#include <itkSTAPLEImageFilter.h>

Detailed Description

template<typename TInputImage, typename TOutputImage>
class itk::STAPLEImageFilter< TInputImage, TOutputImage >

The STAPLE filter implements the Simultaneous Truth and Performance Level Estimation algorithm for generating ground truth volumes from a set of binary expert segmentations.

The STAPLE algorithm treats segmentation as a pixelwise classification, which leads to an averaging scheme that accounts for systematic biases in the behavior of experts in order to generate a fuzzy ground truth volume and simultaneous accuracy assessment of each expert. The ground truth volumes produced by this filter are floating point volumes of values between zero and one that indicate probability of each pixel being in the object targeted by the segmentation.

The STAPLE algorithm is described in [137].

INPUTS: Input volumes to the STAPLE filter must be binary segmentations of an image, that is, there must be a single foreground value that represents positively classified pixels (pixels that are considered to belong inside the segmentation). Any number of background pixel values may be present in the input images. You can, for example, input volumes with many different labels as long as the structure you are interested in creating ground truth for is consistently labeled among all input volumes. Pixel type of the input volumes does not matter. Specify the label value for positively classified pixels using SetForegroundValue. All other labels will be considered to be negatively classified pixels (background).

Input volumes must all contain the same size RequestedRegions.

OUTPUTS: The STAPLE filter produces a single output volume with a range of floating point values from zero to one. IT IS VERY IMPORTANT TO INSTANTIATE THIS FILTER WITH A FLOATING POINT OUTPUT TYPE (floats or doubles). You may threshold the output above some probability threshold if you wish to produce a binary ground truth.

PARAMETERS: The STAPLE algorithm requires a number of inputs. You may specify any number of input volumes using the SetInput(i, p_i) method, where i ranges from zero to N-1, N is the total number of input segmentations, and p_i is the SmartPointer to the i-th segmentation.

The SetConfidenceWeight parameter is a modifier for the prior probability that any pixel would be classified as inside the target object. This implementation of the STAPLE algorithm automatically calculates prior positive classification probability as the average fraction of the image volume filled by the target object in each input segmentation. The ConfidenceWeight parameter allows for scaling the of this default prior probability: if g_t is the prior probability that a pixel would be classified inside the target object, then g_t is set to g_t * ConfidenceWeight before iterating on the solution. In general ConfidenceWeight should be left to the default of 1.0.

You must provide a foreground value using SetForegroundValue that the STAPLE algorithm will use to identify positively classified pixels in the input images. All other values in the image will be treated as background values. For example, if your input segmentations consist of 1's everywhere inside the segmented region, then use SetForegroundValue(1).

The STAPLE algorithm is an iterative E-M algorithm and will converge on a solution after some number of iterations that cannot be known a priori. After updating the filter, the total elapsed iterations taken to converge on the solution can be queried through GetElapsedIterations(). You may also specify a MaximumNumberOfIterations, after which the algorithm will stop iterating regardless of whether or not it has converged. This implementation of the STAPLE algorithm will find the solution to within seven digits of precision unless it is stopped early.

Once updated, the Sensitivity (true positive fraction, q) and Specificity (true negative fraction, q) for each expert input volume can be queried using GetSensitivity(i) and GetSpecificity(i), where i is the i-th input volume.

REQUIRED PARAMETERS: The only required parameters for this filter are the ForegroundValue and the input volumes. All other parameters may be safely left to their default values. Please see the paper cited above for more information on the STAPLE algorithm and its parameters. A proper understanding of the algorithm is important for interpreting the results that it produces.

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.

Definition at line 117 of file itkSTAPLEImageFilter.h.

Inheritance diagram for itk::STAPLEImageFilter< TInputImage, TOutputImage >:

Collaboration diagram for itk::STAPLEImageFilter< TInputImage, TOutputImage >:

Public Types
using	ConstPointer = SmartPointer<const Self>

using	InputImagePointer = typename InputImageType::Pointer

using	InputImageType = TInputImage

using	InputPixelType = typename TInputImage::PixelType

using	OutputImagePointer = typename OutputImageType::Pointer

using	OutputImageRegionType

using	OutputImageType = TOutputImage

using	OutputPixelType = typename TOutputImage::PixelType

using	Pointer = SmartPointer<Self>

using	RealType = typename NumericTraits<InputPixelType>::RealType

using	Self = STAPLEImageFilter

using	Superclass = ImageToImageFilter<TInputImage, TOutputImage>

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

using	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

virtual unsigned int	GetElapsedIterations () const

const char *	GetNameOfClass () const override

const std::vector< double > &	GetSensitivity () const

const std::vector< double > &	GetSpecificity () const


virtual void	SetForegroundValue (InputPixelType _arg)

virtual InputPixelType	GetForegroundValue () const


double	GetSensitivity (unsigned int i)


double	GetSpecificity (unsigned int i)


virtual void	SetMaximumIterations (unsigned int _arg)

virtual unsigned int	GetMaximumIterations () const


virtual void	SetConfidenceWeight (double _arg)

virtual double	GetConfidenceWeight () const

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 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	AbortGenerateDataOff ()

virtual void	AbortGenerateDataOn ()

virtual void	EnlargeOutputRequestedRegion (DataObject *output)

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	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 *cmd) const

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

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
void	GenerateData () override

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

	STAPLEImageFilter ()

	~STAPLEImageFilter () 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)

void	GenerateInputRequestedRegion () override

	ImageToImageFilter ()

void	VerifyInputInformation () const override

	~ImageToImageFilter () override=default

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 ()

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	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 () 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	ThreaderUpdateProgressOff ()

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 Attributes
double	m_ConfidenceWeight {}

unsigned int	m_ElapsedIterations {}

InputPixelType	m_ForegroundValue {}

unsigned int	m_MaximumIterations {}

std::vector< double >	m_Sensitivity {}

std::vector< double >	m_Specificity {}

Additional Inherited Members
Protected Types inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
using	InputToOutputRegionCopierType

using	OutputToInputRegionCopierType

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
template<typename TSourceObject>
static void	MakeRequiredOutputs (TSourceObject &sourceObject, const DataObjectPointerArraySizeType numberOfRequiredOutputs)

static constexpr float	progressFixedToFloat (uint32_t fixed)

static uint32_t	progressFloatToFixed (float f)

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

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

◆ ConstPointer

template<typename TInputImage, typename TOutputImage>

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

Definition at line 126 of file itkSTAPLEImageFilter.h.

◆ InputImagePointer

template<typename TInputImage, typename TOutputImage>

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

Definition at line 146 of file itkSTAPLEImageFilter.h.

◆ InputImageType

template<typename TInputImage, typename TOutputImage>

using itk::STAPLEImageFilter< TInputImage, TOutputImage >::InputImageType = TInputImage

Image type alias support

Definition at line 145 of file itkSTAPLEImageFilter.h.

◆ InputPixelType

template<typename TInputImage, typename TOutputImage>

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

Definition at line 137 of file itkSTAPLEImageFilter.h.

◆ OutputImagePointer

template<typename TInputImage, typename TOutputImage>

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

Definition at line 148 of file itkSTAPLEImageFilter.h.

◆ OutputImageRegionType

template<typename TInputImage, typename TOutputImage>

using itk::ImageSource< TOutputImage >::OutputImageRegionType

Definition at line 125 of file itkImageSource.h.

◆ OutputImageType

template<typename TInputImage, typename TOutputImage>

using itk::STAPLEImageFilter< TInputImage, TOutputImage >::OutputImageType = TOutputImage

Definition at line 147 of file itkSTAPLEImageFilter.h.

◆ OutputPixelType

template<typename TInputImage, typename TOutputImage>

using itk::STAPLEImageFilter< TInputImage, TOutputImage >::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 136 of file itkSTAPLEImageFilter.h.

◆ Pointer

template<typename TInputImage, typename TOutputImage>

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

Definition at line 125 of file itkSTAPLEImageFilter.h.

◆ RealType

template<typename TInputImage, typename TOutputImage>

using itk::STAPLEImageFilter< TInputImage, TOutputImage >::RealType = typename NumericTraits<InputPixelType>::RealType

Definition at line 138 of file itkSTAPLEImageFilter.h.

◆ Self

template<typename TInputImage, typename TOutputImage>

using itk::STAPLEImageFilter< TInputImage, TOutputImage >::Self = STAPLEImageFilter

Standard class type aliases.

Definition at line 123 of file itkSTAPLEImageFilter.h.

◆ Superclass

template<typename TInputImage, typename TOutputImage>

using itk::STAPLEImageFilter< TInputImage, TOutputImage >::Superclass = ImageToImageFilter<TInputImage, TOutputImage>

Definition at line 124 of file itkSTAPLEImageFilter.h.

Constructor & Destructor Documentation

◆ STAPLEImageFilter()

template<typename TInputImage, typename TOutputImage>

itk::STAPLEImageFilter< TInputImage, TOutputImage >::STAPLEImageFilter ( )

inlineprotected

Definition at line 226 of file itkSTAPLEImageFilter.h.

References m_ConfidenceWeight, m_ElapsedIterations, m_ForegroundValue, m_MaximumIterations, itk::NumericTraits< T >::max(), and itk::NumericTraits< T >::OneValue().

Referenced by GetNameOfClass().

◆ ~STAPLEImageFilter()

template<typename TInputImage, typename TOutputImage>

itk::STAPLEImageFilter< TInputImage, TOutputImage >::~STAPLEImageFilter ( )

overrideprotecteddefault

Member Function Documentation

◆ CreateAnother()

template<typename TInputImage, typename TOutputImage>

virtual::itk::LightObject::Pointer itk::STAPLEImageFilter< TInputImage, TOutputImage >::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.

◆ GenerateData()

template<typename TInputImage, typename TOutputImage>

void itk::STAPLEImageFilter< TInputImage, TOutputImage >::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 >.

◆ GetConfidenceWeight()

template<typename TInputImage, typename TOutputImage>

virtual double itk::STAPLEImageFilter< TInputImage, TOutputImage >::GetConfidenceWeight ( ) const

virtual

Scales the estimated prior probability that a pixel will be inside the targeted object of segmentation. The default prior probability g_t is calculated automatically as the average fraction of positively classified pixels to the total size of the volume (across all input volumes). ConfidenceWeight will scale this default value as g_t = g_t * ConfidenceWeight. In general, ConfidenceWeight should be left to the default of 1.0.

◆ GetElapsedIterations()

template<typename TInputImage, typename TOutputImage>

virtual unsigned int itk::STAPLEImageFilter< TInputImage, TOutputImage >::GetElapsedIterations ( ) const

virtual

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

◆ GetForegroundValue()

template<typename TInputImage, typename TOutputImage>

virtual InputPixelType itk::STAPLEImageFilter< TInputImage, TOutputImage >::GetForegroundValue ( ) const

virtual

Set get the binary ON value of the input image.

◆ GetMaximumIterations()

template<typename TInputImage, typename TOutputImage>

virtual unsigned int itk::STAPLEImageFilter< TInputImage, TOutputImage >::GetMaximumIterations ( ) const

virtual

Set/Get the maximum number of iterations after which the STAPLE algorithm will be considered to have converged. In general this SHOULD NOT be set and the algorithm should be allowed to converge on its own.

◆ GetNameOfClass()

template<typename TInputImage, typename TOutputImage>

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

overridevirtual

See also: LightObject::GetNameOfClass()

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

References STAPLEImageFilter().

◆ GetSensitivity() [1/2]

template<typename TInputImage, typename TOutputImage>

const std::vector< double > & itk::STAPLEImageFilter< TInputImage, TOutputImage >::GetSensitivity ( ) const

inline

After the filter is updated, this method returns a std::vector<double> of all Sensitivity (true positive fraction, p) values for the expert input volumes.

Definition at line 171 of file itkSTAPLEImageFilter.h.

References m_Sensitivity.

◆ GetSensitivity() [2/2]

template<typename TInputImage, typename TOutputImage>

double itk::STAPLEImageFilter< TInputImage, TOutputImage >::GetSensitivity ( unsigned int i )

inline

After the filter is updated, this method returns the Sensitivity (true positive fraction, p) value for the i-th expert input volume.

Definition at line 179 of file itkSTAPLEImageFilter.h.

References itk::ProcessObject::GetNumberOfIndexedInputs(), and m_Sensitivity.

◆ GetSpecificity() [1/2]

template<typename TInputImage, typename TOutputImage>

const std::vector< double > & itk::STAPLEImageFilter< TInputImage, TOutputImage >::GetSpecificity ( ) const

inline

After the filter is updated, this method returns a std::vector<double> of all Specificity (true negative fraction, q) values for the expert input volumes.

Definition at line 162 of file itkSTAPLEImageFilter.h.

References m_Specificity.

◆ GetSpecificity() [2/2]

template<typename TInputImage, typename TOutputImage>

double itk::STAPLEImageFilter< TInputImage, TOutputImage >::GetSpecificity ( unsigned int i )

inline

After the filter is updated, this method returns the Specificity (true negative fraction, q) value for the i-th expert input volume.

Definition at line 192 of file itkSTAPLEImageFilter.h.

References itk::ProcessObject::GetNumberOfIndexedInputs(), and m_Specificity.

◆ New()

template<typename TInputImage, typename TOutputImage>

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

static

Method for creation through the object factory.

◆ PrintSelf()

template<typename TInputImage, typename TOutputImage>

void itk::STAPLEImageFilter< TInputImage, TOutputImage >::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 >.

◆ SetConfidenceWeight()

template<typename TInputImage, typename TOutputImage>

virtual void itk::STAPLEImageFilter< TInputImage, TOutputImage >::SetConfidenceWeight ( double _arg )

virtual

Scales the estimated prior probability that a pixel will be inside the targeted object of segmentation. The default prior probability g_t is calculated automatically as the average fraction of positively classified pixels to the total size of the volume (across all input volumes). ConfidenceWeight will scale this default value as g_t = g_t * ConfidenceWeight. In general, ConfidenceWeight should be left to the default of 1.0.

◆ SetForegroundValue()

template<typename TInputImage, typename TOutputImage>

virtual void itk::STAPLEImageFilter< TInputImage, TOutputImage >::SetForegroundValue ( InputPixelType _arg )

virtual

Set get the binary ON value of the input image.

◆ SetMaximumIterations()

template<typename TInputImage, typename TOutputImage>

virtual void itk::STAPLEImageFilter< TInputImage, TOutputImage >::SetMaximumIterations ( unsigned int _arg )

virtual

Set/Get the maximum number of iterations after which the STAPLE algorithm will be considered to have converged. In general this SHOULD NOT be set and the algorithm should be allowed to converge on its own.

References itk::NumericTraits< T >::max().

Member Data Documentation

◆ ImageDimension

template<typename TInputImage, typename TOutputImage>

unsigned int itk::STAPLEImageFilter< TInputImage, TOutputImage >::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 142 of file itkSTAPLEImageFilter.h.

◆ m_ConfidenceWeight

template<typename TInputImage, typename TOutputImage>

double itk::STAPLEImageFilter< TInputImage, TOutputImage >::m_ConfidenceWeight {}

private

Definition at line 246 of file itkSTAPLEImageFilter.h.

Referenced by STAPLEImageFilter().

◆ m_ElapsedIterations

template<typename TInputImage, typename TOutputImage>

unsigned int itk::STAPLEImageFilter< TInputImage, TOutputImage >::m_ElapsedIterations {}

private

Definition at line 243 of file itkSTAPLEImageFilter.h.

Referenced by STAPLEImageFilter().

◆ m_ForegroundValue

template<typename TInputImage, typename TOutputImage>

InputPixelType itk::STAPLEImageFilter< TInputImage, TOutputImage >::m_ForegroundValue {}

private

Definition at line 242 of file itkSTAPLEImageFilter.h.

Referenced by STAPLEImageFilter().

◆ m_MaximumIterations

template<typename TInputImage, typename TOutputImage>

unsigned int itk::STAPLEImageFilter< TInputImage, TOutputImage >::m_MaximumIterations {}

private

Definition at line 244 of file itkSTAPLEImageFilter.h.

Referenced by STAPLEImageFilter().

◆ m_Sensitivity

template<typename TInputImage, typename TOutputImage>

std::vector<double> itk::STAPLEImageFilter< TInputImage, TOutputImage >::m_Sensitivity {}

private

Definition at line 248 of file itkSTAPLEImageFilter.h.

Referenced by GetSensitivity(), and GetSensitivity().

◆ m_Specificity

template<typename TInputImage, typename TOutputImage>

std::vector<double> itk::STAPLEImageFilter< TInputImage, TOutputImage >::m_Specificity {}

private

Definition at line 249 of file itkSTAPLEImageFilter.h.

Referenced by GetSpecificity(), and GetSpecificity().

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

itkSTAPLEImageFilter.h

Detailed Description

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ ConstPointer

◆ InputImagePointer

◆ InputImageType

◆ InputPixelType

◆ OutputImagePointer

◆ OutputImageRegionType

◆ OutputImageType

◆ OutputPixelType

◆ Pointer

◆ RealType

◆ Self

◆ Superclass

Constructor & Destructor Documentation

◆ STAPLEImageFilter()

◆ ~STAPLEImageFilter()

Member Function Documentation

◆ CreateAnother()

◆ GenerateData()

◆ GetConfidenceWeight()

◆ GetElapsedIterations()

◆ GetForegroundValue()

◆ GetMaximumIterations()

◆ GetNameOfClass()

◆ GetSensitivity() [1/2]

◆ GetSensitivity() [2/2]

◆ GetSpecificity() [1/2]

◆ GetSpecificity() [2/2]

◆ New()

◆ PrintSelf()

◆ SetConfidenceWeight()

◆ SetForegroundValue()

◆ SetMaximumIterations()

Member Data Documentation

◆ ImageDimension

◆ m_ConfidenceWeight

◆ m_ElapsedIterations

◆ m_ForegroundValue

◆ m_MaximumIterations

◆ m_Sensitivity

◆ m_Specificity