ITK  6.0.0
Insight Toolkit
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itk::STAPLEImageFilter< TInputImage, TOutputImage > Class Template Reference

#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

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

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 122 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 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 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 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 InputImageTypeGetInput () const
 
const InputImageTypeGetInput (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 >
OutputImageTypeGetOutput (unsigned int idx)
 
OutputImageTypeGetOutput ()
 
const OutputImageTypeGetOutput () 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 void EnlargeOutputRequestedRegion (DataObject *)
 
virtual const bool & GetAbortGenerateData () const
 
DataObjectPointerArray GetIndexedInputs ()
 
DataObjectPointerArray GetIndexedOutputs ()
 
NameArray GetInputNames () const
 
DataObjectPointerArray GetInputs ()
 
MultiThreaderTypeGetMultiThreader () 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 ThreadIdTypeGetNumberOfWorkUnits () 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
 
CommandGetCommand (unsigned long tag)
 
bool GetDebug () const
 
MetaDataDictionaryGetMetaDataDictionary ()
 
const MetaDataDictionaryGetMetaDataDictionary () const
 
virtual ModifiedTimeType GetMTime () const
 
virtual const TimeStampGetTimeStamp () 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 () 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 ImageRegionSplitterBaseGetImageRegionSplitter () 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)
 
DataObjectGetInput (const DataObjectIdentifierType &key)
 
const DataObjectGetInput (const DataObjectIdentifierType &key) const
 
virtual const DataObjectPointerArraySizeTypeGetNumberOfRequiredInputs () const
 
virtual const DataObjectPointerArraySizeTypeGetNumberOfRequiredOutputs () 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
 
DataObjectGetInput (DataObjectPointerArraySizeType idx)
 
const DataObjectGetInput (DataObjectPointerArraySizeType idx) const
 
DataObjectGetPrimaryInput ()
 
const DataObjectGetPrimaryInput () const
 
virtual void SetPrimaryInputName (const DataObjectIdentifierType &key)
 
virtual const char * GetPrimaryInputName () const
 
DataObjectGetOutput (const DataObjectIdentifierType &key)
 
const DataObjectGetOutput (const DataObjectIdentifierType &key) const
 
virtual void SetPrimaryOutputName (const DataObjectIdentifierType &key)
 
virtual const char * GetPrimaryOutputName () const
 
DataObjectGetOutput (DataObjectPointerArraySizeType i)
 
const DataObjectGetOutput (DataObjectPointerArraySizeType i) const
 
DataObjectGetPrimaryOutput ()
 
const DataObjectGetPrimaryOutput () 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 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 = 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 ImageRegionSplitterBaseGetGlobalDefaultSplitter ()
 
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

◆ ConstPointer

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

Definition at line 131 of file itkSTAPLEImageFilter.h.

◆ InputImagePointer

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

Definition at line 151 of file itkSTAPLEImageFilter.h.

◆ InputImageType

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

Image type alias support

Definition at line 150 of file itkSTAPLEImageFilter.h.

◆ InputPixelType

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

Definition at line 142 of file itkSTAPLEImageFilter.h.

◆ OutputImagePointer

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

Definition at line 153 of file itkSTAPLEImageFilter.h.

◆ OutputImageType

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

Definition at line 152 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 141 of file itkSTAPLEImageFilter.h.

◆ Pointer

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

Definition at line 130 of file itkSTAPLEImageFilter.h.

◆ RealType

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

Definition at line 143 of file itkSTAPLEImageFilter.h.

◆ Self

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

Standard class type aliases.

Definition at line 128 of file itkSTAPLEImageFilter.h.

◆ Superclass

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

Definition at line 129 of file itkSTAPLEImageFilter.h.

Constructor & Destructor Documentation

◆ STAPLEImageFilter()

template<typename TInputImage , typename TOutputImage >
itk::STAPLEImageFilter< TInputImage, TOutputImage >::STAPLEImageFilter ( )
inlineprotected

◆ ~STAPLEImageFilter()

template<typename TInputImage , typename TOutputImage >
itk::STAPLEImageFilter< TInputImage, TOutputImage >::~STAPLEImageFilter ( )
overrideprotecteddefault

Member Function Documentation

◆ 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

◆ 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 176 of file itkSTAPLEImageFilter.h.

◆ 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 184 of file itkSTAPLEImageFilter.h.

◆ 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 167 of file itkSTAPLEImageFilter.h.

◆ 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 197 of file itkSTAPLEImageFilter.h.

◆ 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.

Member Data Documentation

◆ ImageDimension

template<typename TInputImage , typename TOutputImage >
constexpr 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 147 of file itkSTAPLEImageFilter.h.

◆ m_ConfidenceWeight

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

Definition at line 255 of file itkSTAPLEImageFilter.h.

◆ m_ElapsedIterations

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

Definition at line 252 of file itkSTAPLEImageFilter.h.

◆ m_ForegroundValue

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

Definition at line 251 of file itkSTAPLEImageFilter.h.

◆ m_MaximumIterations

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

Definition at line 253 of file itkSTAPLEImageFilter.h.

◆ m_Sensitivity

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

Definition at line 257 of file itkSTAPLEImageFilter.h.

◆ m_Specificity

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

Definition at line 258 of file itkSTAPLEImageFilter.h.


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