ITK  5.4.0
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itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights > Class Template Reference

#include <itkMultiLabelSTAPLEImageFilter.h>

Detailed Description

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

This filter performs a pixelwise combination of an arbitrary number of input images, where each of them represents a segmentation of the same scene (i.e., image).

The labelings in the images are weighted relative to each other based on their "performance" as estimated by an expectation-maximization algorithm. In the process, a ground truth segmentation is estimated, and the estimated performances of the individual segmentations are relative to this estimated ground truth.

The algorithm is based on the binary STAPLE algorithm by Warfield et al. as published originally in

S. Warfield, K. Zou, W. Wells, "Validation of image segmentation and expert quality with an expectation-maximization algorithm" in MICCAI 2002: Fifth International Conference on Medical Image Computing and Computer-Assisted Intervention, Springer-Verlag, Heidelberg, Germany, 2002, pp. 298-306

The multi-label algorithm implemented here is described in detail in

T. Rohlfing, D. B. Russakoff, and C. R. Maurer, Jr., "Performance-based classifier combination in atlas-based image segmentation using expectation-maximization parameter estimation," IEEE Transactions on Medical Imaging, vol. 23, pp. 983-994, Aug. 2004.

INPUTS
All input volumes to this filter must be segmentations of an image, that is, they must have discrete pixel values where each value represents a different segmented object.

Input volumes must all contain the same size RequestedRegions. Not all input images must contain all possible labels, but all label values must have the same meaning in all images.

The filter can optionally be provided with estimates for the a priori class probabilities through the SetPriorProbabilities function. If no estimate is provided, one is automatically generated by analyzing the relative frequencies of the labels in the input images.

OUTPUTS
The filter produces a single output volume. Each output pixel contains the label that has the highest probability of being the correct label, based on the performance models of the individual segmentations. If the maximum probability is not unique, i.e., if more than one label have a maximum probability, then an "undecided" label is assigned to that output pixel.

By default, the label used for undecided pixels is the maximum label value used in the input images plus one. Since it is possible for an image with 8 bit pixel values to use all 256 possible label values, it is permissible to combine 8 bit (i.e., byte) images into a 16 bit (i.e., short) output image.

In addition to the combined image, the estimated confusion matrices for each of the input segmentations can be obtained through the GetConfusionMatrix member function.

PARAMETERS
The label used for "undecided" labels can be set using SetLabelForUndecidedPixels. This functionality can be unset by calling UnsetLabelForUndecidedPixels.

A termination threshold for the EM iteration can be defined by calling SetTerminationUpdateThreshold. The iteration terminates once no single parameter of any confusion matrix changes by less than this threshold. Alternatively, a maximum number of iterations can be specified by calling SetMaximumNumberOfIterations. The algorithm may still terminate after a smaller number of iterations if the termination threshold criterion is satisfied.

EVENTS
This filter invokes IterationEvent() at each iteration of the E-M algorithm. Setting the AbortGenerateData() flag will cause the algorithm to halt after the current iteration and produce results just as if it had converged. The algorithm makes no attempt to report its progress since the number of iterations needed cannot be known in advance.
Author
Torsten Rohlfing, SRI International, Neuroscience Program

Definition at line 119 of file itkMultiLabelSTAPLEImageFilter.h.

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

Public Types

using ConfusionMatrixType = Array2D< WeightsType >
 
using ConstPointer = SmartPointer< const Self >
 
using InputConstIteratorType = ImageRegionConstIterator< TInputImage >
 
using InputImagePointer = typename InputImageType::Pointer
 
using InputImageType = TInputImage
 
using InputPixelType = typename TInputImage::PixelType
 
using OutputImagePointer = typename OutputImageType::Pointer
 
using OutputImageType = TOutputImage
 
using OutputIteratorType = ImageRegionIterator< TOutputImage >
 
using OutputPixelType = typename TOutputImage::PixelType
 
using Pointer = SmartPointer< Self >
 
using PriorProbabilitiesType = Array< WeightsType >
 
using Self = MultiLabelSTAPLEImageFilter
 
using Superclass = ImageToImageFilter< TInputImage, TOutputImage >
 
using WeightsType = TWeights
 
- Public Types inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
using ConstPointer = SmartPointer< const Self >
 
using InputImageConstPointer = typename InputImageType::ConstPointer
 
using InputImagePixelType = typename InputImageType::PixelType
 
using InputImagePointer = typename InputImageType::Pointer
 
using InputImageRegionType = typename InputImageType::RegionType
 
using InputImageType = TInputImage
 
using Pointer = SmartPointer< Self >
 
using Self = ImageToImageFilter
 
using Superclass = ImageSource< TOutputImage >
 
- Public Types inherited from itk::ImageSource< TOutputImage >
using ConstPointer = SmartPointer< const Self >
 
using DataObjectIdentifierType = Superclass::DataObjectIdentifierType
 
using DataObjectPointer = DataObject::Pointer
 
using DataObjectPointerArraySizeType = Superclass::DataObjectPointerArraySizeType
 
using OutputImagePixelType = typename OutputImageType::PixelType
 
using OutputImagePointer = typename OutputImageType::Pointer
 
using OutputImageRegionType = typename OutputImageType::RegionType
 
using OutputImageType = TOutputImage
 
using Pointer = SmartPointer< Self >
 
using Self = ImageSource
 
using Superclass = ProcessObject
 
- Public Types inherited from itk::ProcessObject
using ConstPointer = SmartPointer< const Self >
 
using DataObjectIdentifierType = DataObject::DataObjectIdentifierType
 
using DataObjectPointer = DataObject::Pointer
 
using DataObjectPointerArray = std::vector< DataObjectPointer >
 
using DataObjectPointerArraySizeType = DataObjectPointerArray::size_type
 
using MultiThreaderType = MultiThreaderBase
 
using NameArray = std::vector< DataObjectIdentifierType >
 
using Pointer = SmartPointer< Self >
 
using Self = ProcessObject
 
using Superclass = Object
 
- Public Types inherited from itk::Object
using ConstPointer = SmartPointer< const Self >
 
using Pointer = SmartPointer< Self >
 
using Self = Object
 
using Superclass = LightObject
 
- Public Types inherited from itk::LightObject
using ConstPointer = SmartPointer< const Self >
 
using Pointer = SmartPointer< Self >
 
using Self = LightObject
 

Public Member Functions

const ConfusionMatrixTypeGetConfusionMatrix (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 PriorProbabilitiesTypeGetPriorProbabilities () const
 
 itkOverrideGetNameOfClassMacro (MultiLabelSTAPLEImageFilter)
 
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 InputImageTypeGetInput () const
 
const InputImageTypeGetInput (unsigned int idx) const
 
 itkOverrideGetNameOfClassMacro (ImageToImageFilter)
 
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)
 
 itkOverrideGetNameOfClassMacro (ImageSource)
 
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 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)
 
 itkOverrideGetNameOfClassMacro (ProcessObject)
 
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
 
 itkOverrideGetNameOfClassMacro (Object)
 
virtual void Modified () const
 
void Register () const override
 
void RemoveAllObservers ()
 
void RemoveObserver (unsigned long tag)
 
void SetDebug (bool debugFlag) const
 
void SetReferenceCount (int) override
 
void UnRegister () const noexcept override
 
void SetMetaDataDictionary (const MetaDataDictionary &rhs)
 
void SetMetaDataDictionary (MetaDataDictionary &&rrhs)
 
virtual void SetObjectName (std::string _arg)
 
virtual const std::string & GetObjectName () const
 
- Public Member Functions inherited from itk::LightObject
Pointer Clone () const
 
virtual void Delete ()
 
virtual int GetReferenceCount () const
 
 itkVirtualGetNameOfClassMacro (LightObject)
 
void Print (std::ostream &os, Indent indent=0) const
 

Static Public Member Functions

static Pointer New ()
 
- Static Public Member Functions inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
static double GetGlobalDefaultCoordinateTolerance ()
 
static double GetGlobalDefaultDirectionTolerance ()
 
static void SetGlobalDefaultCoordinateTolerance (double)
 
static void SetGlobalDefaultDirectionTolerance (double)
 
- Static Public Member Functions inherited from itk::Object
static bool GetGlobalWarningDisplay ()
 
static void GlobalWarningDisplayOff ()
 
static void GlobalWarningDisplayOn ()
 
static Pointer New ()
 
static void SetGlobalWarningDisplay (bool val)
 
- Static Public Member Functions inherited from itk::LightObject
static void BreakOnError ()
 
static Pointer New ()
 

Static Public Attributes

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

Protected Member Functions

TInputImage::PixelType ComputeMaximumInputValue ()
 
void EnlargeOutputRequestedRegion (DataObject *) override
 
void GenerateData () override
 
void GenerateInputRequestedRegion () override
 
 MultiLabelSTAPLEImageFilter ()
 
void PrintSelf (std::ostream &, Indent) const override
 
 ~MultiLabelSTAPLEImageFilter () override=default
 
- Protected Member Functions inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
virtual void CallCopyInputRegionToOutputRegion (OutputImageRegionType &destRegion, const InputImageRegionType &srcRegion)
 
virtual void CallCopyOutputRegionToInputRegion (InputImageRegionType &destRegion, const OutputImageRegionType &srcRegion)
 
 ImageToImageFilter ()
 
void VerifyInputInformation () ITKv5_CONST override
 
 ~ImageToImageFilter () override=default
 
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 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 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 Member Functions

void AllocateConfusionMatrixArray ()
 
void InitializeConfusionMatrixArrayFromVoting ()
 
void InitializePriorProbabilities ()
 

Private Attributes

std::vector< ConfusionMatrixTypem_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< ConfusionMatrixTypem_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 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

◆ ConfusionMatrixType

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

Definition at line 160 of file itkMultiLabelSTAPLEImageFilter.h.

◆ ConstPointer

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

Definition at line 128 of file itkMultiLabelSTAPLEImageFilter.h.

◆ InputConstIteratorType

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

Iterator types.

Definition at line 155 of file itkMultiLabelSTAPLEImageFilter.h.

◆ InputImagePointer

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

Definition at line 148 of file itkMultiLabelSTAPLEImageFilter.h.

◆ InputImageType

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

Image type alias support

Definition at line 146 of file itkMultiLabelSTAPLEImageFilter.h.

◆ InputPixelType

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

Definition at line 139 of file itkMultiLabelSTAPLEImageFilter.h.

◆ OutputImagePointer

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

Definition at line 149 of file itkMultiLabelSTAPLEImageFilter.h.

◆ OutputImageType

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

Definition at line 147 of file itkMultiLabelSTAPLEImageFilter.h.

◆ OutputIteratorType

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

Definition at line 156 of file itkMultiLabelSTAPLEImageFilter.h.

◆ OutputPixelType

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

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

Definition at line 138 of file itkMultiLabelSTAPLEImageFilter.h.

◆ Pointer

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

Definition at line 127 of file itkMultiLabelSTAPLEImageFilter.h.

◆ PriorProbabilitiesType

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

Definition at line 161 of file itkMultiLabelSTAPLEImageFilter.h.

◆ Self

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

Standard class type aliases.

Definition at line 125 of file itkMultiLabelSTAPLEImageFilter.h.

◆ Superclass

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

Definition at line 126 of file itkMultiLabelSTAPLEImageFilter.h.

◆ WeightsType

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

Confusion matrix type alias.

Definition at line 159 of file itkMultiLabelSTAPLEImageFilter.h.

Constructor & Destructor Documentation

◆ MultiLabelSTAPLEImageFilter()

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::MultiLabelSTAPLEImageFilter ( )
inlineprotected

Definition at line 285 of file itkMultiLabelSTAPLEImageFilter.h.

◆ ~MultiLabelSTAPLEImageFilter()

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::~MultiLabelSTAPLEImageFilter ( )
overrideprotecteddefault

Member Function Documentation

◆ AllocateConfusionMatrixArray()

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::AllocateConfusionMatrixArray ( )
private

◆ ComputeMaximumInputValue()

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
TInputImage::PixelType itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::ComputeMaximumInputValue ( )
protected

Determine maximum value among all input images' pixels

◆ EnlargeOutputRequestedRegion()

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::EnlargeOutputRequestedRegion ( DataObject )
overrideprotectedvirtual

Give the process object a chance to indicate that it will produce more output than it was requested to produce. For example, many imaging filters must compute the entire output at once or can only produce output in complete slices. Such filters cannot handle smaller requested regions. These filters must provide an implementation of this method, setting the output requested region to the size they will produce. By default, a process object does not modify the size of the output requested region.

Reimplemented from itk::ProcessObject.

◆ GenerateData()

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::GenerateData ( )
overrideprotectedvirtual

A version of GenerateData() specific for image processing filters. This implementation will split the processing across multiple threads. The buffer is allocated by this method. Then the BeforeThreadedGenerateData() method is called (if provided). Then, a series of threads are spawned each calling DynamicThreadedGenerateData(). After all the threads have completed processing, the AfterThreadedGenerateData() method is called (if provided). If an image processing filter cannot be threaded, the filter should provide an implementation of GenerateData(). That implementation is responsible for allocating the output buffer. If a filter can be threaded, it should NOT provide a GenerateData() method but should provide a DynamicThreadedGenerateData() instead.

See also
ThreadedGenerateData()

Reimplemented from itk::ImageSource< TOutputImage >.

◆ GenerateInputRequestedRegion()

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::GenerateInputRequestedRegion ( )
overrideprotectedvirtual

What is the input requested region that is required to produce the output requested region? The base assumption for image processing filters is that the input requested region can be set to match the output requested region. If a filter requires more input (for instance a filter that uses neighborhoods needs more input than output to avoid introducing artificial boundary conditions) or less input (for instance a magnify filter) will have to override this method. In doing so, it should call its superclass' implementation as its first step. Note that imaging filters operate differently than the classes to this point in the class hierarchy. Up till now, the base assumption has been that the largest possible region will be requested of the input.

This implementation of GenerateInputRequestedRegion() only processes the inputs that are a subclass of the ImageBase<InputImageDimension>. If an input is another type of DataObject (including an Image of a different dimension), they are skipped by this method. The subclasses of ImageToImageFilter are responsible for providing an implementation of GenerateInputRequestedRegion() when there are multiple inputs of different types.

See also
ProcessObject::GenerateInputRequestedRegion(), ImageSource::GenerateInputRequestedRegion()

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

◆ GetConfusionMatrix()

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
const ConfusionMatrixType& itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::GetConfusionMatrix ( const unsigned int  i) const
inline

Get confusion matrix for the i-th input segmentation.

Definition at line 279 of file itkMultiLabelSTAPLEImageFilter.h.

◆ GetElapsedNumberOfIterations()

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

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

◆ GetHasLabelForUndecidedPixels()

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
virtual bool itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::GetHasLabelForUndecidedPixels ( )
virtual

True if LabelForUndecidedPixels has been manually set.

◆ GetHasMaximumNumberOfIterations()

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
virtual bool itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::GetHasMaximumNumberOfIterations ( ) const
virtual

True if the MaximumNumberOfIterations has been manually set.

◆ GetHasPriorProbabilities()

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
virtual bool itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::GetHasPriorProbabilities ( )
virtual

True if PriorProbabilities has been manually set.

◆ GetLabelForUndecidedPixels()

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
virtual OutputPixelType itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::GetLabelForUndecidedPixels ( )
virtual

Get label value used for undecided pixels.

After updating the filter, this function returns the actual label value used for undecided pixels in the current output. Note that this value is overwritten when SetLabelForUndecidedPixels is called and the new value only becomes effective upon the next filter update.

◆ GetMaximumNumberOfIterations()

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

Set maximum number of iterations.

◆ GetPriorProbabilities()

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

Get prior class probabilities.

After updating the filter, this function returns the actual prior class probabilities. If these were not previously set by a call to SetPriorProbabilities, then they are estimated from the input segmentations and the result is available through this function.

◆ GetTerminationUpdateThreshold()

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
virtual TWeights itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::GetTerminationUpdateThreshold ( ) const
virtual

Set termination threshold based on confusion matrix parameter updates.

◆ InitializeConfusionMatrixArrayFromVoting()

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::InitializeConfusionMatrixArrayFromVoting ( )
private

◆ InitializePriorProbabilities()

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::InitializePriorProbabilities ( )
private

◆ itkOverrideGetNameOfClassMacro()

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::itkOverrideGetNameOfClassMacro ( MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >  )

Run-time type information (and related methods)

◆ New()

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
static Pointer itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::New ( )
static

Method for creation through the object factory.

◆ PrintSelf()

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::PrintSelf ( std::ostream &  os,
Indent  indent 
) const
overrideprotectedvirtual

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

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

◆ SetLabelForUndecidedPixels()

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::SetLabelForUndecidedPixels ( const OutputPixelType  l)
inline

Set label value for undecided pixels.

Definition at line 203 of file itkMultiLabelSTAPLEImageFilter.h.

◆ SetMaximumNumberOfIterations()

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::SetMaximumNumberOfIterations ( const unsigned int  mit)
inline

Set maximum number of iterations.

Definition at line 169 of file itkMultiLabelSTAPLEImageFilter.h.

◆ SetPriorProbabilities()

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::SetPriorProbabilities ( const PriorProbabilitiesType ppa)
inline

Set manual estimates for the a priori class probabilities.

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

Definition at line 243 of file itkMultiLabelSTAPLEImageFilter.h.

◆ SetTerminationUpdateThreshold()

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
virtual void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::SetTerminationUpdateThreshold ( TWeights  _arg)
virtual

Set termination threshold based on confusion matrix parameter updates.

◆ UnsetLabelForUndecidedPixels()

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::UnsetLabelForUndecidedPixels ( )
inline

Unset label value for undecided pixels and turn on automatic selection.

Definition at line 226 of file itkMultiLabelSTAPLEImageFilter.h.

◆ UnsetMaximumNumberOfIterations()

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::UnsetMaximumNumberOfIterations ( )
inline

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

Definition at line 184 of file itkMultiLabelSTAPLEImageFilter.h.

◆ UnsetPriorProbabilities()

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::UnsetPriorProbabilities ( )
inline

Unset prior class probabilities and turn on automatic estimation.

Definition at line 266 of file itkMultiLabelSTAPLEImageFilter.h.

Member Data Documentation

◆ ImageDimension

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
constexpr unsigned int itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::ImageDimension = TOutputImage::ImageDimension
staticconstexpr

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

Definition at line 143 of file itkMultiLabelSTAPLEImageFilter.h.

◆ m_ConfusionMatrixArray

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
std::vector<ConfusionMatrixType> itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::m_ConfusionMatrixArray {}
private

Definition at line 321 of file itkMultiLabelSTAPLEImageFilter.h.

◆ m_ElapsedNumberOfIterations

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
unsigned int itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::m_ElapsedNumberOfIterations { 0u }
private

Definition at line 331 of file itkMultiLabelSTAPLEImageFilter.h.

◆ m_HasLabelForUndecidedPixels

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
bool itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::m_HasLabelForUndecidedPixels { false }
private

Definition at line 313 of file itkMultiLabelSTAPLEImageFilter.h.

◆ m_HasMaximumNumberOfIterations

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
bool itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::m_HasMaximumNumberOfIterations { false }
private

Definition at line 329 of file itkMultiLabelSTAPLEImageFilter.h.

◆ m_HasPriorProbabilities

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
bool itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::m_HasPriorProbabilities { false }
private

Definition at line 315 of file itkMultiLabelSTAPLEImageFilter.h.

◆ m_LabelForUndecidedPixels

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
OutputPixelType itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::m_LabelForUndecidedPixels {}
private

Definition at line 312 of file itkMultiLabelSTAPLEImageFilter.h.

◆ m_MaximumNumberOfIterations

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
unsigned int itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::m_MaximumNumberOfIterations { 0 }
private

Definition at line 330 of file itkMultiLabelSTAPLEImageFilter.h.

◆ m_PriorProbabilities

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
PriorProbabilitiesType itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::m_PriorProbabilities {}
private

Definition at line 316 of file itkMultiLabelSTAPLEImageFilter.h.

◆ m_TerminationUpdateThreshold

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
TWeights itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::m_TerminationUpdateThreshold {}
private

Definition at line 333 of file itkMultiLabelSTAPLEImageFilter.h.

◆ m_TotalLabelCount

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
vcl_size_t itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::m_TotalLabelCount { 0 }
private

Definition at line 310 of file itkMultiLabelSTAPLEImageFilter.h.

◆ m_UpdatedConfusionMatrixArray

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>
std::vector<ConfusionMatrixType> itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::m_UpdatedConfusionMatrixArray {}
private

Definition at line 322 of file itkMultiLabelSTAPLEImageFilter.h.


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