ITK
4.4.0
Insight Segmentation and Registration Toolkit
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#include <itkMultiLabelSTAPLEImageFilter.h>
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.
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.
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.
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.
Definition at line 117 of file itkMultiLabelSTAPLEImageFilter.h.
Static Public Member Functions | |
static Pointer | New () |
Static Public Attributes | |
static const unsigned int | ImageDimension = TOutputImage::ImageDimension |
Static Public Attributes inherited from itk::ImageToImageFilter< TInputImage, TOutputImage > | |
static const unsigned int | InputImageDimension = TInputImage::ImageDimension |
static const unsigned int | OutputImageDimension = TOutputImage::ImageDimension |
Static Public Attributes inherited from itk::ImageSource< TOutputImage > | |
static const unsigned int | OutputImageDimension = TOutputImage::ImageDimension |
Private Member Functions | |
void | AllocateConfusionMatrixArray () |
void | InitializeConfusionMatrixArrayFromVoting () |
void | InitializePriorProbabilities () |
MultiLabelSTAPLEImageFilter (const Self &) | |
void | operator= (const Self &) |
Private Attributes | |
std::vector< ConfusionMatrixType > | m_ConfusionMatrixArray |
bool | m_HasLabelForUndecidedPixels |
bool | m_HasMaximumNumberOfIterations |
bool | m_HasPriorProbabilities |
OutputPixelType | m_LabelForUndecidedPixels |
unsigned int | m_MaximumNumberOfIterations |
PriorProbabilitiesType | m_PriorProbabilities |
TWeights | m_TerminationUpdateThreshold |
vcl_size_t | m_TotalLabelCount |
std::vector< ConfusionMatrixType > | m_UpdatedConfusionMatrixArray |
Additional Inherited Members | |
Protected Types inherited from itk::ImageToImageFilter< TInputImage, TOutputImage > | |
typedef ImageToImageFilterDetail::ImageRegionCopier < itkGetStaticConstMacro(OutputImageDimension), itkGetStaticConstMacro(InputImageDimension) > | InputToOutputRegionCopierType |
typedef ImageToImageFilterDetail::ImageRegionCopier < itkGetStaticConstMacro(InputImageDimension), itkGetStaticConstMacro(OutputImageDimension) > | OutputToInputRegionCopierType |
Static Protected Member Functions inherited from itk::ImageSource< TOutputImage > | |
static const ImageRegionSplitterBase * | GetGlobalDefaultSplitter () |
static ITK_THREAD_RETURN_TYPE | ThreaderCallback (void *arg) |
Protected Attributes inherited from itk::ProcessObject | |
TimeStamp | m_OutputInformationMTime |
bool | m_Updating |
typedef Array2D<WeightsType> itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::ConfusionMatrixType |
Definition at line 158 of file itkMultiLabelSTAPLEImageFilter.h.
typedef SmartPointer< const Self > itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::ConstPointer |
Definition at line 125 of file itkMultiLabelSTAPLEImageFilter.h.
typedef ImageRegionConstIterator< TInputImage > itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::InputConstIteratorType |
Iterator types.
Definition at line 153 of file itkMultiLabelSTAPLEImageFilter.h.
typedef InputImageType::Pointer itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::InputImagePointer |
Definition at line 146 of file itkMultiLabelSTAPLEImageFilter.h.
typedef TInputImage itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::InputImageType |
Image typedef support
Definition at line 144 of file itkMultiLabelSTAPLEImageFilter.h.
typedef TInputImage::PixelType itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::InputPixelType |
Definition at line 136 of file itkMultiLabelSTAPLEImageFilter.h.
typedef OutputImageType::Pointer itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::OutputImagePointer |
Definition at line 147 of file itkMultiLabelSTAPLEImageFilter.h.
typedef Superclass::OutputImageRegionType itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::OutputImageRegionType |
Superclass typedefs.
Definition at line 150 of file itkMultiLabelSTAPLEImageFilter.h.
typedef TOutputImage itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::OutputImageType |
Definition at line 145 of file itkMultiLabelSTAPLEImageFilter.h.
typedef ImageRegionIterator< TOutputImage > itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::OutputIteratorType |
Definition at line 154 of file itkMultiLabelSTAPLEImageFilter.h.
typedef TOutputImage::PixelType itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::OutputPixelType |
Extract some information from the image types. Dimensionality of the two images is assumed to be the same.
Definition at line 131 of file itkMultiLabelSTAPLEImageFilter.h.
typedef SmartPointer< Self > itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::Pointer |
Definition at line 124 of file itkMultiLabelSTAPLEImageFilter.h.
typedef Array<WeightsType> itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::PriorProbabilitiesType |
Definition at line 159 of file itkMultiLabelSTAPLEImageFilter.h.
typedef MultiLabelSTAPLEImageFilter itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::Self |
Standard class typedefs.
Definition at line 122 of file itkMultiLabelSTAPLEImageFilter.h.
typedef ImageToImageFilter< TInputImage, TOutputImage > itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::Superclass |
Definition at line 123 of file itkMultiLabelSTAPLEImageFilter.h.
typedef TWeights itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::WeightsType |
Confusion matrix typedefs.
Definition at line 157 of file itkMultiLabelSTAPLEImageFilter.h.
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Definition at line 266 of file itkMultiLabelSTAPLEImageFilter.h.
References itk::Math::e.
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Definition at line 273 of file itkMultiLabelSTAPLEImageFilter.h.
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Determine maximum value among all input images' pixels
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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.
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Give the process object a chance to indictate that it will produce more output than it was requested to produce. For example, many imaging filters must compute the entire output at once or can only produce output in complete slices. Such filters cannot handle smaller requested regions. These filters must provide an implementation of this method, setting the output requested region to the size they will produce. By default, a process object does not modify the size of the output requested region.
Reimplemented from itk::ProcessObject.
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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 ThreadedGenerateData(). 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 an be threaded, it should NOT provide a GenerateData() method but should provide a ThreadedGenerateData() instead.
Reimplemented from itk::ImageSource< TOutputImage >.
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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.
Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.
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Get confusion matrix for the i-th input segmentation.
Definition at line 260 of file itkMultiLabelSTAPLEImageFilter.h.
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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.
Definition at line 208 of file itkMultiLabelSTAPLEImageFilter.h.
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Run-time type information (and related methods)
Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.
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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.
Definition at line 241 of file itkMultiLabelSTAPLEImageFilter.h.
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Method for creation through the object factory.
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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 >.
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Set label value for undecided pixels.
Definition at line 194 of file itkMultiLabelSTAPLEImageFilter.h.
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Set maximum number of iterations.
Definition at line 163 of file itkMultiLabelSTAPLEImageFilter.h.
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Set label value for undecided pixels.
Definition at line 227 of file itkMultiLabelSTAPLEImageFilter.h.
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Set termination threshold based on confusion matrix parameter updates.
Definition at line 185 of file itkMultiLabelSTAPLEImageFilter.h.
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Unset label value for undecided pixels and turn on automatic selection.
Definition at line 215 of file itkMultiLabelSTAPLEImageFilter.h.
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Unset label value for undecided pixels and turn on automatic selection.
Definition at line 173 of file itkMultiLabelSTAPLEImageFilter.h.
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Unset prior class probabilities and turn on automatic estimation.
Definition at line 248 of file itkMultiLabelSTAPLEImageFilter.h.
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Extract some information from the image types. Dimensionality of the two images is assumed to be the same.
Definition at line 141 of file itkMultiLabelSTAPLEImageFilter.h.
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Definition at line 302 of file itkMultiLabelSTAPLEImageFilter.h.
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Definition at line 295 of file itkMultiLabelSTAPLEImageFilter.h.
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Definition at line 308 of file itkMultiLabelSTAPLEImageFilter.h.
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Definition at line 297 of file itkMultiLabelSTAPLEImageFilter.h.
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Definition at line 294 of file itkMultiLabelSTAPLEImageFilter.h.
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Definition at line 309 of file itkMultiLabelSTAPLEImageFilter.h.
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Definition at line 298 of file itkMultiLabelSTAPLEImageFilter.h.
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Definition at line 311 of file itkMultiLabelSTAPLEImageFilter.h.
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Definition at line 292 of file itkMultiLabelSTAPLEImageFilter.h.
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Definition at line 303 of file itkMultiLabelSTAPLEImageFilter.h.