ITK
4.13.0
Insight Segmentation and Registration Toolkit
|
#include <itkMRFImageFilter.h>
Implementation of a labeller object that uses Markov Random Fields to classify pixels in an image data set.
This object classifies pixels based on a Markov Random Field (MRF) model. This implementation uses the maximum a posteriori (MAP) estimates for modeling the MRF. The object traverses the data set and uses the model generated by the Mahalanobis distance classifier to get the distance between each pixel in the data set to a set of known classes, updates the distances by evaluating the influence of its neighboring pixels (based on a MRF model) and finally, classifies each pixel to the class which has the minimum distance to that pixel (taking the neighborhood influence under consideration). DoNeighborhoodOperation is the function that can be modified to achieve different falvors of MRF filters in derived classes.
The classified initial labeled image is needed. It is important that the number of expected classes be set before calling the classifier. In our case we have used the ImageClassifer using a Gaussian model to generate the initial labels. This classifier requires the user to ensure that an appropriate membership function is provided. See the documentation of the image classifier class for more information.
The influence of a neighborhood on a given pixel's classification (the MRF term) is computed by calculating a weighted sum of number of class labels in a three dimensional neighborhood. The basic idea of this neighborhood influence is that if a large number of neighbors of a pixel are of one class, then the current pixel is likely to be of the same class.
The dimensions of the neighborhood are the same as the input image dimensions, and values of the weighting parameters are either specified by the user or through the beta matrix parameter. The default weighting table is generated during object construction. The following table shows an example of a 3 x 3 x 3 neighborhood and the weighting values used. A 3 x 3 x 3 kernel is used where each value is a nonnegative parameter, which encourages neighbors to be of the same class. In this example, the influence of the pixels in the same slice is assigned a weight 1.7. The influence of the pixels in the same location in the previous and next slice is assigned a weight 1.5. A weight of 1.3 is assigned to the influence of the north, south, east, west, and diagonal pixels in the previous and next slices.
The user needs to set the neighborhood size using the SetNeighborhoodRadius function. The details on the semantics of a neighborhood can be found in the documentation associated with the itkNeighborhood and related objects. NOTE: The size of the neighborhood must match the size of the neighborhood weighting parameters set by the user.
For minimization of the MRF labeling function the MinimizeFunctional virtual method is called. For our current implementation we use the iterated conditional modes (ICM) algorithm described by Besag in the paper "On the Statistical Analysis of Dirty Pictures" in J. Royal Stat. Soc. B, Vol. 48, 1986.
In each iteration, the algorithm visits each pixel in turn and determines whether to update its classification by computing the influence of the classification of the pixel's neighbors and of the intensity data. On each iteration after the first, we reexamine the classification of a pixel only if the classification of some of its neighbors has changed in the previous iteration. The pixels' classification is updated using a synchronous scheme (iteration by iteration) until the error reaches less than the threshold or the number of iteration exceed the maximum set number of iterations. Note: The current implementation supports betaMatrix default weight for two and three dimensional images only. The default for higher dimension is set to unity. This should be overridden by custom weights after filter initialization.
Definition at line 125 of file itkMRFImageFilter.h.
Static Public Member Functions | |
static Pointer | New () |
Static Public Member Functions inherited from itk::Object | |
static bool | GetGlobalWarningDisplay () |
static void | GlobalWarningDisplayOff () |
static void | GlobalWarningDisplayOn () |
static Pointer | New () |
static void | SetGlobalWarningDisplay (bool flag) |
Static Public Member Functions inherited from itk::LightObject | |
static void | BreakOnError () |
static Pointer | New () |
Static Public Attributes | |
static const unsigned int | ClassifiedImageDimension = TClassifiedImage::ImageDimension |
static const unsigned int | InputImageDimension = TInputImage::ImageDimension |
Static Public Attributes inherited from itk::ImageToImageFilter< TInputImage, TClassifiedImage > | |
static const unsigned int | InputImageDimension |
static const unsigned int | OutputImageDimension |
Static Public Attributes inherited from itk::ImageSource< TClassifiedImage > | |
static const unsigned int | OutputImageDimension |
Protected Types | |
typedef ImageRegionIterator < LabelStatusImageType > | LabelStatusImageIterator |
typedef NeighborhoodIterator < LabelStatusImageType > | LabelStatusImageNeighborhoodIterator |
typedef LabelStatusImageType::Pointer | LabelStatusImagePointer |
typedef Image< int, itkGetStaticConstMacro(InputImageDimension) > | LabelStatusImageType |
typedef LabelStatusImageType::IndexType | LabelStatusIndexType |
typedef LabelStatusImageType::RegionType | LabelStatusRegionType |
Protected Types inherited from itk::ImageToImageFilter< TInputImage, TClassifiedImage > | |
typedef ImageToImageFilterDetail::ImageRegionCopier < itkGetStaticConstMacro(OutputImageDimension), itkGetStaticConstMacro(InputImageDimension) > | InputToOutputRegionCopierType |
typedef ImageToImageFilterDetail::ImageRegionCopier < itkGetStaticConstMacro(InputImageDimension), itkGetStaticConstMacro(OutputImageDimension) > | OutputToInputRegionCopierType |
Private Types | |
typedef TInputImage::SizeType | InputImageSizeType |
typedef LabelStatusImageFaceListType::iterator | LabelStatusImageFaceListIterator |
typedef LabelStatusImageFacesCalculator::FaceListType | LabelStatusImageFaceListType |
typedef NeighborhoodAlgorithm::ImageBoundaryFacesCalculator < LabelStatusImageType > | LabelStatusImageFacesCalculator |
typedef LabelStatusImageNeighborhoodIterator::RadiusType | LabelStatusImageNeighborhoodRadiusType |
Private Member Functions | |
void | ApplyICMLabeller () |
virtual void | SetDefaultMRFNeighborhoodWeight () |
Private Attributes | |
ClassifierType::Pointer | m_ClassifierPtr |
double * | m_ClassProbability |
std::vector< double > | m_DummyVector |
int | m_ErrorCounter |
double | m_ErrorTolerance |
InputImageNeighborhoodRadiusType | m_InputImageNeighborhoodRadius |
unsigned int | m_KernelSize |
LabelledImageNeighborhoodRadiusType | m_LabelledImageNeighborhoodRadius |
LabelStatusImagePointer | m_LabelStatusImage |
LabelStatusImageNeighborhoodRadiusType | m_LabelStatusImageNeighborhoodRadius |
std::vector< double > | m_MahalanobisDistance |
unsigned int | m_MaximumNumberOfIterations |
std::vector< double > | m_MRFNeighborhoodWeight |
int | m_NeighborhoodSize |
std::vector< double > | m_NeighborInfluence |
unsigned int | m_NumberOfClasses |
unsigned int | m_NumberOfIterations |
double | m_SmoothingFactor |
StopConditionType | m_StopCondition |
int | m_TotalNumberOfPixelsInInputImage |
int | m_TotalNumberOfValidPixelsInOutputImage |
Additional Inherited Members | |
Static Protected Member Functions inherited from itk::ImageSource< TClassifiedImage > | |
static const ImageRegionSplitterBase * | GetGlobalDefaultSplitter () |
static ITK_THREAD_RETURN_TYPE | ThreaderCallback (void *arg) |
Protected Attributes inherited from itk::ProcessObject | |
TimeStamp | m_OutputInformationMTime |
bool | m_Updating |
Protected Attributes inherited from itk::LightObject | |
AtomicInt< int > | m_ReferenceCount |
typedef ImageClassifierBase< TInputImage, TClassifiedImage > itk::MRFImageFilter< TInputImage, TClassifiedImage >::ClassifierType |
Type definitions for classifier to be used for the MRF lavbelling.
Definition at line 195 of file itkMRFImageFilter.h.
typedef SmartPointer< const Self > itk::MRFImageFilter< TInputImage, TClassifiedImage >::ConstPointer |
Definition at line 133 of file itkMRFImageFilter.h.
typedef LabelledImageIndexType::IndexValueType itk::MRFImageFilter< TInputImage, TClassifiedImage >::IndexValueType |
Definition at line 181 of file itkMRFImageFilter.h.
typedef TInputImage::ConstPointer itk::MRFImageFilter< TInputImage, TClassifiedImage >::InputImageConstPointer |
Definition at line 145 of file itkMRFImageFilter.h.
typedef InputImageFaceListType::iterator itk::MRFImageFilter< TInputImage, TClassifiedImage >::InputImageFaceListIterator |
Definition at line 217 of file itkMRFImageFilter.h.
typedef InputImageFacesCalculator::FaceListType itk::MRFImageFilter< TInputImage, TClassifiedImage >::InputImageFaceListType |
Definition at line 214 of file itkMRFImageFilter.h.
typedef NeighborhoodAlgorithm::ImageBoundaryFacesCalculator< TInputImage > itk::MRFImageFilter< TInputImage, TClassifiedImage >::InputImageFacesCalculator |
Definition at line 211 of file itkMRFImageFilter.h.
typedef ConstNeighborhoodIterator< TInputImage > itk::MRFImageFilter< TInputImage, TClassifiedImage >::InputImageNeighborhoodIterator |
Input image neighborhood iterator and kernel size typedef
Definition at line 205 of file itkMRFImageFilter.h.
typedef InputImageNeighborhoodIterator::RadiusType itk::MRFImageFilter< TInputImage, TClassifiedImage >::InputImageNeighborhoodRadiusType |
Definition at line 208 of file itkMRFImageFilter.h.
typedef TInputImage::PixelType itk::MRFImageFilter< TInputImage, TClassifiedImage >::InputImagePixelType |
Type definition for the input image pixel type.
Definition at line 148 of file itkMRFImageFilter.h.
typedef TInputImage::Pointer itk::MRFImageFilter< TInputImage, TClassifiedImage >::InputImagePointer |
Definition at line 144 of file itkMRFImageFilter.h.
typedef ImageRegionConstIterator< TInputImage > itk::MRFImageFilter< TInputImage, TClassifiedImage >::InputImageRegionConstIterator |
Definition at line 155 of file itkMRFImageFilter.h.
typedef ImageRegionIterator< TInputImage > itk::MRFImageFilter< TInputImage, TClassifiedImage >::InputImageRegionIterator |
Type definition for the input image region iterator
Definition at line 154 of file itkMRFImageFilter.h.
typedef TInputImage::RegionType itk::MRFImageFilter< TInputImage, TClassifiedImage >::InputImageRegionType |
Type definition for the input image region type.
Definition at line 151 of file itkMRFImageFilter.h.
|
private |
Definition at line 364 of file itkMRFImageFilter.h.
typedef TInputImage itk::MRFImageFilter< TInputImage, TClassifiedImage >::InputImageType |
Type definition for the input image.
Definition at line 140 of file itkMRFImageFilter.h.
typedef LabelledImageFaceListType::iterator itk::MRFImageFilter< TInputImage, TClassifiedImage >::LabelledImageFaceListIterator |
Definition at line 233 of file itkMRFImageFilter.h.
typedef LabelledImageFacesCalculator::FaceListType itk::MRFImageFilter< TInputImage, TClassifiedImage >::LabelledImageFaceListType |
Definition at line 230 of file itkMRFImageFilter.h.
typedef NeighborhoodAlgorithm::ImageBoundaryFacesCalculator< TClassifiedImage > itk::MRFImageFilter< TInputImage, TClassifiedImage >::LabelledImageFacesCalculator |
Definition at line 227 of file itkMRFImageFilter.h.
typedef TClassifiedImage::IndexType itk::MRFImageFilter< TInputImage, TClassifiedImage >::LabelledImageIndexType |
Type definition for the classified image index type.
Definition at line 180 of file itkMRFImageFilter.h.
typedef NeighborhoodIterator< TClassifiedImage > itk::MRFImageFilter< TInputImage, TClassifiedImage >::LabelledImageNeighborhoodIterator |
Labelled image neighborhood interator typedef
Definition at line 221 of file itkMRFImageFilter.h.
typedef LabelledImageNeighborhoodIterator::RadiusType itk::MRFImageFilter< TInputImage, TClassifiedImage >::LabelledImageNeighborhoodRadiusType |
Definition at line 224 of file itkMRFImageFilter.h.
typedef TClassifiedImage::OffsetType itk::MRFImageFilter< TInputImage, TClassifiedImage >::LabelledImageOffsetType |
Type definition for the classified image offset type.
Definition at line 184 of file itkMRFImageFilter.h.
typedef TClassifiedImage::PixelType itk::MRFImageFilter< TInputImage, TClassifiedImage >::LabelledImagePixelType |
Type definitions for the classified image pixel type. It has to be the same type as the training image.
Definition at line 173 of file itkMRFImageFilter.h.
typedef TClassifiedImage::Pointer itk::MRFImageFilter< TInputImage, TClassifiedImage >::LabelledImagePointer |
Type definitions for the labelled image. It is derived from the training image.
Definition at line 169 of file itkMRFImageFilter.h.
typedef ImageRegionIterator< TClassifiedImage > itk::MRFImageFilter< TInputImage, TClassifiedImage >::LabelledImageRegionIterator |
Type definition for the input image region iterator
Definition at line 188 of file itkMRFImageFilter.h.
typedef TClassifiedImage::RegionType itk::MRFImageFilter< TInputImage, TClassifiedImage >::LabelledImageRegionType |
Type definitions for the classified image pixel type. It has to be the same type as the training image.
Definition at line 177 of file itkMRFImageFilter.h.
|
private |
Definition at line 378 of file itkMRFImageFilter.h.
|
private |
Definition at line 375 of file itkMRFImageFilter.h.
|
private |
Definition at line 372 of file itkMRFImageFilter.h.
|
protected |
Definition at line 344 of file itkMRFImageFilter.h.
|
protected |
Labelled status image neighborhood interator typedef
Definition at line 348 of file itkMRFImageFilter.h.
|
private |
Definition at line 369 of file itkMRFImageFilter.h.
|
protected |
Definition at line 343 of file itkMRFImageFilter.h.
|
protected |
Definition at line 340 of file itkMRFImageFilter.h.
|
protected |
Definition at line 341 of file itkMRFImageFilter.h.
|
protected |
Definition at line 342 of file itkMRFImageFilter.h.
typedef TInputImage::SizeType itk::MRFImageFilter< TInputImage, TClassifiedImage >::NeighborhoodRadiusType |
Radius typedef support.
Definition at line 201 of file itkMRFImageFilter.h.
typedef Superclass::OutputImagePointer itk::MRFImageFilter< TInputImage, TClassifiedImage >::OutputImagePointer |
Definition at line 134 of file itkMRFImageFilter.h.
typedef SmartPointer< Self > itk::MRFImageFilter< TInputImage, TClassifiedImage >::Pointer |
Definition at line 132 of file itkMRFImageFilter.h.
typedef MRFImageFilter itk::MRFImageFilter< TInputImage, TClassifiedImage >::Self |
Standard class typedefs.
Definition at line 130 of file itkMRFImageFilter.h.
typedef TInputImage::SizeType itk::MRFImageFilter< TInputImage, TClassifiedImage >::SizeType |
Size and value typedef support.
Definition at line 198 of file itkMRFImageFilter.h.
typedef ImageToImageFilter< TInputImage, TClassifiedImage > itk::MRFImageFilter< TInputImage, TClassifiedImage >::Superclass |
Definition at line 131 of file itkMRFImageFilter.h.
typedef TClassifiedImage::PixelType itk::MRFImageFilter< TInputImage, TClassifiedImage >::TrainingImagePixelType |
Type definitions for the training image pixel type.
Definition at line 165 of file itkMRFImageFilter.h.
typedef TClassifiedImage::Pointer itk::MRFImageFilter< TInputImage, TClassifiedImage >::TrainingImagePointer |
Type definitions for the training image.
Definition at line 162 of file itkMRFImageFilter.h.
enum itk::MRFImageFilter::StopConditionType |
Enumerator | |
---|---|
MaximumNumberOfIterations | |
ErrorTolerance |
Definition at line 296 of file itkMRFImageFilter.h.
|
protected |
|
overrideprotected |
|
protected |
Allocate memory for labelled images.
|
private |
|
protectedvirtual |
Apply MRF Classifier. In this example the images are labelled using Iterated Conditional Mode algorithm by J. Besag, "On statistical analysis of dirty pictures," J. Royal Stat. Soc. B, vol. 48, pp. 259-302, 1986.
|
virtual |
Create an object from an instance, potentially deferring to a factory. This method allows you to create an instance of an object that is exactly the same type as the referring object. This is useful in cases where an object has been cast back to a base class.
Reimplemented from itk::Object.
Reimplemented in itk::RGBGibbsPriorFilter< TInputImage, TClassifiedImage >.
|
protectedvirtual |
|
overrideprotectedvirtual |
Give the process object a chance to indictate that it will produce more output than it was requested to produce. For example, many imaging filters must compute the entire output at once or can only produce output in complete slices. Such filters cannot handle smaller requested regions. These filters must provide an implementation of this method, setting the output requested region to the size they will produce. By default, a process object does not modify the size of the output requested region.
Reimplemented from itk::ProcessObject.
|
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 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< TClassifiedImage >.
Reimplemented in itk::RGBGibbsPriorFilter< TInputImage, TClassifiedImage >.
|
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.
Reimplemented from itk::ImageToImageFilter< TInputImage, TClassifiedImage >.
|
overrideprotectedvirtual |
Generate the information describing the output data. The default implementation of this method will copy information from the input to the output. A filter may override this method if its output will have different information than its input. For instance, a filter that shrinks an image will need to provide an implementation for this method that changes the spacing of the pixels. Such filters should call their superclass' implementation of this method prior to changing the information values they need (i.e. GenerateOutputInformation() should call Superclass::GenerateOutputInformation() prior to changing the information.
Reimplemented from itk::ProcessObject.
|
virtual |
Set/Get the error tollerance level which is used as a threshold to quit the iterations
|
virtual |
Set/Get the number of iteration of the Iterated Conditional Mode (ICM) algorithm. A default value is set at 50 iterations.
Reimplemented in itk::RGBGibbsPriorFilter< TInputImage, TClassifiedImage >.
|
inlinevirtual |
Definition at line 290 of file itkMRFImageFilter.h.
|
virtual |
Run-time type information (and related methods).
Reimplemented from itk::ImageToImageFilter< TInputImage, TClassifiedImage >.
Reimplemented in itk::RGBGibbsPriorFilter< TInputImage, TClassifiedImage >.
|
inline |
Get the neighborhood radius
Definition at line 272 of file itkMRFImageFilter.h.
|
virtual |
Set/Get the number of classes.
Reimplemented in itk::RGBGibbsPriorFilter< TInputImage, TClassifiedImage >.
|
virtual |
|
virtual |
Set/Get the degree of smoothing desired
|
virtual |
Get condition that stops the MRF filter (Number of Iterations / Error tolerance )
|
protectedvirtual |
Minimization algorithm to be used.
Reimplemented in itk::RGBGibbsPriorFilter< TInputImage, TClassifiedImage >.
|
static |
Method for creation through the object factory.
|
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, TClassifiedImage >.
Reimplemented in itk::RGBGibbsPriorFilter< TInputImage, TClassifiedImage >.
void itk::MRFImageFilter< TInputImage, TClassifiedImage >::SetClassifier | ( | typename ClassifierType::Pointer | ptrToClassifier | ) |
Set the pointer to the classifer being used.
|
privatevirtual |
Set/Get the weighting parameters (Beta Matrix). A default 3 x 3 x 3 matrix is provided. However, the user is allowed to override it with their choice of weights for a 3 x 3 x 3 matrix.
|
virtual |
Set/Get the error tollerance level which is used as a threshold to quit the iterations
|
virtual |
Set/Get the number of iteration of the Iterated Conditional Mode (ICM) algorithm. A default value is set at 50 iterations.
Reimplemented in itk::RGBGibbsPriorFilter< TInputImage, TClassifiedImage >.
|
virtual |
Set the weighting parameters (used in MRF algorithms). This is a function allowing the users to set the weight matrix by providing a a 1D array of weights. The default implementation supports a 3 x 3 x 3 kernel. The labeler needs to be extended for a different kernel size.
void itk::MRFImageFilter< TInputImage, TClassifiedImage >::SetNeighborhoodRadius | ( | const NeighborhoodRadiusType & | ) |
Set the neighborhood radius
void itk::MRFImageFilter< TInputImage, TClassifiedImage >::SetNeighborhoodRadius | ( | const SizeValueType | ) |
Sets the radius for the neighborhood, calculates size from the radius, and allocates storage.
void itk::MRFImageFilter< TInputImage, TClassifiedImage >::SetNeighborhoodRadius | ( | const SizeValueType * | radiusArray | ) |
|
virtual |
Set/Get the number of classes.
Reimplemented in itk::RGBGibbsPriorFilter< TInputImage, TClassifiedImage >.
|
virtual |
Set/Get the degree of smoothing desired
|
static |
Labelled Image dimension
Definition at line 192 of file itkMRFImageFilter.h.
|
static |
Image dimension
Definition at line 159 of file itkMRFImageFilter.h.
|
private |
Pointer to the classifier to be used for the MRF labelling.
Definition at line 406 of file itkMRFImageFilter.h.
|
private |
Definition at line 394 of file itkMRFImageFilter.h.
|
private |
Definition at line 403 of file itkMRFImageFilter.h.
|
private |
Definition at line 388 of file itkMRFImageFilter.h.
|
private |
Definition at line 392 of file itkMRFImageFilter.h.
|
private |
Definition at line 380 of file itkMRFImageFilter.h.
|
private |
Definition at line 386 of file itkMRFImageFilter.h.
|
private |
Definition at line 381 of file itkMRFImageFilter.h.
|
private |
Definition at line 398 of file itkMRFImageFilter.h.
|
private |
Definition at line 382 of file itkMRFImageFilter.h.
|
private |
Definition at line 402 of file itkMRFImageFilter.h.
|
private |
Definition at line 385 of file itkMRFImageFilter.h.
|
private |
Definition at line 400 of file itkMRFImageFilter.h.
|
private |
Definition at line 389 of file itkMRFImageFilter.h.
|
private |
Definition at line 401 of file itkMRFImageFilter.h.
|
private |
Definition at line 384 of file itkMRFImageFilter.h.
|
private |
Definition at line 395 of file itkMRFImageFilter.h.
|
private |
Definition at line 393 of file itkMRFImageFilter.h.
|
private |
Definition at line 396 of file itkMRFImageFilter.h.
|
private |
Definition at line 391 of file itkMRFImageFilter.h.
|
private |
Definition at line 390 of file itkMRFImageFilter.h.