#include <itkImagePCAShapeModelEstimator.h>

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

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

Detailed Description

template<class TInputImage, class TOutputImage = Image< double, TInputImage::ImageDimension >>
class itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >

Base class for ImagePCAShapeModelEstimator object.

itkImagePCAShapeModelEstimator performs a principal component analysis (PCA) on a set of images. The user specifies the number of training images and also the number of desired largest principal components needed. The ITK pipeline mechanism sets up the storage for both input and output images. The number of output images are the user specified number of desired largest principal components plus 1 (for the mean image).

The algorithm uses the VNL library to perform the eigen analysis. To speed the computation of the instead of performing the eigen analysis of the covariance vector A*A' where A is a matrix with p x t, p = number of pixels or voxels in each images and t = number of training images, we calculate the eigen vectors of the inner product matrix A'*A. The resulting eigen vectors (E) are then multiplied with the the matrix A to get the principal compoenets. The covariance matrix has a dimension of p x p. Since number of pixels in any image being typically very high the eigen decomposition becomes computationally expensive. The inner product on the other hand has the dimension of t x t, where t is typically much smaller that p. Hence the eigen decomposition (most compute intensive part) is an orders of magnitude faster.

The Update() function enables the calculation of the various models, creates the membership function objects and populates them.

Wiki Examples:

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Compute a PCA shape model from a training sample

Definition at line 77 of file itkImagePCAShapeModelEstimator.h.

Public Types
typedef SmartPointer< const Self >	ConstPointer

typedef ImageRegionConstIterator < TInputImage >	InputImageConstIterator

typedef TInputImage::ConstPointer	InputImageConstPointer

typedef ImageRegionIterator < TInputImage >	InputImageIterator

typedef TInputImage::PixelType	InputImagePixelType

typedef TInputImage::Pointer	InputImagePointer

typedef TInputImage	InputImageType

typedef vnl_matrix< double >	MatrixOfDoubleType

typedef vnl_matrix< int >	MatrixOfIntegerType

typedef ImageRegionIterator < TOutputImage >	OutputImageIterator

typedef TOutputImage::Pointer	OutputImagePointer

typedef TOutputImage	OutputImageType

typedef SmartPointer< Self >	Pointer

typedef ImagePCAShapeModelEstimator	Self

typedef ImageShapeModelEstimatorBase < TInputImage, TOutputImage >	Superclass

typedef vnl_vector< double >	VectorOfDoubleType

Public Types inherited from itk::ImageShapeModelEstimatorBase< TInputImage, TOutputImage >
typedef SmartPointer< const Self >	ConstPointer

typedef TInputImage::Pointer	InputImagePointer

typedef TInputImage	InputImageType

typedef SmartPointer< Self >	Pointer

typedef ImageShapeModelEstimatorBase	Self

typedef ImageToImageFilter < TInputImage, TOutputImage >	Superclass

Public Types inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
typedef SmartPointer< const Self >	ConstPointer

typedef InputImageType::ConstPointer	InputImageConstPointer

typedef InputImageType::PixelType	InputImagePixelType

typedef InputImageType::Pointer	InputImagePointer

typedef InputImageType::RegionType	InputImageRegionType

typedef TInputImage	InputImageType

typedef Superclass::OutputImagePixelType	OutputImagePixelType

typedef Superclass::OutputImageRegionType	OutputImageRegionType

typedef SmartPointer< Self >	Pointer

typedef ImageToImageFilter	Self

typedef ImageSource< TOutputImage >	Superclass

Public Types inherited from itk::ImageSource< TOutputImage >
typedef SmartPointer< const Self >	ConstPointer

typedef Superclass::DataObjectIdentifierType	DataObjectIdentifierType

typedef DataObject::Pointer	DataObjectPointer

typedef Superclass::DataObjectPointerArraySizeType	DataObjectPointerArraySizeType

typedef OutputImageType::PixelType	OutputImagePixelType

typedef OutputImageType::Pointer	OutputImagePointer

typedef OutputImageType::RegionType	OutputImageRegionType

typedef TOutputImage	OutputImageType

typedef SmartPointer< Self >	Pointer

typedef ImageSource	Self

typedef ProcessObject	Superclass

Public Types inherited from itk::ProcessObject
typedef SmartPointer< const Self >	ConstPointer

typedef DataObject::DataObjectIdentifierType	DataObjectIdentifierType

typedef DataObject::Pointer	DataObjectPointer

typedef std::vector < DataObjectPointer >	DataObjectPointerArray

typedef DataObjectPointerArray::size_type	DataObjectPointerArraySizeType

typedef std::vector < DataObjectIdentifierType >	NameArray

typedef SmartPointer< Self >	Pointer

typedef ProcessObject	Self

typedef Object	Superclass

Public Types inherited from itk::Object
typedef SmartPointer< const Self >	ConstPointer

typedef SmartPointer< Self >	Pointer

typedef Object	Self

typedef LightObject	Superclass

Public Types inherited from itk::LightObject
typedef SmartPointer< const Self >	ConstPointer

typedef SmartPointer< Self >	Pointer

typedef LightObject	Self

Public Member Functions
virtual ::itk::LightObject::Pointer	CreateAnother (void) const

virtual VectorOfDoubleType	GetEigenValues () const

virtual const char *	GetNameOfClass () const

virtual unsigned int	GetNumberOfPrincipalComponentsRequired () const

virtual unsigned int	GetNumberOfTrainingImages () const

virtual void	SetNumberOfPrincipalComponentsRequired (unsigned int n)

virtual void	SetNumberOfTrainingImages (unsigned int n)

Static Public Member Functions
static Pointer	New ()

Static Public Attributes
static const unsigned int	InputImageDimension = TInputImage::ImageDimension

Protected Member Functions
virtual void	EnlargeOutputRequestedRegion (DataObject *)

void	GenerateData ()

virtual void	GenerateInputRequestedRegion ()

	ImagePCAShapeModelEstimator ()

virtual void	PrintSelf (std::ostream &os, Indent indent) const

	~ImagePCAShapeModelEstimator ()

Protected Member Functions inherited from itk::ImageShapeModelEstimatorBase< TInputImage, TOutputImage >
	ImageShapeModelEstimatorBase ()

void	PrintSelf (std::ostream &os, Indent indent) const

	~ImageShapeModelEstimatorBase ()

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 ()

virtual void	VerifyInputInformation ()

	~ImageToImageFilter ()

void	PushBackInput (const DataObject *input)

void	PushFrontInput (const DataObject *input)

Protected Member Functions inherited from itk::ImageSource< TOutputImage >
virtual void	AfterThreadedGenerateData ()

virtual void	AllocateOutputs ()

virtual void	BeforeThreadedGenerateData ()

virtual const ImageRegionSplitterBase *	GetImageRegionSplitter (void) const

	ImageSource ()

virtual unsigned int	SplitRequestedRegion (unsigned int i, unsigned int num, OutputImageRegionType &splitRegion)

virtual void	ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, ThreadIdType threadId)

virtual	~ImageSource ()

Protected Member Functions inherited from itk::ProcessObject
virtual void	AddInput (DataObject *input)

virtual void	AddOutput (DataObject *output)

virtual void	CacheInputReleaseDataFlags ()

virtual void	GenerateOutputInformation ()

virtual void	GenerateOutputRequestedRegion (DataObject *output)

virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredOutputs ()

bool	IsIndexedInputName (const DataObjectIdentifierType &) const

bool	IsIndexedOutputName (const DataObjectIdentifierType &) const

	itkLegacyMacro (virtual void RemoveOutput(DataObject *output))

	itkLegacyMacro (void SetNumberOfOutputs(DataObjectPointerArraySizeType num))

	itkLegacyMacro (virtual void RemoveInput(DataObject *input))

	itkLegacyMacro (void SetNumberOfInputs(DataObjectPointerArraySizeType num))

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)

virtual void	RestoreInputReleaseDataFlags ()

virtual void	SetInput (const DataObjectIdentifierType &key, DataObject *input)

virtual void	SetNthInput (DataObjectPointerArraySizeType num, DataObject *input)

virtual void	SetNthOutput (DataObjectPointerArraySizeType num, DataObject *output)

void	SetNumberOfIndexedInputs (DataObjectPointerArraySizeType num)

void	SetNumberOfIndexedOutputs (DataObjectPointerArraySizeType num)

virtual void	SetNumberOfRequiredOutputs (DataObjectPointerArraySizeType _arg)

virtual void	SetOutput (const DataObjectIdentifierType &key, DataObject *output)

virtual void	SetPrimaryInput (DataObject *input)

virtual void	SetPrimaryOutput (DataObject *output)

virtual void	VerifyPreconditions ()

	~ProcessObject ()

DataObject *	GetInput (const DataObjectIdentifierType &key)

const DataObject *	GetInput (const DataObjectIdentifierType &key) const

DataObject *	GetInput (DataObjectPointerArraySizeType idx)

const DataObject *	GetInput (DataObjectPointerArraySizeType idx) const

DataObject *	GetPrimaryInput ()

const DataObject *	GetPrimaryInput () const

virtual void	SetPrimaryInputName (const DataObjectIdentifierType &key)

virtual const char *	GetPrimaryInputName (void) const

virtual void	SetNumberOfRequiredInputs (DataObjectPointerArraySizeType)

virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredInputs ()

bool	AddRequiredInputName (const DataObjectIdentifierType &)

bool	AddRequiredInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx)

bool	RemoveRequiredInputName (const DataObjectIdentifierType &)

bool	IsRequiredInputName (const DataObjectIdentifierType &) const

void	SetRequiredInputNames (const NameArray &)

DataObject *	GetOutput (const DataObjectIdentifierType &key)

const DataObject *	GetOutput (const DataObjectIdentifierType &key) const

virtual void	SetPrimaryOutputName (const DataObjectIdentifierType &key)

virtual const char *	GetPrimaryOutputName (void) const

DataObject *	GetOutput (DataObjectPointerArraySizeType idx)

const DataObject *	GetOutput (DataObjectPointerArraySizeType idx) const

DataObject *	GetPrimaryOutput ()

const DataObject *	GetPrimaryOutput () const

Protected Member Functions inherited from itk::Object
	Object ()

bool	PrintObservers (std::ostream &os, Indent indent) const

virtual void	SetTimeStamp (const TimeStamp &time)

virtual	~Object ()

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 Types
typedef TInputImage::SizeType	ImageSizeType

typedef std::vector < InputImageConstIterator >	InputImageIteratorArray

typedef std::vector < InputImageConstPointer >	InputImagePointerArray

typedef TInputImage::PixelType	InputPixelType

Private Member Functions
void	CalculateInnerProduct ()

void	EstimatePCAShapeModelParameters ()

virtual void	EstimateShapeModels ()

	ImagePCAShapeModelEstimator (const Self &)

void	operator= (const Self &)

Private Attributes
VectorOfDoubleType	m_EigenValues

VectorOfDoubleType	m_EigenVectorNormalizedEnergy

MatrixOfDoubleType	m_EigenVectors

MatrixOfDoubleType	m_InnerProduct

InputImageIteratorArray	m_InputImageIteratorArray

ImageSizeType	m_InputImageSize

VectorOfDoubleType	m_Means

unsigned int	m_NumberOfPixels

unsigned int	m_NumberOfPrincipalComponentsRequired

unsigned int	m_NumberOfTrainingImages

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