ITK  4.1.0
Insight Segmentation and Registration Toolkit
Public Types | Public Member Functions | Static Public Member Functions | Static Public Attributes | Protected Member Functions | Private Types | Private Member Functions | Private Attributes
itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage > Class Template Reference

#include <itkImagePCAShapeModelEstimator.h>

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

List of all members.

Public Types

typedef SmartPointer< const SelfConstPointer
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< SelfPointer
typedef ImagePCAShapeModelEstimator Self
typedef
ImageShapeModelEstimatorBase
< TInputImage, TOutputImage > 
Superclass
typedef vnl_vector< double > VectorOfDoubleType

Public Member Functions

virtual ::itk::LightObject::Pointer CreateAnother (void) 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 ()

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
virtual VectorOfDoubleType GetEigenValues () const
 ImagePCAShapeModelEstimator ()
 ~ImagePCAShapeModelEstimator ()
virtual void PrintSelf (std::ostream &os, Indent indent) const

Detailed Description

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< 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:

Definition at line 77 of file itkImagePCAShapeModelEstimator.h.


Member Typedef Documentation

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
typedef SmartPointer< const Self > itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::ConstPointer
template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
typedef TInputImage::SizeType itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::ImageSizeType [private]

Definition at line 169 of file itkImagePCAShapeModelEstimator.h.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
typedef ImageRegionConstIterator< TInputImage > itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::InputImageConstIterator

Definition at line 103 of file itkImagePCAShapeModelEstimator.h.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
typedef TInputImage::ConstPointer itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::InputImageConstPointer
template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
typedef ImageRegionIterator< TInputImage > itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::InputImageIterator

Type definition for the input image iterator type.

Definition at line 102 of file itkImagePCAShapeModelEstimator.h.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
typedef std::vector< InputImageConstIterator > itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::InputImageIteratorArray [private]

Definition at line 167 of file itkImagePCAShapeModelEstimator.h.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
typedef TInputImage::PixelType itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::InputImagePixelType

Type definition for the input image pixel type.

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

Definition at line 99 of file itkImagePCAShapeModelEstimator.h.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
typedef TInputImage::Pointer itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::InputImagePointer

Type definitions for the training image.

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

Definition at line 95 of file itkImagePCAShapeModelEstimator.h.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
typedef std::vector< InputImageConstPointer > itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::InputImagePointerArray [private]

Local variable typedefs

Definition at line 166 of file itkImagePCAShapeModelEstimator.h.

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

Type definition for the input image.

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

Definition at line 91 of file itkImagePCAShapeModelEstimator.h.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
typedef TInputImage::PixelType itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::InputPixelType [private]

Set up the vector to store the image data.

Definition at line 172 of file itkImagePCAShapeModelEstimator.h.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
typedef vnl_matrix< double > itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::MatrixOfDoubleType

Type definition for a double matrix.

Definition at line 117 of file itkImagePCAShapeModelEstimator.h.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
typedef vnl_matrix< int > itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::MatrixOfIntegerType

Type definition for an integer vector.

Definition at line 120 of file itkImagePCAShapeModelEstimator.h.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
typedef ImageRegionIterator< TOutputImage > itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::OutputImageIterator

Type definition for the input image iterator type.

Definition at line 114 of file itkImagePCAShapeModelEstimator.h.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
typedef TOutputImage::Pointer itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::OutputImagePointer

Reimplemented from itk::ImageSource< TOutputImage >.

Definition at line 111 of file itkImagePCAShapeModelEstimator.h.

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

Type definition for the output image

Reimplemented from itk::ImageSource< TOutputImage >.

Definition at line 110 of file itkImagePCAShapeModelEstimator.h.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
typedef SmartPointer< Self > itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::Pointer
template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
typedef ImagePCAShapeModelEstimator itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::Self

Standard class typedefs.

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

Definition at line 82 of file itkImagePCAShapeModelEstimator.h.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
typedef ImageShapeModelEstimatorBase< TInputImage, TOutputImage > itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::Superclass
template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
typedef vnl_vector< double > itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::VectorOfDoubleType

Type definition for a double vector.

Definition at line 123 of file itkImagePCAShapeModelEstimator.h.


Constructor & Destructor Documentation

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::ImagePCAShapeModelEstimator ( ) [protected]

Get the eigen values

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::~ImagePCAShapeModelEstimator ( ) [protected]

Get the eigen values

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::ImagePCAShapeModelEstimator ( const Self ) [private]

Member Function Documentation

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
void itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::CalculateInnerProduct ( ) [private]
template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
virtual::itk::LightObject::Pointer itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::CreateAnother ( void  ) const [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.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
virtual void itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::EnlargeOutputRequestedRegion ( DataObject ) [protected, virtual]

This filter must produce all of the outputs at once, as such it must override the EnlargeOutputRequestedRegion method to enlarge the output request region.

Reimplemented from itk::ProcessObject.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
void itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::EstimatePCAShapeModelParameters ( ) [private]
template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
virtual void itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::EstimateShapeModels ( ) [private, virtual]

Local functions A function that generates the cluster centers (model) corresponding to the estimates of the cluster centers (in the initial codebook). If no codebook is provided, then use the number of classes to determine the cluster centers or the Shape model. This is the the base function to call the K-means classifier.

Implements itk::ImageShapeModelEstimatorBase< TInputImage, TOutputImage >.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
void itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::GenerateData ( ) [protected, virtual]

Starts the image modelling process

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

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
virtual void itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::GenerateInputRequestedRegion ( ) [protected, virtual]

This filter requires all the input image at once, as such it must override the GenerateInputRequestedRegion method. Additionally, this filter assumes that the input images are at least the size as the first input image.

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

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
virtual VectorOfDoubleType itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::GetEigenValues ( ) const [virtual]

Get the eigen values

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
virtual const char* itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::GetNameOfClass ( ) const [virtual]

Run-time type information (and related methods).

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

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
virtual unsigned int itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::GetNumberOfPrincipalComponentsRequired ( ) const [virtual]
template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
virtual unsigned int itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::GetNumberOfTrainingImages ( ) const [virtual]
template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
static Pointer itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::New ( ) [static]

Method for creation through the object factory.

Reimplemented from itk::Object.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
void itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::operator= ( const Self ) [private]

PushBackInput(), PushFronInput() in the public section force the input to be the type expected by an ImageToImageFilter. However, these methods end of "hiding" the versions from the superclass (ProcessObject) whose arguments are DataObjects. Here, we re-expose the versions from ProcessObject to avoid warnings about hiding methods from the superclass.

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

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
virtual void itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::PrintSelf ( std::ostream &  os,
Indent  indent 
) const [protected, virtual]

Get the eigen values

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

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
virtual void itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::SetNumberOfPrincipalComponentsRequired ( unsigned int  n) [virtual]

Set/Get the number of required largest principal components. The filter produces the required number of principal components plus one outputs. Output index 0 represents the mean image and the remaining outputs the requested principal components.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
virtual void itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::SetNumberOfTrainingImages ( unsigned int  n) [virtual]

Set/Get the number of training images in the input.


Member Data Documentation

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
const unsigned int itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::InputImageDimension = TInputImage::ImageDimension [static]

Input Image dimension

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

Definition at line 107 of file itkImagePCAShapeModelEstimator.h.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
VectorOfDoubleType itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::m_EigenValues [private]

Definition at line 197 of file itkImagePCAShapeModelEstimator.h.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
VectorOfDoubleType itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::m_EigenVectorNormalizedEnergy [private]

Definition at line 199 of file itkImagePCAShapeModelEstimator.h.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
MatrixOfDoubleType itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::m_EigenVectors [private]

Definition at line 195 of file itkImagePCAShapeModelEstimator.h.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
MatrixOfDoubleType itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::m_InnerProduct [private]

Definition at line 193 of file itkImagePCAShapeModelEstimator.h.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
InputImageIteratorArray itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::m_InputImageIteratorArray [private]

Local storage variables

Definition at line 189 of file itkImagePCAShapeModelEstimator.h.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
ImageSizeType itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::m_InputImageSize [private]

Definition at line 201 of file itkImagePCAShapeModelEstimator.h.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
VectorOfDoubleType itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::m_Means [private]

Definition at line 191 of file itkImagePCAShapeModelEstimator.h.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
unsigned int itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::m_NumberOfPixels [private]

Definition at line 203 of file itkImagePCAShapeModelEstimator.h.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
unsigned int itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::m_NumberOfPrincipalComponentsRequired [private]

Definition at line 209 of file itkImagePCAShapeModelEstimator.h.

template<class TInputImage, class TOutputImage = Image< double, ::itk::GetImageDimension< TInputImage >::ImageDimension >>
unsigned int itk::ImagePCAShapeModelEstimator< TInputImage, TOutputImage >::m_NumberOfTrainingImages [private]

Definition at line 206 of file itkImagePCAShapeModelEstimator.h.


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