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NA-MICNational Alliance for Medical Image Computing http://na-mic.org

ITK Workshop

October 5-8, 2005

Writing a New ITK Filter

National Alliance for Medical Image Computing http://na-mic.org

ITK Workshop – Extending the Toolkit

• Filters Anatomy– Class Hierarchy– Inputs– Outputs

• UnaryFunctorFilter– Casting Example– Division by 2 Example– Functor with parameters Example

• Regions and Iterators– Defining properties of the Output Image– Allocating the output– Using Iterators


Anatomy of an ITK Filter

Insight Toolkit - Advanced Course


The Class Hierarchy

itk::ProcessObjectitk::DataObject

itk::Object

itk::ImageBase

itk::Image

itk::ImageSource

itk::ImageToImageFilter


The Class Hierarchy

itk::InPlaceImageFilter

itk::UnaryFunctorImageFilter itk::BinaryFunctorImageFilter

itk::TernaryFunctorImageFilter

itk::ImageToImageFilter


Filter Typical Elements

InputImage

OutputImage

Filter

Parameters


InPlace Filter Elements

InputImage

OutputImage

Filter

Parameters


The Unary Functor Image Filter



Image Filter Hierarchy

template <class TInputImage, class TOutputImage>

class ImageToImageFilter : public ImageSource< TOutputImage >

{…};

template <class TInputImage, class TOutputImage>

class InPlaceToImageFilter :

public ImageToImageFilter< TOutputImage , TOutputImage >

{…};

template <class TOutputImage>

class ImageSource : public ProcessObject

{…};


Unary Functor Filter

itk::UnaryFunctorImageFilter

Pixel-WiseImageFilter

Input Image Output Image


It should be enough to specify the

operation to be applied on each pixel


That is the role of the

FUNCTOR



Filter

Functor

template <class TInputImage, class TOutputImage, class TFunctor>

class UnaryFunctorImageFilter :

public InPlaceImageFilter< TInputImage, TOutputImage >{

private:

TFunctor m_Functor;

};


Exercise 23


Create an Image Filter that

performs Casting


namespace itk {

namespace Functor {

template< class TInput, class TOutput> class Cast { public: Cast() {}; ~Cast() {}; inline TOutput operator()( const TInput & A ) { return static_cast<TOutput>( A ); } };

} // end of Functor namespace

Unary Functor Filter Example : Casting



#include “itkUnaryFunctorImageFilter.h”

template<class TInputImage, class TOutputImage>class MyFunctorImageFilter : public UnaryFunctorImageFilter< TInputImage,TOutputImage, Functor::Cast< typename TInputImage::PixelType, typename TOutputImage::PixelType> > {

…


public: typedef MyFunctorImageFilter Self; typedef UnaryFunctorImageFilter< TInputImage, TOutputImage, Functor::Cast< typename TInputImage::PixelType, typename TOutputImage::PixelType > > Superclass;

typedef SmartPointer< Self > Pointer; typedef SmartPointer< const Self > ConstPointer;

itkNewMacro( Self );

itkTypeMacro( MyFunctorImageFilter, UnaryFunctorImageFilter );



Typical Declarations: Traits and Macros

• Traits

• Self

• Superclass

• Pointer

• ConstPointer

• Macros

• NewMacro

• TypeMacro


protected:

MyFunctorImageFilter() {} virtual ~MyFunctorImageFilter() {}

private:

MyFunctorImageFilter( const Self & ); // purposely not implemented void operator=( const Self & ); // purposely not implemented

}; // end of class

} // end of namespace itk



#include “MyFunctorImageFilter.h”

int main() { typedef itk::Image< unsigned char, 2 > InputImageType; typedef itk::Image< unsigned short, 2 > OutputImageType;

typedef itk::MyFunctorImageFilter< InputImageType, OutputImageType > FilterType; FilterType::Pointer filter = FilterType::New();

}



Exercise 24


Create an Image Filter that divides all the intensity values by 2


NOTE


The use of itk::NumericTraits<>

and RealType

and typename


namespace itk {

namespace Functor {

template< class TInput, class TOutput> class Divider { public: Divider() {}; ~Divider() {}; inline TOutput operator()( const TInput & A ) { typedef typename NumericTraits<TInput>::RealType InputRealType; return static_cast<TOutput>( InputRealType( A ) / 2.0 ); } };

} // end of Functor namespace

Exercise


Exercise

#include “itkUnaryFunctorImageFilter.h”

template<class TInputImage, class TOutputImage>class DividerByTwoImageFilter : public UnaryFunctorImageFilter< TInputImage,TOutputImage, Functor::Divider< typename TInputImage::PixelType, typename TOutputImage::PixelType> >{public:

typedef MyFunctorImageFilter Self;

typedef UnaryFunctorImageFilter< TInputImage, TOutputImage, Functor::Divider< typename TInputImage::PixelType, typename TOutputImage::PixelType> > Superclass;…


Exercise 25


Create an Image Filter that divides all the intensity values by a given value


namespace itk { namespace Functor { template< class TInput, class TOutput> class Divider { public: Divider() {}; ~Divider() {}; typedef typename NumericTraits<TInput>::RealType InputRealType; inline TOutput operator()( const TInput & A ) { return static_cast<TOutput>( InputRealType( A ) / m_Divisor ); } void SetDivisor( const InputRealType & value ) { m_Divisor = value; } private: InputRealType m_Divisor; };

Exercise : Functors with parameters



template<class TInputImage, class TOutputImage>class DividerImageFilter : public UnaryFunctorImageFilter< TInputImage,TOutputImage, Divider< typename TInputImage::PixelType, typename TOutputImage::PixelType> >{…public: typedef typename Superclass::FunctorType FunctorType; typedef typename FunctorType::InputRealType InputRealType;

void SetDivisor( const InputRealType & value ) { this->GetFunctor().SetDivisor( value ); }


#include “DividerImageFilter.h”

int main() { typedef itk::Image< unsigned char, 2 > InputImageType; typedef itk::Image< unsigned short, 2 > OutputImageType;

typedef itk::DividerImageFilter< InputImageType, OutputImageType > FilterType; FilterType::Pointer filter = FilterType::New();

filter->SetDivisor( 7.5 );

}



Image Regions



Insight Toolkit – Image Regions

LargestPossibleRegion

BufferedRegion

RequestedRegion


Filter Typical Elements

InputImage

OutputImage

Filter

Parameters

Region Region



InputRegion

OutputRegion

Input Image Output Image


Generate Output Information Method

Filter

virtual voidGenerateOutputInformation(){ Superclass::GenerateOutputInformation();

OutputImagePointer outputPtr = this->GetOutput();

outputPtr->SetLargestPossibleRegion(…); outputPtr->SetSpacing(…); outputPtr->SetOrigin(…);}


Generate Output Information Method

• Spacing

• Origin

• Orientation (Direction)

• LargestPossibleRegion

This method configures the Output Image

by default it copies meta data from the Input


Exercise 26


Create an Image Filter that extractsthe first quadrant of an image


Quadrant Extract Image Filter Example

#include “itkImageToImageFilter.h”

template<class TInputImage>class FirstQuadrantExtractImageFilter : public ImageToImageFilter< TInputImage,TInputImage >{public: typedef FirstQuadrantExtractImageFilter Self; typedef ImageToImageFilter< TInputImage, TInputImage > Superclass;

typedef SmartPointer< Self > Pointer; typedef SmartPointer< const Self > ConstPointer;

itkNewMacro( Self );

itkTypeMacro( FirstQuadrantExtractImageFilter, ImageToImageFilter ); …


Quadrant Extract Image Filter Example

typedef typename TInputImage::RegionType RegionType;typedef typename TInputImage::SizeType SizeType;typedef typename TInputImage::IndexType IndexType;

typedef typename TInputImage::Pointer ImagePointer;typedef typename TInputImage::ConstPointer ImageConstPointer;

protected:

FirstQuadrantExtractImageFilter() {}; ~FirstQuadrantExtractImageFilter() {};

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

void GenerateOutputInformation();

void GenerateData();


GenerateOutputInformation() Method

• Call Superclass::GenerateOutputInformation()

• Set Parameters of the Output Image

• Spacing

• Origin

• Direction

• LargestPossibleRegion



template< class TInputImage >void GenerateOutputInformation(){ Superclass::GenerateOutputInformation();

ImageConstPointer inputImage = this->GetInput(); ImagePointer outputImage = this->GetOutput();

RegionType inputRegion = inputImage->GetLargestPossibleRegion ();

IndexType inputStart = inputRegion.GetIndex(); SizeType inputSize = inputRegion.GetSize();



IndexType outputStart; SizeType outputSize;

const unsigned int Dimension = TInputImage::ImageDimension;

for( unsigned int i = 0; i < Dimension; i++ ) { outputSize[i] = inputSize[i] / 2; outputStart[i] = inputStart[i]; }

RegionType outputRegion;

outputRegion.SetIndex( outputStart ); outputRegion.SetSize( outputSize );



outputImage->SetLargestPossibleRegion( outputRegion );

outputImage->SetSpacing( inputImage->GetSpacing() );

outputImage->SetOrigin( inputImage->GetOrigin() );

outputImage->SetDirection( inputImage->GetDirection() );

} // end of GenerateOutputInformation() method


GenerateData() Method

• Get Input and Output Image pointers

• Invokes GetInput()

• Invokes GetOutput()

• Allocate memory for the Output Image (s)

• Invokes SetRegions()

• Invokes Allocate()

• Computes pixels of Output Image

• Usually requires Image Iterators



template< class TInputImage >void GenerateData(){

ImageConstPointer inputImage = this->GetInput(); ImagePointer outputImage = this->GetOutput();

RegionType outputRegion = outputImage->GetLargestPossibleRegion();

outputImage->SetRegions( outputRegion ); outputImage->Allocate();

typedef ImageRegionIterator< TInputImage > ImageIterator; typedef ImageRegionConstIterator< TInputImage > ImageConstIterator;

ImageIterator outputIterator( outputImage, outputRegion ); ImageConstIterator inputIterator( inputImage, outputRegion );



First Quadrant

InputImageRegion

OutputImageRegion



inputIterator.GoToBegin();outputIterator.GoToBegin();

while( ! outputIterator.IsAtEnd() ) {

outputIterator.Set( inputIterator.Get() );

++inputIterator; ++outputIterator;

}


Exercise 26b


Modify the code for extractingthe central thirds an image



InputImageRegion

OutputImageRegion

Central Third


END


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