itkDiffusionTensorPrincipalDirectionImageFilter.h

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/*===================================================================

The Medical Imaging Interaction Toolkit (MITK)

Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.

This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.

See LICENSE.txt or http://www.mitk.org for details.

===================================================================*/

/*===================================================================

This file is based heavily on a corresponding ITK filter.

===================================================================*/
#ifndef __itkDiffusionTensorPrincipalDirectionImageFilter_h_
#define __itkDiffusionTensorPrincipalDirectionImageFilter_h_

#include <MitkDiffusionCoreExports.h>
#include <itkImageToImageFilter.h>
#include <vnl/vnl_vector_fixed.h>
#include <vnl/vnl_matrix.h>
#include <vnl/algo/vnl_svd.h>
#include <itkVectorContainer.h>
#include <itkVectorImage.h>
#include <itkDiffusionTensor3D.h>
#include <mitkFiberBundle.h>

namespace itk{
template< class TTensorPixelType, class TPDPixelType=float>
class DiffusionTensorPrincipalDirectionImageFilter :
        public ImageToImageFilter< Image< DiffusionTensor3D<TTensorPixelType>, 3 >, Image< Vector< TPDPixelType, 3 >, 3 > >
{

public:

    typedef DiffusionTensorPrincipalDirectionImageFilter Self;
    typedef SmartPointer<Self>                      Pointer;
    typedef SmartPointer<const Self>                ConstPointer;
    typedef ImageToImageFilter< Image< DiffusionTensor3D<TTensorPixelType>, 3 >, Image< Vector< TPDPixelType, 3 >, 3 > >
    Superclass;

    itkFactorylessNewMacro(Self)
    itkCloneMacro(Self)

    itkTypeMacro(DiffusionTensorPrincipalDirectionImageFilter, ImageToImageFilter)

    typedef TTensorPixelType                            TensorComponentType;
    typedef TPDPixelType                                DirectionPixelType;
    typedef typename Superclass::InputImageType         InputImageType;
    typedef typename Superclass::OutputImageType        OutputImageType;
    typedef typename Superclass::OutputImageRegionType  OutputImageRegionType;
    typedef itk::Image<unsigned char, 3>                ItkUcharImgType;
    typedef vnl_vector_fixed< double, 3 >               DirectionType;

    void SetImage( const InputImageType *image );

    // input
    itkSetMacro( MaskImage, ItkUcharImgType::Pointer)
    itkSetMacro( NormalizeVectors, bool)

    // output
    itkGetMacro( OutputFiberBundle, mitk::FiberBundle::Pointer)
    itkGetMacro( NumDirectionsImage, ItkUcharImgType::Pointer)

    protected:
        DiffusionTensorPrincipalDirectionImageFilter();
    ~DiffusionTensorPrincipalDirectionImageFilter() {}
    void PrintSelf(std::ostream& os, Indent indent) const;

    void BeforeThreadedGenerateData();
    void ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, ThreadIdType );
    void AfterThreadedGenerateData();

private:

    bool                                m_NormalizeVectors;     
    mitk::FiberBundle::Pointer         m_OutputFiberBundle;    
    ItkUcharImgType::Pointer            m_NumDirectionsImage;   
    ItkUcharImgType::Pointer            m_MaskImage;            
    float                               m_MaxEigenvalue;
};

}

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkDiffusionTensorPrincipalDirectionImageFilter.txx"
#endif

#endif //__itkDiffusionTensorPrincipalDirectionImageFilter_h_