mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType > Class Template Reference

#include <mitkTeemDiffusionTensor3DReconstructionImageFilter.h>

Collaboration diagram for mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >:

List of all members.

Public Types
typedef TTensorPixelType	TensorPixelType
typedef itk::Vector < TensorPixelType, 7 >	VectorType
typedef itk::Image< VectorType, 3 >	VectorImageType
typedef itk::DiffusionTensor3D < TensorPixelType >	TensorType
typedef itk::Image< TensorType, 3 >	ItkTensorImageType
typedef itk::Vector < TensorPixelType, 6 >	ItkTensorVectorType
typedef itk::Image < ItkTensorVectorType, 3 >	ItkTensorVectorImageType
typedef DiffusionImagePixelType	DiffusionPixelType
typedef itk::VectorImage < DiffusionPixelType, 3 >	DiffusionImageType
typedef TeemDiffusionTensor3DReconstructionImageFilter	Self
typedef itk::Object	Superclass
typedef itk::SmartPointer< Self >	Pointer
typedef itk::SmartPointer < const Self >	ConstPointer
Public Member Functions
virtual const char *	GetClassName () const
virtual DiffusionImage < DiffusionImagePixelType > ::Pointer	GetInput ()
virtual void	SetInput (typename DiffusionImage< DiffusionImagePixelType >::Pointer _arg)
virtual bool	GetEstimateErrorImage ()
virtual void	SetEstimateErrorImage (bool _arg)
virtual float	GetSigma ()
virtual void	SetSigma (float _arg)
virtual TeemTensorEstimationMethods	GetEstimationMethod ()
virtual void	SetEstimationMethod (TeemTensorEstimationMethods _arg)
virtual int	GetNumIterations ()
virtual void	SetNumIterations (int _arg)
virtual double	GetConfidenceThreshold ()
virtual void	SetConfidenceThreshold (double _arg)
virtual float	GetConfidenceFuzzyness ()
virtual void	SetConfidenceFuzzyness (float _arg)
virtual double	GetMinPlausibleValue ()
virtual void	SetMinPlausibleValue (double _arg)
virtual mitk::TensorImage::Pointer	GetOutput ()
virtual mitk::TensorImage::Pointer	GetOutputItk ()
virtual void	Update ()
Static Public Member Functions
static Pointer	New ()
Protected Member Functions
	TeemDiffusionTensor3DReconstructionImageFilter ()
virtual	~TeemDiffusionTensor3DReconstructionImageFilter ()
Protected Attributes
DiffusionImage < DiffusionImagePixelType > ::Pointer	m_Input
bool	m_EstimateErrorImage
float	m_Sigma
TeemTensorEstimationMethods	m_EstimationMethod
int	m_NumIterations
double	m_ConfidenceThreshold
float	m_ConfidenceFuzzyness
double	m_MinPlausibleValue
mitk::TensorImage::Pointer	m_Output
mitk::TensorImage::Pointer	m_OutputItk
mitk::Image::Pointer	m_ErrorImage

---

Detailed Description

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>
class mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >

Definition at line 39 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.h.

---

Member Typedef Documentation

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

typedef itk::SmartPointer<const Self> mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::ConstPointer

Definition at line 58 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.h.

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

typedef itk::VectorImage< DiffusionPixelType, 3 > mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::DiffusionImageType

Definition at line 55 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.h.

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

typedef DiffusionImagePixelType mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::DiffusionPixelType

Definition at line 54 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.h.

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

typedef itk::Image<TensorType,3 > mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::ItkTensorImageType

Definition at line 49 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.h.

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

typedef itk::Image<ItkTensorVectorType,3> mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::ItkTensorVectorImageType

Definition at line 52 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.h.

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

typedef itk::Vector<TensorPixelType,6> mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::ItkTensorVectorType

Definition at line 51 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.h.

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

typedef itk::SmartPointer<Self> mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::Pointer

Definition at line 58 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.h.

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

typedef TeemDiffusionTensor3DReconstructionImageFilter mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::Self

Definition at line 58 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.h.

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

typedef itk::Object mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::Superclass

Definition at line 58 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.h.

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

typedef TTensorPixelType mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::TensorPixelType

Definition at line 43 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.h.

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

typedef itk::DiffusionTensor3D<TensorPixelType> mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::TensorType

Definition at line 48 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.h.

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

typedef itk::Image<VectorType,3> mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::VectorImageType

Definition at line 46 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.h.

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

typedef itk::Vector<TensorPixelType,7> mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::VectorType

Definition at line 45 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.h.

---

Constructor & Destructor Documentation

template<class D , class T >

mitk::TeemDiffusionTensor3DReconstructionImageFilter< D, T >::TeemDiffusionTensor3DReconstructionImageFilter

(

)

[protected]

Definition at line 33 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.cpp.

                                                :
m_EstimateErrorImage(false),m_Sigma(-19191919),
m_EstimationMethod(TeemTensorEstimationMethodsLLS),
m_NumIterations(1),m_ConfidenceThreshold(-19191919.0),
m_ConfidenceFuzzyness(0.0),m_MinPlausibleValue(1.0)
{
}

template<class D , class T >

mitk::TeemDiffusionTensor3DReconstructionImageFilter< D, T >::~TeemDiffusionTensor3DReconstructionImageFilter

(

)

[protected, virtual]

Definition at line 43 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.cpp.

{
}

---

Member Function Documentation

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

virtual const char* mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::GetClassName

(

)

const [virtual]

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

virtual float mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::GetConfidenceFuzzyness

(

)

[virtual]

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

virtual double mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::GetConfidenceThreshold

(

)

[virtual]

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

virtual bool mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::GetEstimateErrorImage

(

)

[virtual]

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

virtual TeemTensorEstimationMethods mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::GetEstimationMethod

(

)

[virtual]

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

virtual DiffusionImage<DiffusionImagePixelType>::Pointer mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::GetInput

(

)

[virtual]

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

virtual double mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::GetMinPlausibleValue

(

)

[virtual]

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

virtual int mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::GetNumIterations

(

)

[virtual]

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

virtual mitk::TensorImage::Pointer mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::GetOutput

(

)

[virtual]

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

virtual mitk::TensorImage::Pointer mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::GetOutputItk

(

)

[virtual]

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

virtual float mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::GetSigma

(

)

[virtual]

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

static Pointer mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::New

(

)

[static]

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

virtual void mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::SetConfidenceFuzzyness

(

float

_arg )

[virtual]

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

virtual void mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::SetConfidenceThreshold

(

double

_arg )

[virtual]

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

virtual void mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::SetEstimateErrorImage

(

bool

_arg )

[virtual]

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

virtual void mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::SetEstimationMethod

(

TeemTensorEstimationMethods

_arg )

[virtual]

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

virtual void mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::SetInput

(

typename DiffusionImage< DiffusionImagePixelType >::Pointer

_arg )

[virtual]

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

virtual void mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::SetMinPlausibleValue

(

double

_arg )

[virtual]

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

virtual void mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::SetNumIterations

(

int

_arg )

[virtual]

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

virtual void mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::SetSigma

(

float

_arg )

[virtual]

template<class D , class T >

void mitk::TeemDiffusionTensor3DReconstructionImageFilter< D, T >::Update

(

)

[virtual]

Definition at line 76 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.cpp.

References file_replace(), MITK_ERROR, mitk::TensorImage::New(), mitk::TeemTensorEstimationMethodsLLS, mitk::TeemTensorEstimationMethodsMLE, mitk::TeemTensorEstimationMethodsNLS, and mitk::TeemTensorEstimationMethodsWLS.

{

  // save input image to nrrd file in temp-folder
  char filename[512];
  srand((unsigned)time(0)); 
  int random_integer = rand();
  sprintf( filename, "dwi_%d.nhdr",random_integer);
  
  typedef mitk::NrrdDiffusionImageWriter<D> WriterType;
  typename WriterType::Pointer nrrdWriter = WriterType::New();
  nrrdWriter->SetInput( m_Input );
  //nrrdWriter->SetDirections(m_Input->GetDirections());
  //nrrdWriter->SetB_Value(m_Input->GetB_Value());
  nrrdWriter->SetFileName(filename);
  try
  {
    nrrdWriter->Update();
  }
  catch (itk::ExceptionObject e)
  {
    std::cout << e << std::endl;
  }

  file_replace(filename,"vector","list");

  // build up correct command from input params
  char command[4096];
  sprintf( command, "tend estim -i %s -B kvp -o tensors_%d.nhdr -knownB0 true",
    filename, random_integer);

  //m_DiffusionImages;
  if(m_EstimateErrorImage)
  {
    sprintf( command, "%s -ee error_image_%d.nhdr", command, random_integer);
  }

  if(m_Sigma != -19191919)
  {
    sprintf( command, "%s -sigma %f", command, m_Sigma);
  }

  switch(m_EstimationMethod)
  {
  case TeemTensorEstimationMethodsLLS:
    sprintf( command, "%s -est lls", command);
    break;
  case TeemTensorEstimationMethodsMLE:
    sprintf( command, "%s -est mle", command);
    break;
  case TeemTensorEstimationMethodsNLS:
    sprintf( command, "%s -est nls", command);
    break;
  case TeemTensorEstimationMethodsWLS:
    sprintf( command, "%s -est wls", command);
    break;
  }
  
  sprintf( command, "%s -wlsi %d", command, m_NumIterations);

  if(m_ConfidenceThreshold != -19191919.0)
  {
    sprintf( command, "%s -t %f", command, m_ConfidenceThreshold);
  }
  
  sprintf( command, "%s -soft %f", command, m_ConfidenceFuzzyness);
  sprintf( command, "%s -mv %f", command, m_MinPlausibleValue);
  
  // call tend estim command
  std::cout << "Calling <" << command << ">" << std::endl;
  int success = system(command);
  if(!success)
  {
    MITK_ERROR << "system command could not be called!";
  }

  remove(filename);
  sprintf( filename, "dwi_%d.raw", random_integer);
  remove(filename);

  // change kind from tensor to vector
  sprintf( filename, "tensors_%d.nhdr", random_integer);
  file_replace(filename,"3D-masked-symmetric-matrix","vector");

  //file_replace(filename,"3D-symmetric-matrix","vector");
  //itksys::SystemTools::ReplaceString(line,"3D-masked-symmetric-matrix","vector");
  //itksys::SystemTools::ReplaceString(line,"vector","domain");

  // read result as mitk::Image and provide it in m_Output
  typedef itk::ImageFileReader<VectorImageType> FileReaderType;
  typename FileReaderType::Pointer reader = FileReaderType::New();
  reader->SetFileName(filename);
  reader->Update();
  typename VectorImageType::Pointer vecImage = reader->GetOutput();
  
  remove(filename);
  sprintf( filename, "tensors_%d.raw", random_integer);
  remove(filename);

  typename ItkTensorImageType::Pointer itkTensorImage = ItkTensorImageType::New();
  itkTensorImage->SetSpacing( vecImage->GetSpacing() );   // Set the image spacing
  itkTensorImage->SetOrigin( vecImage->GetOrigin() );     // Set the image origin
  itkTensorImage->SetDirection( vecImage->GetDirection() );  // Set the image direction
  itkTensorImage->SetLargestPossibleRegion( vecImage->GetLargestPossibleRegion() );
  itkTensorImage->SetBufferedRegion( vecImage->GetLargestPossibleRegion() );
  itkTensorImage->SetRequestedRegion( vecImage->GetLargestPossibleRegion() );
  itkTensorImage->Allocate();
  
  itk::ImageRegionIterator<VectorImageType> it(vecImage,
    vecImage->GetLargestPossibleRegion());

  itk::ImageRegionIterator<ItkTensorImageType> it2(itkTensorImage,
    itkTensorImage->GetLargestPossibleRegion());
  it2 = it2.Begin();

  //#pragma omp parallel private (it)
  {
    for(it=it.Begin();!it.IsAtEnd(); ++it, ++it2)
    {
      //#pragma omp single nowait
      {
        VectorType vec = it.Get();
        TensorType tensor;
        for(int i=1;i<7;i++)
          tensor[i-1] = vec[i] * vec[0];
        it2.Set( tensor );
      }
    } // end for
  } // end ompparallel

  m_OutputItk = mitk::TensorImage::New();
  m_OutputItk->InitializeByItk(itkTensorImage.GetPointer());
  m_OutputItk->SetVolume( itkTensorImage->GetBufferPointer() );

  // in case: read resulting error-image and provide it in m_ErrorImage
  if(m_EstimateErrorImage)
  {
    // open error image here
  }

}

---

Member Data Documentation

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

float mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::m_ConfidenceFuzzyness [protected]

Definition at line 104 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.h.

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

double mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::m_ConfidenceThreshold [protected]

Definition at line 103 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.h.

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

mitk::Image::Pointer mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::m_ErrorImage [protected]

Definition at line 108 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.h.

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

bool mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::m_EstimateErrorImage [protected]

Definition at line 99 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.h.

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

TeemTensorEstimationMethods mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::m_EstimationMethod [protected]

Definition at line 101 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.h.

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

DiffusionImage<DiffusionImagePixelType>::Pointer mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::m_Input [protected]

Definition at line 98 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.h.

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

double mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::m_MinPlausibleValue [protected]

Definition at line 105 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.h.

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

int mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::m_NumIterations [protected]

Definition at line 102 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.h.

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

mitk::TensorImage::Pointer mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::m_Output [protected]

Definition at line 106 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.h.

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

mitk::TensorImage::Pointer mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::m_OutputItk [protected]

Definition at line 107 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.h.

template<class DiffusionImagePixelType = short, class TTensorPixelType = float>

float mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionImagePixelType, TTensorPixelType >::m_Sigma [protected]

Definition at line 100 of file mitkTeemDiffusionTensor3DReconstructionImageFilter.h.

---

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

• mitkTeemDiffusionTensor3DReconstructionImageFilter.h
• mitkTeemDiffusionTensor3DReconstructionImageFilter.cpp