Supplies a 3D surface from pre-processed segmentation. More...

#include <mitkManualSegmentationToSurfaceFilter.h>

Inheritance diagram for mitk::ManualSegmentationToSurfaceFilter:

Collaboration diagram for mitk::ManualSegmentationToSurfaceFilter:

Public Types
typedef ManualSegmentationToSurfaceFilter	Self
typedef ImageToSurfaceFilter	Superclass
typedef itk::SmartPointer< Self >	Pointer
typedef itk::SmartPointer < const Self >	ConstPointer
typedef double	vtkDouble
Public Member Functions
virtual const char *	GetClassName () const
virtual void	GenerateData ()
virtual void	SetMedianFilter3D (bool _arg)
virtual bool	GetMedianFilter3D () const
virtual void	MedianFilter3DOn ()
virtual void	MedianFilter3DOff ()
virtual void	SetInterpolation (bool _arg)
virtual bool	GetInterpolation () const
virtual void	InterpolationOn ()
virtual void	InterpolationOff ()
virtual void	SetUseGaussianImageSmooth (bool _arg)
virtual bool	GetUseGaussianImageSmooth () const
virtual void	UseGaussianImageSmoothOn ()
virtual void	UseGaussianImageSmoothOff ()
virtual void	SetGaussianStandardDeviation (double _arg)
virtual double	GetGaussianStandardDeviation () const
void	SetMedianKernelSize (int x, int y, int z)
virtual int	GetMedianKernelSizeX () const
virtual int	GetMedianKernelSizeY () const
virtual int	GetMedianKernelSizeZ () const
void	SetInterpolation (vtkDouble x, vtkDouble y, vtkDouble z)
Static Public Member Functions
static Pointer	New ()
Protected Member Functions
	ManualSegmentationToSurfaceFilter ()
virtual	~ManualSegmentationToSurfaceFilter ()
Protected Attributes
bool	m_MedianFilter3D
int	m_MedianKernelSizeX
int	m_MedianKernelSizeY
int	m_MedianKernelSizeZ
bool	m_UseGaussianImageSmooth
double	m_GaussianStandardDeviation
bool	m_Interpolation
vtkDouble	m_InterpolationX
vtkDouble	m_InterpolationY
vtkDouble	m_InterpolationZ

Detailed Description

Supplies a 3D surface from pre-processed segmentation.

The resulting surface depends on a filter pipeline based on vtkMedian (1) and a Gaussian filter with vtkImageGaussianSmooth (2). All voxel can be changed to an isotropic representation of the image (ATTANTION: the number of voxels in the will change). The resulting isotropic image has 1mm isotropic voxel by default. But can be varied freely.

Definition at line 44 of file mitkManualSegmentationToSurfaceFilter.h.

Member Typedef Documentation

typedef itk::SmartPointer<const Self> mitk::ManualSegmentationToSurfaceFilter::ConstPointer

Reimplemented from mitk::ImageToSurfaceFilter.

Definition at line 47 of file mitkManualSegmentationToSurfaceFilter.h.

typedef itk::SmartPointer<Self> mitk::ManualSegmentationToSurfaceFilter::Pointer

Reimplemented from mitk::ImageToSurfaceFilter.

Definition at line 47 of file mitkManualSegmentationToSurfaceFilter.h.

typedef ManualSegmentationToSurfaceFilter mitk::ManualSegmentationToSurfaceFilter::Self

Reimplemented from mitk::ImageToSurfaceFilter.

Definition at line 47 of file mitkManualSegmentationToSurfaceFilter.h.

typedef ImageToSurfaceFilter mitk::ManualSegmentationToSurfaceFilter::Superclass

Reimplemented from mitk::ImageToSurfaceFilter.

Definition at line 47 of file mitkManualSegmentationToSurfaceFilter.h.

typedef double mitk::ManualSegmentationToSurfaceFilter::vtkDouble

Definition at line 47 of file mitkManualSegmentationToSurfaceFilter.h.

Constructor & Destructor Documentation

mitk::ManualSegmentationToSurfaceFilter::ManualSegmentationToSurfaceFilter ( ) [protected]

Definition at line 24 of file mitkManualSegmentationToSurfaceFilter.cpp.

References m_GaussianStandardDeviation, m_Interpolation, m_InterpolationX, m_InterpolationY, m_InterpolationZ, m_MedianFilter3D, m_MedianKernelSizeX, m_MedianKernelSizeY, m_MedianKernelSizeZ, and m_UseGaussianImageSmooth.

{
  m_MedianFilter3D = false;
  m_MedianKernelSizeX = 3;
  m_MedianKernelSizeY = 3;
  m_MedianKernelSizeZ = 3;
  m_UseGaussianImageSmooth = false;
  m_GaussianStandardDeviation = 1.5;
  m_Interpolation = false;
  m_InterpolationX = 1.0f;
  m_InterpolationY = 1.0f;
  m_InterpolationZ = 1.0f;
};

mitk::ManualSegmentationToSurfaceFilter::~ManualSegmentationToSurfaceFilter ( ) [protected, virtual]

Definition at line 39 of file mitkManualSegmentationToSurfaceFilter.cpp.

{};

Member Function Documentation

void mitk::ManualSegmentationToSurfaceFilter::GenerateData ( ) [virtual]

Will pre-process a segmentation voxelwise. The segmentation can use a hole fill relating a median filter and smooth by a Gaussian filter. The image can be interpolated to an isotropic image. By default every filter is disabled. This method calls CreateSurface from mitkImageToSurfaceFilter and does not need a manual call since we use Update().

Reimplemented from mitk::ImageToSurfaceFilter.

Definition at line 41 of file mitkManualSegmentationToSurfaceFilter.cpp.

References mitk::ProgressBar::AddStepsToDo(), mitk::ProgressBar::GetInstance(), mitk::SlicedData::GetRequestedRegion(), mitk::Image::GetVtkImageData(), QuadProgPP::median(), MITK_INFO, mitk::ProgressBar::Progress(), and QuadProgPP::t().

{
  mitk::Surface *surface = this->GetOutput();
  mitk::Image * image    =  (mitk::Image*)GetInput();
  mitk::Image::RegionType outputRegion = image->GetRequestedRegion();

  int tstart=outputRegion.GetIndex(3);
  int tmax=tstart+outputRegion.GetSize(3); //GetSize()==1 - will aber 0 haben, wenn nicht zeitaufgeloest

  ScalarType thresholdExpanded = this->m_Threshold;

  if ((tmax-tstart) > 0)
  {
    ProgressBar::GetInstance()->AddStepsToDo( 7 * (tmax - tstart)  );
  }

  for( int t=tstart; t<tmax; t++ )
  {

    vtkSmartPointer<vtkImageData> vtkimage = image->GetVtkImageData(t);

    // Median -->smooth 3D 
    MITK_INFO << (m_MedianFilter3D ? "Applying median..." : "No median filtering");
    if(m_MedianFilter3D)
    {
      vtkImageMedian3D *median = vtkImageMedian3D::New();
      median->SetInput(vtkimage); //RC++ (VTK < 5.0)
      median->SetKernelSize(m_MedianKernelSizeX,m_MedianKernelSizeY,m_MedianKernelSizeZ);//Std: 3x3x3
      median->ReleaseDataFlagOn();
      median->UpdateInformation();
      median->Update();
      vtkimage = median->GetOutput(); //->Out
      median->Delete();
    }
    ProgressBar::GetInstance()->Progress();

    //Interpolate image spacing 
    MITK_INFO << (m_Interpolation ? "Resampling..." : "No resampling");
    if(m_Interpolation)
    {
      vtkImageResample * imageresample = vtkImageResample::New();
      imageresample->SetInput(vtkimage);

      //Set Spacing Manual to 1mm in each direction (Original spacing is lost during image processing)      
      imageresample->SetAxisOutputSpacing(0, m_InterpolationX);
      imageresample->SetAxisOutputSpacing(1, m_InterpolationY);
      imageresample->SetAxisOutputSpacing(2, m_InterpolationZ);
      imageresample->UpdateInformation();
      imageresample->Update();
      vtkimage=imageresample->GetOutput();//->Output
      imageresample->Delete();
    }
    ProgressBar::GetInstance()->Progress();

    MITK_INFO << (m_UseGaussianImageSmooth ? "Applying gaussian smoothing..." : "No gaussian smoothing");
    if(m_UseGaussianImageSmooth)//gauss
    {
      vtkImageThreshold* vtkimagethreshold = vtkImageThreshold::New();
      vtkimagethreshold->SetInput(vtkimage);
      vtkimagethreshold->SetInValue( 100 );
      vtkimagethreshold->SetOutValue( 0 );
      vtkimagethreshold->ThresholdByUpper( this->m_Threshold ); 
      thresholdExpanded = 49;

      vtkimagethreshold->SetOutputScalarTypeToUnsignedChar();
      vtkimagethreshold->ReleaseDataFlagOn();

      vtkImageGaussianSmooth *gaussian = vtkImageGaussianSmooth::New();
      gaussian->SetInput(vtkimagethreshold->GetOutput()); 
      gaussian->SetDimensionality(3);
      gaussian->SetRadiusFactor(0.49);
      gaussian->SetStandardDeviation( m_GaussianStandardDeviation );
      gaussian->ReleaseDataFlagOn();
      gaussian->UpdateInformation();
      gaussian->Update();
      vtkimage = gaussian->GetOutput(); //->Out
      gaussian->Delete();
      vtkimagethreshold->Delete();
    }
    ProgressBar::GetInstance()->Progress();

    // Create sureface for t-Slice
    CreateSurface(t, vtkimage, surface, thresholdExpanded);
    ProgressBar::GetInstance()->Progress();
  }
};

virtual const char* mitk::ManualSegmentationToSurfaceFilter::GetClassName ( ) const [virtual]

Reimplemented from mitk::ImageToSurfaceFilter.

virtual double mitk::ManualSegmentationToSurfaceFilter::GetGaussianStandardDeviation ( ) const [virtual]

Returns the standard deviation of the Gaussian filter which will be used when filter is enabled.

virtual bool mitk::ManualSegmentationToSurfaceFilter::GetInterpolation ( ) const [virtual]

Returns activation state of interpolation filter.

virtual bool mitk::ManualSegmentationToSurfaceFilter::GetMedianFilter3D ( ) const [virtual]

Return state if median filter is enabled.

virtual int mitk::ManualSegmentationToSurfaceFilter::GetMedianKernelSizeX ( ) const [virtual]

Returns the kernel size in the first direction.

virtual int mitk::ManualSegmentationToSurfaceFilter::GetMedianKernelSizeY ( ) const [virtual]

Returns the kernel size in the second direction.

virtual int mitk::ManualSegmentationToSurfaceFilter::GetMedianKernelSizeZ ( ) const [virtual]

Returns the kernel size in the third direction.

virtual bool mitk::ManualSegmentationToSurfaceFilter::GetUseGaussianImageSmooth ( ) const [virtual]

Returns activation state of standard deviation filter.

virtual void mitk::ManualSegmentationToSurfaceFilter::InterpolationOff ( ) [virtual]

virtual void mitk::ManualSegmentationToSurfaceFilter::InterpolationOn ( ) [virtual]

Enable the interpolation filter (second filter in pipeline) for isotropic voxel.

virtual void mitk::ManualSegmentationToSurfaceFilter::MedianFilter3DOff ( ) [virtual]

virtual void mitk::ManualSegmentationToSurfaceFilter::MedianFilter3DOn ( ) [virtual]

Enable the median filter (first filter in pipeline).

static Pointer mitk::ManualSegmentationToSurfaceFilter::New ( ) [static]

Reimplemented from mitk::ImageToSurfaceFilter.

Referenced by QmitkIsoSurface::CreateSurface(), and mitkManualSegmentationToSurfaceFilterTest().

virtual void mitk::ManualSegmentationToSurfaceFilter::SetGaussianStandardDeviation ( double _arg ) [virtual]

Set standard deviation for Gaussian Filter.

Parameters:

_arg	by default 1.5

virtual void mitk::ManualSegmentationToSurfaceFilter::SetInterpolation ( bool _arg ) [virtual]

Supplies a method to enable Interpolation.

void mitk::ManualSegmentationToSurfaceFilter::SetInterpolation	(	vtkDouble	x,
		vtkDouble	y,
		vtkDouble	z
	)

Set the values for Spacing in X, Y and Z-Dimension

Definition at line 136 of file mitkManualSegmentationToSurfaceFilter.cpp.

{
  m_InterpolationX = x;
  m_InterpolationY = y;
  m_InterpolationZ = z;
}

virtual void mitk::ManualSegmentationToSurfaceFilter::SetMedianFilter3D ( bool _arg ) [virtual]

Supplies a method for setting median filter by a bool value.

void mitk::ManualSegmentationToSurfaceFilter::SetMedianKernelSize	(	int	x,
		int	y,
		int	z
	)

Set the Kernel for Median3DFilter. By default kernel is set to 3x3x3. If you choose '1' nothing will be processed in this direction.

Definition at line 129 of file mitkManualSegmentationToSurfaceFilter.cpp.

{
  m_MedianKernelSizeX = x;
  m_MedianKernelSizeY = y;
  m_MedianKernelSizeZ = z;
 }

virtual void mitk::ManualSegmentationToSurfaceFilter::SetUseGaussianImageSmooth ( bool _arg ) [virtual]

Supplies a method for Gaussian filter (third filter in pipeline).

virtual void mitk::ManualSegmentationToSurfaceFilter::UseGaussianImageSmoothOff ( ) [virtual]

virtual void mitk::ManualSegmentationToSurfaceFilter::UseGaussianImageSmoothOn ( ) [virtual]

Enables Gaussian image smooth. As well the threshold for the CreateSurface() method will raise the threshold to 49 and changes the image range set from 0 to 100. It is made for reasons in binary images to prevent conflicts with the used filter. There are better results for dividing fore- and background.