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 double	vtkDouble

Public Types inherited from mitk::ImageToSurfaceFilter
enum	DecimationType { NoDecimation, DecimatePro, QuadricDecimation }

typedef ImageToSurfaceFilter	Self

typedef SurfaceSource	Superclass

typedef itk::SmartPointer< Self >	Pointer

typedef itk::SmartPointer< const Self >	ConstPointer

Public Types inherited from mitk::SurfaceSource
typedef SurfaceSource	Self

typedef BaseDataSource	Superclass

typedef itk::SmartPointer< Self >	Pointer

typedef itk::SmartPointer< const Self >	ConstPointer

typedef Surface	OutputType

Public Types inherited from mitk::BaseDataSource
typedef BaseDataSource	Self

typedef itk::ProcessObject	Superclass

typedef itk::SmartPointer< Self >	Pointer

typedef itk::SmartPointer< const Self >	ConstPointer

typedef BaseData	OutputType

typedef itk::DataObject::DataObjectIdentifierType	DataObjectIdentifierType

Public Member Functions
	mitkClassMacro (ManualSegmentationToSurfaceFilter, ImageToSurfaceFilter)

virtual void	GenerateData () override

Pointer	Clone () const

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)

Public Member Functions inherited from mitk::ImageToSurfaceFilter
virtual std::vector< std::string >	GetClassHierarchy () const override

virtual const char *	GetClassName () const

Pointer	Clone () const

virtual void	GenerateOutputInformation () override

const mitk::Image *	GetInput (void)

virtual void	SetInput (const mitk::Image *image)

void	SetSmoothIteration (int smoothIteration)

void	SetSmoothRelaxation (float smoothRelaxation)

virtual void	SetThreshold (ScalarType _arg)

virtual ScalarType	GetThreshold () const

virtual void	SetSmooth (bool _arg)

virtual void	SmoothOn ()

virtual void	SmoothOff ()

virtual bool	GetSmooth () const

virtual DecimationType	GetDecimate () const

virtual void	SetDecimate (DecimationType _arg)

virtual void	SetTargetReduction (float _arg)

virtual float	GetTargetReduction () const

template<class T1 , class T2 , class T3 >
void	mitkVtkLinearTransformPoint (T1 matrix[4][4], T2 in[3], T3 out[3])

Public Member Functions inherited from mitk::SurfaceSource
Pointer	Clone () const

OutputType *	GetOutput ()

const OutputType *	GetOutput () const

OutputType *	GetOutput (DataObjectPointerArraySizeType idx)

const OutputType *	GetOutput (DataObjectPointerArraySizeType idx) const

virtual itk::DataObject::Pointer	MakeOutput (DataObjectPointerArraySizeType idx) override

virtual itk::DataObject::Pointer	MakeOutput (const DataObjectIdentifierType &name) override

Public Member Functions inherited from mitk::BaseDataSource
OutputType *	GetOutput ()

const OutputType *	GetOutput () const

OutputType *	GetOutput (DataObjectPointerArraySizeType idx)

const OutputType *	GetOutput (DataObjectPointerArraySizeType idx) const

virtual void	GraftOutput (OutputType *output)
	Graft the specified BaseData onto this BaseDataSource's output. More...

virtual void	GraftOutput (const DataObjectIdentifierType &key, OutputType *output)

virtual void	GraftNthOutput (unsigned int idx, OutputType *output)
	Graft the specified base data object onto this BaseDataSource's idx'th output. More...

bool	Updating () const
	Access itk::ProcessObject::m_Updating. More...

Static Public Member Functions
static Pointer	New ()

Static Public Member Functions inherited from mitk::ImageToSurfaceFilter
static const char *	GetStaticNameOfClass ()

static Pointer	New ()

Static Public Member Functions inherited from mitk::SurfaceSource
static const char *	GetStaticNameOfClass ()

static Pointer	New ()

Static Public Member Functions inherited from mitk::BaseDataSource
static const char *	GetStaticNameOfClass ()

Protected Member Functions
	ManualSegmentationToSurfaceFilter ()

virtual	~ManualSegmentationToSurfaceFilter ()

Protected Member Functions inherited from mitk::ImageToSurfaceFilter
	ImageToSurfaceFilter ()

virtual	~ImageToSurfaceFilter ()

void	CreateSurface (int time, vtkImageData vtkimage, mitk::Surface surface, const ScalarType threshold)

Protected Member Functions inherited from mitk::SurfaceSource
	SurfaceSource ()

virtual	~SurfaceSource ()

Protected Member Functions inherited from mitk::BaseDataSource
	BaseDataSource ()

virtual	~BaseDataSource ()

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

Protected Attributes inherited from mitk::ImageToSurfaceFilter
bool	m_Smooth

DecimationType	m_Decimate

ScalarType	m_Threshold

float	m_TargetReduction

int	m_SmoothIteration

float	m_SmoothRelaxation

Additional Inherited Members
Static Protected Member Functions inherited from mitk::BaseDataSource
static Pointer	New ()

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 double mitk::ManualSegmentationToSurfaceFilter::vtkDouble

Definition at line 49 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.

mitk::ManualSegmentationToSurfaceFilter::~ManualSegmentationToSurfaceFilter ( )

protectedvirtual

Definition at line 38 of file mitkManualSegmentationToSurfaceFilter.cpp.

Member Function Documentation

Pointer mitk::ManualSegmentationToSurfaceFilter::Clone ( ) const

void mitk::ManualSegmentationToSurfaceFilter::GenerateData ( )

overridevirtual

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 40 of file mitkManualSegmentationToSurfaceFilter.cpp.

References mitk::ProgressBar::AddStepsToDo(), mitk::ProportionalTimeGeometry::GetFirstTimePoint(), mitk::ProgressBar::GetInstance(), mitk::SlicedData::GetRequestedRegion(), mitk::ProportionalTimeGeometry::GetStepDuration(), mitk::BaseData::GetTimeGeometry(), mitk::Image::GetVtkImageData(), MITK_DEBUG, MITK_INFO, mitk::New(), mitk::ProgressBar::Progress(), mitk::ProportionalTimeGeometry::SetFirstTimePoint(), and mitk::ProportionalTimeGeometry::SetStepDuration().

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).

mitk::ManualSegmentationToSurfaceFilter::mitkClassMacro	(	ManualSegmentationToSurfaceFilter	,
		ImageToSurfaceFilter
	)

static Pointer mitk::ManualSegmentationToSurfaceFilter::New ( )

static

Referenced by mitk::ShowSegmentationAsSurface::ThreadedUpdateFunction().

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 164 of file mitkManualSegmentationToSurfaceFilter.cpp.

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 157 of file mitkManualSegmentationToSurfaceFilter.cpp.

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.