Generates surface representations from labeled (segmented) images. More...

#include <mitkLabeledImageToSurfaceFilter.h>

Inheritance diagram for mitk::LabeledImageToSurfaceFilter:

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Collaboration diagram for mitk::LabeledImageToSurfaceFilter:

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Public Types
typedef int	LabelType

typedef std::map< LabelType, unsigned long >	LabelMapType

typedef std::map< unsigned int, LabelType >	IdxToLabelMapType

Public Types inherited from mitk::ImageToSurfaceFilter
enum	DecimationType { NoDecimation , DecimatePro , QuadricDecimation }
	Enumeration of available polygon decimation strategies. More...

Public Types inherited from mitk::SurfaceSource
typedef Surface	OutputType

Public Types inherited from mitk::BaseDataSource
typedef BaseData	OutputType
	Output data type. More...

typedef itk::DataObject::DataObjectIdentifierType	DataObjectIdentifierType
	Identifier type for named data objects. More...

Public Member Functions
	mitkClassMacro (LabeledImageToSurfaceFilter, ImageToSurfaceFilter)

Pointer	Clone () const

virtual void	SetGenerateAllLabels (bool _arg)

virtual bool	GetGenerateAllLabels ()

virtual void	GenerateAllLabelsOn ()

virtual void	GenerateAllLabelsOff ()

virtual void	SetLabel (LabelType _arg)

virtual LabelType	GetLabel ()

virtual void	SetBackgroundLabel (LabelType _arg)

virtual LabelType	GetBackgroundLabel ()

virtual void	SetGaussianStandardDeviation (double _arg)

virtual double	GetGaussianStandardDeviation ()

LabelType	GetLabelForNthOutput (const unsigned int &i)

mitk::ScalarType	GetVolumeForNthOutput (const unsigned int &i)

mitk::ScalarType	GetVolumeForLabel (const LabelType &label)

Public Member Functions inherited from mitk::ImageToSurfaceFilter
	mitkClassMacro (ImageToSurfaceFilter, SurfaceSource)

Pointer	Clone () const

void	GenerateData () override

void	GenerateOutputInformation () override

const mitk::Image *	GetInput (void)

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

void	SetSmoothIteration (int smoothIteration)
	Set the number of iterations used to smooth the surface. More...

void	SetSmoothRelaxation (float smoothRelaxation)
	Set the relaxation factor for Laplacian smoothing. More...

virtual void	SetThreshold (ScalarType _arg)
	Set the threshold used for surface extraction via vtkMarchingCubes. More...

virtual ScalarType	GetThreshold () const
	Get the threshold used for vtkMarchingCubes surface extraction. More...

virtual void	SetSmooth (bool _arg)
	Enable vtkSmoothPolyDataFilter for Laplacian smoothing. More...

virtual void	SmoothOn ()
	Toggle surface smoothing on/off. More...

virtual void	SmoothOff ()

virtual bool	GetSmooth () const
	Get whether surface smoothing is enabled. More...

virtual DecimationType	GetDecimate () const
	Get the current decimation mode. More...

virtual void	SetDecimate (DecimationType _arg)
	Set the decimation mode to reduce the number of triangles in the mesh. More...

virtual void	SetTargetReduction (float _arg)
	Set the desired target reduction of triangles in the range [0.0, 1.0]. More...

virtual float	GetTargetReduction () const
	Get the target reduction factor for the decimation filter. More...

template<class T1 , class T2 , class T3 >
void	mitkVtkLinearTransformPoint (T1 matrix[4][4], T2 in[3], T3 out[3])
	Transform a 3D point by a 4x4 matrix (affine transformation). More...

Public Member Functions inherited from mitk::SurfaceSource
	mitkClassMacro (SurfaceSource, BaseDataSource)

Pointer	Clone () const

mitkBaseDataSourceGetOutputDeclarations itk::DataObject::Pointer	MakeOutput (DataObjectPointerArraySizeType idx) override
	Allocate a new output object and return it. More...

itk::DataObject::Pointer	MakeOutput (const DataObjectIdentifierType &name) override
	Allocate a new output object by name. More...

Public Member Functions inherited from mitk::BaseDataSource
	mitkClassMacroItkParent (BaseDataSource, itk::ProcessObject)

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)
	Graft the specified base data object onto a named output. More...

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
	Check whether the pipeline is currently executing. More...

Static Public Member Functions
static Pointer	New ()

Static Public Member Functions inherited from mitk::ImageToSurfaceFilter
static Pointer	New ()

Static Public Member Functions inherited from mitk::SurfaceSource
static Pointer	New ()

Protected Member Functions
void	GenerateData () override

void	GenerateOutputInformation () override

virtual void	CreateSurface (int time, vtkImageData vtkimage, mitk::Surface surface, LabelType label)

virtual LabelMapType	GetAvailableLabels ()

	LabeledImageToSurfaceFilter ()

	~LabeledImageToSurfaceFilter () override

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

	~ImageToSurfaceFilter () override
	Destructor. More...

void	CreateSurface (int time, vtkImageData vtkimage, mitk::Surface surface, const ScalarType threshold)
	Create the surface for a single time step using vtkMarchingCubes. More...

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

	~SurfaceSource () override

Protected Member Functions inherited from mitk::BaseDataSource
	BaseDataSource ()
	Constructor. More...

	~BaseDataSource () override
	Destructor. More...

Protected Attributes
double	m_GaussianStandardDeviation

bool	m_GenerateAllLabels

LabelType	m_Label

LabelType	m_BackgroundLabel

LabelMapType	m_AvailableLabels

IdxToLabelMapType	m_IdxToLabels

Protected Attributes inherited from mitk::ImageToSurfaceFilter
bool	m_Smooth
	Flag whether the created surface shall be smoothed (default is false). More...

DecimationType	m_Decimate
	Decimation mode. Default is NoDecimation. More...

ScalarType	m_Threshold
	Threshold for surface extraction. Default value is 1. More...

float	m_TargetReduction
	The reduction factor for the decimation filter. Range [0.0, 1.0]. More...

int	m_SmoothIteration
	The number of iterations for the smoothing filter. Default is 50. More...

float	m_SmoothRelaxation
	The relaxation factor for the smoothing filter. Default is 0.1. More...

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

Detailed Description

Generates surface representations from labeled (segmented) images.

For a labeled image containing N distinct label regions (plus background), this filter creates N surface representations, one per labeled region. Each surface is assigned to a separate output of the filter. The mapping between output index and label can be queried via GetLabelForNthOutput().

Alternatively, surface generation can be restricted to a single specific label by calling GenerateAllLabelsOff() and then SetLabel(label).

The filter also computes the volume (in mm^3) of each labeled region, accessible via GetVolumeForNthOutput() or GetVolumeForLabel().

See also: ImageToSurfaceFilter

Definition at line 40 of file mitkLabeledImageToSurfaceFilter.h.

Member Typedef Documentation

◆ IdxToLabelMapType

typedef std::map<unsigned int, LabelType> mitk::LabeledImageToSurfaceFilter::IdxToLabelMapType

Definition at line 53 of file mitkLabeledImageToSurfaceFilter.h.

◆ LabelMapType

typedef std::map<LabelType, unsigned long> mitk::LabeledImageToSurfaceFilter::LabelMapType

Definition at line 51 of file mitkLabeledImageToSurfaceFilter.h.

◆ LabelType

typedef int mitk::LabeledImageToSurfaceFilter::LabelType

Definition at line 49 of file mitkLabeledImageToSurfaceFilter.h.

Constructor & Destructor Documentation

◆ LabeledImageToSurfaceFilter()

mitk::LabeledImageToSurfaceFilter::LabeledImageToSurfaceFilter ( )

protected

◆ ~LabeledImageToSurfaceFilter()

mitk::LabeledImageToSurfaceFilter::~LabeledImageToSurfaceFilter ( )

overrideprotected

Member Function Documentation

◆ Clone()

Pointer mitk::LabeledImageToSurfaceFilter::Clone ( ) const

◆ CreateSurface()

virtual void mitk::LabeledImageToSurfaceFilter::CreateSurface	(	int	time,
		vtkImageData *	vtkimage,
		mitk::Surface *	surface,
		LabelType	label
	)

protectedvirtual

◆ GenerateAllLabelsOff()

virtual void mitk::LabeledImageToSurfaceFilter::GenerateAllLabelsOff ( )

virtual

◆ GenerateAllLabelsOn()

virtual void mitk::LabeledImageToSurfaceFilter::GenerateAllLabelsOn ( )

virtual

◆ GenerateData()

void mitk::LabeledImageToSurfaceFilter::GenerateData ( )

overrideprotected

◆ GenerateOutputInformation()

void mitk::LabeledImageToSurfaceFilter::GenerateOutputInformation ( )

overrideprotected

◆ GetAvailableLabels()

virtual LabelMapType mitk::LabeledImageToSurfaceFilter::GetAvailableLabels ( )

protectedvirtual

◆ GetBackgroundLabel()

virtual LabelType mitk::LabeledImageToSurfaceFilter::GetBackgroundLabel ( )

virtual

Returns the label of the background. No surface will be generated for this label!

Returns: the label of the background, by default 0

◆ GetGaussianStandardDeviation()

virtual double mitk::LabeledImageToSurfaceFilter::GetGaussianStandardDeviation ( )

virtual

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

◆ GetGenerateAllLabels()

virtual bool mitk::LabeledImageToSurfaceFilter::GetGenerateAllLabels ( )

virtual

Returns: if all labels or only a specific label should be extracted.

◆ GetLabel()

virtual LabelType mitk::LabeledImageToSurfaceFilter::GetLabel ( )

virtual

Returns the label you want to extract. This method only has an effect, if GenerateAllLabels() is set to false

Returns: _arg the label to extract, by default 1

◆ GetLabelForNthOutput()

LabelType mitk::LabeledImageToSurfaceFilter::GetLabelForNthOutput ( const unsigned int & i )

Lets you retrieve the label which was used for generating the Nth output of this filter. If GenerateAllLabels() is set to false, this filter only knows about the label provided via SetLabel(). All other labels in the image are not known.

Parameters

i	the index of the Nth output.

Returns: the label used for calculating the Nth output of the filter. If i is out of range, itk::NumericLimits<LabelType>::max() is returned.

◆ GetVolumeForLabel()

mitk::ScalarType mitk::LabeledImageToSurfaceFilter::GetVolumeForLabel ( const LabelType & label )

Lets you retrieve the volume in milliliters of the region with the given label. If GenerateAllLabels is set to false, you may only call this method for the label provided using the SetLabel() method.

Parameters

label the label of the region you want to get the volume of

Returns: the volume of the region with the given label. If label is invalid, 0.0 is returned.

◆ GetVolumeForNthOutput()

mitk::ScalarType mitk::LabeledImageToSurfaceFilter::GetVolumeForNthOutput ( const unsigned int & i )

Lets you retrieve the volume in milliliters of the region used to generate the Nth output.

Parameters

i	the index of the Nth output.

Returns: the volume of the region used to generate the Nth output of the filter. If i is out of range, 0.0 is returned.

◆ mitkClassMacro()

mitk::LabeledImageToSurfaceFilter::mitkClassMacro	(	LabeledImageToSurfaceFilter	,
		ImageToSurfaceFilter
	)

◆ New()

static Pointer mitk::LabeledImageToSurfaceFilter::New ( )

static

◆ SetBackgroundLabel()

virtual void mitk::LabeledImageToSurfaceFilter::SetBackgroundLabel ( LabelType _arg )

virtual

Set the label of the background. No surface will be generated for this label!

Parameters

_arg	the label of the background, by default 0

◆ SetGaussianStandardDeviation()

virtual void mitk::LabeledImageToSurfaceFilter::SetGaussianStandardDeviation ( double _arg )

virtual

Set standard deviation for Gaussian Filter.

Parameters

_arg	by default 1.5

◆ SetGenerateAllLabels()

virtual void mitk::LabeledImageToSurfaceFilter::SetGenerateAllLabels ( bool _arg )

virtual

Set whether you want to extract all (true) or only a specific label (false)

Parameters

_arg	true by default

◆ SetLabel()

virtual void mitk::LabeledImageToSurfaceFilter::SetLabel ( LabelType _arg )

virtual

Set the label you want to extract. This method only has an effect, if GenerateAllLabels() is set to false

Parameters

_arg	the label to extract, by default 1

Member Data Documentation

◆ m_AvailableLabels

LabelMapType mitk::LabeledImageToSurfaceFilter::m_AvailableLabels

protected

Definition at line 145 of file mitkLabeledImageToSurfaceFilter.h.

◆ m_BackgroundLabel

LabelType mitk::LabeledImageToSurfaceFilter::m_BackgroundLabel

protected

Definition at line 143 of file mitkLabeledImageToSurfaceFilter.h.

◆ m_GaussianStandardDeviation

double mitk::LabeledImageToSurfaceFilter::m_GaussianStandardDeviation

protected

Definition at line 137 of file mitkLabeledImageToSurfaceFilter.h.

◆ m_GenerateAllLabels

bool mitk::LabeledImageToSurfaceFilter::m_GenerateAllLabels

protected

Definition at line 139 of file mitkLabeledImageToSurfaceFilter.h.

◆ m_IdxToLabels

IdxToLabelMapType mitk::LabeledImageToSurfaceFilter::m_IdxToLabels

protected

Definition at line 147 of file mitkLabeledImageToSurfaceFilter.h.

◆ m_Label

LabelType mitk::LabeledImageToSurfaceFilter::m_Label

protected

Definition at line 141 of file mitkLabeledImageToSurfaceFilter.h.

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

mitkLabeledImageToSurfaceFilter.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ IdxToLabelMapType

◆ LabelMapType

◆ LabelType

Constructor & Destructor Documentation

◆ LabeledImageToSurfaceFilter()

◆ ~LabeledImageToSurfaceFilter()

Member Function Documentation

◆ Clone()

◆ CreateSurface()

◆ GenerateAllLabelsOff()

◆ GenerateAllLabelsOn()

◆ GenerateData()

◆ GenerateOutputInformation()

◆ GetAvailableLabels()

◆ GetBackgroundLabel()

◆ GetGaussianStandardDeviation()

◆ GetGenerateAllLabels()

◆ GetLabel()

◆ GetLabelForNthOutput()

◆ GetVolumeForLabel()

◆ GetVolumeForNthOutput()

◆ mitkClassMacro()

◆ New()

◆ SetBackgroundLabel()

◆ SetGaussianStandardDeviation()

◆ SetGenerateAllLabels()

◆ SetLabel()

Member Data Documentation

◆ m_AvailableLabels

◆ m_BackgroundLabel

◆ m_GaussianStandardDeviation

◆ m_GenerateAllLabels

◆ m_IdxToLabels

◆ m_Label