Converts pixel data to surface data by using a threshold The mitkNifTKImageToSurfaceFilter is used to create a new surface out of an mitk image. The filter uses a threshold to define the surface. It can use two algorithms for the extraction: the vtkMarchingCube algorithm (default) and the Corrected Marching Cubes 33 method: Custodio, Lis, et al. "Practical considerations on Marching Cubes 33 topological correctness." Computers & Graphics 37.7 (2013): 840-850. More...

Inheritance diagram for niftk::ImageToSurfaceFilter:

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Collaboration diagram for niftk::ImageToSurfaceFilter:

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Public Types
enum	SurfaceExtractionMethod { StandardExtractor, EnhancedCPUExtractor, GPUExtractor }

enum	SurfaceDecimationMethod { NoDecimation, DecimatePro, QuadricVTK, Quadric, QuadricTri, Melax, ShortestEdge }

enum	SurfaceSmoothingMethod { NoSurfaceSmoothing, TaubinSmoothing, CurvatureNormalSmooth, InverseEdgeLengthSmooth, WindowedSincSmoothing, StandardVTKSmoothing }

enum	InputSmoothingMethod { NoInputSmoothing, GaussianSmoothing, MedianSmoothing }

Public Member Functions
	mitkClassMacro (ImageToSurfaceFilter, SurfaceSource) static Pointer New()

virtual void	GenerateData () override
	For each image time slice a surface will be created. This method is called by Update(). More...

virtual void	GenerateOutputInformation () override
	Initializes the output information ( i.e. the geometry information ) of the output of the filter. More...

const mitk::Image *	GetInput (void)
	Returns a const reference to the input image (e.g. the original input image that ist used to create the surface) More...

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

virtual void	SetThreshold (mitk::ScalarType _arg)
	Set the Marching Cubes threshold value. Threshold can be manipulated by inherited classes. More...

virtual mitk::ScalarType	GetThreshold () const
	Get the Marching Cubes threshold value. Threshold can be manipulated by inherited classes. More...

virtual SurfaceExtractionMethod	GetSurfaceExtractionType () const
	Get the state of the input image smoothing mode. More...

virtual void	SetSurfaceExtractionType (SurfaceExtractionMethod _arg)
	Sets the input image smoothing mode (Gaussian / Median) More...

virtual InputSmoothingMethod	GetInputSmoothingType () const
	Get the state of the input image smoothing mode. More...

virtual void	SetInputSmoothingType (InputSmoothingMethod _arg)
	Sets the input image smoothing mode (Gaussian / Median) More...

virtual void	SetPerformInputSmoothing (bool _arg)
	Enables input image smoothing. The preferred method can be specified, along with the radius. More...

virtual void	PerformInputSmoothingOn ()
	Enable/Disable input image smoothing. More...

virtual void	PerformInputSmoothingOff ()

virtual bool	GetPerformInputSmoothing () const
	Returns if input image smoothing is enabled. More...

virtual void	SetInputSmoothingRadius (float _arg)
	Sets the smoothing radius of the input image smoothing method. More...

virtual float	GetInputSmoothingRadius () const
	Returns the smoothing radius of the input image smoothing method. More...

virtual void	SetInputSmoothingIterations (int _arg)
	Sets the number of iterations for the surface smoothing method. More...

virtual int	GetInputSmoothingIterations () const
	Returns the number of iterations for the surface smoothing method. More...

virtual SurfaceSmoothingMethod	GetSurfaceSmoothingType () const
	Get the state of the surface smoothing mode. More...

virtual void	SetSurfaceSmoothingType (SurfaceSmoothingMethod _arg)
	Sets the surface smoothing mode (Laplacian / Taubin) More...

virtual void	SetPerformSurfaceSmoothing (bool _arg)
	Enables surface smoothing. The preferred method can be specified, along with the parameters. More...

virtual void	PerformSurfaceSmoothingOn ()
	Enable/Disable surface smoothing. More...

virtual void	PerformSurfaceSmoothingOff ()

virtual bool	GetPerformSurfaceSmoothing () const
	Returns if surface smoothing is enabled. More...

virtual void	SetSurfaceSmoothingRadius (float _arg)
	Sets the smoothing radius of the surface smoothing method. More...

virtual float	GetSurfaceSmoothingRadius () const
	Returns the smoothing radius of the surface smoothing method. More...

virtual void	SetSurfaceSmoothingIterations (int _arg)
	Sets the number of iterations for the input image smoothing method. More...

virtual int	GetSurfaceSmoothingIterations () const
	Returns the number of iterations for the input image smoothing method. More...

virtual SurfaceDecimationMethod	GetSurfaceDecimationType () const
	Get the state of decimation mode to reduce the number of triangles in the surface represantation. More...

virtual void	SetSurfaceDecimationType (SurfaceDecimationMethod _arg)
	Sets the surface decimation method to reduce the number of triangles in the mesh and produce a good approximation to the original image. More...

virtual void	SetPerformSurfaceDecimation (bool _arg)
	Enables surface decimation. The preferred method can be specified, along with the radius. More...

virtual void	PerformSurfaceDecimationOn ()
	Enable/Disable surface decimation. More...

virtual void	PerformSurfaceDecimationOff ()

virtual bool	GetPerformSurfaceDecimation () const
	Returns if surface decimation is enabled. More...

virtual void	SetTargetReduction (float _arg)
	Set desired amount of reduction of triangles in the range from 0.0 to 1.0. For example 0.9 will reduce the data set to 10%. More...

virtual float	GetTargetReduction () const
	Returns the reduction factor as a float value. More...

virtual void	SetSamplingRatio (double _arg)
	Set desired downsampling ratio that is applied to the image before surface extraction. More...

virtual double	GetSamplingRatio () const
	Returns the downsampling ratio. More...

virtual void	SetPerformSurfaceCleaning (bool _arg)
	Enable/Disable surface cleaning and small object removal. More...

virtual bool	GetPerformSurfaceCleaning () const
	Returns true if surface cleaning is enabled. More...

virtual void	SetSurfaceCleaningThreshold (int _arg)
	Sets the number threshold for small object removal. More...

virtual int	GetSurfaceCleaningThreshold () const
	Returns the threshold for small object removal. More...

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

Protected Member Functions
	ImageToSurfaceFilter ()
	Default Constructor. More...

virtual	~ImageToSurfaceFilter ()
	Destructor. More...

void	CreateSurface (mitk::Image image, mitk::Surface surface)

void	VTKSurfaceExtraction (mitk::Image *image, vtkSmartPointer< vtkPolyData > vtkSurface)
	Creates a surface using the VTK Marching Cubes method. More...

void	CMC33SurfaceExtraction (mitk::Image inputImage, MeshData meshData)
	Creates a surface using the Corrected Marching Cubes 33 method (C-MC33) More...

void	MeshSmoothing (MeshData *meshData)
	Performs smoothing of the triangle mesh with the previously selected method (SurfaceSmoothingType) More...

void	SurfaceSmoothingVTK (vtkSmartPointer< vtkPolyData > vtkSurface)
	Performs smoothing of the triangle mesh with the VTK smoothing method. More...

void	ComputeSmoothNormals (MeshData *meshData)
	Computes smooth (interpolated) normals for the surface. More...

void	EditSurface (MeshData *meshData, bool recomputeNormals, bool flipNormals, bool reorientFaces, bool fixCracks)
	Utility function for a. Flipping Normals b. Reorienting Faces c. Fixing Cracks. More...

vtkSmartPointer< vtkPolyData >	BuildVTKPolyData (MeshData *meshData)
	Creates a VTK Polydata structure from the set of provided vertices and triangles. More...

Protected Attributes
mitk::ScalarType	m_Threshold

SurfaceExtractionMethod	m_SurfaceExtractionType

InputSmoothingMethod	m_InputSmoothingType

bool	m_PerformInputSmoothing

int	m_InputSmoothingIterations

float	m_InputSmoothingRadius

SurfaceSmoothingMethod	m_SurfaceSmoothingType

bool	m_PerformSurfaceSmoothing

int	m_SurfaceSmoothingIterations

float	m_SurfaceSmoothingRadius

SurfaceDecimationMethod	m_SurfaceDecimationType

bool	m_PerformSurfaceDecimation

double	m_TargetReduction

bool	m_PerformSurfaceCleaning

int	m_SurfaceCleaningThreshold

bool	m_VTKNormalCompute

bool	m_FlipNormals

double	m_SamplingRatio

Detailed Description

Converts pixel data to surface data by using a threshold The mitkNifTKImageToSurfaceFilter is used to create a new surface out of an mitk image. The filter uses a threshold to define the surface. It can use two algorithms for the extraction: the vtkMarchingCube algorithm (default) and the Corrected Marching Cubes 33 method: Custodio, Lis, et al. "Practical considerations on Marching Cubes 33 topological correctness." Computers & Graphics 37.7 (2013): 840-850.

By default a vtkPolyData surface based on an input threshold for the input image will be created. Optionally it is possible to:

Smooth the input image before the extraction take place (Median, Gaussian smoothing methods from VTK)
Reduce the number of triangles/polygons (Decimate Pro or Quadric decimation methods from VTK)
Smooth the surface-data (VTK method or various flavors of Taubin smoothing from Meshlab)
Perform a "Small object removal" that eliminates small, non connected surface fragments that have fewer number of ploygons than a selected threshold

The resulting vtk-surface has the same size as the input image.

Member Enumeration Documentation

enum niftk::ImageToSurfaceFilter::InputSmoothingMethod

Enumerator
NoInputSmoothing
GaussianSmoothing
MedianSmoothing

enum niftk::ImageToSurfaceFilter::SurfaceDecimationMethod

Enumerator
NoDecimation
DecimatePro
QuadricVTK
Quadric
QuadricTri
Melax
ShortestEdge

enum niftk::ImageToSurfaceFilter::SurfaceExtractionMethod

Enumerator
StandardExtractor
EnhancedCPUExtractor
GPUExtractor

enum niftk::ImageToSurfaceFilter::SurfaceSmoothingMethod

Enumerator
NoSurfaceSmoothing
TaubinSmoothing
CurvatureNormalSmooth
InverseEdgeLengthSmooth
WindowedSincSmoothing
StandardVTKSmoothing

Constructor & Destructor Documentation

niftk::ImageToSurfaceFilter::ImageToSurfaceFilter ( )

protected

Default Constructor.

niftk::ImageToSurfaceFilter::~ImageToSurfaceFilter ( )

protectedvirtual

Destructor.

Member Function Documentation

vtkSmartPointer< vtkPolyData > niftk::ImageToSurfaceFilter::BuildVTKPolyData ( MeshData * meshData )

protected

Creates a VTK Polydata structure from the set of provided vertices and triangles.

void niftk::ImageToSurfaceFilter::CMC33SurfaceExtraction	(	mitk::Image *	inputImage,
		MeshData *	meshData
	)

protected

Creates a surface using the Corrected Marching Cubes 33 method (C-MC33)

void niftk::ImageToSurfaceFilter::ComputeSmoothNormals ( MeshData * meshData )

protected

Computes smooth (interpolated) normals for the surface.

void niftk::ImageToSurfaceFilter::CreateSurface	(	mitk::Image *	image,
		mitk::Surface *	surface
	)

protected

With the given threshold vtkMarchingCube creates the surface. By default a vtkPolyData surface based on a threshold of the input image will be created. Optionally it is possible to reduce the number of triangles/polygones [SetDecimate(mitk::NifTKImageToSurfaceFilter::DecimatePro) and SetTargetReduction (float _arg)] or smooth the data [SetSmooth(true), SetSmoothingIteration(int smoothIteration) and SetSmoothRelaxation(float smoothRelaxation)].

Parameters

time	selected slice or "0" for single
*mitk::Image	input image
*mitk::Surface	output
threshold	can be different from SetThreshold()

void niftk::ImageToSurfaceFilter::EditSurface	(	MeshData *	meshData,
		bool	recomputeNormals,
		bool	flipNormals,
		bool	reorientFaces,
		bool	fixCracks
	)

protected

Utility function for a. Flipping Normals b. Reorienting Faces c. Fixing Cracks.

void niftk::ImageToSurfaceFilter::GenerateData ( void )

overridevirtual

For each image time slice a surface will be created. This method is called by Update().

void niftk::ImageToSurfaceFilter::GenerateOutputInformation ( void )

overridevirtual

Initializes the output information ( i.e. the geometry information ) of the output of the filter.

const mitk::Image * niftk::ImageToSurfaceFilter::GetInput ( void )

Returns a const reference to the input image (e.g. the original input image that ist used to create the surface)

virtual int niftk::ImageToSurfaceFilter::GetInputSmoothingIterations ( ) const

virtual

Returns the number of iterations for the surface smoothing method.

virtual float niftk::ImageToSurfaceFilter::GetInputSmoothingRadius ( ) const

virtual

Returns the smoothing radius of the input image smoothing method.

virtual InputSmoothingMethod niftk::ImageToSurfaceFilter::GetInputSmoothingType ( ) const

virtual

Get the state of the input image smoothing mode.

virtual bool niftk::ImageToSurfaceFilter::GetPerformInputSmoothing ( ) const

virtual

Returns if input image smoothing is enabled.

virtual bool niftk::ImageToSurfaceFilter::GetPerformSurfaceCleaning ( ) const

virtual

Returns true if surface cleaning is enabled.

virtual bool niftk::ImageToSurfaceFilter::GetPerformSurfaceDecimation ( ) const

virtual

Returns if surface decimation is enabled.

virtual bool niftk::ImageToSurfaceFilter::GetPerformSurfaceSmoothing ( ) const

virtual

Returns if surface smoothing is enabled.

virtual double niftk::ImageToSurfaceFilter::GetSamplingRatio ( ) const

virtual

Returns the downsampling ratio.

virtual int niftk::ImageToSurfaceFilter::GetSurfaceCleaningThreshold ( ) const

virtual

Returns the threshold for small object removal.

virtual SurfaceDecimationMethod niftk::ImageToSurfaceFilter::GetSurfaceDecimationType ( ) const

virtual

Get the state of decimation mode to reduce the number of triangles in the surface represantation.

virtual SurfaceExtractionMethod niftk::ImageToSurfaceFilter::GetSurfaceExtractionType ( ) const

virtual

Get the state of the input image smoothing mode.

virtual int niftk::ImageToSurfaceFilter::GetSurfaceSmoothingIterations ( ) const

virtual

Returns the number of iterations for the input image smoothing method.

virtual float niftk::ImageToSurfaceFilter::GetSurfaceSmoothingRadius ( ) const

virtual

Returns the smoothing radius of the surface smoothing method.

virtual SurfaceSmoothingMethod niftk::ImageToSurfaceFilter::GetSurfaceSmoothingType ( ) const

virtual

Get the state of the surface smoothing mode.

virtual float niftk::ImageToSurfaceFilter::GetTargetReduction ( ) const

virtual

Returns the reduction factor as a float value.

virtual mitk::ScalarType niftk::ImageToSurfaceFilter::GetThreshold ( ) const

virtual

Get the Marching Cubes threshold value. Threshold can be manipulated by inherited classes.

void niftk::ImageToSurfaceFilter::MeshSmoothing ( MeshData * meshData )

protected

Performs smoothing of the triangle mesh with the previously selected method (SurfaceSmoothingType)

niftk::ImageToSurfaceFilter::mitkClassMacro	(	ImageToSurfaceFilter	,
		SurfaceSource
	)

template<class T1 , class T2 , class T3 >

void niftk::ImageToSurfaceFilter::mitkVtkLinearTransformPoint	(	T1	matrix[4][4],
		T2	in[3],
		T3	out[3]
	)

inline

Transforms a point by a 4x4 matrix.

virtual void niftk::ImageToSurfaceFilter::PerformInputSmoothingOff ( )

virtual

virtual void niftk::ImageToSurfaceFilter::PerformInputSmoothingOn ( )

virtual

Enable/Disable input image smoothing.

virtual void niftk::ImageToSurfaceFilter::PerformSurfaceDecimationOff ( )

virtual

virtual void niftk::ImageToSurfaceFilter::PerformSurfaceDecimationOn ( )

virtual

Enable/Disable surface decimation.

virtual void niftk::ImageToSurfaceFilter::PerformSurfaceSmoothingOff ( )

virtual

virtual void niftk::ImageToSurfaceFilter::PerformSurfaceSmoothingOn ( )

virtual

Enable/Disable surface smoothing.

void niftk::ImageToSurfaceFilter::SetInput ( const mitk::Image * image )

virtual

virtual void niftk::ImageToSurfaceFilter::SetInputSmoothingIterations ( int _arg )

virtual

Sets the number of iterations for the surface smoothing method.

virtual void niftk::ImageToSurfaceFilter::SetInputSmoothingRadius ( float _arg )

virtual

Sets the smoothing radius of the input image smoothing method.

virtual void niftk::ImageToSurfaceFilter::SetInputSmoothingType ( InputSmoothingMethod _arg )

virtual

Sets the input image smoothing mode (Gaussian / Median)

virtual void niftk::ImageToSurfaceFilter::SetPerformInputSmoothing ( bool _arg )

virtual

Enables input image smoothing. The preferred method can be specified, along with the radius.

virtual void niftk::ImageToSurfaceFilter::SetPerformSurfaceCleaning ( bool _arg )

virtual

Enable/Disable surface cleaning and small object removal.

virtual void niftk::ImageToSurfaceFilter::SetPerformSurfaceDecimation ( bool _arg )

virtual

Enables surface decimation. The preferred method can be specified, along with the radius.

virtual void niftk::ImageToSurfaceFilter::SetPerformSurfaceSmoothing ( bool _arg )

virtual

Enables surface smoothing. The preferred method can be specified, along with the parameters.

virtual void niftk::ImageToSurfaceFilter::SetSamplingRatio ( double _arg )

virtual

Set desired downsampling ratio that is applied to the image before surface extraction.

virtual void niftk::ImageToSurfaceFilter::SetSurfaceCleaningThreshold ( int _arg )

virtual

Sets the number threshold for small object removal.

virtual void niftk::ImageToSurfaceFilter::SetSurfaceDecimationType ( SurfaceDecimationMethod _arg )

virtual

Sets the surface decimation method to reduce the number of triangles in the mesh and produce a good approximation to the original image.

virtual void niftk::ImageToSurfaceFilter::SetSurfaceExtractionType ( SurfaceExtractionMethod _arg )

virtual

Sets the input image smoothing mode (Gaussian / Median)

virtual void niftk::ImageToSurfaceFilter::SetSurfaceSmoothingIterations ( int _arg )

virtual

Sets the number of iterations for the input image smoothing method.

virtual void niftk::ImageToSurfaceFilter::SetSurfaceSmoothingRadius ( float _arg )

virtual

Sets the smoothing radius of the surface smoothing method.

virtual void niftk::ImageToSurfaceFilter::SetSurfaceSmoothingType ( SurfaceSmoothingMethod _arg )

virtual

Sets the surface smoothing mode (Laplacian / Taubin)

virtual void niftk::ImageToSurfaceFilter::SetTargetReduction ( float _arg )

virtual

Set desired amount of reduction of triangles in the range from 0.0 to 1.0. For example 0.9 will reduce the data set to 10%.

virtual void niftk::ImageToSurfaceFilter::SetThreshold ( mitk::ScalarType _arg )

virtual

Set the Marching Cubes threshold value. Threshold can be manipulated by inherited classes.

Threshold that is used to create the surface. All pixel in the input image that are higher than that value will be considered in the surface. The threshold referees to vtkMarchingCube. Default value is 1. See also SetThreshold (ScalarType _arg)

void niftk::ImageToSurfaceFilter::SurfaceSmoothingVTK ( vtkSmartPointer< vtkPolyData > vtkSurface )

protected

Performs smoothing of the triangle mesh with the VTK smoothing method.

void niftk::ImageToSurfaceFilter::VTKSurfaceExtraction	(	mitk::Image *	image,
		vtkSmartPointer< vtkPolyData >	vtkSurface
	)

protected

Creates a surface using the VTK Marching Cubes method.

Member Data Documentation

bool niftk::ImageToSurfaceFilter::m_FlipNormals

protected

int niftk::ImageToSurfaceFilter::m_InputSmoothingIterations

protected

float niftk::ImageToSurfaceFilter::m_InputSmoothingRadius

protected

InputSmoothingMethod niftk::ImageToSurfaceFilter::m_InputSmoothingType

protected

bool niftk::ImageToSurfaceFilter::m_PerformInputSmoothing

protected

bool niftk::ImageToSurfaceFilter::m_PerformSurfaceCleaning

protected

bool niftk::ImageToSurfaceFilter::m_PerformSurfaceDecimation

protected

bool niftk::ImageToSurfaceFilter::m_PerformSurfaceSmoothing

protected

double niftk::ImageToSurfaceFilter::m_SamplingRatio

protected

int niftk::ImageToSurfaceFilter::m_SurfaceCleaningThreshold

protected

SurfaceDecimationMethod niftk::ImageToSurfaceFilter::m_SurfaceDecimationType

protected

SurfaceExtractionMethod niftk::ImageToSurfaceFilter::m_SurfaceExtractionType

protected

int niftk::ImageToSurfaceFilter::m_SurfaceSmoothingIterations

protected

float niftk::ImageToSurfaceFilter::m_SurfaceSmoothingRadius

protected

SurfaceSmoothingMethod niftk::ImageToSurfaceFilter::m_SurfaceSmoothingType

protected

double niftk::ImageToSurfaceFilter::m_TargetReduction

protected

mitk::ScalarType niftk::ImageToSurfaceFilter::m_Threshold

protected

Threshold that is used to create the surface. All pixel in the input image that are higher than that value will be considered in the surface. Default value is 1. See also SetThreshold (ScalarType _arg)

bool niftk::ImageToSurfaceFilter::m_VTKNormalCompute

protected

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

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation