#include <itkDeformableSimplexMesh3DFilter.h>

Inheritance diagram for itk::DeformableSimplexMesh3DFilter< TInputMesh, TOutputMesh >:

Collaboration diagram for itk::DeformableSimplexMesh3DFilter< TInputMesh, TOutputMesh >:

Detailed Description

template<typename TInputMesh, typename TOutputMesh>
class itk::DeformableSimplexMesh3DFilter< TInputMesh, TOutputMesh >

Three-dimensional deformable model for image segmentation.

DeformableSimplexMesh3DFilter is a discrete three-dimensional deformable model, which can be used to deform a 3-D SimplexMesh.

The mesh deformation is constrained by internal forces. The interal force can be scaled via SetAlpha (typical values are 0.01 < alpha < 0.3). The external force is derived from the image one wants to delineate. Therefore an image of type GradientImageType needs to be set by calling SetGradientImage(...). The external forces are scaled via SetBeta (typical values are 0.01 < beta < 1). One still needs to play around with these values.

To control the smoothness of the mesh a rigidity parameter can be adjusted. Low values (1 or 0) allow areas with high curvature. Higher values (around 7 or 8) will make the mesh smoother.

By setting the gamma parameter the regularity of the mesh is controlled. Low values (< 0.03) produce more regular mesh. Higher values ( 0.3 < gamma < 0.2) will allow to move the vertices to regions of higher curvature.

This approach for segmentation follows that of Delingette et al. (1997).

This filter currently assumes that the spacing of the input image is 1.

The user has to set the number of iterations for mesh evolution.

Author: Thomas Boettger. Division Medical and Biological Informatics, German Cancer Research Center, Heidelberg.

Definition at line 76 of file itkDeformableSimplexMesh3DFilter.h.

Public Types
typedef Image< unsigned char, 3 >	BinaryOutput

typedef InputMeshType::CellsContainer::Iterator	CellsContainerIterator

typedef InputMeshType::CellsContainerPointer	CellsContainerPointer

typedef SmartPointer< const Self >	ConstPointer

typedef CovariantVector < typename VectorType::ValueType, 3 >	CovariantVectorType

typedef GeometryMapType::Iterator	GeometryMapIterator

typedef GeometryMapType::Pointer	GeometryMapPointer

typedef InputMeshType::GeometryMapType	GeometryMapType

typedef GradientImageType::Pointer	GradientImagePointer

typedef GradientImageType::SizeType	GradientImageSizeType

typedef Image< GradientType, 3 >	GradientImageType

typedef GradientImageType::IndexType	GradientIndexType

typedef GradientIndexType::IndexValueType	GradientIndexValueType

typedef GradientImageType::PixelType	GradientPixelType

typedef CovariantVector < PixelType, 3 >	GradientType

typedef IndexSetType::iterator	IndexSetIterator

typedef std::set< IdentifierType >	IndexSetType

typedef InputMeshType::Pointer	InputMeshPointer

typedef TInputMesh	InputMeshType

typedef InputMeshType::NeighborListType	InputNeighbors

typedef InputMeshType::NeighborListType::iterator	InputNeighborsIterator

typedef InputMeshType::PointsContainer	InputPointsContainer

typedef InputMeshType::PointsContainer::ConstIterator	InputPointsContainerConstIterator

typedef InputMeshType::PointsContainerPointer	InputPointsContainerPointer

typedef Image< float, 3 >	MagnitudeOutput

typedef InputMeshType::PointType	MeshPointType

typedef NeighborSetType::iterator	NeighborSetIterator

typedef std::set< IdentifierType >	NeighborSetType

typedef OutputMeshType::Pointer	OutputMeshPointer

typedef TOutputMesh	OutputMeshType

typedef InputMeshType::PixelType	PixelType

typedef SmartPointer< Self >	Pointer

typedef SimplexMeshGeometry::PointType	PointType

typedef DeformableSimplexMesh3DFilter	Self

typedef MeshToMeshFilter < TInputMesh, TOutputMesh >	Superclass

typedef PointType::VectorType	VectorType

typedef itk::MapContainer < IdentifierType, NeighborSetType >	VertexNeighborListType

Public Types inherited from itk::MeshToMeshFilter< TInputMesh, TOutputMesh >
typedef SmartPointer< const Self >	ConstPointer

typedef InputMeshType::Pointer	InputMeshPointer

typedef TInputMesh	InputMeshType

typedef OutputMeshType::Pointer	OutputMeshPointer

typedef TOutputMesh	OutputMeshType

typedef SmartPointer< Self >	Pointer

typedef MeshToMeshFilter	Self

typedef MeshSource< TOutputMesh >	Superclass

Public Types inherited from itk::MeshSource< TOutputMesh >
typedef SmartPointer< const Self >	ConstPointer

typedef Superclass::DataObjectIdentifierType	DataObjectIdentifierType

typedef DataObject::Pointer	DataObjectPointer

typedef OutputMeshType::Pointer	OutputMeshPointer

typedef TOutputMesh	OutputMeshType

typedef SmartPointer< Self >	Pointer

typedef MeshSource	Self

typedef ProcessObject	Superclass

typedef ProcessObject::DataObjectPointerArraySizeType	DataObjectPointerArraySizeType

Public Types inherited from itk::ProcessObject
typedef SmartPointer< const Self >	ConstPointer

typedef DataObject::DataObjectIdentifierType	DataObjectIdentifierType

typedef DataObject::Pointer	DataObjectPointer

typedef std::vector < DataObjectPointer >	DataObjectPointerArray

typedef DataObjectPointerArray::size_type	DataObjectPointerArraySizeType

typedef std::vector < DataObjectIdentifierType >	NameArray

typedef SmartPointer< Self >	Pointer

typedef ProcessObject	Self

typedef Object	Superclass

Public Types inherited from itk::Object
typedef SmartPointer< const Self >	ConstPointer

typedef SmartPointer< Self >	Pointer

typedef Object	Self

typedef LightObject	Superclass

Public Types inherited from itk::LightObject
typedef SmartPointer< const Self >	ConstPointer

typedef SmartPointer< Self >	Pointer

typedef LightObject	Self

Public Member Functions
virtual ::itk::LightObject::Pointer	CreateAnother (void) const

virtual double	GetAlpha () const

virtual double	GetBeta () const

virtual double	GetDamping () const

virtual const GeometryMapType *	GetData () const

virtual double	GetGamma () const

const GradientImageType *	GetGradient () const

virtual GeometryMapType *	GetModifiableData ()

virtual const char *	GetNameOfClass () const

virtual unsigned int	GetRigidity () const

virtual int	GetStep () const

virtual void	SetAlpha (double _arg)

virtual void	SetBeta (double _arg)

virtual void	SetDamping (double _arg)

virtual void	SetData (GeometryMapType *_arg)

virtual void	SetGamma (double _arg)

void	SetGradient (const GradientImageType *gradientImage)

virtual void	SetRigidity (unsigned int _arg)


virtual void	SetIterations (int _arg)

virtual int	GetIterations () const


virtual int	GetImageWidth () const

virtual int	GetImageHeight () const

virtual int	GetImageDepth () const

Public Member Functions inherited from itk::MeshToMeshFilter< TInputMesh, TOutputMesh >
const InputMeshType *	GetInput (void) const

const InputMeshType *	GetInput (unsigned int idx) const

void	SetInput (const InputMeshType *input)

Public Member Functions inherited from itk::MeshSource< TOutputMesh >
OutputMeshType *	GetOutput (void)

OutputMeshType *	GetOutput (unsigned int idx)

virtual void	GraftNthOutput (unsigned int idx, DataObject *output)

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

void	SetOutput (TOutputMesh *output)

virtual void	GraftOutput (DataObject *output)

virtual DataObjectPointer	MakeOutput (DataObjectPointerArraySizeType idx) ITK_OVERRIDE

Public Member Functions inherited from itk::ProcessObject
virtual void	AbortGenerateDataOff ()

virtual void	AbortGenerateDataOn ()

virtual void	EnlargeOutputRequestedRegion (DataObject *)

virtual const bool &	GetAbortGenerateData () const

NameArray	GetInputNames () const

MultiThreader *	GetMultiThreader () const

DataObjectPointerArraySizeType	GetNumberOfIndexedInputs () const

DataObjectPointerArraySizeType	GetNumberOfInputs () const

DataObjectPointerArraySizeType	GetNumberOfOutputs () const

virtual DataObjectPointerArraySizeType	GetNumberOfValidRequiredInputs () const

NameArray	GetOutputNames () const

virtual const float &	GetProgress () const

NameArray	GetRequiredInputNames () const

bool	HasInput (const DataObjectIdentifierType &key) const

bool	HasOutput (const DataObjectIdentifierType &key) const

virtual DataObjectPointer	MakeOutput (const DataObjectIdentifierType &)

virtual void	PrepareOutputs ()

virtual void	PropagateRequestedRegion (DataObject *output)

virtual void	ResetPipeline ()

virtual void	SetAbortGenerateData (bool _arg)

virtual void	Update ()

virtual void	UpdateLargestPossibleRegion ()

virtual void	UpdateOutputData (DataObject *output)

virtual void	UpdateOutputInformation ()

void	UpdateProgress (float progress)

DataObjectPointerArray	GetInputs ()

DataObjectPointerArray	GetOutputs ()

DataObjectPointerArray	GetIndexedInputs ()

DataObjectPointerArray	GetIndexedOutputs ()

DataObjectPointerArraySizeType	GetNumberOfIndexedOutputs () const

void	SetProgress (float progress)

virtual void	SetReleaseDataFlag (bool flag)

virtual bool	GetReleaseDataFlag () const

void	ReleaseDataFlagOn ()

void	ReleaseDataFlagOff ()

virtual void	SetReleaseDataBeforeUpdateFlag (bool _arg)

virtual const bool &	GetReleaseDataBeforeUpdateFlag () const

virtual void	ReleaseDataBeforeUpdateFlagOn ()

virtual void	ReleaseDataBeforeUpdateFlagOff ()

virtual void	SetNumberOfThreads (ThreadIdType _arg)

virtual const ThreadIdType &	GetNumberOfThreads () const

Public Member Functions inherited from itk::Object
unsigned long	AddObserver (const EventObject &event, Command *)

unsigned long	AddObserver (const EventObject &event, Command *) const

virtual void	DebugOff () const

virtual void	DebugOn () const

Command *	GetCommand (unsigned long tag)

bool	GetDebug () const

MetaDataDictionary &	GetMetaDataDictionary (void)

const MetaDataDictionary &	GetMetaDataDictionary (void) const

virtual ModifiedTimeType	GetMTime () const

virtual const TimeStamp &	GetTimeStamp () const

bool	HasObserver (const EventObject &event) const

void	InvokeEvent (const EventObject &)

void	InvokeEvent (const EventObject &) const

virtual void	Modified () const

virtual void	Register () const ITK_OVERRIDE

void	RemoveAllObservers ()

void	RemoveObserver (unsigned long tag)

void	SetDebug (bool debugFlag) const

void	SetMetaDataDictionary (const MetaDataDictionary &rhs)

virtual void	SetReferenceCount (int) ITK_OVERRIDE

virtual void	UnRegister () const ITK_OVERRIDE

virtual void	SetObjectName (std::string _arg)

virtual const std::string &	GetObjectName () const

Public Member Functions inherited from itk::LightObject
virtual void	Delete ()

virtual int	GetReferenceCount () const

	itkCloneMacro (Self)

void	Print (std::ostream &os, Indent indent=0) const

Static Public Member Functions
static Pointer	New ()

Static Public Member Functions inherited from itk::MeshToMeshFilter< TInputMesh, TOutputMesh >
static Pointer	New ()

Static Public Member Functions inherited from itk::MeshSource< TOutputMesh >
static Pointer	New ()

Static Public Member Functions inherited from itk::Object
static bool	GetGlobalWarningDisplay ()

static void	GlobalWarningDisplayOff ()

static void	GlobalWarningDisplayOn ()

static Pointer	New ()

static void	SetGlobalWarningDisplay (bool flag)

Static Public Member Functions inherited from itk::LightObject
static void	BreakOnError ()

static Pointer	New ()

Protected Member Functions
PointType	ComputeBarycentricCoordinates (PointType p, SimplexMeshGeometry *data)

virtual void	ComputeDisplacement ()

virtual void	ComputeExternalForce (SimplexMeshGeometry data, const GradientImageType gradient)

virtual void	ComputeGeometry ()

virtual void	ComputeInternalForce (SimplexMeshGeometry *data)

virtual void	ComputeOutput ()

	DeformableSimplexMesh3DFilter ()

	DeformableSimplexMesh3DFilter (const Self &)

virtual void	GenerateData ()

virtual void	Initialize ()

double	L_Func (double r, double d, double phi)

void	operator= (const Self &)

void	PrintSelf (std::ostream &os, Indent indent) const

virtual void	UpdateReferenceMetrics ()

	~DeformableSimplexMesh3DFilter ()

Protected Member Functions inherited from itk::MeshToMeshFilter< TInputMesh, TOutputMesh >
void	CopyInputMeshToOutputMeshCellData ()

void	CopyInputMeshToOutputMeshCellLinks ()

void	CopyInputMeshToOutputMeshCells ()

void	CopyInputMeshToOutputMeshPointData ()

void	CopyInputMeshToOutputMeshPoints ()

	MeshToMeshFilter ()

	~MeshToMeshFilter ()

Protected Member Functions inherited from itk::MeshSource< TOutputMesh >
virtual void	GenerateInputRequestedRegion () ITK_OVERRIDE

	MeshSource ()

virtual	~MeshSource ()

Protected Member Functions inherited from itk::ProcessObject
virtual void	AddInput (DataObject *input)

virtual void	AddOutput (DataObject *output)

virtual void	CacheInputReleaseDataFlags ()

virtual void	GenerateOutputInformation ()

virtual void	GenerateOutputRequestedRegion (DataObject *output)

virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredOutputs () const

bool	IsIndexedInputName (const DataObjectIdentifierType &) const

bool	IsIndexedOutputName (const DataObjectIdentifierType &) const

	itkLegacyMacro (virtual void RemoveOutput(DataObject *output))

	itkLegacyMacro (void SetNumberOfOutputs(DataObjectPointerArraySizeType num))

	itkLegacyMacro (virtual void RemoveInput(DataObject *input))

	itkLegacyMacro (void SetNumberOfInputs(DataObjectPointerArraySizeType num))

DataObjectPointerArraySizeType	MakeIndexFromInputName (const DataObjectIdentifierType &name) const

DataObjectPointerArraySizeType	MakeIndexFromOutputName (const DataObjectIdentifierType &name) const

DataObjectIdentifierType	MakeNameFromInputIndex (DataObjectPointerArraySizeType idx) const

DataObjectIdentifierType	MakeNameFromOutputIndex (DataObjectPointerArraySizeType idx) const

	ProcessObject ()

virtual void	PropagateResetPipeline ()

virtual void	ReleaseInputs ()

virtual void	RemoveInput (const DataObjectIdentifierType &key)

virtual void	RemoveInput (DataObjectPointerArraySizeType)

virtual void	RemoveOutput (const DataObjectIdentifierType &key)

virtual void	RemoveOutput (DataObjectPointerArraySizeType idx)

virtual void	RestoreInputReleaseDataFlags ()

virtual void	SetInput (const DataObjectIdentifierType &key, DataObject *input)

virtual void	SetNthInput (DataObjectPointerArraySizeType num, DataObject *input)

virtual void	SetNthOutput (DataObjectPointerArraySizeType num, DataObject *output)

void	SetNumberOfIndexedInputs (DataObjectPointerArraySizeType num)

void	SetNumberOfIndexedOutputs (DataObjectPointerArraySizeType num)

virtual void	SetNumberOfRequiredOutputs (DataObjectPointerArraySizeType _arg)

virtual void	SetOutput (const DataObjectIdentifierType &key, DataObject *output)

virtual void	SetPrimaryInput (DataObject *input)

virtual void	SetPrimaryOutput (DataObject *output)

virtual void	VerifyInputInformation ()

virtual void	VerifyPreconditions ()

	~ProcessObject ()

DataObject *	GetInput (const DataObjectIdentifierType &key)

const DataObject *	GetInput (const DataObjectIdentifierType &key) const

DataObject *	GetInput (DataObjectPointerArraySizeType idx)

const DataObject *	GetInput (DataObjectPointerArraySizeType idx) const

virtual void	PushBackInput (const DataObject *input)

virtual void	PopBackInput ()

virtual void	PushFrontInput (const DataObject *input)

virtual void	PopFrontInput ()

DataObject *	GetPrimaryInput ()

const DataObject *	GetPrimaryInput () const

virtual void	SetPrimaryInputName (const DataObjectIdentifierType &key)

virtual const char *	GetPrimaryInputName (void) const

virtual void	SetNumberOfRequiredInputs (DataObjectPointerArraySizeType)

virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredInputs () const

bool	AddRequiredInputName (const DataObjectIdentifierType &)

bool	AddRequiredInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx)

bool	RemoveRequiredInputName (const DataObjectIdentifierType &)

bool	IsRequiredInputName (const DataObjectIdentifierType &) const

void	SetRequiredInputNames (const NameArray &)

DataObject *	GetOutput (const DataObjectIdentifierType &key)

const DataObject *	GetOutput (const DataObjectIdentifierType &key) const

virtual void	SetPrimaryOutputName (const DataObjectIdentifierType &key)

virtual const char *	GetPrimaryOutputName (void) const

DataObject *	GetOutput (DataObjectPointerArraySizeType idx)

const DataObject *	GetOutput (DataObjectPointerArraySizeType idx) const

DataObject *	GetPrimaryOutput ()

const DataObject *	GetPrimaryOutput () const

Protected Member Functions inherited from itk::Object
	Object ()

bool	PrintObservers (std::ostream &os, Indent indent) const

virtual void	SetTimeStamp (const TimeStamp &time)

virtual	~Object ()

Protected Member Functions inherited from itk::LightObject
virtual LightObject::Pointer	InternalClone () const

	LightObject ()

virtual void	PrintHeader (std::ostream &os, Indent indent) const

virtual void	PrintTrailer (std::ostream &os, Indent indent) const

virtual	~LightObject ()

Protected Attributes
double	m_Alpha

double	m_Beta

double	m_Damping

GeometryMapPointer	m_Data

double	m_Gamma

int	m_ImageDepth

int	m_ImageHeight

int	m_ImageWidth

int	m_Iterations

unsigned int	m_Rigidity

int	m_Step

Protected Attributes inherited from itk::ProcessObject
TimeStamp	m_OutputInformationMTime

bool	m_Updating

Protected Attributes inherited from itk::LightObject
InternalReferenceCountType	m_ReferenceCount

SimpleFastMutexLock	m_ReferenceCountLock

Additional Inherited Members
Protected Types inherited from itk::LightObject
typedef int	InternalReferenceCountType