#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
using	BinaryOutput = Image< unsigned char, 3 >

using	CellsContainerIterator = typename InputMeshType::CellsContainer::Iterator

using	CellsContainerPointer = typename InputMeshType::CellsContainerPointer

using	ConstPointer = SmartPointer< const Self >

using	CovariantVectorType = CovariantVector< typename VectorType::ValueType, 3 >

using	GeometryMapIterator = typename GeometryMapType::Iterator

using	GeometryMapPointer = typename GeometryMapType::Pointer

using	GeometryMapType = typename InputMeshType::GeometryMapType

using	GradientImagePointer = typename GradientImageType::Pointer

using	GradientImageSizeType = typename GradientImageType::SizeType

using	GradientImageType = Image< GradientType, 3 >

using	GradientIndexType = typename GradientImageType::IndexType

using	GradientIndexValueType = typename GradientIndexType::IndexValueType

using	GradientPixelType = typename GradientImageType::PixelType

using	GradientType = CovariantVector< PixelType, 3 >

using	IndexSetIterator = typename IndexSetType::iterator

using	IndexSetType = std::set< IdentifierType >

using	InputMeshPointer = typename InputMeshType::Pointer

using	InputMeshType = TInputMesh

using	InputNeighbors = typename InputMeshType::NeighborListType

using	InputNeighborsIterator = typename InputMeshType::NeighborListType::iterator

using	InputPointsContainer = typename InputMeshType::PointsContainer

using	InputPointsContainerConstIterator = typename InputMeshType::PointsContainer::ConstIterator

using	InputPointsContainerPointer = typename InputMeshType::PointsContainerPointer

using	MagnitudeOutput = Image< float, 3 >

using	MeshPointType = typename InputMeshType::PointType

using	NeighborSetIterator = typename NeighborSetType::iterator

using	NeighborSetType = std::set< IdentifierType >

using	OutputMeshPointer = typename OutputMeshType::Pointer

using	OutputMeshType = TOutputMesh

using	PixelType = typename InputMeshType::PixelType

using	Pointer = SmartPointer< Self >

using	PointType = typename SimplexMeshGeometry::PointType

using	Self = DeformableSimplexMesh3DFilter

using	Superclass = MeshToMeshFilter< TInputMesh, TOutputMesh >

using	VectorType = typename PointType::VectorType

using	VertexNeighborListType = itk::MapContainer< IdentifierType, NeighborSetType >

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

using	InputMeshPointer = typename InputMeshType::Pointer

using	InputMeshType = TInputMesh

using	OutputMeshPointer = typename OutputMeshType::Pointer

using	OutputMeshType = TOutputMesh

using	Pointer = SmartPointer< Self >

using	Self = MeshToMeshFilter

using	Superclass = MeshSource< TOutputMesh >

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

using	DataObjectIdentifierType = Superclass::DataObjectIdentifierType

using	DataObjectPointer = DataObject::Pointer

using	OutputMeshPointer = typename OutputMeshType::Pointer

using	OutputMeshType = TOutputMesh

using	Pointer = SmartPointer< Self >

using	Self = MeshSource

using	Superclass = ProcessObject

using	DataObjectPointerArraySizeType = ProcessObject::DataObjectPointerArraySizeType

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

using	DataObjectIdentifierType = DataObject::DataObjectIdentifierType

using	DataObjectPointer = DataObject::Pointer

using	DataObjectPointerArray = std::vector< DataObjectPointer >

using	DataObjectPointerArraySizeType = DataObjectPointerArray::size_type

using	MultiThreaderType = MultiThreaderBase

using	NameArray = std::vector< DataObjectIdentifierType >

using	Pointer = SmartPointer< Self >

using	Self = ProcessObject

using	Superclass = Object

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

using	Pointer = SmartPointer< Self >

using	Self = Object

using	Superclass = LightObject

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

using	Pointer = SmartPointer< Self >

using	Self = LightObject

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

const InputMeshType *	GetInput (unsigned int idx) const

void	SetInput (const InputMeshType *input)

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

OutputMeshType *	GetOutput (unsigned int idx)

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

virtual void	GraftOutput (DataObject *output)

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

void	SetOutput (TOutputMesh *output)

DataObjectPointer	MakeOutput (DataObjectPointerArraySizeType idx) override

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

virtual void	AbortGenerateDataOn ()

virtual void	EnlargeOutputRequestedRegion (DataObject *)

virtual const bool &	GetAbortGenerateData () const

DataObjectPointerArray	GetIndexedInputs ()

DataObjectPointerArray	GetIndexedOutputs ()

NameArray	GetInputNames () const

DataObjectPointerArray	GetInputs ()

MultiThreaderType *	GetMultiThreader () const

DataObjectPointerArraySizeType	GetNumberOfIndexedInputs () const

DataObjectPointerArraySizeType	GetNumberOfIndexedOutputs () const

DataObjectPointerArraySizeType	GetNumberOfInputs () const

DataObjectPointerArraySizeType	GetNumberOfOutputs () const

virtual DataObjectPointerArraySizeType	GetNumberOfValidRequiredInputs () const

NameArray	GetOutputNames () const

DataObjectPointerArray	GetOutputs ()

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)

void	SetMultiThreader (MultiThreaderType *threader)

virtual void	Update ()

virtual void	UpdateLargestPossibleRegion ()

virtual void	UpdateOutputData (DataObject *output)

virtual void	UpdateOutputInformation ()

void	UpdateProgress (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	SetNumberOfWorkUnits (ThreadIdType _arg)

virtual const ThreadIdType &	GetNumberOfWorkUnits () 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 ()

const MetaDataDictionary &	GetMetaDataDictionary () 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

void	Register () const override

void	RemoveAllObservers ()

void	RemoveObserver (unsigned long tag)

void	SetDebug (bool debugFlag) const

void	SetReferenceCount (int) override

void	UnRegister () const noexceptoverride

void	SetMetaDataDictionary (const MetaDataDictionary &rhs)

void	SetMetaDataDictionary (MetaDataDictionary &&rrhs)

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 ()

void	GenerateData () override

virtual void	Initialize ()

bool	L_Func (const double r, const double d, const double phi, double &output)

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

virtual void	UpdateReferenceMetrics ()

	~DeformableSimplexMesh3DFilter () override=default

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

void	CopyInputMeshToOutputMeshCellLinks ()

void	CopyInputMeshToOutputMeshCells ()

void	CopyInputMeshToOutputMeshPointData ()

void	CopyInputMeshToOutputMeshPoints ()

	MeshToMeshFilter ()

	~MeshToMeshFilter () override=default

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

	MeshSource ()

	~MeshSource () override=default

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

void	AddOptionalInputName (const DataObjectIdentifierType &)

void	AddOptionalInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx)

virtual void	AddOutput (DataObject *output)

bool	AddRequiredInputName (const DataObjectIdentifierType &)

bool	AddRequiredInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx)

virtual void	CacheInputReleaseDataFlags ()

virtual void	GenerateOutputInformation ()

virtual void	GenerateOutputRequestedRegion (DataObject *output)

DataObject *	GetInput (const DataObjectIdentifierType &key)

const DataObject *	GetInput (const DataObjectIdentifierType &key) const

virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredInputs () const

virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredOutputs () const

bool	IsIndexedInputName (const DataObjectIdentifierType &) const

bool	IsIndexedOutputName (const DataObjectIdentifierType &) const

bool	IsRequiredInputName (const DataObjectIdentifierType &) const

DataObjectPointerArraySizeType	MakeIndexFromInputName (const DataObjectIdentifierType &name) const

DataObjectPointerArraySizeType	MakeIndexFromOutputName (const DataObjectIdentifierType &name) const

DataObjectIdentifierType	MakeNameFromInputIndex (DataObjectPointerArraySizeType idx) const

DataObjectIdentifierType	MakeNameFromOutputIndex (DataObjectPointerArraySizeType idx) const

virtual void	PopBackInput ()

virtual void	PopFrontInput ()

	ProcessObject ()

virtual void	PropagateResetPipeline ()

virtual void	PushBackInput (const DataObject *input)

virtual void	PushFrontInput (const DataObject *input)

virtual void	ReleaseInputs ()

virtual void	RemoveInput (const DataObjectIdentifierType &key)

virtual void	RemoveInput (DataObjectPointerArraySizeType)

virtual void	RemoveOutput (const DataObjectIdentifierType &key)

virtual void	RemoveOutput (DataObjectPointerArraySizeType idx)

bool	RemoveRequiredInputName (const DataObjectIdentifierType &)

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	SetNumberOfRequiredInputs (DataObjectPointerArraySizeType)

virtual void	SetNumberOfRequiredOutputs (DataObjectPointerArraySizeType _arg)

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

virtual void	SetPrimaryInput (DataObject *input)

virtual void	SetPrimaryOutput (DataObject *output)

void	SetRequiredInputNames (const NameArray &)

virtual void	VerifyInputInformation () ITKv5_CONST

virtual void	VerifyPreconditions () ITKv5_CONST

	~ProcessObject () override

DataObject *	GetInput (DataObjectPointerArraySizeType idx)

const DataObject *	GetInput (DataObjectPointerArraySizeType idx) const

DataObject *	GetPrimaryInput ()

const DataObject *	GetPrimaryInput () const

virtual void	SetPrimaryInputName (const DataObjectIdentifierType &key)

virtual const char *	GetPrimaryInputName () const

DataObject *	GetOutput (const DataObjectIdentifierType &key)

const DataObject *	GetOutput (const DataObjectIdentifierType &key) const

virtual void	SetPrimaryOutputName (const DataObjectIdentifierType &key)

virtual const char *	GetPrimaryOutputName () 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)

	~Object () override

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
std::atomic< int >	m_ReferenceCount