#include <itkFastMarchingBase.h>

Inheritance diagram for itk::FastMarchingBase< TInput, TOutput >:

Collaboration diagram for itk::FastMarchingBase< TInput, TOutput >:

Detailed Description

template<class TInput, class TOutput>
class itk::FastMarchingBase< TInput, TOutput >

Abstract class to solve an Eikonal based-equation using Fast Marching Method.

Fast marching solves an Eikonal equation where the speed is always non-negative and depends on the position only. Starting from an initial position on the front, fast marching systematically moves the front forward one node at a time.

Updates are preformed using an entropy satisfy scheme where only "upwind" neighborhoods are used. This implementation of Fast Marching uses a std::priority_queue to locate the next proper node to update.

Fast Marching sweeps through N points in (N log N) steps to obtain the arrival time value as the front propagates through the domain.

The initial front is specified by two containers:

one containing the known nodes (Alive Nodes: nodes that are already part of the object),
one containing the trial nodes (Trial Nodes: nodes that are considered for inclusion).

In order for the filter to evolve, at least some trial nodes must be specified. These can for instance be specified as the layer of nodes around the alive ones.

The algorithm is terminated early by setting an appropriate stopping criterion, or if there are no more nodes to process.

Template Parameters

TTraits

traits which includes definition such as:

InputDomainType (itk::Image or itk::QuadEdgeMesh)
OutputDomainType (similar to InputDomainType)
NodeType (itk::Index if itk::Image and PointIdentifier if itk::QuadEdgeMesh)
NodePairType std::pair< NodeType, OutputPixelType >
Superclass (itk::ImageToImageFilter or itk::QuadEdgeMeshToQuadEdgeMeshFilter )

Todo:: In the current implemenation, std::priority_queue only allows taking nodes out from the front and putting nodes in from the back. Use itk::PriorityQueueContainer instead.

Topology constraints:: Additional flexibiility in this class includes the implementation of topology constraints for image-based fast marching. Further details can be found in the paper

NJ Tustison, BA Avants, MF Siqueira, JC Gee. "Topological Well- Composedness and Glamorous Glue: A Digital Gluing Algorithm for Topologically Constrained Front Propagation, IEEE Transactions on Image Processing, 20(6):1756-1761, June 2011.

Essentially, one can constrain the propagating front(s) such that they either:

don't merge (using the "Strict" option)
don't create handles (using the "NoHandles" option)

Whereas the majority of related work uses the digital topological concept of "simple points" to constrain the evolving front, this filter uses the concept of "well-composedness". Advantages of the latter over the former includes being able to use the standard marching cubes algorithm to produce a mesh whose genus is identical to that of the evolved front(s).

See Also: FastMarchingStoppingCriterionBase

Definition at line 102 of file itkFastMarchingBase.h.

Public Types
typedef SmartPointer< const Self >	ConstPointer

typedef Traits::InputDomainPointer	InputDomainPointer

typedef Traits::InputDomainType	InputDomainType

typedef Traits::InputPixelType	InputPixelType

typedef Traits::LabelType	LabelType

typedef Traits::NodePairContainerConstIterator	NodePairContainerConstIterator

typedef Traits::NodePairContainerPointer	NodePairContainerPointer

typedef Traits::NodePairContainerType	NodePairContainerType

typedef Traits::NodePairType	NodePairType

typedef Traits::NodeType	NodeType

typedef Traits::OutputDomainPointer	OutputDomainPointer

typedef Traits::OutputDomainType	OutputDomainType

typedef Traits::OutputPixelType	OutputPixelType

typedef SmartPointer< Self >	Pointer

typedef FastMarchingBase	Self

typedef StoppingCriterionType::Pointer	StoppingCriterionPointer

typedef FastMarchingStoppingCriterionBase < TInput, TOutput >	StoppingCriterionType

typedef SuperclassType	Superclass

typedef Traits::SuperclassType	SuperclassType

enum	TopologyCheckType { Nothing = 0, NoHandles, Strict }

typedef FastMarchingTraits < TInput, TOutput >	Traits

Public Member Functions
virtual double	GetNormalizationFactor ()

virtual double	GetSpeedConstant ()

virtual StoppingCriterionType *	GetStoppingCriterion ()

virtual OutputPixelType	GetTargetReachedValue ()

virtual void	SetCollectPoints (bool _arg)

virtual void	SetNormalizationFactor (double _arg)

virtual void	SetSpeedConstant (double _arg)

virtual void	SetStoppingCriterion (StoppingCriterionType *_arg)


virtual void	SetTopologyCheck (TopologyCheckType _arg)

virtual const TopologyCheckType &	GetTopologyCheck ()


virtual void	SetTrialPoints (NodePairContainerType *_arg)

virtual NodePairContainerType *	GetTrialPoints ()


virtual void	SetAlivePoints (NodePairContainerType *_arg)

virtual NodePairContainerType *	GetAlivePoints ()


virtual void	SetProcessedPoints (NodePairContainerType *_arg)

virtual NodePairContainerType *	GetProcessedPoints ()


virtual void	SetForbiddenPoints (NodePairContainerType *_arg)

virtual NodePairContainerType *	GetForbiddenPoints ()


virtual const bool &	GetCollectPoints ()

virtual void	CollectPointsOn ()

virtual void	CollectPointsOff ()

Protected Types
typedef std::vector< NodePairType >	HeapContainerType

typedef std::greater < NodePairType >	NodeComparerType

typedef std::priority_queue < NodeType, HeapContainerType, NodeComparerType >	PriorityQueueType

Protected Member Functions
virtual bool	CheckTopology (OutputDomainType *oDomain, const NodeType &iNode)=0

	FastMarchingBase ()

void	GenerateData ()

virtual unsigned char	GetLabelValueForGivenNode (const NodeType &iNode) const =0

virtual const OutputPixelType	GetOutputValue (OutputDomainType *oDomain, const NodeType &iNode) const =0

virtual IdentifierType	GetTotalNumberOfNodes () const =0

void	Initialize (OutputDomainType *oDomain)

virtual void	InitializeOutput (OutputDomainType *oDomain)=0

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

virtual void	SetLabelValueForGivenNode (const NodeType &iNode, const LabelType &iLabel)=0

virtual void	SetOutputValue (OutputDomainType *oDomain, const NodeType &iNode, const OutputPixelType &iValue)=0

virtual void	UpdateNeighbors (OutputDomainType *oDomain, const NodeType &iNode)=0

virtual void	UpdateValue (OutputDomainType *oDomain, const NodeType &iNode)=0

virtual	~FastMarchingBase ()

Private Member Functions
	FastMarchingBase (const Self &)

void	operator= (const Self &)

Member Typedef Documentation

template<class TInput , class TOutput >

typedef SmartPointer< const Self > itk::FastMarchingBase< TInput, TOutput >::ConstPointer

Definition at line 112 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

typedef std::vector< NodePairType > itk::FastMarchingBase< TInput, TOutput >::HeapContainerType

protected

Definition at line 244 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

typedef Traits::InputDomainPointer itk::FastMarchingBase< TInput, TOutput >::InputDomainPointer

Definition at line 116 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

typedef Traits::InputDomainType itk::FastMarchingBase< TInput, TOutput >::InputDomainType

Input Domain related definitions

Definition at line 115 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

typedef Traits::InputPixelType itk::FastMarchingBase< TInput, TOutput >::InputPixelType

Definition at line 117 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

typedef Traits::LabelType itk::FastMarchingBase< TInput, TOutput >::LabelType

Definition at line 134 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

typedef std::greater< NodePairType > itk::FastMarchingBase< TInput, TOutput >::NodeComparerType

protected

Definition at line 245 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

typedef Traits::NodePairContainerConstIterator itk::FastMarchingBase< TInput, TOutput >::NodePairContainerConstIterator

Definition at line 132 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

typedef Traits::NodePairContainerPointer itk::FastMarchingBase< TInput, TOutput >::NodePairContainerPointer

Definition at line 130 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

typedef Traits::NodePairContainerType itk::FastMarchingBase< TInput, TOutput >::NodePairContainerType

Definition at line 129 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

typedef Traits::NodePairType itk::FastMarchingBase< TInput, TOutput >::NodePairType

NodePairType pair of node and corresponding value

Definition at line 128 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

typedef Traits::NodeType itk::FastMarchingBase< TInput, TOutput >::NodeType

NodeType type of node

Definition at line 125 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

typedef Traits::OutputDomainPointer itk::FastMarchingBase< TInput, TOutput >::OutputDomainPointer

Definition at line 121 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

typedef Traits::OutputDomainType itk::FastMarchingBase< TInput, TOutput >::OutputDomainType

Output Domain related definitions

Definition at line 120 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

typedef Traits::OutputPixelType itk::FastMarchingBase< TInput, TOutput >::OutputPixelType

Definition at line 122 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

typedef SmartPointer< Self > itk::FastMarchingBase< TInput, TOutput >::Pointer

Definition at line 111 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

typedef std::priority_queue< NodeType, HeapContainerType, NodeComparerType > itk::FastMarchingBase< TInput, TOutput >::PriorityQueueType

protected

Definition at line 251 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

typedef FastMarchingBase itk::FastMarchingBase< TInput, TOutput >::Self

Definition at line 109 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

typedef StoppingCriterionType::Pointer itk::FastMarchingBase< TInput, TOutput >::StoppingCriterionPointer

Definition at line 138 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

typedef FastMarchingStoppingCriterionBase< TInput, TOutput > itk::FastMarchingBase< TInput, TOutput >::StoppingCriterionType

StoppingCriterionType stopping criterion

Definition at line 137 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

typedef SuperclassType itk::FastMarchingBase< TInput, TOutput >::Superclass

Definition at line 110 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

typedef Traits::SuperclassType itk::FastMarchingBase< TInput, TOutput >::SuperclassType

Definition at line 106 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

typedef FastMarchingTraits<TInput, TOutput> itk::FastMarchingBase< TInput, TOutput >::Traits

Definition at line 105 of file itkFastMarchingBase.h.

Member Enumeration Documentation

template<class TInput , class TOutput >

enum itk::FastMarchingBase::TopologyCheckType

Enumerator:

Nothing	`Nothing`
NoHandles	`NoHandles`
Strict	`Strict`

Definition at line 155 of file itkFastMarchingBase.h.

Constructor & Destructor Documentation

template<class TInput , class TOutput >

itk::FastMarchingBase< TInput, TOutput >::FastMarchingBase ( )

protected

Constructor.

template<class TInput , class TOutput >

virtual itk::FastMarchingBase< TInput, TOutput >::~FastMarchingBase ( )

protectedvirtual

Destructor.

template<class TInput , class TOutput >

itk::FastMarchingBase< TInput, TOutput >::FastMarchingBase ( const Self & )

private

Member Function Documentation

template<class TInput , class TOutput >

virtual bool itk::FastMarchingBase< TInput, TOutput >::CheckTopology	(	OutputDomainType *	oDomain,
		const NodeType &	iNode
	)

protectedpure virtual

Check if the current node violate topological criterion.

Parameters

[in]	oDomain
[in]	iNode

Implemented in itk::FastMarchingImageFilterBase< TInput, TOutput >.

template<class TInput , class TOutput >

virtual void itk::FastMarchingBase< TInput, TOutput >::CollectPointsOff ( )

virtual

Get the Collect Points flag.

template<class TInput , class TOutput >

virtual void itk::FastMarchingBase< TInput, TOutput >::CollectPointsOn ( )

virtual

Get the Collect Points flag.

template<class TInput , class TOutput >

void itk::FastMarchingBase< TInput, TOutput >::GenerateData ( )

protected

template<class TInput , class TOutput >

virtual NodePairContainerType* itk::FastMarchingBase< TInput, TOutput >::GetAlivePoints ( )

virtual

Set/Get AlivePoints

template<class TInput , class TOutput >

virtual const bool& itk::FastMarchingBase< TInput, TOutput >::GetCollectPoints ( )

virtual

Get the Collect Points flag.

template<class TInput , class TOutput >

virtual NodePairContainerType* itk::FastMarchingBase< TInput, TOutput >::GetForbiddenPoints ( )

virtual

Set/Get ForbiddenPoints

template<class TInput , class TOutput >

virtual unsigned char itk::FastMarchingBase< TInput, TOutput >::GetLabelValueForGivenNode ( const NodeType & iNode ) const

protectedpure virtual

Get the LabelType Value for a given node.

Parameters

[in] iNode

Returns: its label value

Implemented in itk::FastMarchingImageFilterBase< TInput, TOutput >, and itk::FastMarchingQuadEdgeMeshFilterBase< TInput, TOutput >.

template<class TInput , class TOutput >

virtual double itk::FastMarchingBase< TInput, TOutput >::GetNormalizationFactor ( )

virtual

Set/Get NormalizationFactor.

template<class TInput , class TOutput >

virtual const OutputPixelType itk::FastMarchingBase< TInput, TOutput >::GetOutputValue	(	OutputDomainType *	oDomain,
		const NodeType &	iNode
	)		const

protectedpure virtual

Get the ouput value (front value) for a given node.

Implemented in itk::FastMarchingImageFilterBase< TInput, TOutput >.

template<class TInput , class TOutput >

virtual NodePairContainerType* itk::FastMarchingBase< TInput, TOutput >::GetProcessedPoints ( )

virtual

Set/Get ProcessedPoints

template<class TInput , class TOutput >

virtual double itk::FastMarchingBase< TInput, TOutput >::GetSpeedConstant ( )

virtual

Set/Get SpeedConstant.

template<class TInput , class TOutput >

virtual StoppingCriterionType* itk::FastMarchingBase< TInput, TOutput >::GetStoppingCriterion ( )

virtual

Set/Get the Stopping Criterion.

template<class TInput , class TOutput >

virtual OutputPixelType itk::FastMarchingBase< TInput, TOutput >::GetTargetReachedValue ( )

virtual

Get the value reached by the front when it stops propagating.

template<class TInput , class TOutput >

virtual const TopologyCheckType& itk::FastMarchingBase< TInput, TOutput >::GetTopologyCheck ( )

virtual

Set/Get the TopologyCheckType macro indicating whether the user wants to check topology (and which one).

template<class TInput , class TOutput >

virtual IdentifierType itk::FastMarchingBase< TInput, TOutput >::GetTotalNumberOfNodes ( ) const

protectedpure virtual

Get the total number of nodes in the domain.

Implemented in itk::FastMarchingImageFilterBase< TInput, TOutput >, and itk::FastMarchingQuadEdgeMeshFilterBase< TInput, TOutput >.

template<class TInput , class TOutput >

virtual NodePairContainerType* itk::FastMarchingBase< TInput, TOutput >::GetTrialPoints ( )

virtual

Set/Get TrialPoints

template<class TInput , class TOutput >

void itk::FastMarchingBase< TInput, TOutput >::Initialize ( OutputDomainType * oDomain )

protected

template<class TInput , class TOutput >

virtual void itk::FastMarchingBase< TInput, TOutput >::InitializeOutput ( OutputDomainType * oDomain )

protectedpure virtual

Implemented in itk::FastMarchingImageFilterBase< TInput, TOutput >.

template<class TInput , class TOutput >

void itk::FastMarchingBase< TInput, TOutput >::operator= ( const Self & )

private

template<class TInput , class TOutput >

void itk::FastMarchingBase< TInput, TOutput >::PrintSelf	(	std::ostream &	os,
		Indent	indent
	)		const

protected

PrintSelf method.

template<class TInput , class TOutput >

virtual void itk::FastMarchingBase< TInput, TOutput >::SetAlivePoints ( NodePairContainerType * _arg )

virtual

Set/Get AlivePoints

template<class TInput , class TOutput >

virtual void itk::FastMarchingBase< TInput, TOutput >::SetCollectPoints ( bool _arg )

virtual

Set the Collect Points flag. Instrument the algorithm to collect a container of all nodes which it has visited. Useful for creating Narrowbands for level set algorithms that supports narrow banding.

template<class TInput , class TOutput >

virtual void itk::FastMarchingBase< TInput, TOutput >::SetForbiddenPoints ( NodePairContainerType * _arg )

virtual

Set/Get ForbiddenPoints

template<class TInput , class TOutput >

virtual void itk::FastMarchingBase< TInput, TOutput >::SetLabelValueForGivenNode	(	const NodeType &	iNode,
		const LabelType &	iLabel
	)

protectedpure virtual

Set the Label Value for a given node.

Parameters

[in]	iNode
[in]	iLabel

Implemented in itk::FastMarchingImageFilterBase< TInput, TOutput >, and itk::FastMarchingQuadEdgeMeshFilterBase< TInput, TOutput >.

template<class TInput , class TOutput >

virtual void itk::FastMarchingBase< TInput, TOutput >::SetNormalizationFactor ( double _arg )

virtual

template<class TInput , class TOutput >

virtual void itk::FastMarchingBase< TInput, TOutput >::SetOutputValue	(	OutputDomainType *	oDomain,
		const NodeType &	iNode,
		const OutputPixelType &	iValue
	)

protectedpure virtual

Set the output value (front value) for a given node.

Implemented in itk::FastMarchingImageFilterBase< TInput, TOutput >.

template<class TInput , class TOutput >

virtual void itk::FastMarchingBase< TInput, TOutput >::SetProcessedPoints ( NodePairContainerType * _arg )

virtual

Set/Get ProcessedPoints

template<class TInput , class TOutput >

virtual void itk::FastMarchingBase< TInput, TOutput >::SetSpeedConstant ( double _arg )

virtual

template<class TInput , class TOutput >

virtual void itk::FastMarchingBase< TInput, TOutput >::SetStoppingCriterion ( StoppingCriterionType * _arg )

virtual

template<class TInput , class TOutput >

virtual void itk::FastMarchingBase< TInput, TOutput >::SetTopologyCheck ( TopologyCheckType _arg )

virtual

Set/Get the TopologyCheckType macro indicating whether the user wants to check topology (and which one).

template<class TInput , class TOutput >

virtual void itk::FastMarchingBase< TInput, TOutput >::SetTrialPoints ( NodePairContainerType * _arg )

virtual

Set/Get TrialPoints

template<class TInput , class TOutput >

virtual void itk::FastMarchingBase< TInput, TOutput >::UpdateNeighbors	(	OutputDomainType *	oDomain,
		const NodeType &	iNode
	)

protectedpure virtual

Update neighbors to a given node.

Parameters

[in]	oDomain
[in]	iNode

Implemented in itk::FastMarchingImageFilterBase< TInput, TOutput >.

template<class TInput , class TOutput >

virtual void itk::FastMarchingBase< TInput, TOutput >::UpdateValue	(	OutputDomainType *	oDomain,
		const NodeType &	iNode
	)

protectedpure virtual

Update value for a given node.

Parameters

[in]	oDomain
[in]	iNode

Implemented in itk::FastMarchingImageFilterBase< TInput, TOutput >.

Member Data Documentation

template<class TInput , class TOutput >

NodePairContainerPointer itk::FastMarchingBase< TInput, TOutput >::m_AlivePoints

protected

Definition at line 237 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

bool itk::FastMarchingBase< TInput, TOutput >::m_CollectPoints

protected

Definition at line 241 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

NodePairContainerPointer itk::FastMarchingBase< TInput, TOutput >::m_ForbiddenPoints

protected

Definition at line 239 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

PriorityQueueType itk::FastMarchingBase< TInput, TOutput >::m_Heap

protected

Definition at line 253 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

double itk::FastMarchingBase< TInput, TOutput >::m_InverseSpeed

protected

Definition at line 229 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

OutputPixelType itk::FastMarchingBase< TInput, TOutput >::m_LargeValue

protected

Definition at line 233 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

double itk::FastMarchingBase< TInput, TOutput >::m_NormalizationFactor

protected

Definition at line 230 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

NodePairContainerPointer itk::FastMarchingBase< TInput, TOutput >::m_ProcessedPoints

protected

Definition at line 238 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

double itk::FastMarchingBase< TInput, TOutput >::m_SpeedConstant

protected

Definition at line 228 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

StoppingCriterionPointer itk::FastMarchingBase< TInput, TOutput >::m_StoppingCriterion

protected

Definition at line 226 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

OutputPixelType itk::FastMarchingBase< TInput, TOutput >::m_TargetReachedValue

protected

Definition at line 232 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

TopologyCheckType itk::FastMarchingBase< TInput, TOutput >::m_TopologyCheck

protected

Definition at line 255 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

OutputPixelType itk::FastMarchingBase< TInput, TOutput >::m_TopologyValue

protected

Definition at line 234 of file itkFastMarchingBase.h.

template<class TInput , class TOutput >

NodePairContainerPointer itk::FastMarchingBase< TInput, TOutput >::m_TrialPoints

protected

Definition at line 236 of file itkFastMarchingBase.h.

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

itkFastMarchingBase.h

Protected Attributes
NodePairContainerPointer	m_AlivePoints

bool	m_CollectPoints

NodePairContainerPointer	m_ForbiddenPoints

PriorityQueueType	m_Heap

double	m_InverseSpeed

OutputPixelType	m_LargeValue

double	m_NormalizationFactor

NodePairContainerPointer	m_ProcessedPoints

double	m_SpeedConstant

StoppingCriterionPointer	m_StoppingCriterion

OutputPixelType	m_TargetReachedValue

TopologyCheckType	m_TopologyCheck

OutputPixelType	m_TopologyValue

NodePairContainerPointer	m_TrialPoints

Detailed Description

template<class TInput, class TOutput> class itk::FastMarchingBase< TInput, TOutput >

Public Types

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Private Member Functions

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<class TInput, class TOutput>
class itk::FastMarchingBase< TInput, TOutput >