#include <itkVesselEnhancingDiffusion3DImageFilter.h>

Inheritance diagram for itk::VesselEnhancingDiffusion3DImageFilter< PixelType, NDimension >:

Collaboration diagram for itk::VesselEnhancingDiffusion3DImageFilter< PixelType, NDimension >:

Detailed Description

template<class PixelType = short int, unsigned int NDimension = 3>
class itk::VesselEnhancingDiffusion3DImageFilter< PixelType, NDimension >

Complete rewrite of previous versions, only using itk/vnl routines for derivatives, eigensystem calculations and diffusion. Internally, the input image image is converted to internalprecision (float) for calculation, and converted back when returning the results.

Uses simple forward Euler scheme (explicit) with 3x3x3 stencil, see eg phd of Joachim Weickert for theory and implementation regarding the construction of this discretization scheme. See 'Vessel Enhancing Diffusion', Manniesing, media 2006, for information regarding the construction of the diffusion tensor.

Stores all elements of the Hessian of the complete image during diffusion. An alternative implementation is to only store the scale for which the vesselness has maximum response, and to recalculate the hessian (locally) during diffusion. Also stores the current image, ie at iteration i + temp image, therefore the complete memory consumption approximately peaks at 8 times the input image (input image in float)
The hessian is stored as six individual images, an alternative implementation is to use the itk symmetric second rank tensor as pixeltype (and eg using the class SymmetricEigenAnalysisImage Filter). However, we are lazy, and using this since we rely on vnl datatypes and its eigensystem calculations
note: most of computation time is spent at calculation of vesselness response

9 feb 2009 changed imagetype to precisionimage type of function call, thanks to Mark Rabotnikov
PixelType short, 3D Precision float, 3D
todo
- using parallelism/threading eg over scales
- completely itk-fying, eg eigenvalues calculation
- possibly embedding within itk-diffusion framework
- itk expert to have a look at use of iterators (there must be a potential gain there)

email: r.man.nosp@m.nies.nosp@m.ing@e.nosp@m.rasm.nosp@m.usmc..nosp@m.nl

Definition at line 74 of file itkVesselEnhancingDiffusion3DImageFilter.h.

Public Types
typedef SmartPointer< const Self >	ConstPointer

typedef Image< PixelType, NDimension >	ImageType

typedef SmartPointer< Self >	Pointer

typedef float	Precision

typedef Image< Precision, NDimension >	PrecisionImageType

typedef VesselEnhancingDiffusion3DImageFilter	Self

typedef ImageToImageFilter < ImageType, ImageType >	Superclass

Public Types inherited from itk::ImageToImageFilter< Image< PixelType, NDimension >, Image< PixelType, NDimension > >
typedef SmartPointer< const Self >	ConstPointer

typedef InputImageType::ConstPointer	InputImageConstPointer

typedef InputImageType::PixelType	InputImagePixelType

typedef InputImageType::Pointer	InputImagePointer

typedef InputImageType::RegionType	InputImageRegionType

typedef Image< PixelType, NDimension >	InputImageType

typedef Superclass::OutputImagePixelType	OutputImagePixelType

typedef Superclass::OutputImageRegionType	OutputImageRegionType

typedef SmartPointer< Self >	Pointer

typedef ImageToImageFilter	Self

typedef ImageSource< Image < PixelType, NDimension > >	Superclass

Public Types inherited from itk::ImageSource< Image< PixelType, NDimension > >
typedef SmartPointer< const Self >	ConstPointer

typedef Superclass::DataObjectIdentifierType	DataObjectIdentifierType

typedef DataObject::Pointer	DataObjectPointer

typedef Superclass::DataObjectPointerArraySizeType	DataObjectPointerArraySizeType

typedef OutputImageType::PixelType	OutputImagePixelType

typedef OutputImageType::Pointer	OutputImagePointer

typedef OutputImageType::RegionType	OutputImageRegionType

typedef Image< PixelType, NDimension >	OutputImageType

typedef SmartPointer< Self >	Pointer

typedef ImageSource	Self

typedef ProcessObject	Superclass

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 void	DarkObjectLightBackgroundOff ()

virtual void	DarkObjectLightBackgroundOn ()

virtual const char *	GetNameOfClass () const

virtual void	SetAlpha (Precision _arg)

virtual void	SetBeta (Precision _arg)

virtual void	SetDarkObjectLightBackground (bool _arg)

void	SetDefaultPars ()

virtual void	SetEpsilon (Precision _arg)

virtual void	SetGamma (Precision _arg)

virtual void	SetIterations (unsigned int _arg)

virtual void	SetOmega (Precision _arg)

virtual void	SetRecalculateVesselness (unsigned int _arg)

void	SetScales (const std::vector< Precision > scales)

virtual void	SetSensitivity (Precision _arg)

virtual void	SetTimeStep (Precision _arg)

virtual void	SetVerbose (bool _arg)

virtual void	VerboseOff ()

virtual void	VerboseOn ()

Public Member Functions inherited from itk::ImageToImageFilter< Image< PixelType, NDimension >, Image< PixelType, NDimension > >
const InputImageType *	GetInput (void) const

const InputImageType *	GetInput (unsigned int idx) const

virtual void	PopBackInput ()

virtual void	PopFrontInput ()

virtual void	PushBackInput (const InputImageType *image)

virtual void	PushFrontInput (const InputImageType *image)

virtual void	SetInput (const InputImageType *image)

virtual void	SetInput (unsigned int, const Image< PixelType, NDimension > *image)

virtual void	SetCoordinateTolerance (double _arg)

virtual double	GetCoordinateTolerance () const

virtual void	SetDirectionTolerance (double _arg)

virtual double	GetDirectionTolerance () const

Public Member Functions inherited from itk::ImageSource< Image< PixelType, NDimension > >
OutputImageType *	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)

OutputImageType *	GetOutput (void)

const OutputImageType *	GetOutput (void) const

virtual ProcessObject::DataObjectPointer	MakeOutput (ProcessObject::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::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
void	GenerateData ()

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

	VesselEnhancingDiffusion3DImageFilter ()

	~VesselEnhancingDiffusion3DImageFilter ()

Protected Member Functions inherited from itk::ImageToImageFilter< Image< PixelType, NDimension >, Image< PixelType, NDimension > >
virtual void	CallCopyInputRegionToOutputRegion (OutputImageRegionType &destRegion, const InputImageRegionType &srcRegion)

virtual void	CallCopyOutputRegionToInputRegion (InputImageRegionType &destRegion, const OutputImageRegionType &srcRegion)

virtual void	GenerateInputRequestedRegion ()

	ImageToImageFilter ()

virtual void	VerifyInputInformation ()

	~ImageToImageFilter ()

void	PushBackInput (const DataObject *input)

void	PushFrontInput (const DataObject *input)

Protected Member Functions inherited from itk::ImageSource< Image< PixelType, NDimension > >
virtual void	AfterThreadedGenerateData ()

virtual void	AllocateOutputs ()

virtual void	BeforeThreadedGenerateData ()

virtual const ImageRegionSplitterBase *	GetImageRegionSplitter (void) const

	ImageSource ()

virtual unsigned int	SplitRequestedRegion (unsigned int i, unsigned int pieces, OutputImageRegionType &splitRegion)

virtual void	ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, ThreadIdType threadId)

virtual	~ImageSource ()

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	VerifyPreconditions ()

	~ProcessObject ()

DataObject *	GetInput (const DataObjectIdentifierType &key)

const DataObject *	GetInput (const DataObjectIdentifierType &key) const

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 (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 ()

Private Member Functions
void	DiffusionTensor ()

void	MaxVesselResponse (const typename PrecisionImageType::Pointer)

void	operator= (const Self &)

void	VED3DSingleIteration (typename PrecisionImageType::Pointer)

	VesselEnhancingDiffusion3DImageFilter (const Self &)

Precision	VesselnessFunction3D (Precision, Precision, Precision)

Private Attributes
Precision	m_Alpha

Precision	m_Beta

unsigned int	m_CurrentIteration

bool	m_DarkObjectLightBackground

PrecisionImageType::Pointer	m_Dxx

PrecisionImageType::Pointer	m_Dxy

PrecisionImageType::Pointer	m_Dxz

PrecisionImageType::Pointer	m_Dyy

PrecisionImageType::Pointer	m_Dyz

PrecisionImageType::Pointer	m_Dzz

Precision	m_Epsilon

Precision	m_Gamma

unsigned int	m_Iterations

Precision	m_Omega

unsigned int	m_RecalculateVesselness

std::vector< Precision >	m_Scales

Precision	m_Sensitivity

Precision	m_TimeStep

bool	m_Verbose

Additional Inherited Members
Static Public Attributes inherited from itk::ImageToImageFilter< Image< PixelType, NDimension >, Image< PixelType, NDimension > >
static const unsigned int	InputImageDimension

static const unsigned int	OutputImageDimension

Static Public Attributes inherited from itk::ImageSource< Image< PixelType, NDimension > >
static const unsigned int	OutputImageDimension

Protected Types inherited from itk::ImageToImageFilter< Image< PixelType, NDimension >, Image< PixelType, NDimension > >
typedef ImageToImageFilterDetail::ImageRegionCopier < itkGetStaticConstMacro(OutputImageDimension), itkGetStaticConstMacro(InputImageDimension) >	InputToOutputRegionCopierType

typedef ImageToImageFilterDetail::ImageRegionCopier < itkGetStaticConstMacro(InputImageDimension), itkGetStaticConstMacro(OutputImageDimension) >	OutputToInputRegionCopierType

Protected Types inherited from itk::LightObject
typedef int	InternalReferenceCountType

Static Protected Member Functions inherited from itk::ImageSource< Image< PixelType, NDimension > >
static const ImageRegionSplitterBase *	GetGlobalDefaultSplitter ()

static ITK_THREAD_RETURN_TYPE	ThreaderCallback (void *arg)

Protected Attributes inherited from itk::ProcessObject
TimeStamp	m_OutputInformationMTime

bool	m_Updating

Protected Attributes inherited from itk::LightObject
InternalReferenceCountType	m_ReferenceCount

SimpleFastMutexLock	m_ReferenceCountLock