#include <itkVesselEnhancingDiffusion3DImageFilter.h>

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

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

Detailed Description

template<typename 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
using	ConstPointer = SmartPointer< const Self >

using	ImageType = Image< PixelType, NDimension >

using	Pointer = SmartPointer< Self >

using	Precision = float

using	PrecisionImageType = Image< Precision, NDimension >

using	Self = VesselEnhancingDiffusion3DImageFilter

using	Superclass = ImageToImageFilter< ImageType, ImageType >

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

using	InputImageConstPointer = typename InputImageType::ConstPointer

using	InputImagePixelType = typename InputImageType::PixelType

using	InputImagePointer = typename InputImageType::Pointer

using	InputImageRegionType = typename InputImageType::RegionType

using	InputImageType = Image< PixelType, NDimension >

using	OutputImagePixelType = typename Superclass::OutputImagePixelType

using	OutputImageRegionType = typename Superclass::OutputImageRegionType

using	Pointer = SmartPointer< Self >

using	Self = ImageToImageFilter

using	Superclass = ImageSource< Image< PixelType, NDimension > >

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

using	DataObjectIdentifierType = Superclass::DataObjectIdentifierType

using	DataObjectPointer = DataObject::Pointer

using	DataObjectPointerArraySizeType = Superclass::DataObjectPointerArraySizeType

using	OutputImagePixelType = typename OutputImageType::PixelType

using	OutputImagePointer = typename OutputImageType::Pointer

using	OutputImageRegionType = typename OutputImageType::RegionType

using	OutputImageType = Image< PixelType, NDimension >

using	Pointer = SmartPointer< Self >

using	Self = ImageSource

using	Superclass = ProcessObject

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 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 () const

const InputImageType *	GetInput (unsigned int idx) const

void	PopBackInput () override

void	PopFrontInput () override

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)

OutputImageType *	GetOutput ()

const OutputImageType *	GetOutput () const

virtual void	GraftOutput (DataObject *output)

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

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

ProcessObject::DataObjectPointer	MakeOutput (ProcessObject::DataObjectPointerArraySizeType idx) override

ProcessObject::DataObjectPointer	MakeOutput (const ProcessObject::DataObjectIdentifierType &) 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 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::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 () override

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

	VesselEnhancingDiffusion3DImageFilter ()

	~VesselEnhancingDiffusion3DImageFilter () override

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)

void	GenerateInputRequestedRegion () override

	ImageToImageFilter ()

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

void	VerifyInputInformation () ITKv5_CONST override

	~ImageToImageFilter () override

void	PushBackInput (const DataObject *input) override

void	PushFrontInput (const DataObject *input) override

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

virtual void	AllocateOutputs ()

virtual void	BeforeThreadedGenerateData ()

void	ClassicMultiThread (ThreadFunctionType callbackFunction)

void	GenerateData () override

virtual const ImageRegionSplitterBase *	GetImageRegionSplitter () const

	ImageSource ()

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

	~ImageSource () override=default

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

virtual void	DynamicThreadedGenerateData (const OutputImageRegionType &outputRegionForThread)

virtual bool	GetDynamicMultiThreading () const

virtual void	SetDynamicMultiThreading (bool _arg)

virtual void	DynamicMultiThreadingOn ()

virtual void	DynamicMultiThreadingOff ()

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

	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)

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	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 ()

Private Member Functions
void	DiffusionTensor ()

void	MaxVesselResponse (const typename PrecisionImageType::Pointer)

void	VED3DSingleIteration (typename PrecisionImageType::Pointer)

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 constexpr unsigned int	InputImageDimension

static constexpr unsigned int	OutputImageDimension

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

Protected Types inherited from itk::ImageToImageFilter< Image< PixelType, NDimension >, Image< PixelType, NDimension > >
using	InputToOutputRegionCopierType = ImageToImageFilterDetail::ImageRegionCopier< Self::OutputImageDimension, Self::InputImageDimension >

using	OutputToInputRegionCopierType = ImageToImageFilterDetail::ImageRegionCopier< Self::InputImageDimension, Self::OutputImageDimension >

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

static ITK_THREAD_RETURN_FUNCTION_CALL_CONVENTION	ThreaderCallback (void *arg)

Protected Attributes inherited from itk::ImageSource< Image< PixelType, NDimension > >
bool	m_DynamicMultiThreading

Protected Attributes inherited from itk::ProcessObject
TimeStamp	m_OutputInformationMTime

bool	m_Updating

Protected Attributes inherited from itk::LightObject
std::atomic< int >	m_ReferenceCount