itk::GibbsTrackingFilter< ItkQBallImageType > Class Template Reference

Performes global fiber tractography on the input Q-Ball or tensor image (Gibbs tracking, Reisert 2010). More...

#include <itkGibbsTrackingFilter.h>

Inheritance diagram for itk::GibbsTrackingFilter< ItkQBallImageType >:

Collaboration diagram for itk::GibbsTrackingFilter< ItkQBallImageType >:

Public Types
typedef GibbsTrackingFilter	Self
typedef ProcessObject	Superclass
typedef SmartPointer< Self >	Pointer
typedef SmartPointer< const Self >	ConstPointer
typedef Image< DiffusionTensor3D< float >, 3 >	ItkTensorImage
typedef ItkQBallImageType::Pointer	ItkQBallImageTypePointer
typedef Image< float, 3 >	ItkFloatImageType
typedef vtkSmartPointer< vtkPolyData >	FiberPolyDataType

Public Member Functions
Pointer	Clone () const
virtual const char *	GetClassName () const
virtual void	SetStartTemperature (float _arg)
	Start temperature of simulated annealing process. More...
virtual void	SetEndTemperature (float _arg)
	End temperature of simulated annealing process. More...
virtual void	SetIterations (double _arg)
	Number of iterations. More iterations usually mean better results. More...
virtual void	SetParticleWeight (float _arg)
	Smaller particle weights result in a higher sensitivity if the method. More...
virtual void	SetParticleWidth (float _arg)
	Thinner particles cause more reconstructed fibers. More...
virtual void	SetParticleLength (float _arg)
virtual void	SetConnectionPotential (float _arg)
virtual void	SetInexBalance (float _arg)
	Values < 0 result in a stronger weighting of the internal energy, values > 0 cause a stronger weighting of the external energy,. More...
virtual void	SetParticlePotential (float _arg)
virtual void	SetMinFiberLength (int _arg)
	Shorter fibers are discarded. More...
virtual void	SetAbortTracking (bool _arg)
	Set flag to prematurely abort tracking. More...
virtual void	SetCurvatureThreshold (float _arg)
	Absolute angular threshold between two particles (in radians). More...
virtual void	SetDuplicateImage (bool _arg)
	Work on copy of input image. More...
virtual void	SetRandomSeed (int _arg)
	Seed for random generator. More...
virtual void	SetLoadParameterFile (std::string _arg)
	Parameter file. More...
virtual void	SetSaveParameterFile (std::string _arg)
virtual void	SetLutPath (std::string _arg)
	Path to lookuptables. Default is binary directory. More...
virtual float	GetParticleWeight ()
virtual float	GetParticleWidth ()
virtual float	GetParticleLength ()
virtual int	GetNumParticles ()
virtual int	GetNumConnections ()
virtual int	GetNumAcceptedFibers ()
virtual float	GetProposalAcceptance ()
virtual double	GetCurrentIteration ()
virtual double	GetIterations ()
virtual bool	GetIsInValidState ()
FiberPolyDataType	GetFiberBundle ()
	Output fibers. More...
virtual void	SetQBallImage (typename ItkQBallImageType::Pointer _arg)
virtual void	SetMaskImage (ItkFloatImageType::Pointer _arg)
virtual void	SetTensorImage (ItkTensorImage::Pointer _arg)
virtual void	Update () override

Static Public Member Functions
static Pointer	New ()

Protected Member Functions
void	GenerateData () override
	GibbsTrackingFilter ()
virtual	~GibbsTrackingFilter ()
void	EstimateParticleWeight ()
void	PrepareMaskImage ()
bool	LoadParameters ()
bool	SaveParameters ()

Protected Attributes
ItkQBallImageType::Pointer	m_QBallImage
ItkFloatImageType::Pointer	m_MaskImage
ItkTensorImage::Pointer	m_TensorImage
float	m_StartTemperature
	Start temperature. More...
float	m_EndTemperature
	End temperature. More...
double	m_Iterations
	Total number of iterations. More...
double	m_CurrentIteration
	Current iteration. More...
unsigned long	m_CurrentStep
	current tracking step More...
float	m_ParticleWeight
	w (unitless) More...
float	m_ParticleWidth
	sigma (mm) More...
float	m_ParticleLength
	l (mm) More...
float	m_ConnectionPotential
	gross L (chemisches potential, default 10) More...
float	m_InexBalance
	gewichtung zwischen den lambdas; -5 ... 5 -> nur intern ... nur extern,default 0 More...
float	m_ParticlePotential
	default 0.2 More...
int	m_MinFiberLength
	discard all fibers shortan than the specified length in mm More...
bool	m_AbortTracking
	set flag to abort tracking More...
int	m_NumAcceptedFibers
	number of reconstructed fibers generated by the FiberBuilder More...
volatile bool	m_BuildFibers
	set flag to generate fibers from particle grid More...
float	m_ProposalAcceptance
	proposal acceptance rate (0-1) More...
float	m_CurvatureThreshold
	curvature threshold in radians (1 -> no curvature is accepted, -1 all curvature angles are accepted) More...
bool	m_DuplicateImage
	generates a working copy of the qball image so that the original image won't be changed by the mean subtraction More...
int	m_NumParticles
	current number of particles in grid More...
int	m_NumConnections
	current number of connections between particles in grid More...
int	m_RandomSeed
	seed value for random generator (-1 for standard seeding) More...
std::string	m_LoadParameterFile
	filename of parameter file (reader) More...
std::string	m_SaveParameterFile
	filename of parameter file (writer) More...
std::string	m_LutPath
	path to lookuptables used by the sphere interpolator More...
bool	m_IsInValidState
	Whether the filter is in a valid state, false if error occured. More...
FiberPolyDataType	m_FiberPolyData
	container for reconstructed fibers More...

Static Protected Attributes
static const int	m_ParticleGridCellCapacity

Detailed Description

template<class ItkQBallImageType>
class itk::GibbsTrackingFilter< ItkQBallImageType >

Performes global fiber tractography on the input Q-Ball or tensor image (Gibbs tracking, Reisert 2010).

Definition at line 41 of file itkGibbsTrackingFilter.h.

Member Typedef Documentation

template<class ItkQBallImageType>

typedef SmartPointer< const Self > itk::GibbsTrackingFilter< ItkQBallImageType >::ConstPointer

Definition at line 47 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

typedef vtkSmartPointer< vtkPolyData > itk::GibbsTrackingFilter< ItkQBallImageType >::FiberPolyDataType

Definition at line 56 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

typedef Image< float, 3 > itk::GibbsTrackingFilter< ItkQBallImageType >::ItkFloatImageType

Definition at line 55 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

typedef ItkQBallImageType::Pointer itk::GibbsTrackingFilter< ItkQBallImageType >::ItkQBallImageTypePointer

Definition at line 54 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

typedef Image< DiffusionTensor3D<float>, 3 > itk::GibbsTrackingFilter< ItkQBallImageType >::ItkTensorImage

Definition at line 53 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

typedef SmartPointer< Self > itk::GibbsTrackingFilter< ItkQBallImageType >::Pointer

Definition at line 46 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

typedef GibbsTrackingFilter itk::GibbsTrackingFilter< ItkQBallImageType >::Self

Definition at line 44 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

typedef ProcessObject itk::GibbsTrackingFilter< ItkQBallImageType >::Superclass

Definition at line 45 of file itkGibbsTrackingFilter.h.

Constructor & Destructor Documentation

template<class ItkQBallImageType >

itk::GibbsTrackingFilter< ItkQBallImageType >::GibbsTrackingFilter ( )

protected

Definition at line 45 of file itkGibbsTrackingFilter.cpp.

template<class ItkQBallImageType >

itk::GibbsTrackingFilter< ItkQBallImageType >::~GibbsTrackingFilter ( )

protectedvirtual

Definition at line 75 of file itkGibbsTrackingFilter.cpp.

Member Function Documentation

template<class ItkQBallImageType>

Pointer itk::GibbsTrackingFilter< ItkQBallImageType >::Clone

(

)

const

template<class ItkQBallImageType >

void itk::GibbsTrackingFilter< ItkQBallImageType >::EstimateParticleWeight ( )

protected

Definition at line 96 of file itkGibbsTrackingFilter.cpp.

References SphereInterpolator::IsInValidState(), mitk::ParticleGrid::m_NumParticles, mitk::MetropolisHastingsSampler::MakeProposal(), MITK_INFO, mitkThrow, mitk::New(), mitk::ParticleGrid::ResetGrid(), EnergyComputer::SetParameters(), and mitk::MetropolisHastingsSampler::SetTemperature().

template<class ItkQBallImageType >

void itk::GibbsTrackingFilter< ItkQBallImageType >::GenerateData ( )

overrideprotected

Definition at line 168 of file itkGibbsTrackingFilter.cpp.

References mitk::eps, itk::OrientationDistributionFunction< TComponent, NOdfDirections >::GetMeanValue(), mitk::MetropolisHastingsSampler::GetNumAcceptedProposals(), SphereInterpolator::IsInValidState(), mitk::FiberBuilder::iterate(), mitk::ParticleGrid::m_NumConnections, mitk::ParticleGrid::m_NumParticles, mitk::MetropolisHastingsSampler::MakeProposal(), MITK_ERROR, MITK_INFO, mitkThrow, mitk::New(), itk::TensorImageToQBallImageFilter< TInputScalarType, TOutputScalarType >::New(), EnergyComputer::SetParameters(), and mitk::MetropolisHastingsSampler::SetTemperature().

Referenced by itk::GibbsTrackingFilter< ItkQBallImageType >::Update().

template<class ItkQBallImageType>

virtual const char* itk::GibbsTrackingFilter< ItkQBallImageType >::GetClassName ( ) const

virtual

template<class ItkQBallImageType>

virtual double itk::GibbsTrackingFilter< ItkQBallImageType >::GetCurrentIteration ( )

virtual

template<class ItkQBallImageType >

GibbsTrackingFilter< ItkQBallImageType >::FiberPolyDataType itk::GibbsTrackingFilter< ItkQBallImageType >::GetFiberBundle

(

)

Output fibers.

Definition at line 82 of file itkGibbsTrackingFilter.cpp.

template<class ItkQBallImageType>

virtual bool itk::GibbsTrackingFilter< ItkQBallImageType >::GetIsInValidState ( )

virtual

template<class ItkQBallImageType>

virtual double itk::GibbsTrackingFilter< ItkQBallImageType >::GetIterations ( )

virtual

template<class ItkQBallImageType>

virtual int itk::GibbsTrackingFilter< ItkQBallImageType >::GetNumAcceptedFibers ( )

virtual

template<class ItkQBallImageType>

virtual int itk::GibbsTrackingFilter< ItkQBallImageType >::GetNumConnections ( )

virtual

template<class ItkQBallImageType>

virtual int itk::GibbsTrackingFilter< ItkQBallImageType >::GetNumParticles ( )

virtual

template<class ItkQBallImageType>

virtual float itk::GibbsTrackingFilter< ItkQBallImageType >::GetParticleLength ( )

virtual

template<class ItkQBallImageType>

virtual float itk::GibbsTrackingFilter< ItkQBallImageType >::GetParticleWeight ( )

virtual

Getter.

template<class ItkQBallImageType>

virtual float itk::GibbsTrackingFilter< ItkQBallImageType >::GetParticleWidth ( )

virtual

template<class ItkQBallImageType>

virtual float itk::GibbsTrackingFilter< ItkQBallImageType >::GetProposalAcceptance ( )

virtual

template<class ItkQBallImageType >

bool itk::GibbsTrackingFilter< ItkQBallImageType >::LoadParameters ( )

protected

Definition at line 383 of file itkGibbsTrackingFilter.cpp.

References M_PI, and MITK_INFO.

template<class ItkQBallImageType>

static Pointer itk::GibbsTrackingFilter< ItkQBallImageType >::New ( )

static

template<class ItkQBallImageType >

void itk::GibbsTrackingFilter< ItkQBallImageType >::PrepareMaskImage ( )

protected

Definition at line 345 of file itkGibbsTrackingFilter.cpp.

References MITK_INFO, and mitk::New().

template<class ItkQBallImageType >

bool itk::GibbsTrackingFilter< ItkQBallImageType >::SaveParameters ( )

protected

Definition at line 446 of file itkGibbsTrackingFilter.cpp.

References MITK_INFO.

template<class ItkQBallImageType>

virtual void itk::GibbsTrackingFilter< ItkQBallImageType >::SetAbortTracking ( bool  _arg )

virtual

Set flag to prematurely abort tracking.

template<class ItkQBallImageType>

virtual void itk::GibbsTrackingFilter< ItkQBallImageType >::SetConnectionPotential ( float  _arg )

virtual

template<class ItkQBallImageType>

virtual void itk::GibbsTrackingFilter< ItkQBallImageType >::SetCurvatureThreshold ( float  _arg )

virtual

Absolute angular threshold between two particles (in radians).

template<class ItkQBallImageType>

virtual void itk::GibbsTrackingFilter< ItkQBallImageType >::SetDuplicateImage ( bool  _arg )

virtual

Work on copy of input image.

template<class ItkQBallImageType>

virtual void itk::GibbsTrackingFilter< ItkQBallImageType >::SetEndTemperature ( float  _arg )

virtual

End temperature of simulated annealing process.

template<class ItkQBallImageType>

virtual void itk::GibbsTrackingFilter< ItkQBallImageType >::SetInexBalance ( float  _arg )

virtual

Values < 0 result in a stronger weighting of the internal energy, values > 0 cause a stronger weighting of the external energy,.

template<class ItkQBallImageType>

virtual void itk::GibbsTrackingFilter< ItkQBallImageType >::SetIterations ( double  _arg )

virtual

Number of iterations. More iterations usually mean better results.

template<class ItkQBallImageType>

virtual void itk::GibbsTrackingFilter< ItkQBallImageType >::SetLoadParameterFile ( std::string  _arg )

virtual

Parameter file.

template<class ItkQBallImageType>

virtual void itk::GibbsTrackingFilter< ItkQBallImageType >::SetLutPath ( std::string  _arg )

virtual

Path to lookuptables. Default is binary directory.

template<class ItkQBallImageType>

virtual void itk::GibbsTrackingFilter< ItkQBallImageType >::SetMaskImage ( ItkFloatImageType::Pointer  _arg )

virtual

template<class ItkQBallImageType>

virtual void itk::GibbsTrackingFilter< ItkQBallImageType >::SetMinFiberLength ( int  _arg )

virtual

Shorter fibers are discarded.

template<class ItkQBallImageType>

virtual void itk::GibbsTrackingFilter< ItkQBallImageType >::SetParticleLength ( float  _arg )

virtual

template<class ItkQBallImageType>

virtual void itk::GibbsTrackingFilter< ItkQBallImageType >::SetParticlePotential ( float  _arg )

virtual

template<class ItkQBallImageType>

virtual void itk::GibbsTrackingFilter< ItkQBallImageType >::SetParticleWeight ( float  _arg )

virtual

Smaller particle weights result in a higher sensitivity if the method.

template<class ItkQBallImageType>

virtual void itk::GibbsTrackingFilter< ItkQBallImageType >::SetParticleWidth ( float  _arg )

virtual

Thinner particles cause more reconstructed fibers.

template<class ItkQBallImageType>

virtual void itk::GibbsTrackingFilter< ItkQBallImageType >::SetQBallImage ( typename ItkQBallImageType::Pointer  _arg )

virtual

Input images.

template<class ItkQBallImageType>

virtual void itk::GibbsTrackingFilter< ItkQBallImageType >::SetRandomSeed ( int  _arg )

virtual

Seed for random generator.

template<class ItkQBallImageType>

virtual void itk::GibbsTrackingFilter< ItkQBallImageType >::SetSaveParameterFile ( std::string  _arg )

virtual

template<class ItkQBallImageType>

virtual void itk::GibbsTrackingFilter< ItkQBallImageType >::SetStartTemperature ( float  _arg )

virtual

Start temperature of simulated annealing process.

Setter.

template<class ItkQBallImageType>

virtual void itk::GibbsTrackingFilter< ItkQBallImageType >::SetTensorImage ( ItkTensorImage::Pointer  _arg )

virtual

template<class ItkQBallImageType>

virtual void itk::GibbsTrackingFilter< ItkQBallImageType >::Update ( )

inlineoverridevirtual

Definition at line 95 of file itkGibbsTrackingFilter.h.

References itk::GibbsTrackingFilter< ItkQBallImageType >::GenerateData().

Member Data Documentation

template<class ItkQBallImageType>

bool itk::GibbsTrackingFilter< ItkQBallImageType >::m_AbortTracking

protected

set flag to abort tracking

Definition at line 128 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

volatile bool itk::GibbsTrackingFilter< ItkQBallImageType >::m_BuildFibers

protected

set flag to generate fibers from particle grid

Definition at line 130 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

float itk::GibbsTrackingFilter< ItkQBallImageType >::m_ConnectionPotential

protected

gross L (chemisches potential, default 10)

Definition at line 124 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

double itk::GibbsTrackingFilter< ItkQBallImageType >::m_CurrentIteration

protected

Current iteration.

Definition at line 119 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

unsigned long itk::GibbsTrackingFilter< ItkQBallImageType >::m_CurrentStep

protected

current tracking step

Definition at line 120 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

float itk::GibbsTrackingFilter< ItkQBallImageType >::m_CurvatureThreshold

protected

curvature threshold in radians (1 -> no curvature is accepted, -1 all curvature angles are accepted)

Definition at line 132 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

bool itk::GibbsTrackingFilter< ItkQBallImageType >::m_DuplicateImage

protected

generates a working copy of the qball image so that the original image won't be changed by the mean subtraction

Definition at line 133 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

float itk::GibbsTrackingFilter< ItkQBallImageType >::m_EndTemperature

protected

End temperature.

Definition at line 117 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

FiberPolyDataType itk::GibbsTrackingFilter< ItkQBallImageType >::m_FiberPolyData

protected

container for reconstructed fibers

Definition at line 142 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

float itk::GibbsTrackingFilter< ItkQBallImageType >::m_InexBalance

protected

gewichtung zwischen den lambdas; -5 ... 5 -> nur intern ... nur extern,default 0

Definition at line 125 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

bool itk::GibbsTrackingFilter< ItkQBallImageType >::m_IsInValidState

protected

Whether the filter is in a valid state, false if error occured.

Definition at line 140 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

double itk::GibbsTrackingFilter< ItkQBallImageType >::m_Iterations

protected

Total number of iterations.

Definition at line 118 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

std::string itk::GibbsTrackingFilter< ItkQBallImageType >::m_LoadParameterFile

protected

filename of parameter file (reader)

Definition at line 137 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

std::string itk::GibbsTrackingFilter< ItkQBallImageType >::m_LutPath

protected

path to lookuptables used by the sphere interpolator

Definition at line 139 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

ItkFloatImageType::Pointer itk::GibbsTrackingFilter< ItkQBallImageType >::m_MaskImage

protected

Definition at line 112 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

int itk::GibbsTrackingFilter< ItkQBallImageType >::m_MinFiberLength

protected

discard all fibers shortan than the specified length in mm

Definition at line 127 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

int itk::GibbsTrackingFilter< ItkQBallImageType >::m_NumAcceptedFibers

protected

number of reconstructed fibers generated by the FiberBuilder

Definition at line 129 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

int itk::GibbsTrackingFilter< ItkQBallImageType >::m_NumConnections

protected

current number of connections between particles in grid

Definition at line 135 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

int itk::GibbsTrackingFilter< ItkQBallImageType >::m_NumParticles

protected

current number of particles in grid

Definition at line 134 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

const int itk::GibbsTrackingFilter< ItkQBallImageType >::m_ParticleGridCellCapacity

staticprotected

Definition at line 145 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

float itk::GibbsTrackingFilter< ItkQBallImageType >::m_ParticleLength

protected

l (mm)

Definition at line 123 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

float itk::GibbsTrackingFilter< ItkQBallImageType >::m_ParticlePotential

protected

default 0.2

Definition at line 126 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

float itk::GibbsTrackingFilter< ItkQBallImageType >::m_ParticleWeight

protected

w (unitless)

Definition at line 121 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

float itk::GibbsTrackingFilter< ItkQBallImageType >::m_ParticleWidth

protected

sigma (mm)

Definition at line 122 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

float itk::GibbsTrackingFilter< ItkQBallImageType >::m_ProposalAcceptance

protected

proposal acceptance rate (0-1)

Definition at line 131 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

ItkQBallImageType::Pointer itk::GibbsTrackingFilter< ItkQBallImageType >::m_QBallImage

protected

Definition at line 111 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

int itk::GibbsTrackingFilter< ItkQBallImageType >::m_RandomSeed

protected

seed value for random generator (-1 for standard seeding)

Definition at line 136 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

std::string itk::GibbsTrackingFilter< ItkQBallImageType >::m_SaveParameterFile

protected

filename of parameter file (writer)

Definition at line 138 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

float itk::GibbsTrackingFilter< ItkQBallImageType >::m_StartTemperature

protected

Start temperature.

Definition at line 116 of file itkGibbsTrackingFilter.h.

template<class ItkQBallImageType>

ItkTensorImage::Pointer itk::GibbsTrackingFilter< ItkQBallImageType >::m_TensorImage

protected

Definition at line 113 of file itkGibbsTrackingFilter.h.

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

• itkGibbsTrackingFilter.h
• itkGibbsTrackingFilter.cpp