#include <itkSamplingSchemeQSpace.h>

Inheritance diagram for itk::SamplingSchemeQSpace< TPixelType >:

Collaboration diagram for itk::SamplingSchemeQSpace< TPixelType >:

Detailed Description

template<class TPixelType = double>
class itk::SamplingSchemeQSpace< TPixelType >

this class describes sampling in Q space.

The sampling in Q space can be single shell sampling or multiple shell sampling, which is determined by m_IndicesInShells.

Author: Jian Cheng

Definition at line 38 of file itkSamplingSchemeQSpace.h.

Public Types
typedef SmartPointer< const Self >	ConstPointer

typedef Superclass::Index2DVectorPointer	Index2DVectorPointer

typedef Superclass::Index2DVectorType	Index2DVectorType

typedef Superclass::IndexVectorType	IndexVectorType

typedef SmartPointer< Self >	Pointer

typedef SamplingSchemeQSpace	Self

typedef Superclass::STDVectorPointer	STDVectorPointer

typedef Superclass::STDVectorType	STDVectorType

typedef SamplingScheme3D< TPixelType >	Superclass

Public Types inherited from itk::SamplingScheme3D< TPixelType >
typedef SmartPointer< const Self >	ConstPointer

typedef utl_shared_ptr< Index2DVectorType >	Index2DVectorPointer

typedef std::vector< IndexVectorType >	Index2DVectorType

typedef std::vector< int >	IndexVectorType

typedef utl_shared_ptr< MatrixType >	MatrixPointer

typedef utl::NDArray< double, 2 >	MatrixType

typedef SmartPointer< Self >	Pointer

typedef VectorContainer< IdentifierType, Point< TPixelType, 3 > >	PointsContainer

typedef PointsContainer::ConstIterator	PointsContainerConstIterator

typedef PointsContainer::ConstPointer	PointsContainerConstPointer

typedef PointsContainer::Iterator	PointsContainerIterator

typedef PointsContainer::Pointer	PointsContainerPointer

typedef Point< TPixelType, 3 >	PointType

typedef SamplingScheme3D	Self

typedef utl_shared_ptr< STDVectorType >	STDVectorPointer

typedef std::vector< double >	STDVectorType

typedef VectorContainer< IdentifierType, Point< TPixelType, 3 > >	Superclass

typedef TPixelType	ValueType

Public Member Functions
void	Clear ()

void	ConvertBVectorToQVector ()

void	ConvertQVectorToBVector ()

void	CorrectBValues ()

void	CorrectRadiusValues () ITK_OVERRIDE

virtual ::itk::LightObject::Pointer	CreateAnother (void) const

virtual double	GetBThresholdSingleShell ()

virtual STDVectorPointer	GetBVector ()

STDVectorPointer	GetBVectorInShell (unsigned int shellIndex)

virtual const char *	GetNameOfClass () const

std::vector< STDVectorType >	GroupBValues ()

void	RemoveSamplesNotIndexed ()

virtual void	SetBThresholdSingleShell (double _arg)

void	SetBVector (const STDVectorPointer bVec)

void	SetSamplingScheme3D (typename Superclass::Pointer scheme3D)

Public Member Functions inherited from itk::SamplingScheme3D< TPixelType >
void	AppendOrientation (const double x, const double y, const double z, const int shell=-1)

void	AppendOrientation (const PointType &point, const int shell=-1)

void	AppendOrientationAndRadiusValue (const double x, const double y, const double z, const double radius, const int shell=-1)

double	CalculateElectrostaticEnergy (const double order=2.0, const bool isNormalize=true, const bool countHalf=true) const

double	CalculateElectrostaticEnergyInShell (const unsigned int shellIndex, const double order=2.0, const bool isNormalize=true, const bool countHalf=true) const

MatrixPointer	CalculateElectrostaticEnergyMatrix (const double order=2.0) const

MatrixPointer	CalculateInnerProductMatrix (const bool isAbsolute=true) const

double	CalculateMaxDot (const unsigned int index, const bool isSymmetric=true) const

double	CalculateMaxDotInShell (const unsigned int sampleIndex, const unsigned int shellIndex, const bool isSymmetric=true) const

double	CalculateMinDistance (const unsigned int index, const bool isSymmetric=true) const

STDVectorType	CalculateMinDistance (const bool isSymmetric=true) const

double	CalculateMinDistanceInShell (const unsigned int sampleIndex, const unsigned int shellIndex, const bool isSymmetric=true) const

STDVectorType	CalculateMinDistanceInShell (const unsigned int shellIndex, const bool isSymmetric=true) const

double	CalculatePackingDensity (const bool isSymmetric=true) const

double	CalculatePackingDensityInShell (const unsigned int shellIndex, const bool isSymmetric=true) const

double	CalculateSphericalCodeEntropy (const bool isSymmetric=true) const

double	CalculateSphericalCodeEntropyInShell (const unsigned int shellIndex, const bool isSymmetric=true) const

double	CalculateVoronoiEntropy (const int tess=7, const bool isSymmetric=true)

double	CalculateVoronoiEntropyInShell (const unsigned int shellIndex, const int tess=7, const bool isSymmetric=true)

void	Clear ()

virtual ::itk::LightObject::Pointer	CreateAnother (void) const

void	GenerateFromRandomPoints (const std::vector< int > &numberOfPoints)

virtual double	GetDeltaBig ()

virtual double	GetDeltaSmall ()

virtual Index2DVectorPointer	GetIndicesInShells ()

unsigned int	GetNumberOfSamples () const

IndexVectorType	GetNumberOfSamplesAtEachShell () const

unsigned int	GetNumberOfSamplesInShell (const unsigned int shellIndex) const

unsigned int	GetNumberOfShells () const

void	GetNumbers (int &numberUniqueSamples, int &numberAntipodalSamples, int &numberRepeatedSamples) const

PointType	GetOrientation (unsigned int index)

MatrixPointer	GetOrientationsCartesian (const bool alwarysReCalculate=false)

MatrixPointer	GetOrientationsCartesianInShell (const unsigned int shellIndex) const

MatrixPointer	GetOrientationsSpherical (const bool alwarysReCalculate=false)

MatrixPointer	GetOrientationsSphericalInShell (const unsigned int shellIndex)

virtual double	GetRadiusThresholdSingleShell ()

double	GetRadiusValue (unsigned int index)

virtual STDVectorPointer	GetRadiusVector ()

STDVectorPointer	GetRadiusVectorInShell (unsigned int shellIndex)

virtual double	GetTau ()

std::vector< STDVectorType >	GroupRadiusValues ()

void	NormalizeDirections ()

void	ReadOrientationFile (const std::string &gradFile, const int NoSymmetricDuple=DIRECTION_NODUPLICATE, const int flipx=DIRECTION_NOFLIP, const int flipy=DIRECTION_NOFLIP, const int flipz=DIRECTION_NOFLIP, const bool need_normalize=true)

void	ReadOrientationFileList (const std::vector< std::string > &gradFileVec, const int NoSymmetricDuple=DIRECTION_NODUPLICATE, const int flipx=DIRECTION_NOFLIP, const int flipy=DIRECTION_NOFLIP, const int flipz=DIRECTION_NOFLIP, const bool need_normalize=true)

void	RemoveSamplesNotIndexed ()

virtual void	SetDeltaBig (double _arg)

virtual void	SetDeltaSmall (double _arg)

virtual void	SetIndicesInShells (Index2DVectorPointer _arg)

void	SetOrientationsCartesian (const MatrixPointer mat)

void	SetOrientationsSpherical (const MatrixPointer mat)

virtual void	SetRadiusThresholdSingleShell (double _arg)

void	SetRadiusVector (const STDVectorPointer radiusVec)

virtual void	SetTau (double _arg)

Static Public Member Functions
static Pointer	New ()

Static Public Member Functions inherited from itk::SamplingScheme3D< TPixelType >
static double	CalculateMinDistanceUpperBound (const unsigned int numberOfPoints, const bool isSphericalDistance=true)

static double	CalculateVoronoiEntropy (const MatrixType &grad, const MatrixType &gradTess, const bool isSymmetric=true)

static Pointer	New ()

Protected Member Functions
LightObject::Pointer	InternalClone () const ITK_OVERRIDE

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

	SamplingSchemeQSpace ()

virtual	~SamplingSchemeQSpace ()

Protected Member Functions inherited from itk::SamplingScheme3D< TPixelType >
LightObject::Pointer	InternalClone () const ITK_OVERRIDE

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

	SamplingScheme3D ()

virtual	~SamplingScheme3D ()

Protected Attributes
double	m_BThresholdSingleShell

STDVectorPointer	m_BVector

Protected Attributes inherited from itk::SamplingScheme3D< TPixelType >
double	m_DeltaBig

double	m_DeltaSmall

Index2DVectorPointer	m_IndicesInShells

MatrixPointer	m_OrientationsCartesian

MatrixPointer	m_OrientationsSpherical

double	m_RadiusThresholdSingleShell

STDVectorPointer	m_RadiusVector

double	m_Tau

Private Member Functions
void	operator= (const Self &)

	SamplingSchemeQSpace (const Self &)

Member Typedef Documentation

template<class TPixelType = double>

typedef SmartPointer<const Self> itk::SamplingSchemeQSpace< TPixelType >::ConstPointer

Definition at line 45 of file itkSamplingSchemeQSpace.h.

template<class TPixelType = double>

typedef Superclass::Index2DVectorPointer itk::SamplingSchemeQSpace< TPixelType >::Index2DVectorPointer

Definition at line 57 of file itkSamplingSchemeQSpace.h.

template<class TPixelType = double>

typedef Superclass::Index2DVectorType itk::SamplingSchemeQSpace< TPixelType >::Index2DVectorType

Definition at line 56 of file itkSamplingSchemeQSpace.h.

template<class TPixelType = double>

typedef Superclass::IndexVectorType itk::SamplingSchemeQSpace< TPixelType >::IndexVectorType

Definition at line 55 of file itkSamplingSchemeQSpace.h.

template<class TPixelType = double>

typedef SmartPointer<Self> itk::SamplingSchemeQSpace< TPixelType >::Pointer

Definition at line 44 of file itkSamplingSchemeQSpace.h.

template<class TPixelType = double>

typedef SamplingSchemeQSpace itk::SamplingSchemeQSpace< TPixelType >::Self

Standard class typedefs.

Definition at line 42 of file itkSamplingSchemeQSpace.h.

template<class TPixelType = double>

typedef Superclass::STDVectorPointer itk::SamplingSchemeQSpace< TPixelType >::STDVectorPointer

Definition at line 54 of file itkSamplingSchemeQSpace.h.

template<class TPixelType = double>

typedef Superclass::STDVectorType itk::SamplingSchemeQSpace< TPixelType >::STDVectorType

Definition at line 51 of file itkSamplingSchemeQSpace.h.

template<class TPixelType = double>

typedef SamplingScheme3D<TPixelType> itk::SamplingSchemeQSpace< TPixelType >::Superclass

Definition at line 43 of file itkSamplingSchemeQSpace.h.

Constructor & Destructor Documentation

template<class TPixelType >

itk::SamplingSchemeQSpace< TPixelType >::SamplingSchemeQSpace ( )

protected

Definition at line 28 of file itkSamplingSchemeQSpace.hxx.

References itk::SamplingSchemeQSpace< TPixelType >::InternalClone().

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template<class TPixelType = double>

virtual itk::SamplingSchemeQSpace< TPixelType >::~SamplingSchemeQSpace ( )

inlineprotectedvirtual

Definition at line 85 of file itkSamplingSchemeQSpace.h.

References ITK_OVERRIDE.

template<class TPixelType = double>

itk::SamplingSchemeQSpace< TPixelType >::SamplingSchemeQSpace ( const Self & )

private

Member Function Documentation

template<class TPixelType >

void itk::SamplingSchemeQSpace< TPixelType >::Clear ( )

Definition at line 117 of file itkSamplingSchemeQSpace.hxx.

References itk::SamplingSchemeQSpace< TPixelType >::ConvertBVectorToQVector().

Referenced by itk::SamplingSchemeQSpace< TPixelType >::SetSamplingScheme3D().

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template<class TPixelType >

void itk::SamplingSchemeQSpace< TPixelType >::ConvertBVectorToQVector ( )

Definition at line 127 of file itkSamplingSchemeQSpace.hxx.

References itk::SamplingSchemeQSpace< TPixelType >::ConvertQVectorToBVector(), and M_PI.

Referenced by itk::SamplingSchemeQSpace< TPixelType >::Clear().

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template<class TPixelType >

void itk::SamplingSchemeQSpace< TPixelType >::ConvertQVectorToBVector ( )

Definition at line 141 of file itkSamplingSchemeQSpace.hxx.

References itk::SamplingSchemeQSpace< TPixelType >::GroupBValues(), and M_PI.

Referenced by itk::SamplingSchemeQSpace< TPixelType >::ConvertBVectorToQVector().

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template<class TPixelType >

void itk::SamplingSchemeQSpace< TPixelType >::CorrectBValues ( )

Definition at line 220 of file itkSamplingSchemeQSpace.hxx.

References itk::SamplingSchemeQSpace< TPixelType >::CorrectRadiusValues(), and utlGlobalException.

Referenced by itk::SamplingSchemeQSpace< TPixelType >::GroupBValues().

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template<class TPixelType >

void itk::SamplingSchemeQSpace< TPixelType >::CorrectRadiusValues ( )

virtual

Reimplemented from itk::SamplingScheme3D< TPixelType >.

Definition at line 245 of file itkSamplingSchemeQSpace.hxx.

References itk::SamplingSchemeQSpace< TPixelType >::RemoveSamplesNotIndexed(), and utlGlobalException.

Referenced by itk::SamplingSchemeQSpace< TPixelType >::CorrectBValues().

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template<class TPixelType = double>

virtual::itk::LightObject::Pointer itk::SamplingSchemeQSpace< TPixelType >::CreateAnother ( void ) const

template<class TPixelType = double>

virtual double itk::SamplingSchemeQSpace< TPixelType >::GetBThresholdSingleShell ( )

virtual

template<class TPixelType = double>

virtual STDVectorPointer itk::SamplingSchemeQSpace< TPixelType >::GetBVector ( )

virtual

template<class TPixelType >

SamplingSchemeQSpace< TPixelType >::STDVectorPointer itk::SamplingSchemeQSpace< TPixelType >::GetBVectorInShell ( unsigned int shellIndex )

Definition at line 80 of file itkSamplingSchemeQSpace.hxx.

References itk::SamplingSchemeQSpace< TPixelType >::SetSamplingScheme3D().

Referenced by itk::SamplingSchemeQSpace< TPixelType >::SetBVector().

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template<class TPixelType = double>

virtual const char* itk::SamplingSchemeQSpace< TPixelType >::GetNameOfClass ( ) const

virtual

Standard part of every itk Object.

Reimplemented from itk::SamplingScheme3D< TPixelType >.

template<class TPixelType >

std::vector< typename SamplingSchemeQSpace< TPixelType >::STDVectorType > itk::SamplingSchemeQSpace< TPixelType >::GroupBValues ( )

Definition at line 153 of file itkSamplingSchemeQSpace.hxx.

References itk::SamplingSchemeQSpace< TPixelType >::CorrectBValues(), and utlSAGlobalException.

Referenced by itk::SamplingSchemeQSpace< TPixelType >::ConvertQVectorToBVector().

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template<class TPixelType >

LightObject::Pointer itk::SamplingSchemeQSpace< TPixelType >::InternalClone ( ) const

protected

Definition at line 37 of file itkSamplingSchemeQSpace.hxx.

References itk::SamplingSchemeQSpace< TPixelType >::PrintSelf().

Referenced by itk::SamplingSchemeQSpace< TPixelType >::SamplingSchemeQSpace().

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template<class TPixelType = double>

static Pointer itk::SamplingSchemeQSpace< TPixelType >::New ( )

static

Method for creation through the object factory.

template<class TPixelType = double>

void itk::SamplingSchemeQSpace< TPixelType >::operator= ( const Self & )

private

template<class TPixelType >

void itk::SamplingSchemeQSpace< TPixelType >::PrintSelf	(	std::ostream &	os,
		Indent	indent
	)		const

protected

Definition at line 56 of file itkSamplingSchemeQSpace.hxx.

References utl::PrintVector(), and itk::SamplingSchemeQSpace< TPixelType >::SetBVector().

Referenced by itk::SamplingSchemeQSpace< TPixelType >::InternalClone().

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template<class TPixelType >

void itk::SamplingSchemeQSpace< TPixelType >::RemoveSamplesNotIndexed ( )

remove samples not in m_IndicesInShells

Definition at line 257 of file itkSamplingSchemeQSpace.hxx.

References utlGlobalException.

Referenced by itk::SamplingSchemeQSpace< TPixelType >::CorrectRadiusValues().

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template<class TPixelType = double>

virtual void itk::SamplingSchemeQSpace< TPixelType >::SetBThresholdSingleShell ( double _arg )

virtual

template<class TPixelType >

void itk::SamplingSchemeQSpace< TPixelType >::SetBVector ( const STDVectorPointer bVec )

Definition at line 65 of file itkSamplingSchemeQSpace.hxx.

References itk::SamplingSchemeQSpace< TPixelType >::GetBVectorInShell().

Referenced by itk::SamplingSchemeQSpace< TPixelType >::PrintSelf().

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template<class TPixelType >

void itk::SamplingSchemeQSpace< TPixelType >::SetSamplingScheme3D ( typename Superclass::Pointer scheme3D )

Definition at line 98 of file itkSamplingSchemeQSpace.hxx.

References itk::SamplingSchemeQSpace< TPixelType >::Clear().

Referenced by itk::SamplingSchemeQSpace< TPixelType >::GetBVectorInShell().

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Member Data Documentation

template<class TPixelType = double>

double itk::SamplingSchemeQSpace< TPixelType >::m_BThresholdSingleShell

protected

b values whose distance is smallter the threshold will be considered in the same shell, and they will be replaced as their mean b value.

Definition at line 95 of file itkSamplingSchemeQSpace.h.

template<class TPixelType = double>

STDVectorPointer itk::SamplingSchemeQSpace< TPixelType >::m_BVector

protected

Definition at line 97 of file itkSamplingSchemeQSpace.h.

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

Modules/SamplingScheme/include/itkSamplingSchemeQSpace.h
Modules/SamplingScheme/include/itkSamplingSchemeQSpace.hxx

Detailed Description

template<class TPixelType = double> class itk::SamplingSchemeQSpace< TPixelType >

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<class TPixelType = double>
class itk::SamplingSchemeQSpace< TPixelType >