itk::SamplingScheme3D< TPixelType > Class Template Reference

#include <itkSamplingScheme3D.h>

Inheritance diagram for itk::SamplingScheme3D< TPixelType >:

Collaboration diagram for itk::SamplingScheme3D< TPixelType >:

Detailed Description

template<class TPixelType = double>
class itk::SamplingScheme3D< TPixelType >

this class describes sampling in a 3D space (Q space or R space).

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

Author

Jian Cheng (JC), jian..nosp@m.chen.nosp@m.g.198.nosp@m.3@gm.nosp@m.ail.c.nosp@m.om

Definition at line 43 of file itkSamplingScheme3D.h.

Public Types
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	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 void	CorrectRadiusValues ()
virtual ::itk::LightObject::Pointer	CreateAnother (void) const
void	GenerateFromRandomPoints (const std::vector< int > &numberOfPoints)
virtual double	GetDeltaBig ()
virtual double	GetDeltaSmall ()
virtual Index2DVectorPointer	GetIndicesInShells ()
virtual const char *	GetNameOfClass () const
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 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
	SamplingScheme3D ()
virtual	~SamplingScheme3D ()

Protected Attributes
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
PointType &	CreateElementAt (IdentifierType)
void	InsertElement (IdentifierType, PointType)
void	operator= (const Self &)
	SamplingScheme3D (const Self &)
void	SetElement (IdentifierType, PointType)

Member Typedef Documentation

template<class TPixelType = double>

typedef SmartPointer< const Self > itk::SamplingScheme3D< TPixelType >::ConstPointer

Definition at line 52 of file itkSamplingScheme3D.h.

template<class TPixelType = double>

typedef utl_shared_ptr<Index2DVectorType> itk::SamplingScheme3D< TPixelType >::Index2DVectorPointer

Definition at line 78 of file itkSamplingScheme3D.h.

template<class TPixelType = double>

typedef std::vector<IndexVectorType > itk::SamplingScheme3D< TPixelType >::Index2DVectorType

Definition at line 77 of file itkSamplingScheme3D.h.

template<class TPixelType = double>

typedef std::vector<int> itk::SamplingScheme3D< TPixelType >::IndexVectorType

Definition at line 76 of file itkSamplingScheme3D.h.

template<class TPixelType = double>

typedef utl_shared_ptr<MatrixType > itk::SamplingScheme3D< TPixelType >::MatrixPointer

Definition at line 73 of file itkSamplingScheme3D.h.

template<class TPixelType = double>

typedef utl::NDArray<double,2> itk::SamplingScheme3D< TPixelType >::MatrixType

Definition at line 72 of file itkSamplingScheme3D.h.

template<class TPixelType = double>

typedef SmartPointer< Self > itk::SamplingScheme3D< TPixelType >::Pointer

Definition at line 51 of file itkSamplingScheme3D.h.

template<class TPixelType = double>

typedef VectorContainer<IdentifierType, Point< TPixelType, 3 > > itk::SamplingScheme3D< TPixelType >::PointsContainer

Definition at line 58 of file itkSamplingScheme3D.h.

template<class TPixelType = double>

typedef PointsContainer::ConstIterator itk::SamplingScheme3D< TPixelType >::PointsContainerConstIterator

Create types that are iterators for each of the container types.

Definition at line 69 of file itkSamplingScheme3D.h.

template<class TPixelType = double>

typedef PointsContainer::ConstPointer itk::SamplingScheme3D< TPixelType >::PointsContainerConstPointer

Definition at line 66 of file itkSamplingScheme3D.h.

template<class TPixelType = double>

typedef PointsContainer::Iterator itk::SamplingScheme3D< TPixelType >::PointsContainerIterator

Definition at line 70 of file itkSamplingScheme3D.h.

template<class TPixelType = double>

typedef PointsContainer::Pointer itk::SamplingScheme3D< TPixelType >::PointsContainerPointer

Create types that are pointers to each of the container types.

Definition at line 65 of file itkSamplingScheme3D.h.

template<class TPixelType = double>

typedef Point<TPixelType, 3> itk::SamplingScheme3D< TPixelType >::PointType

Definition at line 61 of file itkSamplingScheme3D.h.

template<class TPixelType = double>

typedef SamplingScheme3D itk::SamplingScheme3D< TPixelType >::Self

Standard class typedefs.

Definition at line 49 of file itkSamplingScheme3D.h.

template<class TPixelType = double>

typedef utl_shared_ptr<STDVectorType > itk::SamplingScheme3D< TPixelType >::STDVectorPointer

Definition at line 75 of file itkSamplingScheme3D.h.

template<class TPixelType = double>

typedef std::vector<double> itk::SamplingScheme3D< TPixelType >::STDVectorType

Definition at line 74 of file itkSamplingScheme3D.h.

template<class TPixelType = double>

typedef VectorContainer<IdentifierType, Point< TPixelType, 3 > > itk::SamplingScheme3D< TPixelType >::Superclass

Definition at line 50 of file itkSamplingScheme3D.h.

template<class TPixelType = double>

typedef TPixelType itk::SamplingScheme3D< TPixelType >::ValueType

Definition at line 62 of file itkSamplingScheme3D.h.

Constructor & Destructor Documentation

template<class TPixelType >

itk::SamplingScheme3D< TPixelType >::SamplingScheme3D ( )

protected

Definition at line 31 of file itkSamplingScheme3D.hxx.

References ONE_OVER_4_PI_2, and itk::SamplingScheme3D< TPixelType >::SetRadiusVector().

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template<class TPixelType = double>

virtual itk::SamplingScheme3D< TPixelType >::~SamplingScheme3D ( )

inlineprotectedvirtual

Definition at line 225 of file itkSamplingScheme3D.h.

References ITK_OVERRIDE.

template<class TPixelType = double>

itk::SamplingScheme3D< TPixelType >::SamplingScheme3D ( const Self &  )

private

Member Function Documentation

template<class TPixelType >

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

push_back a new orientation

Definition at line 463 of file itkSamplingScheme3D.hxx.

Referenced by itk::SamplingScheme3D< TPixelType >::GenerateFromRandomPoints().

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template<class TPixelType >

void itk::SamplingScheme3D< TPixelType >::AppendOrientation	(	const PointType &	point,
		const int	shell = -1
	)

push_back a new orientation

Definition at line 473 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::AppendOrientationAndRadiusValue(), utlException, and utlSAException.

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template<class TPixelType >

void itk::SamplingScheme3D< TPixelType >::AppendOrientationAndRadiusValue	(	const double	x,
		const double	y,
		const double	z,
		const double	radius,
		const int	shell = -1
	)

push_back a new orientation and a radius value

Definition at line 504 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::CalculateInnerProductMatrix().

Referenced by itk::SamplingScheme3D< TPixelType >::AppendOrientation().

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template<class TPixelType >

double itk::SamplingScheme3D< TPixelType >::CalculateElectrostaticEnergy	(	const double	order = 2.0,
		const bool	isNormalize = true,
		const bool	countHalf = true
	)		const

calculate electrostatic energy

Definition at line 878 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::CalculateElectrostaticEnergyInShell(), and utlWarning.

Referenced by itk::SamplingScheme3D< TPixelType >::GetNumbers(), and processOrientation().

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template<class TPixelType >

double itk::SamplingScheme3D< TPixelType >::CalculateElectrostaticEnergyInShell	(	const unsigned int	shellIndex,
		const double	order = 2.0,
		const bool	isNormalize = true,
		const bool	countHalf = true
	)		const

Definition at line 912 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::CalculateMinDistanceUpperBound(), and utlWarning.

Referenced by itk::SamplingScheme3D< TPixelType >::CalculateElectrostaticEnergy().

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template<class TPixelType >

SamplingScheme3D< TPixelType >::MatrixPointer itk::SamplingScheme3D< TPixelType >::CalculateElectrostaticEnergyMatrix

(

const double

order = 2.0

)

const

return electrostatic energy matrix, the diagonal elements are maximal double value

Definition at line 546 of file itkSamplingScheme3D.hxx.

References spams::abs(), itk::SamplingScheme3D< TPixelType >::CalculatePackingDensity(), utl::max(), and utlWarning.

Referenced by itk::SamplingScheme3D< TPixelType >::CalculateInnerProductMatrix().

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template<class TPixelType >

SamplingScheme3D< TPixelType >::MatrixPointer itk::SamplingScheme3D< TPixelType >::CalculateInnerProductMatrix

(

const bool

isAbsolute = true

)

const

return dot products between samples.

Definition at line 516 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::CalculateElectrostaticEnergyMatrix().

Referenced by itk::SamplingScheme3D< TPixelType >::AppendOrientationAndRadiusValue().

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template<class TPixelType >

double itk::SamplingScheme3D< TPixelType >::CalculateMaxDot	(	const unsigned int	index,
		const bool	isSymmetric = true
	)		const

Definition at line 716 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::CalculateMaxDotInShell(), M_EPS, and utlGlobalException.

Referenced by itk::SamplingScheme3D< TPixelType >::CalculateVoronoiEntropyInShell().

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template<class TPixelType >

double itk::SamplingScheme3D< TPixelType >::CalculateMaxDotInShell	(	const unsigned int	sampleIndex,
		const unsigned int	shellIndex,
		const bool	isSymmetric = true
	)		const

Definition at line 749 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::CalculateMinDistance(), M_EPS, and utlGlobalException.

Referenced by itk::SamplingScheme3D< TPixelType >::CalculateMaxDot().

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template<class TPixelType >

double itk::SamplingScheme3D< TPixelType >::CalculateMinDistance	(	const unsigned int	index,
		const bool	isSymmetric = true
	)		const

calculate the minimum distance for the point with a given index.

Definition at line 783 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::CalculateMinDistanceInShell(), M_EPS, and M_PI.

Referenced by itk::SamplingScheme3D< TPixelType >::CalculateMaxDotInShell(), itk::SamplingScheme3D< TPixelType >::CalculateMinDistanceInShell(), and processOrientation().

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template<class TPixelType >

SamplingScheme3D< TPixelType >::STDVectorType itk::SamplingScheme3D< TPixelType >::CalculateMinDistance

(

const bool

isSymmetric = true

)

const

calculate the minimum distance for all points.

Definition at line 815 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::CalculateMinDistanceInShell().

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template<class TPixelType >

double itk::SamplingScheme3D< TPixelType >::CalculateMinDistanceInShell	(	const unsigned int	sampleIndex,
		const unsigned int	shellIndex,
		const bool	isSymmetric = true
	)		const

Definition at line 799 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::CalculateMinDistance(), M_EPS, and M_PI.

Referenced by itk::SamplingScheme3D< TPixelType >::CalculateMinDistance().

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template<class TPixelType >

SamplingScheme3D< TPixelType >::STDVectorType itk::SamplingScheme3D< TPixelType >::CalculateMinDistanceInShell	(	const unsigned int	shellIndex,
		const bool	isSymmetric = true
	)		const

calculate the minimum distance for all points in a single shell.

Definition at line 829 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::GetNumbers().

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template<class TPixelType >

double itk::SamplingScheme3D< TPixelType >::CalculateMinDistanceUpperBound ( const unsigned int  numberOfPoints, const bool  isSphericalDistance = true  )

static

calculate an upper bound of the minimal distance for a given number of points. If isSphericalDistance is true, return spherical distance instead of Euclidean distance. http://mathworld.wolfram.com/SphericalCode.html

Definition at line 948 of file itkSamplingScheme3D.hxx.

References M_PI, and itk::SamplingScheme3D< TPixelType >::PrintSelf().

Referenced by itk::SamplingScheme3D< TPixelType >::CalculateElectrostaticEnergyInShell().

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template<class TPixelType >

double itk::SamplingScheme3D< TPixelType >::CalculatePackingDensity

(

const bool

isSymmetric = true

)

const

Packing density: https://en.wikipedia.org/wiki/Packing_density https://en.wikipedia.org/wiki/Spherical_cap

Definition at line 578 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::CalculatePackingDensityInShell().

Referenced by itk::SamplingScheme3D< TPixelType >::CalculateElectrostaticEnergyMatrix(), and processOrientation().

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template<class TPixelType >

double itk::SamplingScheme3D< TPixelType >::CalculatePackingDensityInShell	(	const unsigned int	shellIndex,
		const bool	isSymmetric = true
	)		const

Definition at line 597 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::CalculateSphericalCodeEntropy().

Referenced by itk::SamplingScheme3D< TPixelType >::CalculatePackingDensity().

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template<class TPixelType >

double itk::SamplingScheme3D< TPixelType >::CalculateSphericalCodeEntropy

(

const bool

isSymmetric = true

)

const

Calculate entropy based on spherical cap. https://en.wikipedia.org/wiki/Spherical_cap

Definition at line 614 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::CalculateSphericalCodeEntropyInShell(), and utl::Entropy().

Referenced by itk::SamplingScheme3D< TPixelType >::CalculatePackingDensityInShell().

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template<class TPixelType >

double itk::SamplingScheme3D< TPixelType >::CalculateSphericalCodeEntropyInShell	(	const unsigned int	shellIndex,
		const bool	isSymmetric = true
	)		const

Definition at line 637 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::CalculateVoronoiEntropy(), and utl::Entropy().

Referenced by itk::SamplingScheme3D< TPixelType >::CalculateSphericalCodeEntropy().

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template<class TPixelType >

double itk::SamplingScheme3D< TPixelType >::CalculateVoronoiEntropy ( const MatrixType &  grad, const MatrixType &  gradTess, const bool  isSymmetric = true  )

static

Definition at line 656 of file itkSamplingScheme3D.hxx.

References utl::Entropy().

Referenced by itk::SamplingScheme3D< TPixelType >::CalculateSphericalCodeEntropyInShell().

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template<class TPixelType >

double itk::SamplingScheme3D< TPixelType >::CalculateVoronoiEntropy	(	const int	tess = 7,
		const bool	isSymmetric = true
	)

Definition at line 694 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::CalculateVoronoiEntropyInShell(), CARTESIAN_TO_CARTESIAN, DIRECTION_NODUPLICATE, utl::GradientTable< T >::GetGrad(), and utl::GradientTable< T >::Initialize().

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template<class TPixelType >

double itk::SamplingScheme3D< TPixelType >::CalculateVoronoiEntropyInShell	(	const unsigned int	shellIndex,
		const int	tess = 7,
		const bool	isSymmetric = true
	)

Definition at line 705 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::CalculateMaxDot(), CARTESIAN_TO_CARTESIAN, DIRECTION_NODUPLICATE, utl::GradientTable< T >::GetGrad(), and utl::GradientTable< T >::Initialize().

Referenced by itk::SamplingScheme3D< TPixelType >::CalculateVoronoiEntropy().

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template<class TPixelType >

void itk::SamplingScheme3D< TPixelType >::Clear

(

)

Definition at line 264 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::RemoveSamplesNotIndexed().

Referenced by itk::SamplingScheme3D< TPixelType >::InternalClone().

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template<class TPixelType >

void itk::SamplingScheme3D< TPixelType >::CorrectRadiusValues ( )

virtual

Reimplemented in itk::SamplingSchemeQSpace< TPixelType >.

Definition at line 369 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::ReadOrientationFile(), and utlGlobalException.

Referenced by itk::SamplingScheme3D< TPixelType >::GroupRadiusValues().

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template<class TPixelType = double>

virtual::itk::LightObject::Pointer itk::SamplingScheme3D< TPixelType >::CreateAnother

(

void

)

const

template<class TPixelType = double>

PointType& itk::SamplingScheme3D< TPixelType >::CreateElementAt ( IdentifierType  )

private

template<class TPixelType >

void itk::SamplingScheme3D< TPixelType >::GenerateFromRandomPoints

(

const std::vector< int > &

numberOfPoints

)

generate sampling scheme from random points in sphere

Definition at line 440 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::AppendOrientation(), and utl::RandomPointInSphere().

Referenced by itk::SamplingScheme3D< TPixelType >::ReadOrientationFileList().

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template<class TPixelType = double>

virtual double itk::SamplingScheme3D< TPixelType >::GetDeltaBig ( )

virtual

template<class TPixelType = double>

virtual double itk::SamplingScheme3D< TPixelType >::GetDeltaSmall ( )

virtual

template<class TPixelType = double>

virtual Index2DVectorPointer itk::SamplingScheme3D< TPixelType >::GetIndicesInShells ( )

virtual

template<class TPixelType = double>

virtual const char* itk::SamplingScheme3D< TPixelType >::GetNameOfClass ( ) const

virtual

Standard part of every itk Object.

Reimplemented in itk::SamplingSchemeQSpace< TPixelType >.

template<class TPixelType = double>

unsigned int itk::SamplingScheme3D< TPixelType >::GetNumberOfSamples ( ) const

inline

Definition at line 109 of file itkSamplingScheme3D.h.

Referenced by processOrientation().

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template<class TPixelType = double>

IndexVectorType itk::SamplingScheme3D< TPixelType >::GetNumberOfSamplesAtEachShell ( ) const

inline

Definition at line 125 of file itkSamplingScheme3D.h.

References DIRECTION_NODUPLICATE, and DIRECTION_NOFLIP.

template<class TPixelType = double>

unsigned int itk::SamplingScheme3D< TPixelType >::GetNumberOfSamplesInShell ( const unsigned int  shellIndex ) const

inline

Definition at line 113 of file itkSamplingScheme3D.h.

template<class TPixelType = double>

unsigned int itk::SamplingScheme3D< TPixelType >::GetNumberOfShells ( ) const

inline

Definition at line 120 of file itkSamplingScheme3D.h.

template<class TPixelType >

void itk::SamplingScheme3D< TPixelType >::GetNumbers	(	int &	numberUniqueSamples,
		int &	numberAntipodalSamples,
		int &	numberRepeatedSamples
	)		const

Definition at line 845 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::CalculateElectrostaticEnergy().

Referenced by itk::SamplingScheme3D< TPixelType >::CalculateMinDistanceInShell(), and processOrientation().

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template<class TPixelType = double>

PointType itk::SamplingScheme3D< TPixelType >::GetOrientation ( unsigned int  index )

inline

Definition at line 167 of file itkSamplingScheme3D.h.

template<class TPixelType >

SamplingScheme3D< TPixelType >::MatrixPointer itk::SamplingScheme3D< TPixelType >::GetOrientationsCartesian

(

const bool

alwarysReCalculate = false

)

Orientations as matrix, return a pointer

Definition at line 78 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::GetOrientationsSpherical(), utl::SphericalToCartesian(), and utlGlobalException.

Referenced by itk::SamplingScheme3D< TPixelType >::GetRadiusVectorInShell().

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template<class TPixelType >

SamplingScheme3D< TPixelType >::MatrixPointer itk::SamplingScheme3D< TPixelType >::GetOrientationsCartesianInShell

(

const unsigned int

shellIndex

)

const

Definition at line 185 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::NormalizeDirections(), utlException, and utlGlobalException.

Referenced by itk::SamplingScheme3D< TPixelType >::SetOrientationsSpherical().

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template<class TPixelType >

SamplingScheme3D< TPixelType >::MatrixPointer itk::SamplingScheme3D< TPixelType >::GetOrientationsSpherical

(

const bool

alwarysReCalculate = false

)

Definition at line 111 of file itkSamplingScheme3D.hxx.

References utl::CartesianToSpherical(), itk::SamplingScheme3D< TPixelType >::SetOrientationsCartesian(), and utlGlobalException.

Referenced by itk::SamplingScheme3D< TPixelType >::GetOrientationsCartesian().

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template<class TPixelType >

SamplingScheme3D< TPixelType >::MatrixPointer itk::SamplingScheme3D< TPixelType >::GetOrientationsSphericalInShell

(

const unsigned int

shellIndex

)

Definition at line 159 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::SetOrientationsSpherical(), utlException, and utlGlobalException.

Referenced by itk::SamplingScheme3D< TPixelType >::SetOrientationsCartesian().

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template<class TPixelType = double>

virtual double itk::SamplingScheme3D< TPixelType >::GetRadiusThresholdSingleShell ( )

virtual

template<class TPixelType = double>

double itk::SamplingScheme3D< TPixelType >::GetRadiusValue ( unsigned int  index )

inline

Definition at line 171 of file itkSamplingScheme3D.h.

template<class TPixelType = double>

virtual STDVectorPointer itk::SamplingScheme3D< TPixelType >::GetRadiusVector ( )

virtual

template<class TPixelType >

SamplingScheme3D< TPixelType >::STDVectorPointer itk::SamplingScheme3D< TPixelType >::GetRadiusVectorInShell

(

unsigned int

shellIndex

)

Definition at line 60 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::GetOrientationsCartesian().

Referenced by itk::SamplingScheme3D< TPixelType >::SetRadiusVector().

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template<class TPixelType = double>

virtual double itk::SamplingScheme3D< TPixelType >::GetTau ( )

virtual

template<class TPixelType >

std::vector< typename SamplingScheme3D< TPixelType >::STDVectorType > itk::SamplingScheme3D< TPixelType >::GroupRadiusValues

(

)

Definition at line 306 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::CorrectRadiusValues(), and utlGlobalException.

Referenced by itk::SamplingScheme3D< TPixelType >::RemoveSamplesNotIndexed().

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template<class TPixelType = double>

void itk::SamplingScheme3D< TPixelType >::InsertElement ( IdentifierType  , PointType    )

private

template<class TPixelType >

LightObject::Pointer itk::SamplingScheme3D< TPixelType >::InternalClone ( ) const

protected

Definition at line 234 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::Clear().

Referenced by itk::SamplingScheme3D< TPixelType >::NormalizeDirections().

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template<class TPixelType = double>

static Pointer itk::SamplingScheme3D< TPixelType >::New ( )

static

Method for creation through the object factory.

template<class TPixelType >

void itk::SamplingScheme3D< TPixelType >::NormalizeDirections

(

)

Definition at line 204 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::InternalClone().

Referenced by itk::SamplingScheme3D< TPixelType >::GetOrientationsCartesianInShell().

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template<class TPixelType = double>

void itk::SamplingScheme3D< TPixelType >::operator= ( const Self &  )

private

template<class TPixelType >

void itk::SamplingScheme3D< TPixelType >::PrintSelf ( std::ostream &  os, Indent  indent  ) const

protected

Definition at line 961 of file itkSamplingScheme3D.hxx.

References utl::PrintUtlMatrix(), PrintVar3, and utl::PrintVector().

Referenced by itk::SamplingScheme3D< TPixelType >::CalculateMinDistanceUpperBound().

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template<class TPixelType >

void itk::SamplingScheme3D< TPixelType >::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
	)

Nx3 gradient file, each row is a point in S^2, catesian format

Definition at line 391 of file itkSamplingScheme3D.hxx.

References CARTESIAN_TO_CARTESIAN, and itk::SamplingScheme3D< TPixelType >::ReadOrientationFileList().

Referenced by itk::SamplingScheme3D< TPixelType >::CorrectRadiusValues().

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template<class TPixelType >

void itk::SamplingScheme3D< TPixelType >::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
	)

Read a list of gradient files. Each file contains gradients for a single shell.

Definition at line 409 of file itkSamplingScheme3D.hxx.

References CARTESIAN_TO_CARTESIAN, itk::SamplingScheme3D< TPixelType >::GenerateFromRandomPoints(), and utlGlobalException.

Referenced by itk::SamplingScheme3D< TPixelType >::ReadOrientationFile().

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template<class TPixelType >

void itk::SamplingScheme3D< TPixelType >::RemoveSamplesNotIndexed

(

)

remove samples not in m_IndicesInShells

Definition at line 277 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::GroupRadiusValues(), and utlGlobalException.

Referenced by itk::SamplingScheme3D< TPixelType >::Clear().

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template<class TPixelType = double>

virtual void itk::SamplingScheme3D< TPixelType >::SetDeltaBig ( double  _arg )

virtual

template<class TPixelType = double>

virtual void itk::SamplingScheme3D< TPixelType >::SetDeltaSmall ( double  _arg )

virtual

template<class TPixelType = double>

void itk::SamplingScheme3D< TPixelType >::SetElement ( IdentifierType  , PointType    )

private

template<class TPixelType = double>

virtual void itk::SamplingScheme3D< TPixelType >::SetIndicesInShells ( Index2DVectorPointer  _arg )

virtual

template<class TPixelType >

void itk::SamplingScheme3D< TPixelType >::SetOrientationsCartesian

(

const MatrixPointer

mat

)

Definition at line 148 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::GetOrientationsSphericalInShell().

Referenced by itk::SamplingScheme3D< TPixelType >::GetOrientationsSpherical().

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template<class TPixelType >

void itk::SamplingScheme3D< TPixelType >::SetOrientationsSpherical

(

const MatrixPointer

mat

)

Definition at line 173 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::GetOrientationsCartesianInShell(), and utl::SphericalToCartesian().

Referenced by itk::SamplingScheme3D< TPixelType >::GetOrientationsSphericalInShell().

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template<class TPixelType = double>

virtual void itk::SamplingScheme3D< TPixelType >::SetRadiusThresholdSingleShell ( double  _arg )

virtual

template<class TPixelType >

void itk::SamplingScheme3D< TPixelType >::SetRadiusVector

(

const STDVectorPointer

radiusVec

)

Definition at line 46 of file itkSamplingScheme3D.hxx.

References itk::SamplingScheme3D< TPixelType >::GetRadiusVectorInShell().

Referenced by itk::SamplingScheme3D< TPixelType >::SamplingScheme3D().

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template<class TPixelType = double>

virtual void itk::SamplingScheme3D< TPixelType >::SetTau ( double  _arg )

virtual

Member Data Documentation

template<class TPixelType = double>

double itk::SamplingScheme3D< TPixelType >::m_DeltaBig

protected

big delta

Definition at line 238 of file itkSamplingScheme3D.h.

template<class TPixelType = double>

double itk::SamplingScheme3D< TPixelType >::m_DeltaSmall

protected

small delta

Definition at line 235 of file itkSamplingScheme3D.h.

template<class TPixelType = double>

Index2DVectorPointer itk::SamplingScheme3D< TPixelType >::m_IndicesInShells

protected

2D vector, each element is a vector containing the indices for orientations in each shell. If m_IndicesInShells is empty, single shell sampling is used.

Note

: There may be some samples whose indices are not in m_IndicesInShells. These samples which are not indexed can be removed by using RemoveSamplesNotIndexed().

Definition at line 249 of file itkSamplingScheme3D.h.

template<class TPixelType = double>

MatrixPointer itk::SamplingScheme3D< TPixelType >::m_OrientationsCartesian

protected

Orientation matrix

Definition at line 258 of file itkSamplingScheme3D.h.

template<class TPixelType = double>

MatrixPointer itk::SamplingScheme3D< TPixelType >::m_OrientationsSpherical

protected

Definition at line 259 of file itkSamplingScheme3D.h.

template<class TPixelType = double>

double itk::SamplingScheme3D< TPixelType >::m_RadiusThresholdSingleShell

protected

threshould to separate radius values into different shells. If it is positive, radius 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 255 of file itkSamplingScheme3D.h.

template<class TPixelType = double>

STDVectorPointer itk::SamplingScheme3D< TPixelType >::m_RadiusVector

protected

radius values

Definition at line 241 of file itkSamplingScheme3D.h.

template<class TPixelType = double>

double itk::SamplingScheme3D< TPixelType >::m_Tau

protected

tau value

Definition at line 232 of file itkSamplingScheme3D.h.

---

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

• Modules/SamplingScheme/include/itkSamplingScheme3D.h
• Modules/SamplingScheme/include/itkSamplingScheme3D.hxx