vtkDiffusionTensorMathematics Class Reference

#include <vtkDiffusionTensorMathematics.h>

Inheritance diagram for vtkDiffusionTensorMathematics:

List of all members.

Public Types
enum	{   VTK_TENS_TRACE, VTK_TENS_DETERMINANT, VTK_TENS_RELATIVE_ANISOTROPY, VTK_TENS_FRACTIONAL_ANISOTROPY,   VTK_TENS_MAX_EIGENVALUE, VTK_TENS_MID_EIGENVALUE, VTK_TENS_MIN_EIGENVALUE, VTK_TENS_LINEAR_MEASURE,   VTK_TENS_PLANAR_MEASURE, VTK_TENS_SPHERICAL_MEASURE, VTK_TENS_COLOR_ORIENTATION, VTK_TENS_D11,   VTK_TENS_D22, VTK_TENS_D33, VTK_TENS_MODE, VTK_TENS_COLOR_MODE,   VTK_TENS_MAX_EIGENVALUE_PROJX, VTK_TENS_MAX_EIGENVALUE_PROJY, VTK_TENS_MAX_EIGENVALUE_PROJZ, VTK_TENS_RAI_MAX_EIGENVEC_PROJX,   VTK_TENS_RAI_MAX_EIGENVEC_PROJY, VTK_TENS_RAI_MAX_EIGENVEC_PROJZ, VTK_TENS_PARALLEL_DIFFUSIVITY, VTK_TENS_PERPENDICULAR_DIFFUSIVITY }
	Operation options. More...
Public Member Functions
void	ComputeTensorIncrements (vtkImageData *imageData, vtkIdType incr[3])
void	PrintSelf (ostream &os, vtkIndent indent)
void	SetOperationToColorByMode ()
void	SetOperationToColorByOrientation ()
void	SetOperationToD11 ()
void	SetOperationToD22 ()
void	SetOperationToD33 ()
void	SetOperationToDeterminant ()
void	SetOperationToFractionalAnisotropy ()
void	SetOperationToLinearMeasure ()
void	SetOperationToMaxEigenvalue ()
void	SetOperationToMaxEigenvalueProjectionX ()
void	SetOperationToMaxEigenvalueProjectionY ()
void	SetOperationToMaxEigenvalueProjectionZ ()
void	SetOperationToMiddleEigenvalue ()
void	SetOperationToMinEigenvalue ()
void	SetOperationToMode ()
void	SetOperationToParallelDiffusivity ()
void	SetOperationToPerpendicularDiffusivity ()
void	SetOperationToPlanarMeasure ()
void	SetOperationToRAIMaxEigenvecX ()
void	SetOperationToRAIMaxEigenvecY ()
void	SetOperationToRAIMaxEigenvecZ ()
void	SetOperationToRelativeAnisotropy ()
void	SetOperationToSphericalMeasure ()
void	SetOperationToTrace ()
virtual void	SetScalarMask (vtkImageData *)
virtual void	SetTensorRotationMatrix (vtkMatrix4x4 *)
	vtkBooleanMacro (FixNegativeEigenvalues, int)
	vtkBooleanMacro (MaskWithScalars, int)
	vtkBooleanMacro (ExtractEigenvalues, int)
	vtkGetMacro (MaskLabelValue, int)
	vtkGetMacro (FixNegativeEigenvalues, int)
	vtkGetMacro (MaskWithScalars, int)
	vtkGetMacro (ExtractEigenvalues, int)
	vtkGetMacro (ScaleFactor, double)
	vtkGetMacro (Operation, int)
	vtkGetObjectMacro (ScalarMask, vtkImageData)
	vtkGetObjectMacro (TensorRotationMatrix, vtkMatrix4x4)
	vtkSetClampMacro (Operation, int, VTK_TENS_TRACE, VTK_TENS_PERPENDICULAR_DIFFUSIVITY)
	vtkSetMacro (MaskLabelValue, int)
	vtkSetMacro (FixNegativeEigenvalues, int)
	vtkSetMacro (MaskWithScalars, int)
	vtkSetMacro (ExtractEigenvalues, int)
	vtkSetMacro (ScaleFactor, double)
	vtkTypeMacro (vtkDiffusionTensorMathematics, vtkThreadedImageAlgorithm)
Static Public Member Functions
static void	ColorByMode (double w[3], double &R, double &G, double &B)
static double	Determinant (double D[3][3])
static int	FixNegativeEigenvaluesMethod (double w[3])
static double	FractionalAnisotropy (double w[3])
static double	LinearMeasure (double w[3])
static double	MaxEigenvalue (double w[3])
static double	MaxEigenvalueProjectionX (double **v, double w[3])
static double	MaxEigenvalueProjectionY (double **v, double w[3])
static double	MaxEigenvalueProjectionZ (double **v, double w[3])
static double	MiddleEigenvalue (double w[3])
static double	MinEigenvalue (double w[3])
static double	Mode (double w[3])
static void	ModeToRGB (double Mode, double FA, double &R, double &G, double &B)
	Public for access from threads.
static vtkDiffusionTensorMathematics *	New ()
static double	ParallelDiffusivity (double w[3])
static double	PerpendicularDiffusivity (double w[3])
static double	PlanarMeasure (double w[3])
static double	RAIMaxEigenvecX (double **v, double w[3])
static double	RAIMaxEigenvecY (double **v, double w[3])
static double	RAIMaxEigenvecZ (double **v, double w[3])
static double	RelativeAnisotropy (double w[3])
static double	SphericalMeasure (double w[3])
static int	TeemEigenSolver (double **m, double *w, double **v)
static double	Trace (double w[3])
static double	Trace (double D[3][3])
Protected Member Functions
int	FillInputPortInformation (int port, vtkInformation *info)
virtual int	RequestInformation (vtkInformation *, vtkInformationVector **, vtkInformationVector *)
virtual void	ThreadedRequestData (vtkInformation *request, vtkInformationVector **inputVector, vtkInformationVector *outputVector, vtkImageData ***inData, vtkImageData **outData, int extent[6], int threadId)
	vtkDiffusionTensorMathematics ()
	~vtkDiffusionTensorMathematics ()
Protected Attributes
int	ExtractEigenvalues
	Scale factor for output scalars.
int	FixNegativeEigenvalues
int	MaskLabelValue
int	MaskWithScalars
	Boolean controls eigenfunction extraction.
int	Operation
vtkImageData *	ScalarMask
double	ScaleFactor
	math operation to perform
vtkMatrix4x4 *	TensorRotationMatrix
Private Member Functions
void	operator= (const vtkDiffusionTensorMathematics &)
	vtkDiffusionTensorMathematics (const vtkDiffusionTensorMathematics &)

---

Member Enumeration Documentation

anonymous enum

Operation options.

Enumerator:

VTK_TENS_TRACE
VTK_TENS_DETERMINANT
VTK_TENS_RELATIVE_ANISOTROPY
VTK_TENS_FRACTIONAL_ANISOTROPY
VTK_TENS_MAX_EIGENVALUE
VTK_TENS_MID_EIGENVALUE
VTK_TENS_MIN_EIGENVALUE
VTK_TENS_LINEAR_MEASURE
VTK_TENS_PLANAR_MEASURE
VTK_TENS_SPHERICAL_MEASURE
VTK_TENS_COLOR_ORIENTATION
VTK_TENS_D11
VTK_TENS_D22
VTK_TENS_D33
VTK_TENS_MODE
VTK_TENS_COLOR_MODE
VTK_TENS_MAX_EIGENVALUE_PROJX
VTK_TENS_MAX_EIGENVALUE_PROJY
VTK_TENS_MAX_EIGENVALUE_PROJZ
VTK_TENS_RAI_MAX_EIGENVEC_PROJX
VTK_TENS_RAI_MAX_EIGENVEC_PROJY
VTK_TENS_RAI_MAX_EIGENVEC_PROJZ
VTK_TENS_PARALLEL_DIFFUSIVITY
VTK_TENS_PERPENDICULAR_DIFFUSIVITY

---

Constructor & Destructor Documentation

vtkDiffusionTensorMathematics::vtkDiffusionTensorMathematics

(

)

[protected]

References ExtractEigenvalues, FixNegativeEigenvalues, MaskLabelValue, MaskWithScalars, Operation, ScalarMask, ScaleFactor, TensorRotationMatrix, and VTK_TENS_TRACE.

vtkDiffusionTensorMathematics::~vtkDiffusionTensorMathematics

(

)

[protected]

References ScalarMask, and TensorRotationMatrix.

vtkDiffusionTensorMathematics::vtkDiffusionTensorMathematics

(

const vtkDiffusionTensorMathematics &

)

[private]

---

Member Function Documentation

void vtkDiffusionTensorMathematics::ColorByMode	(	double	w[3],
		double &	R,
		double &	G,
		double &	B
	)			[static]

References FractionalAnisotropy(), Mode(), and ModeToRGB().

Referenced by vtkDiffusionTensorMathematicsExecute1Eigen().

void vtkDiffusionTensorMathematics::ComputeTensorIncrements	(	vtkImageData *	imageData,
		vtkIdType	incr[3]
	)

double vtkDiffusionTensorMathematics::Determinant

(

double

D[3][3]

)

[static]

Referenced by vtkDiffusionTensorMathematicsExecute1().

int vtkDiffusionTensorMathematics::FillInputPortInformation	(	int	port,
		vtkInformation *	info
	)			[protected]

int vtkDiffusionTensorMathematics::FixNegativeEigenvaluesMethod

(

double

w[3]

)

[static]

Helper functions to perform operations pixel-wise

Referenced by vtkDiffusionTensorMathematicsExecute1Eigen().

double vtkDiffusionTensorMathematics::FractionalAnisotropy

(

double

w[3]

)

[static]

References VTK_EPS.

Referenced by ColorByMode(), and vtkDiffusionTensorMathematicsExecute1Eigen().

double vtkDiffusionTensorMathematics::LinearMeasure

(

double

w[3]

)

[static]

References VTK_EPS.

Referenced by vtkSeedTracts::SeedStreamlinesInROI(), and vtkDiffusionTensorMathematicsExecute1Eigen().

double vtkDiffusionTensorMathematics::MaxEigenvalue

(

double

w[3]

)

[static]

double vtkDiffusionTensorMathematics::MaxEigenvalueProjectionX	(	double **	v,
		double	w[3]
	)			[static]

Referenced by vtkDiffusionTensorMathematicsExecute1Eigen().

double vtkDiffusionTensorMathematics::MaxEigenvalueProjectionY	(	double **	v,
		double	w[3]
	)			[static]

Referenced by vtkDiffusionTensorMathematicsExecute1Eigen().

double vtkDiffusionTensorMathematics::MaxEigenvalueProjectionZ	(	double **	v,
		double	w[3]
	)			[static]

Referenced by vtkDiffusionTensorMathematicsExecute1Eigen().

double vtkDiffusionTensorMathematics::MiddleEigenvalue

(

double

w[3]

)

[static]

double vtkDiffusionTensorMathematics::MinEigenvalue

(

double

w[3]

)

[static]

double vtkDiffusionTensorMathematics::Mode

(

double

w[3]

)

[static]

References M_SQRT2, and VTK_EPS.

Referenced by ColorByMode(), and vtkDiffusionTensorMathematicsExecute1Eigen().

void vtkDiffusionTensorMathematics::ModeToRGB	(	double	Mode,
		double	FA,
		double &	R,
		double &	G,
		double &	B
	)			[static]

Public for access from threads.

Referenced by ColorByMode().

vtkDiffusionTensorMathematics * vtkDiffusionTensorMathematics::New

(

)

[static]

References autoSlicerTracto2regions::ret.

void vtkDiffusionTensorMathematics::operator=

(

const vtkDiffusionTensorMathematics &

)

[private]

double vtkDiffusionTensorMathematics::ParallelDiffusivity

(

double

w[3]

)

[static]

Referenced by vtkDiffusionTensorMathematicsExecute1Eigen().

double vtkDiffusionTensorMathematics::PerpendicularDiffusivity

(

double

w[3]

)

[static]

Referenced by vtkDiffusionTensorMathematicsExecute1Eigen().

double vtkDiffusionTensorMathematics::PlanarMeasure

(

double

w[3]

)

[static]

References VTK_EPS.

Referenced by vtkDiffusionTensorMathematicsExecute1Eigen().

void vtkDiffusionTensorMathematics::PrintSelf	(	ostream &	os,
		vtkIndent	indent
	)

References Operation.

double vtkDiffusionTensorMathematics::RAIMaxEigenvecX	(	double **	v,
		double	w[3]
	)			[static]

References RelativeAnisotropy().

Referenced by vtkDiffusionTensorMathematicsExecute1Eigen().

double vtkDiffusionTensorMathematics::RAIMaxEigenvecY	(	double **	v,
		double	w[3]
	)			[static]

References RelativeAnisotropy().

Referenced by vtkDiffusionTensorMathematicsExecute1Eigen().

double vtkDiffusionTensorMathematics::RAIMaxEigenvecZ	(	double **	v,
		double	w[3]
	)			[static]

References RelativeAnisotropy().

Referenced by vtkDiffusionTensorMathematicsExecute1Eigen().

double vtkDiffusionTensorMathematics::RelativeAnisotropy

(

double

w[3]

)

[static]

References trace(), and VTK_EPS.

Referenced by RAIMaxEigenvecX(), RAIMaxEigenvecY(), RAIMaxEigenvecZ(), and vtkDiffusionTensorMathematicsExecute1Eigen().

virtual int vtkDiffusionTensorMathematics::RequestInformation	(	vtkInformation *	,
		vtkInformationVector **	,
		vtkInformationVector *
	)			[protected, virtual]

void vtkDiffusionTensorMathematics::SetOperationToColorByMode

(

)

[inline]

Output RGB color according to colormapping of mode, with final RGB being a linear combination of gray and this color. Amount of gray is determined by FA. Thanks to Gordon Lothar Kindlmann for this method.

void vtkDiffusionTensorMathematics::SetOperationToColorByOrientation

(

)

[inline]

Output RGB color according to XYZ of eigenvectors. Output A (alpha, or transparency) according to anisotropy (1-spherical measure).

void vtkDiffusionTensorMathematics::SetOperationToD11

(

)

[inline]

Output a matrix (tensor) component

void vtkDiffusionTensorMathematics::SetOperationToD22

(

)

[inline]

void vtkDiffusionTensorMathematics::SetOperationToD33

(

)

[inline]

void vtkDiffusionTensorMathematics::SetOperationToDeterminant

(

)

[inline]

Output the determinant

void vtkDiffusionTensorMathematics::SetOperationToFractionalAnisotropy

(

)

[inline]

void vtkDiffusionTensorMathematics::SetOperationToLinearMeasure

(

)

[inline]

void vtkDiffusionTensorMathematics::SetOperationToMaxEigenvalue

(

)

[inline]

Output a selected eigenvalue

void vtkDiffusionTensorMathematics::SetOperationToMaxEigenvalueProjectionX

(

)

[inline]

Output Maxeigenvalue*Maxeigenvec_projection also known as L1Z

void vtkDiffusionTensorMathematics::SetOperationToMaxEigenvalueProjectionY

(

)

[inline]

void vtkDiffusionTensorMathematics::SetOperationToMaxEigenvalueProjectionZ

(

)

[inline]

void vtkDiffusionTensorMathematics::SetOperationToMiddleEigenvalue

(

)

[inline]

void vtkDiffusionTensorMathematics::SetOperationToMinEigenvalue

(

)

[inline]

void vtkDiffusionTensorMathematics::SetOperationToMode

(

)

[inline]

This is the skewness of the eigenvalues (thanks to Gordon Lothar (of the Hill People) Kindlmann)

void vtkDiffusionTensorMathematics::SetOperationToParallelDiffusivity

(

)

[inline]

void vtkDiffusionTensorMathematics::SetOperationToPerpendicularDiffusivity

(

)

[inline]

void vtkDiffusionTensorMathematics::SetOperationToPlanarMeasure

(

)

[inline]

void vtkDiffusionTensorMathematics::SetOperationToRAIMaxEigenvecX

(

)

[inline]

Output Relative_anisotropy*Maxeigenvec_projection also known as L1z

void vtkDiffusionTensorMathematics::SetOperationToRAIMaxEigenvecY

(

)

[inline]

void vtkDiffusionTensorMathematics::SetOperationToRAIMaxEigenvecZ

(

)

[inline]

void vtkDiffusionTensorMathematics::SetOperationToRelativeAnisotropy

(

)

[inline]

Output various anisotropy and shape measures

void vtkDiffusionTensorMathematics::SetOperationToSphericalMeasure

(

)

[inline]

void vtkDiffusionTensorMathematics::SetOperationToTrace

(

)

[inline]

Output the trace (sum of eigenvalues = sum along diagonal)

virtual void vtkDiffusionTensorMathematics::SetScalarMask

(

vtkImageData *

)

[virtual]

Scalar mask

virtual void vtkDiffusionTensorMathematics::SetTensorRotationMatrix

(

vtkMatrix4x4 *

)

[virtual]

Description This matrix is only used for ColorByOrientation. We transform the tensor orientation by this matrix before setting the output RGB values. This is useful to put the output colors into a standard coordinate system (i.e. RAS) regardless of the data scan order. Example usage is as follows: 1) If tensors are to be displayed in a coordinate system that is not IJK (array-based), and the whole volume is being rotated, each tensor needs also to be rotated. First find the matrix that positions your volume. (This is how the entire volume is positioned, not the matrix that positions an arbitrary reformatted slice.) 2) Remove scaling and translation from this matrix; we just need to rotate each tensor. 3) Set TensorRotationMatrix to this rotation matrix.

double vtkDiffusionTensorMathematics::SphericalMeasure

(

double

w[3]

)

[static]

References VTK_EPS.

Referenced by vtkDiffusionTensorMathematicsExecute1Eigen().

int vtkDiffusionTensorMathematics::TeemEigenSolver	(	double **	m,
		double *	w,
		double **	v
	)			[static]

References NodeSelector::t, and teem::tenEigensolve_d.

Referenced by vtkPreciseHyperStreamline::Execute(), vtkTensorImplicitFunctionToFunctionSet::FunctionValues(), vtkSeedTracts::SeedStreamlinesInROI(), and vtkDiffusionTensorMathematicsExecute1Eigen().

virtual void vtkDiffusionTensorMathematics::ThreadedRequestData	(	vtkInformation *	request,
		vtkInformationVector **	inputVector,
		vtkInformationVector *	outputVector,
		vtkImageData ***	inData,
		vtkImageData **	outData,
		int	extent[6],
		int	threadId
	)			[protected, virtual]

double vtkDiffusionTensorMathematics::Trace

(

double

w[3]

)

[static]

double vtkDiffusionTensorMathematics::Trace

(

double

D[3][3]

)

[static]

Referenced by vtkDiffusionTensorMathematicsExecute1().

vtkDiffusionTensorMathematics::vtkBooleanMacro	(	FixNegativeEigenvalues	,
		int
	)

vtkDiffusionTensorMathematics::vtkBooleanMacro	(	MaskWithScalars	,
		int
	)

Description Input scalars are a binary mask: 0 prevents display of tensor quantity at that point

vtkDiffusionTensorMathematics::vtkBooleanMacro	(	ExtractEigenvalues	,
		int
	)

vtkDiffusionTensorMathematics::vtkGetMacro	(	MaskLabelValue	,
		int
	)

vtkDiffusionTensorMathematics::vtkGetMacro	(	FixNegativeEigenvalues	,
		int
	)

vtkDiffusionTensorMathematics::vtkGetMacro	(	MaskWithScalars	,
		int
	)

vtkDiffusionTensorMathematics::vtkGetMacro	(	ExtractEigenvalues	,
		int
	)

vtkDiffusionTensorMathematics::vtkGetMacro	(	ScaleFactor	,
		double
	)

vtkDiffusionTensorMathematics::vtkGetMacro	(	Operation	,
		int
	)

Get the Operation to perform.

vtkDiffusionTensorMathematics::vtkGetObjectMacro	(	ScalarMask	,
		vtkImageData
	)

vtkDiffusionTensorMathematics::vtkGetObjectMacro	(	TensorRotationMatrix	,
		vtkMatrix4x4
	)

vtkDiffusionTensorMathematics::vtkSetClampMacro	(	Operation	,
		int	,
		VTK_TENS_TRACE	,
		VTK_TENS_PERPENDICULAR_DIFFUSIVITY
	)

vtkDiffusionTensorMathematics::vtkSetMacro	(	MaskLabelValue	,
		int
	)

Label value defining ROI for mask

vtkDiffusionTensorMathematics::vtkSetMacro	(	FixNegativeEigenvalues	,
		int
	)

vtkDiffusionTensorMathematics::vtkSetMacro	(	MaskWithScalars	,
		int
	)

vtkDiffusionTensorMathematics::vtkSetMacro	(	ExtractEigenvalues	,
		int
	)

Turn on/off extraction of eigenvalues from tensor.

vtkDiffusionTensorMathematics::vtkSetMacro	(	ScaleFactor	,
		double
	)

Specify scale factor to scale output (float) scalars by. This is not used when the output is RGBA (char color data).

vtkDiffusionTensorMathematics::vtkTypeMacro	(	vtkDiffusionTensorMathematics	,
		vtkThreadedImageAlgorithm
	)

---

Member Data Documentation

int vtkDiffusionTensorMathematics::ExtractEigenvalues [protected]

Scale factor for output scalars.

Referenced by vtkDiffusionTensorMathematics().

int vtkDiffusionTensorMathematics::FixNegativeEigenvalues [protected]

Referenced by vtkDiffusionTensorMathematics().

int vtkDiffusionTensorMathematics::MaskLabelValue [protected]

Referenced by vtkDiffusionTensorMathematics().

int vtkDiffusionTensorMathematics::MaskWithScalars [protected]

Boolean controls eigenfunction extraction.

Referenced by vtkDiffusionTensorMathematics().

int vtkDiffusionTensorMathematics::Operation [protected]

Referenced by PrintSelf(), and vtkDiffusionTensorMathematics().

vtkImageData* vtkDiffusionTensorMathematics::ScalarMask [protected]

Referenced by vtkDiffusionTensorMathematics(), and ~vtkDiffusionTensorMathematics().

double vtkDiffusionTensorMathematics::ScaleFactor [protected]

math operation to perform

Referenced by vtkDiffusionTensorMathematics().

vtkMatrix4x4* vtkDiffusionTensorMathematics::TensorRotationMatrix [protected]

Referenced by vtkDiffusionTensorMathematics(), and ~vtkDiffusionTensorMathematics().

---

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

• Libs/vtkTeem/vtkDiffusionTensorMathematics.h
• Libs/vtkTeem/vtkDiffusionTensorMathematics.cxx