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itk::DiffusionTensor3D< TComponent > Class Template Reference
Image Representation Objects | Objects Related to Tensor Images | Geometry Representation Objects

Represent a diffusion tensor as used in DTI images. More...

#include <itkDiffusionTensor3D.h>

+ Inheritance diagram for itk::DiffusionTensor3D< TComponent >:
+ Collaboration diagram for itk::DiffusionTensor3D< TComponent >:

Public Types

typedef
Superclass::AccumulateValueType 		AccumulateValueType
 
typedef FixedArray< TComponent,
itkGetStaticConstMacro(InternalDimension)> 		BaseArray
 
typedef ValueType CArray [VLength]
 
typedef
Superclass::ComponentArrayType 		ComponentArrayType
 
typedef Superclass::ComponentType ComponentType
 
typedef const ValueType * const_pointer
 
typedef const ValueType & const_reference
 
typedef const ValueType * ConstIterator
 
typedef
Superclass::EigenValuesArrayType 		EigenValuesArrayType
 
typedef
Superclass::EigenVectorsMatrixType 		EigenVectorsMatrixType
 
typedef ValueType * Iterator
 
typedef Matrix< TComponent,
NDimension, NDimension > 		MatrixType
 
typedef ValueType * pointer
 
typedef Superclass::RealValueType RealValueType
 
typedef ValueType & reference
 
typedef DiffusionTensor3D Self
 
typedef unsigned int SizeType
 
typedef
SymmetricSecondRankTensor
< TComponent, 3 > 		Superclass
 
typedef SymmetricEigenAnalysis
< MatrixType,
EigenValuesArrayType,
EigenVectorsMatrixType > 		SymmetricEigenAnalysisType
 
typedef Superclass::ValueType ValueType
 

Public Member Functions

 DiffusionTensor3D ()
 
 DiffusionTensor3D (const Superclass &r)
 
 DiffusionTensor3D (const ComponentType &r)
 
 DiffusionTensor3D (const ComponentArrayType r)
 
template<typename TCoordRepB >
 DiffusionTensor3D (const DiffusionTensor3D< TCoordRepB > &pa)
 
Iterator Begin ()
 
ConstIterator Begin () const
 
void ComputeEigenAnalysis (EigenValuesArrayType &eigenValues, EigenVectorsMatrixType &eigenVectors) const
 
void ComputeEigenValues (EigenValuesArrayType &eigenValues) const
 
Iterator End ()
 
ConstIterator End () const
 
void Fill (const ValueType &)
 
ValueType * GetDataPointer ()
 
const ValueType * GetDataPointer () const
 
const_reference GetElement (unsigned short index) const
 
RealValueType GetFractionalAnisotropy () const
 
RealValueType GetInnerScalarProduct () const
 
ComponentType GetNthComponent (int c) const
 
RealValueType GetRelativeAnisotropy () const
 
AccumulateValueType GetTrace () const
 
bool operator!= (const FixedArray &r) const
 
ValueType & operator() (unsigned int row, unsigned int col)
 
const ValueType & operator() (unsigned int row, unsigned int col) const
 
Self operator* (const RealValueType &scalar) const
 
const Self & operator*= (const RealValueType &scalar)
 
Self operator+ (const Self &vec) const
 
const Self & operator+= (const Self &vec)
 
Self operator- (const Self &vec) const
 
const Self & operator-= (const Self &vec)
 
Self operator/ (const RealValueType &scalar) const
 
const Self & operator/= (const RealValueType &scalar)
 
Self & operator= (const Superclass &r)
 
Self & operator= (const ComponentType &r)
 
Self & operator= (const ComponentArrayType r)
 
template<typename TCoordRepB >
Self & operator= (const DiffusionTensor3D< TCoordRepB > &pa)
 
bool operator== (const FixedArray &r) const
 
reference operator[] (short index)
 
const_reference operator[] (short index) const
 
reference operator[] (unsigned short index)
 
const_reference operator[] (unsigned short index) const
 
reference operator[] (int index)
 
const_reference operator[] (int index) const
 
reference operator[] (unsigned int index)
 
const_reference operator[] (unsigned int index) const
 
reference operator[] (long index)
 
const_reference operator[] (long index) const
 
reference operator[] (unsigned long index)
 
const_reference operator[] (unsigned long index) const
 
Self PostMultiply (const MatrixType &m) const
 
Self PreMultiply (const MatrixType &m) const
 
ReverseIterator rBegin ()
 
ConstReverseIterator rBegin () const
 
ReverseIterator rEnd ()
 
ConstReverseIterator rEnd () const
 
void SetElement (unsigned short index, const_reference value)
 
void SetIdentity ()
 
void SetNthComponent (int c, const ComponentType &v)
 
SizeType Size () const
 

Static Public Member Functions

static FixedArray Filled (const ValueType &)
 
static unsigned int GetNumberOfComponents ()
 

Static Public Attributes

static const unsigned int Dimension
 
static const unsigned int InternalDimension
 
static const unsigned int Length
 

Detailed Description

template<typename TComponent>
class itk::DiffusionTensor3D< TComponent >

Represent a diffusion tensor as used in DTI images.

This class implements a 3D symmetric tensor as it is used for representing diffusion of water molecules in Diffusion Tensor Images.

This class derive from the SymmetricSecondRankTensor and from it inherit most of the Tensor related behavior. At this level we add the methods that are specific to 3D and that are closely related to the concept of diffusion.

Author
Jeffrey Duda from School of Engineering at University of Pennsylvania
Torsten Rohlfing from SRI International Neuroscience Program.

This class was mostly based on files that Jeffrey Duda, Torsten Rohlfing and Martin Styner contributed to the ITK users list during a discussion on support for DiffusionTensorImages. A discussion on the design of this class can be found in the WIKI pages of NAMIC:

http://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:ITK-DiffusionTensorPixelType

Note
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics.
Contributions by Torsten Rohlfing were funded by the following NIH grants

Alcohol, HIV and the Brain, NIAAA AA12999, PI: A. Pfefferbaum

Normal Aging of Brain Structure and Function NIA AG 17919, PI: E.V. Sullivan.

References
E. R. Melhem, S. Mori, G. Mukundan, M. A. Kraut, M. G. Pomper, and P. C. M. van Zijl, "Diffusion tensor MR imaging of the brain and white matter tractography," Am. J. Roentgenol., vol. 178, pp. 3-16, 2002.
See Also
SymmetricSecondRankTensor

Definition at line 79 of file itkDiffusionTensor3D.h.

Member Typedef Documentation

template<typename TComponent>
typedef Superclass::AccumulateValueType itk::DiffusionTensor3D< TComponent >::AccumulateValueType

Definition at line 94 of file itkDiffusionTensor3D.h.

typedef FixedArray<TComponent, itkGetStaticConstMacro(InternalDimension)> itk::SymmetricSecondRankTensor< TComponent, NDimension >::BaseArray
inherited

Convenience typedefs.

Definition at line 88 of file itkSymmetricSecondRankTensor.h.

typedef ValueType itk::FixedArray< TComponent , VLength >::CArray[VLength]
inherited

A type representing the C-array version of this FixedArray.

Definition at line 77 of file itkFixedArray.h.

template<typename TComponent>
typedef Superclass::ComponentArrayType itk::DiffusionTensor3D< TComponent >::ComponentArrayType

Definition at line 92 of file itkDiffusionTensor3D.h.

template<typename TComponent>
typedef Superclass::ComponentType itk::DiffusionTensor3D< TComponent >::ComponentType

Definition at line 88 of file itkDiffusionTensor3D.h.

typedef const ValueType* itk::FixedArray< TComponent , VLength >::const_pointer
inherited

A const pointer to the ValueType.

Definition at line 129 of file itkFixedArray.h.

typedef const ValueType& itk::FixedArray< TComponent , VLength >::const_reference
inherited

A const reference to the ValueType.

Definition at line 135 of file itkFixedArray.h.

typedef const ValueType* itk::FixedArray< TComponent , VLength >::ConstIterator
inherited

A const iterator through the array.

Definition at line 83 of file itkFixedArray.h.

template<typename TComponent>
typedef Superclass::EigenValuesArrayType itk::DiffusionTensor3D< TComponent >::EigenValuesArrayType

Definition at line 97 of file itkDiffusionTensor3D.h.

template<typename TComponent>
typedef Superclass::EigenVectorsMatrixType itk::DiffusionTensor3D< TComponent >::EigenVectorsMatrixType

Definition at line 98 of file itkDiffusionTensor3D.h.

typedef ValueType* itk::FixedArray< TComponent , VLength >::Iterator
inherited

An iterator through the array.

Definition at line 80 of file itkFixedArray.h.

typedef Matrix<TComponent, NDimension, NDimension> itk::SymmetricSecondRankTensor< TComponent, NDimension >::MatrixType
inherited

Matrix of eigen-vectors.

Definition at line 94 of file itkSymmetricSecondRankTensor.h.

typedef ValueType* itk::FixedArray< TComponent , VLength >::pointer
inherited

A pointer to the ValueType.

Definition at line 126 of file itkFixedArray.h.

template<typename TComponent>
typedef Superclass::RealValueType itk::DiffusionTensor3D< TComponent >::RealValueType

Definition at line 95 of file itkDiffusionTensor3D.h.

typedef ValueType& itk::FixedArray< TComponent , VLength >::reference
inherited

A reference to the ValueType.

Definition at line 132 of file itkFixedArray.h.

template<typename TComponent>
typedef DiffusionTensor3D itk::DiffusionTensor3D< TComponent >::Self

Standard class typedefs.

Definition at line 83 of file itkDiffusionTensor3D.h.

typedef unsigned int itk::FixedArray< TComponent , VLength >::SizeType
inherited

Definition at line 137 of file itkFixedArray.h.

template<typename TComponent>
typedef SymmetricSecondRankTensor<TComponent, 3> itk::DiffusionTensor3D< TComponent >::Superclass

Definition at line 84 of file itkDiffusionTensor3D.h.

typedef SymmetricEigenAnalysis< MatrixType, EigenValuesArrayType, EigenVectorsMatrixType > itk::SymmetricSecondRankTensor< TComponent, NDimension >::SymmetricEigenAnalysisType
inherited

Definition at line 104 of file itkSymmetricSecondRankTensor.h.

template<typename TComponent>
typedef Superclass::ValueType itk::DiffusionTensor3D< TComponent >::ValueType

Propagating some typedef from the superclass

Definition at line 87 of file itkDiffusionTensor3D.h.

Constructor & Destructor Documentation

template<class T >
itk::DiffusionTensor3D< T >::DiffusionTensor3D ( )

Default Constructor.

Default Constructor

Definition at line 32 of file itkDiffusionTensor3D.txx.

template<class T >
itk::DiffusionTensor3D< T >::DiffusionTensor3D ( const Superclass &  r)

Constructor with initialization.

Constructor with initialization

Definition at line 42 of file itkDiffusionTensor3D.txx.

template<class T >
itk::DiffusionTensor3D< T >::DiffusionTensor3D ( const ComponentType &  r)

Constructor with initialization

Definition at line 52 of file itkDiffusionTensor3D.txx.

template<class T >
itk::DiffusionTensor3D< T >::DiffusionTensor3D ( const ComponentArrayType  r)

Constructor with initialization

Definition at line 62 of file itkDiffusionTensor3D.txx.

template<typename TComponent>
template<typename TCoordRepB >
itk::DiffusionTensor3D< TComponent >::DiffusionTensor3D ( const DiffusionTensor3D< TCoordRepB > &  pa)
inline

Constructor to enable casting...

Definition at line 110 of file itkDiffusionTensor3D.h.

Member Function Documentation

Iterator itk::FixedArray< TComponent , VLength >::Begin ( void  )
inherited

Get various iterators to the array.

Get an Iterator for the beginning of the FixedArray.

Referenced by itk::DTITubeSpatialObjectPoint< TPointDimension >::SetTensorMatrix().

ConstIterator itk::FixedArray< TComponent , VLength >::Begin ( void  ) const
inherited

Get a ConstIterator for the beginning of the FixedArray.

void itk::SymmetricSecondRankTensor< TComponent, NDimension >::ComputeEigenAnalysis ( EigenValuesArrayType &  eigenValues,
EigenVectorsMatrixType &  eigenVectors 
) const
inherited

Return an array containing EigenValues, and a matrix containing Eigen vectors.

Compute Eigen analysis, it returns an array with eigen values and a Matrix with eigen vectors

void itk::SymmetricSecondRankTensor< TComponent, NDimension >::ComputeEigenValues ( EigenValuesArrayType &  eigenValues) const
inherited

Return an array containing EigenValues.

Compute Eigen Values

Iterator itk::FixedArray< TComponent , VLength >::End ( void  )
inherited

Get an Iterator for the end of the FixedArray.

Referenced by itk::DTITubeSpatialObjectPoint< TPointDimension >::SetTensorMatrix().

ConstIterator itk::FixedArray< TComponent , VLength >::End ( void  ) const
inherited

Get a ConstIterator for the end of the FixedArray.

void itk::FixedArray< TComponent , VLength >::Fill ( const ValueType &  )
inherited

Fill all elements of the array with the given value.

Referenced by itk::SymmetricSecondRankTensor< TComponent, 3 >::SymmetricSecondRankTensor().

static FixedArray itk::FixedArray< TComponent , VLength >::Filled ( const ValueType &  )
staticinherited

Return an FixedArray with all elements assigned to the given value.

ValueType* itk::FixedArray< TComponent , VLength >::GetDataPointer ( )
inlineinherited

Return a pointer to the data.

Definition at line 216 of file itkFixedArray.h.

const ValueType* itk::FixedArray< TComponent , VLength >::GetDataPointer ( ) const
inlineinherited

Definition at line 217 of file itkFixedArray.h.

const_reference itk::FixedArray< TComponent , VLength >::GetElement ( unsigned short  index) const
inlineinherited

Definition at line 213 of file itkFixedArray.h.

template<class T >
DiffusionTensor3D< T >::RealValueType itk::DiffusionTensor3D< T >::GetFractionalAnisotropy ( ) const

Get the value of Fractional Anisotropy from the Tensor.

Compute the value of fractional anisotropy

Definition at line 139 of file itkDiffusionTensor3D.txx.

template<class T >
DiffusionTensor3D< T >::RealValueType itk::DiffusionTensor3D< T >::GetInnerScalarProduct ( ) const

Get the Inner Scalar Product from the Tensor.

Compute the inner scalar product

Definition at line 201 of file itkDiffusionTensor3D.txx.

ComponentType itk::SymmetricSecondRankTensor< TComponent, NDimension >::GetNthComponent ( int  c) const
inlineinherited

Return the value for the Nth component.

Definition at line 152 of file itkSymmetricSecondRankTensor.h.

References itk::FixedArray< TComponent, NDimension *(NDimension+1)/2 >::operator[]().

static unsigned int itk::SymmetricSecondRankTensor< TComponent, NDimension >::GetNumberOfComponents ( void  )
inlinestaticinherited

Return the number of components.

Definition at line 146 of file itkSymmetricSecondRankTensor.h.

References itk::SymmetricSecondRankTensor< TComponent, NDimension >::InternalDimension.

template<class T >
DiffusionTensor3D< T >::RealValueType itk::DiffusionTensor3D< T >::GetRelativeAnisotropy ( ) const

Get the value of Relative Anisotropy from the Tensor.

Compute the value of relative anisotropy

Definition at line 166 of file itkDiffusionTensor3D.txx.

template<class T >
DiffusionTensor3D< T >::AccumulateValueType itk::DiffusionTensor3D< T >::GetTrace ( ) const

Get Trace value

Get the Trace, specialized version for 3D.

Note that the indices are related to the fact that we store only the upper-right triangle of the matrix. Like 

  | 0  1  2  |
  | X  3  4  |
  | X  X  5  |

The trace is therefore the sum of the components M[0], M[3] and M[5].

Definition at line 124 of file itkDiffusionTensor3D.txx.

bool itk::FixedArray< TComponent , VLength >::operator!= ( const FixedArray< TComponent, NDimension *(NDimension+1)/2 > &  r) const
inlineinherited

Definition at line 191 of file itkFixedArray.h.

ValueType& itk::SymmetricSecondRankTensor< TComponent, NDimension >::operator() ( unsigned int  row,
unsigned int  col 
)
inherited

Matrix notation, in const and non-const forms.

Matrix notation access to elements

const ValueType& itk::SymmetricSecondRankTensor< TComponent, NDimension >::operator() ( unsigned int  row,
unsigned int  col 
) const
inherited

Matrix notation access to elements

Self itk::SymmetricSecondRankTensor< TComponent, NDimension >::operator* ( const RealValueType &  scalar) const
inherited

Arithmetic operations between tensors and scalars

Performs multiplication with a scalar

const Self& itk::SymmetricSecondRankTensor< TComponent, NDimension >::operator*= ( const RealValueType &  scalar)
inherited

Performs multiplication by a scalar, in place

Self itk::SymmetricSecondRankTensor< TComponent, NDimension >::operator+ ( const Self &  vec) const
inherited

Aritmetic operations between pixels. Return a new SymmetricSecondRankTensor.

Returns a temporary copy of a vector

const Self& itk::SymmetricSecondRankTensor< TComponent, NDimension >::operator+= ( const Self &  vec)
inherited

Performs addition in place

Self itk::SymmetricSecondRankTensor< TComponent, NDimension >::operator- ( const Self &  vec) const
inherited

Returns a temporary copy of a vector

const Self& itk::SymmetricSecondRankTensor< TComponent, NDimension >::operator-= ( const Self &  vec)
inherited

Performs subtraction in place

Self itk::SymmetricSecondRankTensor< TComponent, NDimension >::operator/ ( const RealValueType &  scalar) const
inherited

Performs division by a scalar

const Self& itk::SymmetricSecondRankTensor< TComponent, NDimension >::operator/= ( const RealValueType &  scalar)
inherited

Performs division by a scalar, in place

template<class T >
DiffusionTensor3D< T > & itk::DiffusionTensor3D< T >::operator= ( const Superclass &  r)

Pass-through assignment operator for the Array base class.

Assignment Operator

Definition at line 99 of file itkDiffusionTensor3D.txx.

template<class T >
DiffusionTensor3D< T > & itk::DiffusionTensor3D< T >::operator= ( const ComponentType &  r)

Assignment Operator

Definition at line 73 of file itkDiffusionTensor3D.txx.

template<class T >
DiffusionTensor3D< T > & itk::DiffusionTensor3D< T >::operator= ( const ComponentArrayType  r)

Assignment Operator

Definition at line 86 of file itkDiffusionTensor3D.txx.

template<typename TComponent>
template<typename TCoordRepB >
Self& itk::DiffusionTensor3D< TComponent >::operator= ( const DiffusionTensor3D< TCoordRepB > &  pa)
inline

Templated Pass-through assignment for the Array base class.

Definition at line 120 of file itkDiffusionTensor3D.h.

References itk::SymmetricSecondRankTensor< TComponent, NDimension >::operator=().

bool itk::FixedArray< TComponent , VLength >::operator== ( const FixedArray< TComponent, NDimension *(NDimension+1)/2 > &  r) const
inherited

Operators == and != are used to compare whether two arrays are equal. Note that arrays are equal when the number of components (size) is the same, and each component value is equal.

Operator != compares different types of arrays.

reference itk::FixedArray< TComponent , VLength >::operator[] ( short  index)
inlineinherited

Allow the FixedArray to be indexed normally. No bounds checking is done. The separate versions are a work-around for an integer conversion bug in Visual C++.

Definition at line 197 of file itkFixedArray.h.

Referenced by itk::SymmetricSecondRankTensor< TComponent, 3 >::GetNthComponent(), and itk::SymmetricSecondRankTensor< TComponent, 3 >::SetNthComponent().

const_reference itk::FixedArray< TComponent , VLength >::operator[] ( short  index) const
inlineinherited

Definition at line 198 of file itkFixedArray.h.

reference itk::FixedArray< TComponent , VLength >::operator[] ( unsigned short  index)
inlineinherited

Definition at line 199 of file itkFixedArray.h.

const_reference itk::FixedArray< TComponent , VLength >::operator[] ( unsigned short  index) const
inlineinherited

Definition at line 200 of file itkFixedArray.h.

reference itk::FixedArray< TComponent , VLength >::operator[] ( int  index)
inlineinherited

Definition at line 201 of file itkFixedArray.h.

const_reference itk::FixedArray< TComponent , VLength >::operator[] ( int  index) const
inlineinherited

Definition at line 202 of file itkFixedArray.h.

reference itk::FixedArray< TComponent , VLength >::operator[] ( unsigned int  index)
inlineinherited

Definition at line 203 of file itkFixedArray.h.

const_reference itk::FixedArray< TComponent , VLength >::operator[] ( unsigned int  index) const
inlineinherited

Definition at line 204 of file itkFixedArray.h.

reference itk::FixedArray< TComponent , VLength >::operator[] ( long  index)
inlineinherited

Definition at line 205 of file itkFixedArray.h.

const_reference itk::FixedArray< TComponent , VLength >::operator[] ( long  index) const
inlineinherited

Definition at line 206 of file itkFixedArray.h.

reference itk::FixedArray< TComponent , VLength >::operator[] ( unsigned long  index)
inlineinherited

Definition at line 207 of file itkFixedArray.h.

const_reference itk::FixedArray< TComponent , VLength >::operator[] ( unsigned long  index) const
inlineinherited

Definition at line 208 of file itkFixedArray.h.

Self itk::SymmetricSecondRankTensor< TComponent, NDimension >::PostMultiply ( const MatrixType &  m) const
inherited

Post-Multiply by a Matrix as ResultingTensor = ThisTensor * Matrix.

Post-multiply the Tensor by a Matrix

Self itk::SymmetricSecondRankTensor< TComponent, NDimension >::PreMultiply ( const MatrixType &  m) const
inherited

Pre-Multiply by a Matrix as ResultingTensor = Matrix * ThisTensor.

Pre-multiply the Tensor by a Matrix

ReverseIterator itk::FixedArray< TComponent , VLength >::rBegin ( )
inherited

Get a begin ReverseIterator.

ConstReverseIterator itk::FixedArray< TComponent , VLength >::rBegin ( ) const
inherited

Get a begin ConstReverseIterator.

ReverseIterator itk::FixedArray< TComponent , VLength >::rEnd ( )
inherited

Get an end ReverseIterator.

ConstReverseIterator itk::FixedArray< TComponent , VLength >::rEnd ( ) const
inherited

Get an end ConstReverseIterator.

void itk::FixedArray< TComponent , VLength >::SetElement ( unsigned short  index,
const_reference  value 
)
inlineinherited

Set/Get element methods are more convenient in wrapping languages

Definition at line 211 of file itkFixedArray.h.

void itk::SymmetricSecondRankTensor< TComponent, NDimension >::SetIdentity ( void  )
inherited

Set the tensor to an identity tensor. This has 1 in its diagonal elements zero elsewhere

Set the Tensor to an Identity. Set ones in the diagonal and zeroes every where else.

void itk::SymmetricSecondRankTensor< TComponent, NDimension >::SetNthComponent ( int  c,
const ComponentType &  v 
)
inlineinherited

Set the Nth component to v.

Definition at line 156 of file itkSymmetricSecondRankTensor.h.

References itk::FixedArray< TComponent, NDimension *(NDimension+1)/2 >::operator[]().

SizeType itk::FixedArray< TComponent , VLength >::Size ( void  ) const
inherited

Get the size of the FixedArray.

Member Data Documentation

const unsigned int itk::SymmetricSecondRankTensor< TComponent, NDimension >::Dimension
staticinherited

Dimension of the vector space.

Definition at line 83 of file itkSymmetricSecondRankTensor.h.

const unsigned int itk::SymmetricSecondRankTensor< TComponent, NDimension >::InternalDimension
staticinherited

Definition at line 84 of file itkSymmetricSecondRankTensor.h.

const unsigned int itk::FixedArray< TComponent , VLength >::Length
staticinherited

Length constant

Definition at line 68 of file itkFixedArray.h.

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