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elastix::AffineDTITransformElastix< TElastix > Class Template Reference

#include <elxAffineDTITransform.h>

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Public Types

typedef
AffineDTITransformType::Pointer 
AffineDTITransformPointer
typedef AffineDTITransform
< typename elx::TransformBase
< TElastix >::CoordRepType,
elx::TransformBase< TElastix >
::FixedImageDimension > 
AffineDTITransformType
typedef
Superclass2::CombinationTransformType 
CombinationTransformType
typedef
Superclass2::ConfigurationPointer 
ConfigurationPointer
typedef
Superclass2::ConfigurationType 
ConfigurationType
typedef SmartPointer< const SelfConstPointer
typedef Superclass2::CoordRepType CoordRepType
typedef
FixedImageType::DirectionType 
DirectionType
typedef Superclass2::ElastixPointer ElastixPointer
typedef Superclass2::ElastixType ElastixType
typedef Superclass2::FixedImageType FixedImageType
typedef FixedImageType::IndexType IndexType
typedef IndexType::IndexValueType IndexValueType
typedef
Superclass1::InputCovariantVectorType 
InputCovariantVectorType
typedef Superclass1::InputPointType InputPointType
typedef
Superclass1::InputVectorType 
InputVectorType
typedef
Superclass1::InputVnlVectorType 
InputVnlVectorType
typedef Superclass2::ITKBaseType ITKBaseType
typedef Superclass1::JacobianType JacobianType
typedef
Superclass2::MovingImageType 
MovingImageType
typedef
AffineDTITransformType::OffsetType 
OffsetType
typedef
Superclass1::OutputCovariantVectorType 
OutputCovariantVectorType
typedef
Superclass1::OutputPointType 
OutputPointType
typedef
Superclass1::OutputVectorType 
OutputVectorType
typedef
Superclass1::OutputVnlVectorType 
OutputVnlVectorType
typedef Superclass1::ParametersType ParametersType
typedef SmartPointer< SelfPointer
typedef FixedImageType::PointType PointType
typedef FixedImageType::RegionType RegionType
typedef
Superclass2::RegistrationPointer 
RegistrationPointer
typedef
Superclass2::RegistrationType 
RegistrationType
typedef Superclass1::ScalarType ScalarType
typedef Superclass2::ScalesType ScalesType
typedef AffineDTITransformElastix Self
typedef FixedImageType::SizeType SizeType
typedef FixedImageType::SpacingType SpacingType
typedef
AdvancedCombinationTransform
< typename elx::TransformBase
< TElastix >::CoordRepType,
elx::TransformBase< TElastix >
::FixedImageDimension > 
Superclass1
typedef elx::TransformBase
< TElastix > 
Superclass2
typedef
TransformInitializerType::Pointer 
TransformInitializerPointer
typedef
CenteredTransformInitializer
< AffineDTITransformType,
FixedImageType,
MovingImageType
TransformInitializerType

Public Member Functions

virtual void BeforeRegistration (void)
 elxClassNameMacro ("AffineDTITransform")
virtual const char * GetClassName () const
virtual void InitializeTransform (void)
 itkStaticConstMacro (SpaceDimension, unsigned int, Superclass2::FixedImageDimension)
virtual void ReadFromFile (void)
virtual void SetScales (void)
virtual void WriteToFile (const ParametersType &param) const

Static Public Member Functions

static Pointer New ()

Protected Member Functions

 AffineDTITransformElastix ()
virtual bool ReadCenterOfRotationPoint (InputPointType &rotationPoint) const
virtual ~AffineDTITransformElastix ()

Private Member Functions

 AffineDTITransformElastix (const Self &)
void operator= (const Self &)

Private Attributes

AffineDTITransformPointer m_AffineDTITransform

Detailed Description

template<class TElastix>
class elastix::AffineDTITransformElastix< TElastix >

A transform based on the itk AffineDTITransform.

This transform is an affine transformation, with a different parametrisation than the usual one. It is specialised for MR-DTI applications. See also the description of the itk::AffineDTI3DTransform.

Warning:
: the behaviour of this transform might still change in the future. It is still experimental.

The parameters used in this class are:

Parameters:
Transform: Select this transform as follows:
(Transform "AffineDTITransform")
Parameters:
Scales: the scale factor for each parameter, used by the optimizer.
example: (Scales -1 -1 -1 100000000 -1 -1 -1 -1 -1 -1 -1 -1)
The scales work a bit different in this transformation, compared with the other transformations like the EulerTransform. By default, if no scales are supplied, the scales are estimated automatically. With the scales parameter, the user can override the automatically determined scales. Values smaller than or equal to 0 are ignored: the automatically estimated value is used for these parameters. Positive values override the automatically estimated scales. So, in the example above, the shear_x parameter is given a very large scale, which effectively turns off the optimization of that parameters. This might be useful in some MR-DTI application.
Parameters:
CenterOfRotation: an index around which the image is rotated.
example: (CenterOfRotation 128 128 90)
By default the CenterOfRotation is set to the geometric center of the image.
Parameters:
AutomaticTransformInitialization: whether or not the initial translation between images should be estimated as the distance between their centers.
example: (AutomaticTransformInitialization "true")
By default "false" is assumed. So, no initial translation.

The transform parameters necessary for transformix, additionally defined by this class, are: *

Transform Parameters:
CenterOfRotation: stores the center of rotation as an index.
example: (CenterOfRotation 128 128 90)
depecrated! From elastix version 3.402 this is changed to CenterOfRotationPoint!
Transform Parameters:
CenterOfRotationPoint: stores the center of rotation, expressed in world coordinates.
example: (CenterOfRotationPoint 10.555 6.666 12.345)
Transform Parameters:
MatrixTranslation: the parameters as matrix and translation, so written in the same way as the parameters of the normal AffineTransform.
example: (MatrixTranslation 1 0 0 0 1 0 0 0 0.9 0.1 0.1 0.2)
This parameter is just for convenience, so that the user can compare the results between the AffineTransform and AffineDTITransform. It is not a mandatory parameter.
See also:
AffineDTI3DTransform

Definition at line 76 of file elxAffineDTITransform.h.


Member Typedef Documentation

template<class TElastix >
typedef AffineDTITransformType::Pointer elastix::AffineDTITransformElastix< TElastix >::AffineDTITransformPointer

Definition at line 134 of file elxAffineDTITransform.h.

template<class TElastix >
typedef AffineDTITransform< typename elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension > elastix::AffineDTITransformElastix< TElastix >::AffineDTITransformType

The ITK-class that provides most of the functionality, and that is set as the "CurrentTransform" in the CombinationTransform

Definition at line 97 of file elxAffineDTITransform.h.

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 148 of file elxAffineDTITransform.h.

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 141 of file elxAffineDTITransform.h.

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 140 of file elxAffineDTITransform.h.

template<class TElastix >
typedef SmartPointer<const Self> elastix::AffineDTITransformElastix< TElastix >::ConstPointer
template<class TElastix >
typedef Superclass2::CoordRepType elastix::AffineDTITransformElastix< TElastix >::CoordRepType

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 144 of file elxAffineDTITransform.h.

template<class TElastix >
typedef FixedImageType::DirectionType elastix::AffineDTITransformElastix< TElastix >::DirectionType

Definition at line 157 of file elxAffineDTITransform.h.

template<class TElastix >
typedef Superclass2::ElastixPointer elastix::AffineDTITransformElastix< TElastix >::ElastixPointer

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 139 of file elxAffineDTITransform.h.

template<class TElastix >
typedef Superclass2::ElastixType elastix::AffineDTITransformElastix< TElastix >::ElastixType

Typedef's inherited from TransformBase.

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 138 of file elxAffineDTITransform.h.

template<class TElastix >
typedef Superclass2::FixedImageType elastix::AffineDTITransformElastix< TElastix >::FixedImageType

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 145 of file elxAffineDTITransform.h.

template<class TElastix >
typedef FixedImageType::IndexType elastix::AffineDTITransformElastix< TElastix >::IndexType

Other typedef's.

Definition at line 151 of file elxAffineDTITransform.h.

template<class TElastix >
typedef IndexType::IndexValueType elastix::AffineDTITransformElastix< TElastix >::IndexValueType

Definition at line 152 of file elxAffineDTITransform.h.

template<class TElastix >
typedef Superclass1::InputPointType elastix::AffineDTITransformElastix< TElastix >::InputPointType

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 125 of file elxAffineDTITransform.h.

template<class TElastix >
typedef Superclass2::ITKBaseType elastix::AffineDTITransformElastix< TElastix >::ITKBaseType

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 147 of file elxAffineDTITransform.h.

template<class TElastix >
typedef Superclass1::JacobianType elastix::AffineDTITransformElastix< TElastix >::JacobianType

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 146 of file elxAffineDTITransform.h.

template<class TElastix >
typedef AffineDTITransformType::OffsetType elastix::AffineDTITransformElastix< TElastix >::OffsetType

Definition at line 135 of file elxAffineDTITransform.h.

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 126 of file elxAffineDTITransform.h.

template<class TElastix >
typedef Superclass1::ParametersType elastix::AffineDTITransformElastix< TElastix >::ParametersType

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 122 of file elxAffineDTITransform.h.

template<class TElastix >
typedef SmartPointer<Self> elastix::AffineDTITransformElastix< TElastix >::Pointer
template<class TElastix >
typedef FixedImageType::PointType elastix::AffineDTITransformElastix< TElastix >::PointType

Definition at line 154 of file elxAffineDTITransform.h.

template<class TElastix >
typedef FixedImageType::RegionType elastix::AffineDTITransformElastix< TElastix >::RegionType

Definition at line 156 of file elxAffineDTITransform.h.

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 143 of file elxAffineDTITransform.h.

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 142 of file elxAffineDTITransform.h.

template<class TElastix >
typedef Superclass1::ScalarType elastix::AffineDTITransformElastix< TElastix >::ScalarType

Typedefs inherited from the superclass. These are both in AffineDTI2D and AffineDTI3D.

Reimplemented from itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >.

Definition at line 121 of file elxAffineDTITransform.h.

template<class TElastix >
typedef Superclass2::ScalesType elastix::AffineDTITransformElastix< TElastix >::ScalesType

For scales setting in the optimizer

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 164 of file elxAffineDTITransform.h.

template<class TElastix >
typedef AffineDTITransformElastix elastix::AffineDTITransformElastix< TElastix >::Self

Standard ITK-stuff.

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 85 of file elxAffineDTITransform.h.

template<class TElastix >
typedef FixedImageType::SizeType elastix::AffineDTITransformElastix< TElastix >::SizeType

Definition at line 153 of file elxAffineDTITransform.h.

template<class TElastix >
typedef FixedImageType::SpacingType elastix::AffineDTITransformElastix< TElastix >::SpacingType

Definition at line 155 of file elxAffineDTITransform.h.

template<class TElastix >
typedef AdvancedCombinationTransform< typename elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension > elastix::AffineDTITransformElastix< TElastix >::Superclass1

Definition at line 89 of file elxAffineDTITransform.h.

template<class TElastix >
typedef elx::TransformBase< TElastix > elastix::AffineDTITransformElastix< TElastix >::Superclass2

Definition at line 91 of file elxAffineDTITransform.h.

template<class TElastix >
typedef TransformInitializerType::Pointer elastix::AffineDTITransformElastix< TElastix >::TransformInitializerPointer

Definition at line 161 of file elxAffineDTITransform.h.

template<class TElastix >
typedef CenteredTransformInitializer< AffineDTITransformType, FixedImageType, MovingImageType> elastix::AffineDTITransformElastix< TElastix >::TransformInitializerType

Definition at line 160 of file elxAffineDTITransform.h.


Constructor & Destructor Documentation

template<class TElastix >
elastix::AffineDTITransformElastix< TElastix >::AffineDTITransformElastix ( ) [protected]

The constructor.

template<class TElastix >
virtual elastix::AffineDTITransformElastix< TElastix >::~AffineDTITransformElastix ( ) [inline, protected, virtual]

The destructor.

Definition at line 214 of file elxAffineDTITransform.h.

template<class TElastix >
elastix::AffineDTITransformElastix< TElastix >::AffineDTITransformElastix ( const Self ) [private]

The private constructor.


Member Function Documentation

template<class TElastix >
virtual void elastix::AffineDTITransformElastix< TElastix >::BeforeRegistration ( void  ) [virtual]

Execute stuff before the actual registration:

  • Call InitializeTransform
  • Set the scales.

Reimplemented from elastix::BaseComponent.

template<class TElastix >
elastix::AffineDTITransformElastix< TElastix >::elxClassNameMacro ( "AffineDTITransform"  )

Name of this class. Use this name in the parameter file to select this specific transform.
example: (Transform "AffineDTITransform")

template<class TElastix >
virtual const char* elastix::AffineDTITransformElastix< TElastix >::GetClassName ( ) const [virtual]

Run-time type information (and related methods).

Reimplemented from elastix::TransformBase< TElastix >.

template<class TElastix >
virtual void elastix::AffineDTITransformElastix< TElastix >::InitializeTransform ( void  ) [virtual]

Initialize Transform.

  • Set all parameters to zero.
  • Set center of rotation: automatically initialized to the geometric center of the image, or assigned a user entered voxel index, given by the parameter (CenterOfRotation <index-x> <index-y> ...); If an initial transform is present and HowToCombineTransforms is set to "Compose", the initial transform is taken into account while setting the center of rotation.
  • Set initial translation: the initial translation between fixed and moving image is guessed, if the user has set (AutomaticTransformInitialization "true").

It is not yet possible to enter an initial rotation angle.

template<class TElastix >
elastix::AffineDTITransformElastix< TElastix >::itkStaticConstMacro ( SpaceDimension  ,
unsigned  int,
Superclass2::FixedImageDimension   
)

Dimension of the fixed image.

template<class TElastix >
static Pointer elastix::AffineDTITransformElastix< TElastix >::New ( ) [static]
template<class TElastix >
void elastix::AffineDTITransformElastix< TElastix >::operator= ( const Self ) [private]

The private copy constructor.

template<class TElastix >
virtual bool elastix::AffineDTITransformElastix< TElastix >::ReadCenterOfRotationPoint ( InputPointType rotationPoint) const [protected, virtual]

Try to read the CenterOfRotationPoint from the transform parameter file The CenterOfRotationPoint is already in world coordinates.

template<class TElastix >
virtual void elastix::AffineDTITransformElastix< TElastix >::ReadFromFile ( void  ) [virtual]

Function to read transform-parameters from a file.

It reads the center of rotation and calls the superclass' implementation.

Reimplemented from elastix::TransformBase< TElastix >.

template<class TElastix >
virtual void elastix::AffineDTITransformElastix< TElastix >::SetScales ( void  ) [virtual]

Set the scales

  • If AutomaticScalesEstimation is "true" estimate scales
  • If scales are provided by the user use those,
  • Otherwise use some default value This function is called by BeforeRegistration, after the InitializeTransform function is called
template<class TElastix >
virtual void elastix::AffineDTITransformElastix< TElastix >::WriteToFile ( const ParametersType param) const [virtual]

Function to write transform-parameters to a file. It writes the center of rotation to file and calls the superclass' implementation.

Reimplemented from elastix::TransformBase< TElastix >.


Field Documentation

template<class TElastix >
AffineDTITransformPointer elastix::AffineDTITransformElastix< TElastix >::m_AffineDTITransform [private]

Definition at line 227 of file elxAffineDTITransform.h.



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