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elastix::ElastixBase Class Referenceabstract

#include <elxElastixBase.h>

Detailed Description

This class creates an interface for elastix.

The ElastixBase class creates an interface for elastix. This is specified in ElastixTemplate, where all functions are defined. Functionality that does not depend on the pixel type and the dimension of the images to be registered, is defined in this class.

The parameters used by this class are:

Parameters:

RandomSeed: Sets a global seed for the random generator.
example: (RandomSeed 121212)
It must be a positive integer number. Default: 121212.

DefaultOutputPrecision: Set the default precision of floating values in the output. Most importantly, it affects the output precision of the parameters in the transform parameter file.
example: (DefaultOutputPrecision 6)
Default value: 6.

The command line arguments used by this class are:

Command line arguments:

-f: mandatory argument for elastix with the file name of the fixed image.
example: -f fixedImage.mhd

-m: mandatory argument for elastix with the file name of the moving image.
example: -m movingImage.mhd

-out: mandatory argument for both elastix and transformix with the name of the directory that is going to contain everything that elastix or tranformix returns as output.
example: -out outputdirectory

-p: mandatory argument for elastix with the name of the parameter file.
example: -p parameters.txt
Multiple parameter files are allowed. It means that multiple registrations are runned in sequence, with the output of some registration as input to the next.

-fMask: Optional argument for elastix with the file name of a mask for the fixed image. The mask image should contain of zeros and ones, zeros indicating pixels that are not used for the registration.
example: -fMask fixedmask.mhd

-mMask: Optional argument for elastix with the file name of a mask for the moving image. The mask image should contain of zeros and ones, zeros indicating pixels that are not used for the registration.
example: -mMask movingmask.mhd

-tp: mandatory argument for transformix with the name of the transform parameter file.
example: -tp TransformParameters.txt
In one such a transform parameter file a reference can be used to another transform parameter file, which is then used as an initial transform.

-priority: optional argument for both elastix and transformix to specify the priority setting of this process. Choose one from {belownormal, high}.
example: -priority high
This argument is only valid for running under Windows. For Linux, run elastix with "nice".

-threads: optional argument for both elastix and transformix to specify the maximum number of threads used by this process. Default: no maximum.
example: -threads 2

-in: optional argument for transformix with the file name of an input image.
example: -in inputImage.mhd
If this option is skipped, a deformation field of the transform will be generated.

Definition at line 143 of file elxElastixBase.h.

Inheritance diagram for elastix::ElastixBase:
Inheritance graph
[legend]

Data Structures

class  MultipleDataObjectFiller
 
class  MultipleImageLoader
 

Public Types

typedef ComponentDatabaseType::Pointer ComponentDatabasePointer
 
typedef ComponentDatabase ComponentDatabaseType
 
typedef ConfigurationType::Pointer ConfigurationPointer
 
typedef Configuration ConfigurationType
 
typedef DataObjectContainerType::Pointer DataObjectContainerPointer
 
typedef itk::VectorContainer< unsigned int, DataObjectPointerDataObjectContainerType
 
typedef DataObjectType::Pointer DataObjectPointer
 
typedef itk::DataObject DataObjectType
 
typedef ComponentDatabaseType::IndexType DBIndexType
 
typedef FileNameContainerType::Pointer FileNameContainerPointer
 
typedef itk::VectorContainer< unsigned int, std::string > FileNameContainerType
 
typedef std::vector< doubleFlatDirectionCosinesType
 
typedef itk::Object ITKBaseType
 
typedef ObjectContainerType::Pointer ObjectContainerPointer
 
typedef itk::VectorContainer< unsigned int, ObjectPointerObjectContainerType
 
typedef ObjectType::Pointer ObjectPointer
 
typedef itk::Object ObjectType
 
typedef itk::ParameterMapInterface::ParameterMapType ParameterMapType
 
typedef ElastixBase Self
 
typedef BaseComponent Superclass
 

Public Member Functions

virtual void AfterRegistrationBase (void)
 
virtual int ApplyTransform (void)=0
 
virtual int BeforeAllBase (void)
 
virtual int BeforeAllTransformixBase (void)
 
virtual void BeforeRegistrationBase (void)
 
virtual void CreateTransformParametersMap (void)=0
 
 elxGetNumberOfMacro (Registration)
 
 elxGetNumberOfMacro (FixedImagePyramid)
 
 elxGetNumberOfMacro (MovingImagePyramid)
 
 elxGetNumberOfMacro (Interpolator)
 
 elxGetNumberOfMacro (ImageSampler)
 
 elxGetNumberOfMacro (Metric)
 
 elxGetNumberOfMacro (Optimizer)
 
 elxGetNumberOfMacro (Resampler)
 
 elxGetNumberOfMacro (ResampleInterpolator)
 
 elxGetNumberOfMacro (Transform)
 
 elxGetNumberOfMacro (FixedImage)
 
 elxGetNumberOfMacro (MovingImage)
 
 elxGetNumberOfMacro (FixedImageFileName)
 
 elxGetNumberOfMacro (MovingImageFileName)
 
 elxGetNumberOfMacro (FixedMask)
 
 elxGetNumberOfMacro (MovingMask)
 
 elxGetNumberOfMacro (FixedMaskFileName)
 
 elxGetNumberOfMacro (MovingMaskFileName)
 
 elxGetNumberOfMacro (ResultImage)
 
 elxGetObjectMacro (Configuration, ConfigurationType)
 
 elxGetObjectMacro (ComponentDatabase, ComponentDatabaseType)
 
 elxGetObjectMacro (RegistrationContainer, ObjectContainerType)
 
 elxGetObjectMacro (FixedImagePyramidContainer, ObjectContainerType)
 
 elxGetObjectMacro (MovingImagePyramidContainer, ObjectContainerType)
 
 elxGetObjectMacro (InterpolatorContainer, ObjectContainerType)
 
 elxGetObjectMacro (ImageSamplerContainer, ObjectContainerType)
 
 elxGetObjectMacro (MetricContainer, ObjectContainerType)
 
 elxGetObjectMacro (OptimizerContainer, ObjectContainerType)
 
 elxGetObjectMacro (ResamplerContainer, ObjectContainerType)
 
 elxGetObjectMacro (ResampleInterpolatorContainer, ObjectContainerType)
 
 elxGetObjectMacro (TransformContainer, ObjectContainerType)
 
 elxGetObjectMacro (FixedImageContainer, DataObjectContainerType)
 
 elxGetObjectMacro (MovingImageContainer, DataObjectContainerType)
 
 elxGetObjectMacro (FixedMaskContainer, DataObjectContainerType)
 
 elxGetObjectMacro (MovingMaskContainer, DataObjectContainerType)
 
 elxGetObjectMacro (ResultImageContainer, DataObjectContainerType)
 
 elxGetObjectMacro (FixedImageFileNameContainer, FileNameContainerType)
 
 elxGetObjectMacro (MovingImageFileNameContainer, FileNameContainerType)
 
 elxGetObjectMacro (FixedMaskFileNameContainer, FileNameContainerType)
 
 elxGetObjectMacro (MovingMaskFileNameContainer, FileNameContainerType)
 
 elxGetObjectMacro (InitialTransform, ObjectType)
 
 elxGetObjectMacro (FinalTransform, ObjectType)
 
 elxSetObjectMacro (Configuration, ConfigurationType)
 
 elxSetObjectMacro (ComponentDatabase, ComponentDatabaseType)
 
 elxSetObjectMacro (RegistrationContainer, ObjectContainerType)
 
 elxSetObjectMacro (FixedImagePyramidContainer, ObjectContainerType)
 
 elxSetObjectMacro (MovingImagePyramidContainer, ObjectContainerType)
 
 elxSetObjectMacro (InterpolatorContainer, ObjectContainerType)
 
 elxSetObjectMacro (ImageSamplerContainer, ObjectContainerType)
 
 elxSetObjectMacro (MetricContainer, ObjectContainerType)
 
 elxSetObjectMacro (OptimizerContainer, ObjectContainerType)
 
 elxSetObjectMacro (ResamplerContainer, ObjectContainerType)
 
 elxSetObjectMacro (ResampleInterpolatorContainer, ObjectContainerType)
 
 elxSetObjectMacro (TransformContainer, ObjectContainerType)
 
 elxSetObjectMacro (FixedImageContainer, DataObjectContainerType)
 
 elxSetObjectMacro (MovingImageContainer, DataObjectContainerType)
 
 elxSetObjectMacro (FixedMaskContainer, DataObjectContainerType)
 
 elxSetObjectMacro (MovingMaskContainer, DataObjectContainerType)
 
 elxSetObjectMacro (ResultImageContainer, DataObjectContainerType)
 
 elxSetObjectMacro (FixedImageFileNameContainer, FileNameContainerType)
 
 elxSetObjectMacro (MovingImageFileNameContainer, FileNameContainerType)
 
 elxSetObjectMacro (FixedMaskFileNameContainer, FileNameContainerType)
 
 elxSetObjectMacro (MovingMaskFileNameContainer, FileNameContainerType)
 
 elxSetObjectMacro (InitialTransform, ObjectType)
 
 elxSetObjectMacro (FinalTransform, ObjectType)
 
virtual ITKBaseTypeGetAsITKBaseType (void)
 
virtual DBIndexType GetDBIndex (void)
 
virtual int GetDefaultOutputPrecision (void) const
 
virtual const FlatDirectionCosinesTypeGetOriginalFixedImageDirectionFlat (void) const
 
virtual ParameterMapType GetTransformParametersMap (void) const =0
 
virtual bool GetUseDirectionCosines (void) const
 
virtual int Run (void)=0
 
virtual void SetConfigurations (std::vector< ConfigurationPointer > &configurations)=0
 
virtual void SetDBIndex (DBIndexType _arg)
 
virtual void SetOriginalFixedImageDirectionFlat (const FlatDirectionCosinesType &arg)
 
- Public Member Functions inherited from elastix::BaseComponent
virtual void AfterEachIteration (void)
 
virtual void AfterEachIterationBase (void)
 
virtual void AfterEachResolution (void)
 
virtual void AfterEachResolutionBase (void)
 
virtual void AfterRegistration (void)
 
virtual int BeforeAll (void)
 
virtual void BeforeEachResolution (void)
 
virtual void BeforeEachResolutionBase (void)
 
virtual void BeforeRegistration (void)
 
std::string ConvertSecondsToDHMS (const double totalSeconds, const unsigned int precision) const
 
virtual const char * elxGetClassName (void) const
 
virtual const char * GetComponentLabel (void) const
 
virtual void SetComponentLabel (const char *label, unsigned int idx)
 

Protected Member Functions

 ElastixBase ()
 
virtual ~ElastixBase ()
 
- Protected Member Functions inherited from elastix::BaseComponent
 BaseComponent ()
 
virtual ~BaseComponent ()
 

Protected Attributes

ComponentDatabasePointer m_ComponentDatabase
 
ConfigurationPointer m_Configuration
 
DBIndexType m_DBIndex
 
FlatDirectionCosinesType m_OriginalFixedImageDirection
 

Private Member Functions

 ElastixBase (const Self &)
 
FileNameContainerPointer GenerateFileNameContainer (const std::string &optionkey, int &errorcode, bool printerrors, bool printinfo) const
 
void operator= (const Self &)
 

Private Attributes

int m_DefaultOutputPrecision
 
ObjectPointer m_FinalTransform
 
DataObjectContainerPointer m_FixedImageContainer
 
FileNameContainerPointer m_FixedImageFileNameContainer
 
ObjectContainerPointer m_FixedImagePyramidContainer
 
DataObjectContainerPointer m_FixedMaskContainer
 
FileNameContainerPointer m_FixedMaskFileNameContainer
 
ObjectContainerPointer m_ImageSamplerContainer
 
ObjectPointer m_InitialTransform
 
ObjectContainerPointer m_InterpolatorContainer
 
xl::xoutrow_type m_IterationInfo
 
ObjectContainerPointer m_MetricContainer
 
DataObjectContainerPointer m_MovingImageContainer
 
FileNameContainerPointer m_MovingImageFileNameContainer
 
ObjectContainerPointer m_MovingImagePyramidContainer
 
DataObjectContainerPointer m_MovingMaskContainer
 
FileNameContainerPointer m_MovingMaskFileNameContainer
 
ObjectContainerPointer m_OptimizerContainer
 
ObjectContainerPointer m_RegistrationContainer
 
ObjectContainerPointer m_ResampleInterpolatorContainer
 
ObjectContainerPointer m_ResamplerContainer
 
DataObjectContainerPointer m_ResultImageContainer
 
ObjectContainerPointer m_TransformContainer
 
bool m_UseDirectionCosines
 

Member Typedef Documentation

Definition at line 170 of file elxElastixBase.h.

Other typedef's.

Definition at line 169 of file elxElastixBase.h.

Definition at line 153 of file elxElastixBase.h.

Typedefs used in this class.

Definition at line 152 of file elxElastixBase.h.

typedef DataObjectContainerType::Pointer elastix::ElastixBase::DataObjectContainerPointer

Definition at line 163 of file elxElastixBase.h.

typedef itk::VectorContainer< unsigned int, DataObjectPointer > elastix::ElastixBase::DataObjectContainerType

Definition at line 162 of file elxElastixBase.h.

typedef DataObjectType::Pointer elastix::ElastixBase::DataObjectPointer

Definition at line 157 of file elxElastixBase.h.

typedef itk::DataObject elastix::ElastixBase::DataObjectType

Definition at line 156 of file elxElastixBase.h.

Definition at line 171 of file elxElastixBase.h.

typedef FileNameContainerType::Pointer elastix::ElastixBase::FileNameContainerPointer

Definition at line 166 of file elxElastixBase.h.

typedef itk::VectorContainer< unsigned int, std::string > elastix::ElastixBase::FileNameContainerType

Definition at line 165 of file elxElastixBase.h.

Definition at line 172 of file elxElastixBase.h.

typedef itk::Object elastix::ElastixBase::ITKBaseType

The itk class that ElastixTemplate is expected to inherit from Of course ElastixTemplate also inherits from this class (ElastixBase).

Definition at line 180 of file elxElastixBase.h.

typedef ObjectContainerType::Pointer elastix::ElastixBase::ObjectContainerPointer

Definition at line 160 of file elxElastixBase.h.

typedef itk::VectorContainer< unsigned int, ObjectPointer > elastix::ElastixBase::ObjectContainerType

Definition at line 159 of file elxElastixBase.h.

typedef ObjectType::Pointer elastix::ElastixBase::ObjectPointer

Definition at line 155 of file elxElastixBase.h.

typedef itk::Object elastix::ElastixBase::ObjectType

Definition at line 154 of file elxElastixBase.h.

Typedef that is used in the elastix dll version.

Definition at line 175 of file elxElastixBase.h.

Standard typedefs etc.

Definition at line 148 of file elxElastixBase.h.

Definition at line 149 of file elxElastixBase.h.

Constructor & Destructor Documentation

elastix::ElastixBase::ElastixBase ( )
protected
virtual elastix::ElastixBase::~ElastixBase ( )
inlineprotectedvirtual

Definition at line 365 of file elxElastixBase.h.

elastix::ElastixBase::ElastixBase ( const Self )
private

Member Function Documentation

virtual void elastix::ElastixBase::AfterRegistrationBase ( void  )
virtual

Reimplemented from elastix::BaseComponent.

virtual int elastix::ElastixBase::ApplyTransform ( void  )
pure virtual

Empty ApplyTransform()-function to be overridden.

Implemented in elastix::ElastixTemplate< TFixedImage, TMovingImage >.

virtual int elastix::ElastixBase::BeforeAllBase ( void  )
virtual

Function that is called at the very beginning of ElastixTemplate::Run(). It checks the command line input arguments.

Reimplemented from elastix::BaseComponent.

virtual int elastix::ElastixBase::BeforeAllTransformixBase ( void  )
virtual

Function that is called at the very beginning of ElastixTemplate::ApplyTransform(). It checks the command line input arguments.

virtual void elastix::ElastixBase::BeforeRegistrationBase ( void  )
virtual

Functions called before and after registration. They install/uninstall the xout["iteration"] field.

Reimplemented from elastix::BaseComponent.

virtual void elastix::ElastixBase::CreateTransformParametersMap ( void  )
pure virtual

Creates transformation parameters map.

Implemented in elastix::ElastixTemplate< TFixedImage, TMovingImage >.

elastix::ElastixBase::elxGetNumberOfMacro ( Registration  )

Define some convenience functions: GetNumberOfMetrics() for example.

elastix::ElastixBase::elxGetNumberOfMacro ( FixedImagePyramid  )
elastix::ElastixBase::elxGetNumberOfMacro ( MovingImagePyramid  )
elastix::ElastixBase::elxGetNumberOfMacro ( Interpolator  )
elastix::ElastixBase::elxGetNumberOfMacro ( ImageSampler  )
elastix::ElastixBase::elxGetNumberOfMacro ( Metric  )
elastix::ElastixBase::elxGetNumberOfMacro ( Optimizer  )
elastix::ElastixBase::elxGetNumberOfMacro ( Resampler  )
elastix::ElastixBase::elxGetNumberOfMacro ( ResampleInterpolator  )
elastix::ElastixBase::elxGetNumberOfMacro ( Transform  )
elastix::ElastixBase::elxGetNumberOfMacro ( FixedImage  )
elastix::ElastixBase::elxGetNumberOfMacro ( MovingImage  )
elastix::ElastixBase::elxGetNumberOfMacro ( FixedImageFileName  )
elastix::ElastixBase::elxGetNumberOfMacro ( MovingImageFileName  )
elastix::ElastixBase::elxGetNumberOfMacro ( FixedMask  )
elastix::ElastixBase::elxGetNumberOfMacro ( MovingMask  )
elastix::ElastixBase::elxGetNumberOfMacro ( FixedMaskFileName  )
elastix::ElastixBase::elxGetNumberOfMacro ( MovingMaskFileName  )
elastix::ElastixBase::elxGetNumberOfMacro ( ResultImage  )
elastix::ElastixBase::elxGetObjectMacro ( Configuration  ,
ConfigurationType   
)

Set/Get the Configuration Object.

elastix::ElastixBase::elxGetObjectMacro ( ComponentDatabase  ,
ComponentDatabaseType   
)

Functions to get/set the ComponentDatabase The component database contains pointers to functions that create components.

elastix::ElastixBase::elxGetObjectMacro ( RegistrationContainer  ,
ObjectContainerType   
)

Get the component containers. The component containers store components, such as the metric, in the form of an itk::Object::Pointer.

elastix::ElastixBase::elxGetObjectMacro ( FixedImagePyramidContainer  ,
ObjectContainerType   
)
elastix::ElastixBase::elxGetObjectMacro ( MovingImagePyramidContainer  ,
ObjectContainerType   
)
elastix::ElastixBase::elxGetObjectMacro ( InterpolatorContainer  ,
ObjectContainerType   
)
elastix::ElastixBase::elxGetObjectMacro ( ImageSamplerContainer  ,
ObjectContainerType   
)
elastix::ElastixBase::elxGetObjectMacro ( MetricContainer  ,
ObjectContainerType   
)
elastix::ElastixBase::elxGetObjectMacro ( OptimizerContainer  ,
ObjectContainerType   
)
elastix::ElastixBase::elxGetObjectMacro ( ResamplerContainer  ,
ObjectContainerType   
)
elastix::ElastixBase::elxGetObjectMacro ( ResampleInterpolatorContainer  ,
ObjectContainerType   
)
elastix::ElastixBase::elxGetObjectMacro ( TransformContainer  ,
ObjectContainerType   
)
elastix::ElastixBase::elxGetObjectMacro ( FixedImageContainer  ,
DataObjectContainerType   
)

Set/Get the fixed/moving image containers.

elastix::ElastixBase::elxGetObjectMacro ( MovingImageContainer  ,
DataObjectContainerType   
)
elastix::ElastixBase::elxGetObjectMacro ( FixedMaskContainer  ,
DataObjectContainerType   
)

Set/Get the fixed/moving mask containers.

elastix::ElastixBase::elxGetObjectMacro ( MovingMaskContainer  ,
DataObjectContainerType   
)
elastix::ElastixBase::elxGetObjectMacro ( ResultImageContainer  ,
DataObjectContainerType   
)

Set/Get the result image container.

elastix::ElastixBase::elxGetObjectMacro ( FixedImageFileNameContainer  ,
FileNameContainerType   
)

Set/Get The Image FileName containers. Normally, these are filled in the BeforeAllBase function.

elastix::ElastixBase::elxGetObjectMacro ( MovingImageFileNameContainer  ,
FileNameContainerType   
)
elastix::ElastixBase::elxGetObjectMacro ( FixedMaskFileNameContainer  ,
FileNameContainerType   
)

Set/Get The Mask FileName containers. Normally, these are filled in the BeforeAllBase function.

elastix::ElastixBase::elxGetObjectMacro ( MovingMaskFileNameContainer  ,
FileNameContainerType   
)
elastix::ElastixBase::elxGetObjectMacro ( InitialTransform  ,
ObjectType   
)
elastix::ElastixBase::elxGetObjectMacro ( FinalTransform  ,
ObjectType   
)
elastix::ElastixBase::elxSetObjectMacro ( Configuration  ,
ConfigurationType   
)
elastix::ElastixBase::elxSetObjectMacro ( ComponentDatabase  ,
ComponentDatabaseType   
)
elastix::ElastixBase::elxSetObjectMacro ( RegistrationContainer  ,
ObjectContainerType   
)

Set the component containers. The component containers store components, such as the metric, in the form of an itk::Object::Pointer.

elastix::ElastixBase::elxSetObjectMacro ( FixedImagePyramidContainer  ,
ObjectContainerType   
)
elastix::ElastixBase::elxSetObjectMacro ( MovingImagePyramidContainer  ,
ObjectContainerType   
)
elastix::ElastixBase::elxSetObjectMacro ( InterpolatorContainer  ,
ObjectContainerType   
)
elastix::ElastixBase::elxSetObjectMacro ( ImageSamplerContainer  ,
ObjectContainerType   
)
elastix::ElastixBase::elxSetObjectMacro ( MetricContainer  ,
ObjectContainerType   
)
elastix::ElastixBase::elxSetObjectMacro ( OptimizerContainer  ,
ObjectContainerType   
)
elastix::ElastixBase::elxSetObjectMacro ( ResamplerContainer  ,
ObjectContainerType   
)
elastix::ElastixBase::elxSetObjectMacro ( ResampleInterpolatorContainer  ,
ObjectContainerType   
)
elastix::ElastixBase::elxSetObjectMacro ( TransformContainer  ,
ObjectContainerType   
)
elastix::ElastixBase::elxSetObjectMacro ( FixedImageContainer  ,
DataObjectContainerType   
)
elastix::ElastixBase::elxSetObjectMacro ( MovingImageContainer  ,
DataObjectContainerType   
)
elastix::ElastixBase::elxSetObjectMacro ( FixedMaskContainer  ,
DataObjectContainerType   
)
elastix::ElastixBase::elxSetObjectMacro ( MovingMaskContainer  ,
DataObjectContainerType   
)
elastix::ElastixBase::elxSetObjectMacro ( ResultImageContainer  ,
DataObjectContainerType   
)
elastix::ElastixBase::elxSetObjectMacro ( FixedImageFileNameContainer  ,
FileNameContainerType   
)
elastix::ElastixBase::elxSetObjectMacro ( MovingImageFileNameContainer  ,
FileNameContainerType   
)
elastix::ElastixBase::elxSetObjectMacro ( FixedMaskFileNameContainer  ,
FileNameContainerType   
)
elastix::ElastixBase::elxSetObjectMacro ( MovingMaskFileNameContainer  ,
FileNameContainerType   
)
elastix::ElastixBase::elxSetObjectMacro ( InitialTransform  ,
ObjectType   
)

Set/Get the initial transform The type is ObjectType, but the pointer should actually point to an itk::Transform type (or inherited from that one).

elastix::ElastixBase::elxSetObjectMacro ( FinalTransform  ,
ObjectType   
)

Set/Get the final transform The type is ObjectType, but the pointer should actually point to an itk::Transform type (or inherited from that one). You can use this to set it as an initial transform in another ElastixBase instantiation.

FileNameContainerPointer elastix::ElastixBase::GenerateFileNameContainer ( const std::string &  optionkey,
int errorcode,
bool  printerrors,
bool  printinfo 
) const
private

Read a series of command line options that satisfy the following syntax: {-f,-f0} <filename0> [-f1 <filename1> [ -f2 <filename2> ... ] ]

This function is used by BeforeAllBase, and is not meant be used at other locations. The errorcode remains the input value if no errors occur. It is set to errorcode | 1 if the option was not given.

virtual ITKBaseType* elastix::ElastixBase::GetAsITKBaseType ( void  )
inlinevirtual

Cast to ITKBaseType.

Definition at line 183 of file elxElastixBase.h.

virtual DBIndexType elastix::ElastixBase::GetDBIndex ( void  )
inlinevirtual

Definition at line 196 of file elxElastixBase.h.

virtual int elastix::ElastixBase::GetDefaultOutputPrecision ( void  ) const
inlinevirtual

Get the default precision of xout. (The value assumed when no DefaultOutputPrecision is given in the parameter file.

Definition at line 335 of file elxElastixBase.h.

virtual const FlatDirectionCosinesType& elastix::ElastixBase::GetOriginalFixedImageDirectionFlat ( void  ) const
virtual
virtual ParameterMapType elastix::ElastixBase::GetTransformParametersMap ( void  ) const
pure virtual

Gets transformation parameters map.

Implemented in elastix::ElastixTemplate< TFixedImage, TMovingImage >.

virtual bool elastix::ElastixBase::GetUseDirectionCosines ( void  ) const
virtual

Get whether direction cosines should be taken into account (true) or ignored (false). This depends on the UseDirectionCosines parameter.

void elastix::ElastixBase::operator= ( const Self )
private
virtual int elastix::ElastixBase::Run ( void  )
pure virtual

Empty Run()-function to be overridden.

Implemented in elastix::ElastixTemplate< TFixedImage, TMovingImage >.

virtual void elastix::ElastixBase::SetConfigurations ( std::vector< ConfigurationPointer > &  configurations)
pure virtual

Set configuration vector. Library only.

Implemented in elastix::ElastixTemplate< TFixedImage, TMovingImage >.

virtual void elastix::ElastixBase::SetDBIndex ( DBIndexType  _arg)
virtual

Set the database index of the instantiated elastix object.

virtual void elastix::ElastixBase::SetOriginalFixedImageDirectionFlat ( const FlatDirectionCosinesType arg)
virtual

Set/Get the original fixed image direction as a flat array (d11 d21 d31 d21 d22 etc )

Field Documentation

ComponentDatabasePointer elastix::ElastixBase::m_ComponentDatabase
protected

Definition at line 369 of file elxElastixBase.h.

ConfigurationPointer elastix::ElastixBase::m_Configuration
protected

Definition at line 367 of file elxElastixBase.h.

DBIndexType elastix::ElastixBase::m_DBIndex
protected

Definition at line 368 of file elxElastixBase.h.

int elastix::ElastixBase::m_DefaultOutputPrecision
private

Definition at line 503 of file elxElastixBase.h.

ObjectPointer elastix::ElastixBase::m_FinalTransform
private

Definition at line 536 of file elxElastixBase.h.

DataObjectContainerPointer elastix::ElastixBase::m_FixedImageContainer
private

The Image and Mask containers. These are stored as pointers to itk::DataObject.

Definition at line 520 of file elxElastixBase.h.

FileNameContainerPointer elastix::ElastixBase::m_FixedImageFileNameContainer
private

The image and mask FileNameContainers.

Definition at line 529 of file elxElastixBase.h.

ObjectContainerPointer elastix::ElastixBase::m_FixedImagePyramidContainer
private

The component containers. These containers contain SmartPointer's to itk::Object.

Definition at line 508 of file elxElastixBase.h.

DataObjectContainerPointer elastix::ElastixBase::m_FixedMaskContainer
private

Definition at line 522 of file elxElastixBase.h.

FileNameContainerPointer elastix::ElastixBase::m_FixedMaskFileNameContainer
private

Definition at line 531 of file elxElastixBase.h.

ObjectContainerPointer elastix::ElastixBase::m_ImageSamplerContainer
private

Definition at line 511 of file elxElastixBase.h.

ObjectPointer elastix::ElastixBase::m_InitialTransform
private

The initial and final transform.

Definition at line 535 of file elxElastixBase.h.

ObjectContainerPointer elastix::ElastixBase::m_InterpolatorContainer
private

Definition at line 510 of file elxElastixBase.h.

xl::xoutrow_type elastix::ElastixBase::m_IterationInfo
private

Definition at line 501 of file elxElastixBase.h.

ObjectContainerPointer elastix::ElastixBase::m_MetricContainer
private

Definition at line 512 of file elxElastixBase.h.

DataObjectContainerPointer elastix::ElastixBase::m_MovingImageContainer
private

Definition at line 521 of file elxElastixBase.h.

FileNameContainerPointer elastix::ElastixBase::m_MovingImageFileNameContainer
private

Definition at line 530 of file elxElastixBase.h.

ObjectContainerPointer elastix::ElastixBase::m_MovingImagePyramidContainer
private

Definition at line 509 of file elxElastixBase.h.

DataObjectContainerPointer elastix::ElastixBase::m_MovingMaskContainer
private

Definition at line 523 of file elxElastixBase.h.

FileNameContainerPointer elastix::ElastixBase::m_MovingMaskFileNameContainer
private

Definition at line 532 of file elxElastixBase.h.

ObjectContainerPointer elastix::ElastixBase::m_OptimizerContainer
private

Definition at line 513 of file elxElastixBase.h.

FlatDirectionCosinesType elastix::ElastixBase::m_OriginalFixedImageDirection
protected

Definition at line 371 of file elxElastixBase.h.

ObjectContainerPointer elastix::ElastixBase::m_RegistrationContainer
private

Definition at line 514 of file elxElastixBase.h.

ObjectContainerPointer elastix::ElastixBase::m_ResampleInterpolatorContainer
private

Definition at line 516 of file elxElastixBase.h.

ObjectContainerPointer elastix::ElastixBase::m_ResamplerContainer
private

Definition at line 515 of file elxElastixBase.h.

DataObjectContainerPointer elastix::ElastixBase::m_ResultImageContainer
private

The result image container. These are stored as pointers to itk::DataObject.

Definition at line 526 of file elxElastixBase.h.

ObjectContainerPointer elastix::ElastixBase::m_TransformContainer
private

Definition at line 517 of file elxElastixBase.h.

bool elastix::ElastixBase::m_UseDirectionCosines
private

Use or ignore direction cosines.

Definition at line 539 of file elxElastixBase.h.



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