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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  MultipleImageLoader
 

Public Types

using ComponentDatabasePointer = ComponentDatabase::Pointer
 
using ConfigurationPointer = Configuration::Pointer
 
using CoordRepType = double
 
using DataObjectContainerPointer = DataObjectContainerType::Pointer
 
using DataObjectContainerType = itk::VectorContainer< unsigned int, DataObjectPointer >
 
using DataObjectPointer = itk::DataObject::Pointer
 
using DBIndexType = ComponentDatabase::IndexType
 
using FileNameContainerPointer = FileNameContainerType::Pointer
 
using FileNameContainerType = itk::VectorContainer< unsigned int, std::string >
 
using FlatDirectionCosinesType = std::vector< double >
 
using ObjectContainerPointer = ObjectContainerType::Pointer
 
using ObjectContainerType = itk::VectorContainer< unsigned int, ObjectPointer >
 
using ObjectPointer = itk::Object::Pointer
 
using ParameterMapType = itk::ParameterMapInterface::ParameterMapType
 
using ResultDeformationFieldType = itk::DataObject
 
using ResultImageType = itk::DataObject
 
using Self = ElastixBase
 
using Superclass = BaseComponent
 

Public Member Functions

void AddTargetCellToIterationInfo (const char *const name)
 
virtual int ApplyTransform (bool doReadTransform)=0
 
int BeforeAllBase () override
 
int BeforeAllTransformixBase ()
 
void BeforeRegistrationBase () override
 
virtual void CreateTransformParametersMap ()=0
 
 elxGetNumberOfMacro (FixedImage)
 
 elxGetNumberOfMacro (FixedImageFileName)
 
 elxGetNumberOfMacro (FixedImagePyramid)
 
 elxGetNumberOfMacro (FixedMask)
 
 elxGetNumberOfMacro (FixedMaskFileName)
 
 elxGetNumberOfMacro (ImageSampler)
 
 elxGetNumberOfMacro (Interpolator)
 
 elxGetNumberOfMacro (Metric)
 
 elxGetNumberOfMacro (MovingImage)
 
 elxGetNumberOfMacro (MovingImageFileName)
 
 elxGetNumberOfMacro (MovingImagePyramid)
 
 elxGetNumberOfMacro (MovingMask)
 
 elxGetNumberOfMacro (MovingMaskFileName)
 
 elxGetNumberOfMacro (Optimizer)
 
 elxGetNumberOfMacro (Registration)
 
 elxGetNumberOfMacro (ResampleInterpolator)
 
 elxGetNumberOfMacro (Resampler)
 
 elxGetNumberOfMacro (ResultDeformationField)
 
 elxGetNumberOfMacro (ResultImage)
 
 elxGetNumberOfMacro (Transform)
 
 elxGetObjectMacro (Configuration, Configuration)
 
 elxGetObjectMacro (FinalTransform, itk::Object)
 
 elxGetObjectMacro (FixedImageContainer, DataObjectContainerType)
 
 elxGetObjectMacro (FixedImageFileNameContainer, FileNameContainerType)
 
 elxGetObjectMacro (FixedImagePyramidContainer, ObjectContainerType)
 
 elxGetObjectMacro (FixedMaskContainer, DataObjectContainerType)
 
 elxGetObjectMacro (FixedMaskFileNameContainer, FileNameContainerType)
 
 elxGetObjectMacro (ImageSamplerContainer, ObjectContainerType)
 
 elxGetObjectMacro (InitialTransform, itk::Object)
 
 elxGetObjectMacro (InterpolatorContainer, ObjectContainerType)
 
 elxGetObjectMacro (MetricContainer, ObjectContainerType)
 
 elxGetObjectMacro (MovingImageContainer, DataObjectContainerType)
 
 elxGetObjectMacro (MovingImageFileNameContainer, FileNameContainerType)
 
 elxGetObjectMacro (MovingImagePyramidContainer, ObjectContainerType)
 
 elxGetObjectMacro (MovingMaskContainer, DataObjectContainerType)
 
 elxGetObjectMacro (MovingMaskFileNameContainer, FileNameContainerType)
 
 elxGetObjectMacro (OptimizerContainer, ObjectContainerType)
 
 elxGetObjectMacro (RegistrationContainer, ObjectContainerType)
 
 elxGetObjectMacro (ResampleInterpolatorContainer, ObjectContainerType)
 
 elxGetObjectMacro (ResamplerContainer, ObjectContainerType)
 
 elxGetObjectMacro (ResultDeformationFieldContainer, DataObjectContainerType)
 
 elxGetObjectMacro (ResultImageContainer, DataObjectContainerType)
 
 elxGetObjectMacro (TransformContainer, ObjectContainerType)
 
 elxSetObjectMacro (Configuration, Configuration)
 
 elxSetObjectMacro (FinalTransform, itk::Object)
 
 elxSetObjectMacro (FixedImageContainer, DataObjectContainerType)
 
 elxSetObjectMacro (FixedImageFileNameContainer, FileNameContainerType)
 
 elxSetObjectMacro (FixedImagePyramidContainer, ObjectContainerType)
 
 elxSetObjectMacro (FixedMaskContainer, DataObjectContainerType)
 
 elxSetObjectMacro (FixedMaskFileNameContainer, FileNameContainerType)
 
 elxSetObjectMacro (ImageSamplerContainer, ObjectContainerType)
 
 elxSetObjectMacro (InitialTransform, itk::Object)
 
 elxSetObjectMacro (InterpolatorContainer, ObjectContainerType)
 
 elxSetObjectMacro (MetricContainer, ObjectContainerType)
 
 elxSetObjectMacro (MovingImageContainer, DataObjectContainerType)
 
 elxSetObjectMacro (MovingImageFileNameContainer, FileNameContainerType)
 
 elxSetObjectMacro (MovingImagePyramidContainer, ObjectContainerType)
 
 elxSetObjectMacro (MovingMaskContainer, DataObjectContainerType)
 
 elxSetObjectMacro (MovingMaskFileNameContainer, FileNameContainerType)
 
 elxSetObjectMacro (OptimizerContainer, ObjectContainerType)
 
 elxSetObjectMacro (RegistrationContainer, ObjectContainerType)
 
 elxSetObjectMacro (ResampleInterpolatorContainer, ObjectContainerType)
 
 elxSetObjectMacro (ResamplerContainer, ObjectContainerType)
 
 elxSetObjectMacro (ResultDeformationFieldContainer, DataObjectContainerType)
 
 elxSetObjectMacro (ResultImageContainer, DataObjectContainerType)
 
 elxSetObjectMacro (TransformContainer, ObjectContainerType)
 
ConfigurationPointer GetConfiguration (const vcl_size_t index) const
 
DBIndexType GetDBIndex ()
 
int GetDefaultOutputPrecision () const
 
xl::xoutrowGetIterationInfo ()
 
xl::xoutbaseGetIterationInfoAt (const char *const name)
 
const FlatDirectionCosinesTypeGetOriginalFixedImageDirectionFlat () const
 
ResultDeformationFieldTypeGetResultDeformationField (unsigned int idx=0) const
 
ResultImageTypeGetResultImage (const unsigned int idx=0) const
 
ParameterMapType GetTransformParametersMap () const
 
bool GetUseDirectionCosines () const
 
 ITK_DISALLOW_COPY_AND_MOVE (ElastixBase)
 
virtual int Run ()=0
 
void SetConfigurations (const std::vector< ConfigurationPointer > &configurations)
 
void SetDBIndex (DBIndexType _arg)
 
void SetOriginalFixedImageDirectionFlat (const FlatDirectionCosinesType &arg)
 
void SetResultDeformationField (DataObjectPointer result_deformationfield)
 
void SetResultImage (DataObjectPointer result_image)
 
- Public Member Functions inherited from elastix::BaseComponent
virtual void AfterEachIteration ()
 
virtual void AfterEachIterationBase ()
 
virtual void AfterEachResolution ()
 
virtual void AfterEachResolutionBase ()
 
virtual void AfterRegistration ()
 
virtual void AfterRegistrationBase ()
 
virtual int BeforeAll ()
 
virtual int BeforeAllBase ()
 
virtual void BeforeEachResolution ()
 
virtual void BeforeEachResolutionBase ()
 
virtual void BeforeRegistration ()
 
virtual void BeforeRegistrationBase ()
 
virtual const char * elxGetClassName () const
 
const char * GetComponentLabel () const
 
 ITK_DISALLOW_COPY_AND_MOVE (BaseComponent)
 
 itkTypeMacroNoParent (BaseComponent)
 
void SetComponentLabel (const char *label, unsigned int idx)
 

Protected Member Functions

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

Static Protected Member Functions

static DataObjectContainerPointer GenerateDataObjectContainer (DataObjectPointer dataObject)
 

Protected Attributes

ConfigurationPointer m_Configuration { nullptr }
 
std::vector< ConfigurationPointerm_Configurations
 
std::string m_CurrentTransformParameterFileName
 
DBIndexType m_DBIndex { 0 }
 
unsigned int m_IterationCounter {}
 
std::ofstream m_IterationInfoFile
 
itk::TimeProbe m_IterationTimer {}
 
FlatDirectionCosinesType m_OriginalFixedImageDirection
 
itk::TimeProbe m_ResolutionTimer {}
 
itk::TimeProbe m_Timer0 {}
 
ParameterMapType m_TransformParametersMap
 

Private Attributes

int m_DefaultOutputPrecision { 6 }
 
ObjectPointer m_FinalTransform { nullptr }
 
DataObjectContainerPointer m_FixedImageContainer { DataObjectContainerType::New() }
 
FileNameContainerPointer m_FixedImageFileNameContainer { FileNameContainerType::New() }
 
ObjectContainerPointer m_FixedImagePyramidContainer { ObjectContainerType::New() }
 
DataObjectContainerPointer m_FixedMaskContainer { DataObjectContainerType::New() }
 
FileNameContainerPointer m_FixedMaskFileNameContainer { FileNameContainerType::New() }
 
ObjectContainerPointer m_ImageSamplerContainer { ObjectContainerType::New() }
 
ObjectPointer m_InitialTransform { nullptr }
 
ObjectContainerPointer m_InterpolatorContainer { ObjectContainerType::New() }
 
xl::xoutrow m_IterationInfo
 
ObjectContainerPointer m_MetricContainer { ObjectContainerType::New() }
 
DataObjectContainerPointer m_MovingImageContainer { DataObjectContainerType::New() }
 
FileNameContainerPointer m_MovingImageFileNameContainer { FileNameContainerType::New() }
 
ObjectContainerPointer m_MovingImagePyramidContainer { ObjectContainerType::New() }
 
DataObjectContainerPointer m_MovingMaskContainer { DataObjectContainerType::New() }
 
FileNameContainerPointer m_MovingMaskFileNameContainer { FileNameContainerType::New() }
 
ObjectContainerPointer m_OptimizerContainer { ObjectContainerType::New() }
 
ObjectContainerPointer m_RegistrationContainer { ObjectContainerType::New() }
 
ObjectContainerPointer m_ResampleInterpolatorContainer { ObjectContainerType::New() }
 
ObjectContainerPointer m_ResamplerContainer { ObjectContainerType::New() }
 
DataObjectContainerPointer m_ResultDeformationFieldContainer
 
DataObjectContainerPointer m_ResultImageContainer { DataObjectContainerType::New() }
 
ObjectContainerPointer m_TransformContainer { ObjectContainerType::New() }
 
bool m_UseDirectionCosines { true }
 

Additional Inherited Members

- Static Public Member Functions inherited from elastix::BaseComponent
template<typename TBaseComponent >
static auto AsITKBaseType (TBaseComponent *const baseComponent) -> decltype(baseComponent->GetAsITKBaseType())
 
static void InitializeElastixExecutable ()
 
static bool IsElastixLibrary ()
 

Member Typedef Documentation

◆ ComponentDatabasePointer

Other typedef's.

Definition at line 172 of file elxElastixBase.h.

◆ ConfigurationPointer

Typedefs used in this class.

Definition at line 155 of file elxElastixBase.h.

◆ CoordRepType

Type for representation of the transform coordinates.

Definition at line 177 of file elxElastixBase.h.

◆ DataObjectContainerPointer

using elastix::ElastixBase::DataObjectContainerPointer = DataObjectContainerType::Pointer

Definition at line 161 of file elxElastixBase.h.

◆ DataObjectContainerType

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

Definition at line 160 of file elxElastixBase.h.

◆ DataObjectPointer

using elastix::ElastixBase::DataObjectPointer = itk::DataObject::Pointer

Definition at line 157 of file elxElastixBase.h.

◆ DBIndexType

Definition at line 173 of file elxElastixBase.h.

◆ FileNameContainerPointer

using elastix::ElastixBase::FileNameContainerPointer = FileNameContainerType::Pointer

Definition at line 163 of file elxElastixBase.h.

◆ FileNameContainerType

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

Definition at line 162 of file elxElastixBase.h.

◆ FlatDirectionCosinesType

Definition at line 174 of file elxElastixBase.h.

◆ ObjectContainerPointer

using elastix::ElastixBase::ObjectContainerPointer = ObjectContainerType::Pointer

Definition at line 159 of file elxElastixBase.h.

◆ ObjectContainerType

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

Definition at line 158 of file elxElastixBase.h.

◆ ObjectPointer

using elastix::ElastixBase::ObjectPointer = itk::Object::Pointer

Definition at line 156 of file elxElastixBase.h.

◆ ParameterMapType

Typedef that is used in the elastix dll version.

Definition at line 180 of file elxElastixBase.h.

◆ ResultDeformationFieldType

Result deformation field

Definition at line 169 of file elxElastixBase.h.

◆ ResultImageType

using elastix::ElastixBase::ResultImageType = itk::DataObject

Result image

Definition at line 166 of file elxElastixBase.h.

◆ Self

Standard typedefs etc.

Definition at line 151 of file elxElastixBase.h.

◆ Superclass

Definition at line 152 of file elxElastixBase.h.

Constructor & Destructor Documentation

◆ ElastixBase()

elastix::ElastixBase::ElastixBase ( )
protected

◆ ~ElastixBase()

elastix::ElastixBase::~ElastixBase ( )
overrideprotecteddefault

Member Function Documentation

◆ AddTargetCellToIterationInfo()

void elastix::ElastixBase::AddTargetCellToIterationInfo ( const char *const  name)
inline

Definition at line 393 of file elxElastixBase.h.

◆ ApplyTransform()

virtual int elastix::ElastixBase::ApplyTransform ( bool  doReadTransform)
pure virtual

Empty ApplyTransform()-function to be overridden.

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

◆ BeforeAllBase()

int elastix::ElastixBase::BeforeAllBase ( )
overridevirtual

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

Reimplemented from elastix::BaseComponent.

◆ BeforeAllTransformixBase()

int elastix::ElastixBase::BeforeAllTransformixBase ( )

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

◆ BeforeRegistrationBase()

void elastix::ElastixBase::BeforeRegistrationBase ( )
overridevirtual

Function called before registration. It installs the IterationInfo field.

Reimplemented from elastix::BaseComponent.

◆ CreateTransformParametersMap()

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

Creates transformation parameters map.

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

◆ elxGetNumberOfMacro() [1/20]

elastix::ElastixBase::elxGetNumberOfMacro ( FixedImage  )

◆ elxGetNumberOfMacro() [2/20]

elastix::ElastixBase::elxGetNumberOfMacro ( FixedImageFileName  )

◆ elxGetNumberOfMacro() [3/20]

elastix::ElastixBase::elxGetNumberOfMacro ( FixedImagePyramid  )

◆ elxGetNumberOfMacro() [4/20]

elastix::ElastixBase::elxGetNumberOfMacro ( FixedMask  )

◆ elxGetNumberOfMacro() [5/20]

elastix::ElastixBase::elxGetNumberOfMacro ( FixedMaskFileName  )

◆ elxGetNumberOfMacro() [6/20]

elastix::ElastixBase::elxGetNumberOfMacro ( ImageSampler  )

◆ elxGetNumberOfMacro() [7/20]

elastix::ElastixBase::elxGetNumberOfMacro ( Interpolator  )

◆ elxGetNumberOfMacro() [8/20]

elastix::ElastixBase::elxGetNumberOfMacro ( Metric  )

◆ elxGetNumberOfMacro() [9/20]

elastix::ElastixBase::elxGetNumberOfMacro ( MovingImage  )

◆ elxGetNumberOfMacro() [10/20]

elastix::ElastixBase::elxGetNumberOfMacro ( MovingImageFileName  )

◆ elxGetNumberOfMacro() [11/20]

elastix::ElastixBase::elxGetNumberOfMacro ( MovingImagePyramid  )

◆ elxGetNumberOfMacro() [12/20]

elastix::ElastixBase::elxGetNumberOfMacro ( MovingMask  )

◆ elxGetNumberOfMacro() [13/20]

elastix::ElastixBase::elxGetNumberOfMacro ( MovingMaskFileName  )

◆ elxGetNumberOfMacro() [14/20]

elastix::ElastixBase::elxGetNumberOfMacro ( Optimizer  )

◆ elxGetNumberOfMacro() [15/20]

elastix::ElastixBase::elxGetNumberOfMacro ( Registration  )

Define some convenience functions: GetNumberOfMetrics() for example.

◆ elxGetNumberOfMacro() [16/20]

elastix::ElastixBase::elxGetNumberOfMacro ( ResampleInterpolator  )

◆ elxGetNumberOfMacro() [17/20]

elastix::ElastixBase::elxGetNumberOfMacro ( Resampler  )

◆ elxGetNumberOfMacro() [18/20]

elastix::ElastixBase::elxGetNumberOfMacro ( ResultDeformationField  )

◆ elxGetNumberOfMacro() [19/20]

elastix::ElastixBase::elxGetNumberOfMacro ( ResultImage  )

◆ elxGetNumberOfMacro() [20/20]

elastix::ElastixBase::elxGetNumberOfMacro ( Transform  )

◆ elxGetObjectMacro() [1/23]

elastix::ElastixBase::elxGetObjectMacro ( Configuration  ,
Configuration   
)

Set/Get the Configuration Object.

◆ elxGetObjectMacro() [2/23]

elastix::ElastixBase::elxGetObjectMacro ( FinalTransform  ,
itk::Object   
)

◆ elxGetObjectMacro() [3/23]

elastix::ElastixBase::elxGetObjectMacro ( FixedImageContainer  ,
DataObjectContainerType   
)

Set/Get the fixed/moving image containers.

◆ elxGetObjectMacro() [4/23]

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

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

◆ elxGetObjectMacro() [5/23]

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

◆ elxGetObjectMacro() [6/23]

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

Set/Get the fixed/moving mask containers.

◆ elxGetObjectMacro() [7/23]

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

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

◆ elxGetObjectMacro() [8/23]

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

◆ elxGetObjectMacro() [9/23]

elastix::ElastixBase::elxGetObjectMacro ( InitialTransform  ,
itk::Object   
)

◆ elxGetObjectMacro() [10/23]

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

◆ elxGetObjectMacro() [11/23]

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

◆ elxGetObjectMacro() [12/23]

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

◆ elxGetObjectMacro() [13/23]

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

◆ elxGetObjectMacro() [14/23]

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

◆ elxGetObjectMacro() [15/23]

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

◆ elxGetObjectMacro() [16/23]

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

◆ elxGetObjectMacro() [17/23]

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

◆ elxGetObjectMacro() [18/23]

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.

◆ elxGetObjectMacro() [19/23]

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

◆ elxGetObjectMacro() [20/23]

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

◆ elxGetObjectMacro() [21/23]

elastix::ElastixBase::elxGetObjectMacro ( ResultDeformationFieldContainer  ,
DataObjectContainerType   
)

Set/Get the result image container.

◆ elxGetObjectMacro() [22/23]

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

Set/Get the result image container.

◆ elxGetObjectMacro() [23/23]

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

◆ elxSetObjectMacro() [1/23]

elastix::ElastixBase::elxSetObjectMacro ( Configuration  ,
Configuration   
)

◆ elxSetObjectMacro() [2/23]

elastix::ElastixBase::elxSetObjectMacro ( FinalTransform  ,
itk::Object   
)

Set/Get the final transform The type is itk::Object, 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.

◆ elxSetObjectMacro() [3/23]

elastix::ElastixBase::elxSetObjectMacro ( FixedImageContainer  ,
DataObjectContainerType   
)

◆ elxSetObjectMacro() [4/23]

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

◆ elxSetObjectMacro() [5/23]

elastix::ElastixBase::elxSetObjectMacro ( FixedImagePyramidContainer  ,
ObjectContainerType   
)

◆ elxSetObjectMacro() [6/23]

elastix::ElastixBase::elxSetObjectMacro ( FixedMaskContainer  ,
DataObjectContainerType   
)

◆ elxSetObjectMacro() [7/23]

elastix::ElastixBase::elxSetObjectMacro ( FixedMaskFileNameContainer  ,
FileNameContainerType   
)

◆ elxSetObjectMacro() [8/23]

elastix::ElastixBase::elxSetObjectMacro ( ImageSamplerContainer  ,
ObjectContainerType   
)

◆ elxSetObjectMacro() [9/23]

elastix::ElastixBase::elxSetObjectMacro ( InitialTransform  ,
itk::Object   
)

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

◆ elxSetObjectMacro() [10/23]

elastix::ElastixBase::elxSetObjectMacro ( InterpolatorContainer  ,
ObjectContainerType   
)

◆ elxSetObjectMacro() [11/23]

elastix::ElastixBase::elxSetObjectMacro ( MetricContainer  ,
ObjectContainerType   
)

◆ elxSetObjectMacro() [12/23]

elastix::ElastixBase::elxSetObjectMacro ( MovingImageContainer  ,
DataObjectContainerType   
)

◆ elxSetObjectMacro() [13/23]

elastix::ElastixBase::elxSetObjectMacro ( MovingImageFileNameContainer  ,
FileNameContainerType   
)

◆ elxSetObjectMacro() [14/23]

elastix::ElastixBase::elxSetObjectMacro ( MovingImagePyramidContainer  ,
ObjectContainerType   
)

◆ elxSetObjectMacro() [15/23]

elastix::ElastixBase::elxSetObjectMacro ( MovingMaskContainer  ,
DataObjectContainerType   
)

◆ elxSetObjectMacro() [16/23]

elastix::ElastixBase::elxSetObjectMacro ( MovingMaskFileNameContainer  ,
FileNameContainerType   
)

◆ elxSetObjectMacro() [17/23]

elastix::ElastixBase::elxSetObjectMacro ( OptimizerContainer  ,
ObjectContainerType   
)

◆ elxSetObjectMacro() [18/23]

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.

◆ elxSetObjectMacro() [19/23]

elastix::ElastixBase::elxSetObjectMacro ( ResampleInterpolatorContainer  ,
ObjectContainerType   
)

◆ elxSetObjectMacro() [20/23]

elastix::ElastixBase::elxSetObjectMacro ( ResamplerContainer  ,
ObjectContainerType   
)

◆ elxSetObjectMacro() [21/23]

elastix::ElastixBase::elxSetObjectMacro ( ResultDeformationFieldContainer  ,
DataObjectContainerType   
)

◆ elxSetObjectMacro() [22/23]

elastix::ElastixBase::elxSetObjectMacro ( ResultImageContainer  ,
DataObjectContainerType   
)

◆ elxSetObjectMacro() [23/23]

elastix::ElastixBase::elxSetObjectMacro ( TransformContainer  ,
ObjectContainerType   
)

◆ GenerateDataObjectContainer()

static DataObjectContainerPointer elastix::ElastixBase::GenerateDataObjectContainer ( DataObjectPointer  dataObject)
staticprotected

Generates a container that contains the specified data object

◆ GetConfiguration()

ConfigurationPointer elastix::ElastixBase::GetConfiguration ( const vcl_size_t  index) const

Return configuration from vector of configurations. Library only.

◆ GetDBIndex()

DBIndexType elastix::ElastixBase::GetDBIndex ( )
inline

Definition at line 191 of file elxElastixBase.h.

◆ GetDefaultOutputPrecision()

int elastix::ElastixBase::GetDefaultOutputPrecision ( ) const
inline

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

Definition at line 344 of file elxElastixBase.h.

◆ GetIterationInfo()

xl::xoutrow & elastix::ElastixBase::GetIterationInfo ( )
inline

Definition at line 381 of file elxElastixBase.h.

◆ GetIterationInfoAt()

xl::xoutbase & elastix::ElastixBase::GetIterationInfoAt ( const char *const  name)
inline

Definition at line 387 of file elxElastixBase.h.

◆ GetOriginalFixedImageDirectionFlat()

const FlatDirectionCosinesType & elastix::ElastixBase::GetOriginalFixedImageDirectionFlat ( ) const

◆ GetResultDeformationField()

ResultDeformationFieldType * elastix::ElastixBase::GetResultDeformationField ( unsigned int  idx = 0) const

◆ GetResultImage()

ResultImageType * elastix::ElastixBase::GetResultImage ( const unsigned int  idx = 0) const

◆ GetTransformParametersMap()

ParameterMapType elastix::ElastixBase::GetTransformParametersMap ( ) const

Gets transformation parameters map.

◆ GetUseDirectionCosines()

bool elastix::ElastixBase::GetUseDirectionCosines ( ) const

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

◆ ITK_DISALLOW_COPY_AND_MOVE()

elastix::ElastixBase::ITK_DISALLOW_COPY_AND_MOVE ( ElastixBase  )

◆ Run()

virtual int elastix::ElastixBase::Run ( )
pure virtual

Empty Run()-function to be overridden.

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

◆ SetConfigurations()

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

Set configuration vector. Library only.

◆ SetDBIndex()

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

Set the database index of the instantiated elastix object.

◆ SetOriginalFixedImageDirectionFlat()

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

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

◆ SetResultDeformationField()

void elastix::ElastixBase::SetResultDeformationField ( DataObjectPointer  result_deformationfield)

◆ SetResultImage()

void elastix::ElastixBase::SetResultImage ( DataObjectPointer  result_image)

Field Documentation

◆ m_Configuration

ConfigurationPointer elastix::ElastixBase::m_Configuration { nullptr }
protected

Definition at line 402 of file elxElastixBase.h.

◆ m_Configurations

std::vector<ConfigurationPointer> elastix::ElastixBase::m_Configurations
protected

A vector of configuration objects, needed when transformix is used as library.

Definition at line 416 of file elxElastixBase.h.

◆ m_CurrentTransformParameterFileName

std::string elastix::ElastixBase::m_CurrentTransformParameterFileName
protected

Store the CurrentTransformParameterFileName.

Definition at line 413 of file elxElastixBase.h.

◆ m_DBIndex

DBIndexType elastix::ElastixBase::m_DBIndex { 0 }
protected

Definition at line 403 of file elxElastixBase.h.

◆ m_DefaultOutputPrecision

int elastix::ElastixBase::m_DefaultOutputPrecision { 6 }
private

The default output precision of elxout is set to 6.

Definition at line 505 of file elxElastixBase.h.

◆ m_FinalTransform

ObjectPointer elastix::ElastixBase::m_FinalTransform { nullptr }
private

Definition at line 541 of file elxElastixBase.h.

◆ m_FixedImageContainer

DataObjectContainerPointer elastix::ElastixBase::m_FixedImageContainer { DataObjectContainerType::New() }
private

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

Definition at line 522 of file elxElastixBase.h.

◆ m_FixedImageFileNameContainer

FileNameContainerPointer elastix::ElastixBase::m_FixedImageFileNameContainer { FileNameContainerType::New() }
private

The image and mask FileNameContainers.

Definition at line 534 of file elxElastixBase.h.

◆ m_FixedImagePyramidContainer

ObjectContainerPointer elastix::ElastixBase::m_FixedImagePyramidContainer { ObjectContainerType::New() }
private

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

Definition at line 510 of file elxElastixBase.h.

◆ m_FixedMaskContainer

DataObjectContainerPointer elastix::ElastixBase::m_FixedMaskContainer { DataObjectContainerType::New() }
private

Definition at line 524 of file elxElastixBase.h.

◆ m_FixedMaskFileNameContainer

FileNameContainerPointer elastix::ElastixBase::m_FixedMaskFileNameContainer { FileNameContainerType::New() }
private

Definition at line 536 of file elxElastixBase.h.

◆ m_ImageSamplerContainer

ObjectContainerPointer elastix::ElastixBase::m_ImageSamplerContainer { ObjectContainerType::New() }
private

Definition at line 513 of file elxElastixBase.h.

◆ m_InitialTransform

ObjectPointer elastix::ElastixBase::m_InitialTransform { nullptr }
private

The initial and final transform.

Definition at line 540 of file elxElastixBase.h.

◆ m_InterpolatorContainer

ObjectContainerPointer elastix::ElastixBase::m_InterpolatorContainer { ObjectContainerType::New() }
private

Definition at line 512 of file elxElastixBase.h.

◆ m_IterationCounter

unsigned int elastix::ElastixBase::m_IterationCounter {}
protected

Count the number of iterations.

Definition at line 419 of file elxElastixBase.h.

◆ m_IterationInfo

xl::xoutrow elastix::ElastixBase::m_IterationInfo
private

Definition at line 502 of file elxElastixBase.h.

◆ m_IterationInfoFile

std::ofstream elastix::ElastixBase::m_IterationInfoFile
protected

Definition at line 424 of file elxElastixBase.h.

◆ m_IterationTimer

itk::TimeProbe elastix::ElastixBase::m_IterationTimer {}
protected

Definition at line 409 of file elxElastixBase.h.

◆ m_MetricContainer

ObjectContainerPointer elastix::ElastixBase::m_MetricContainer { ObjectContainerType::New() }
private

Definition at line 514 of file elxElastixBase.h.

◆ m_MovingImageContainer

DataObjectContainerPointer elastix::ElastixBase::m_MovingImageContainer { DataObjectContainerType::New() }
private

Definition at line 523 of file elxElastixBase.h.

◆ m_MovingImageFileNameContainer

FileNameContainerPointer elastix::ElastixBase::m_MovingImageFileNameContainer { FileNameContainerType::New() }
private

Definition at line 535 of file elxElastixBase.h.

◆ m_MovingImagePyramidContainer

ObjectContainerPointer elastix::ElastixBase::m_MovingImagePyramidContainer { ObjectContainerType::New() }
private

Definition at line 511 of file elxElastixBase.h.

◆ m_MovingMaskContainer

DataObjectContainerPointer elastix::ElastixBase::m_MovingMaskContainer { DataObjectContainerType::New() }
private

Definition at line 525 of file elxElastixBase.h.

◆ m_MovingMaskFileNameContainer

FileNameContainerPointer elastix::ElastixBase::m_MovingMaskFileNameContainer { FileNameContainerType::New() }
private

Definition at line 537 of file elxElastixBase.h.

◆ m_OptimizerContainer

ObjectContainerPointer elastix::ElastixBase::m_OptimizerContainer { ObjectContainerType::New() }
private

Definition at line 515 of file elxElastixBase.h.

◆ m_OriginalFixedImageDirection

FlatDirectionCosinesType elastix::ElastixBase::m_OriginalFixedImageDirection
protected

Definition at line 405 of file elxElastixBase.h.

◆ m_RegistrationContainer

ObjectContainerPointer elastix::ElastixBase::m_RegistrationContainer { ObjectContainerType::New() }
private

Definition at line 516 of file elxElastixBase.h.

◆ m_ResampleInterpolatorContainer

ObjectContainerPointer elastix::ElastixBase::m_ResampleInterpolatorContainer { ObjectContainerType::New() }
private

Definition at line 518 of file elxElastixBase.h.

◆ m_ResamplerContainer

ObjectContainerPointer elastix::ElastixBase::m_ResamplerContainer { ObjectContainerType::New() }
private

Definition at line 517 of file elxElastixBase.h.

◆ m_ResolutionTimer

itk::TimeProbe elastix::ElastixBase::m_ResolutionTimer {}
protected

Definition at line 410 of file elxElastixBase.h.

◆ m_ResultDeformationFieldContainer

DataObjectContainerPointer elastix::ElastixBase::m_ResultDeformationFieldContainer
private

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

Definition at line 531 of file elxElastixBase.h.

◆ m_ResultImageContainer

DataObjectContainerPointer elastix::ElastixBase::m_ResultImageContainer { DataObjectContainerType::New() }
private

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

Definition at line 528 of file elxElastixBase.h.

◆ m_Timer0

itk::TimeProbe elastix::ElastixBase::m_Timer0 {}
protected

Timers.

Definition at line 408 of file elxElastixBase.h.

◆ m_TransformContainer

ObjectContainerPointer elastix::ElastixBase::m_TransformContainer { ObjectContainerType::New() }
private

Definition at line 519 of file elxElastixBase.h.

◆ m_TransformParametersMap

ParameterMapType elastix::ElastixBase::m_TransformParametersMap
protected

Stores transformation parameters map.

Definition at line 422 of file elxElastixBase.h.

◆ m_UseDirectionCosines

bool elastix::ElastixBase::m_UseDirectionCosines { true }
private

Use or ignore direction cosines. From Elastix 4.3 to 4.7: Ignore direction cosines by default, for backward compatability. From Elastix 4.8: set it to true by default.

Definition at line 546 of file elxElastixBase.h.



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