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This class creates an interface for elastix. More...
#include <elxElastixBase.h>
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:
(RandomSeed 121212)
(DefaultOutputPrecision 6)
The command line arguments used by this class are:
-f fixedImage.mhd
-m movingImage.mhd
-out outputdirectory
-p parameters.txt
-fMask fixedmask.mhd
-mMask movingmask.mhd
-tp TransformParameters.txt
-priority high
-threads 2
-in inputImage.mhd
Definition at line 141 of file elxElastixBase.h.
Definition at line 168 of file elxElastixBase.h.
Other typedef's.
Definition at line 167 of file elxElastixBase.h.
Reimplemented in elastix::ElastixTemplate< TFixedImage, TMovingImage >.
Definition at line 151 of file elxElastixBase.h.
Typedefs used in this class.
Reimplemented in elastix::ElastixTemplate< TFixedImage, TMovingImage >.
Definition at line 150 of file elxElastixBase.h.
typedef DataObjectContainerType::Pointer elastix::ElastixBase::DataObjectContainerPointer |
Reimplemented in elastix::ElastixTemplate< TFixedImage, TMovingImage >.
Definition at line 161 of file elxElastixBase.h.
typedef itk::VectorContainer< unsigned int, DataObjectPointer> elastix::ElastixBase::DataObjectContainerType |
Reimplemented in elastix::ElastixTemplate< TFixedImage, TMovingImage >.
Definition at line 160 of file elxElastixBase.h.
typedef DataObjectType::Pointer elastix::ElastixBase::DataObjectPointer |
Reimplemented in elastix::ElastixTemplate< TFixedImage, TMovingImage >.
Definition at line 155 of file elxElastixBase.h.
typedef itk::DataObject elastix::ElastixBase::DataObjectType |
Reimplemented in elastix::ElastixTemplate< TFixedImage, TMovingImage >.
Definition at line 154 of file elxElastixBase.h.
Definition at line 169 of file elxElastixBase.h.
typedef FileNameContainerType::Pointer elastix::ElastixBase::FileNameContainerPointer |
Reimplemented in elastix::ElastixTemplate< TFixedImage, TMovingImage >.
Definition at line 164 of file elxElastixBase.h.
typedef itk::VectorContainer< unsigned int, std::string > elastix::ElastixBase::FileNameContainerType |
Reimplemented in elastix::ElastixTemplate< TFixedImage, TMovingImage >.
Definition at line 163 of file elxElastixBase.h.
typedef std::vector<double> elastix::ElastixBase::FlatDirectionCosinesType |
Definition at line 170 of file elxElastixBase.h.
typedef 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 175 of file elxElastixBase.h.
typedef ObjectContainerType::Pointer elastix::ElastixBase::ObjectContainerPointer |
Reimplemented in elastix::ElastixTemplate< TFixedImage, TMovingImage >.
Definition at line 158 of file elxElastixBase.h.
typedef itk::VectorContainer< unsigned int, ObjectPointer> elastix::ElastixBase::ObjectContainerType |
Reimplemented in elastix::ElastixTemplate< TFixedImage, TMovingImage >.
Definition at line 157 of file elxElastixBase.h.
typedef ObjectType::Pointer elastix::ElastixBase::ObjectPointer |
Reimplemented in elastix::ElastixTemplate< TFixedImage, TMovingImage >.
Definition at line 153 of file elxElastixBase.h.
typedef itk::Object elastix::ElastixBase::ObjectType |
Reimplemented in elastix::ElastixTemplate< TFixedImage, TMovingImage >.
Definition at line 152 of file elxElastixBase.h.
Standard typedefs etc.
Reimplemented in elastix::ElastixTemplate< TFixedImage, TMovingImage >.
Definition at line 146 of file elxElastixBase.h.
Definition at line 147 of file elxElastixBase.h.
elastix::ElastixBase::ElastixBase | ( | ) | [protected] |
virtual elastix::ElastixBase::~ElastixBase | ( | ) | [inline, protected, virtual] |
Definition at line 341 of file elxElastixBase.h.
elastix::ElastixBase::ElastixBase | ( | const Self & | ) | [private] |
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.
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::elxGetObjectMacro | ( | ResampleInterpolatorContainer | , |
ObjectContainerType | |||
) |
elastix::ElastixBase::elxGetObjectMacro | ( | FinalTransform | , |
ObjectType | |||
) |
elastix::ElastixBase::elxGetObjectMacro | ( | FixedMaskContainer | , |
DataObjectContainerType | |||
) |
Set/Get the fixed/moving mask containers.
elastix::ElastixBase::elxGetObjectMacro | ( | MovingMaskContainer | , |
DataObjectContainerType | |||
) |
elastix::ElastixBase::elxGetObjectMacro | ( | FixedImagePyramidContainer | , |
ObjectContainerType | |||
) |
elastix::ElastixBase::elxGetObjectMacro | ( | TransformContainer | , |
ObjectContainerType | |||
) |
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 | ( | 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 | ( | FixedMaskFileNameContainer | , |
FileNameContainerType | |||
) |
Set/Get The Mask FileName containers. Normally, these are filled in the BeforeAllBase function.
elastix::ElastixBase::elxGetObjectMacro | ( | MovingMaskFileNameContainer | , |
FileNameContainerType | |||
) |
elastix::ElastixBase::elxGetObjectMacro | ( | MovingImagePyramidContainer | , |
ObjectContainerType | |||
) |
elastix::ElastixBase::elxGetObjectMacro | ( | InterpolatorContainer | , |
ObjectContainerType | |||
) |
elastix::ElastixBase::elxGetObjectMacro | ( | Configuration | , |
ConfigurationType | |||
) |
Set/Get the Configuration Object.
elastix::ElastixBase::elxGetObjectMacro | ( | ImageSamplerContainer | , |
ObjectContainerType | |||
) |
elastix::ElastixBase::elxGetObjectMacro | ( | ComponentDatabase | , |
ComponentDatabaseType | |||
) |
Functions to get/set the ComponentDatabase The component database contains pointers to functions that create components.
elastix::ElastixBase::elxGetObjectMacro | ( | MetricContainer | , |
ObjectContainerType | |||
) |
elastix::ElastixBase::elxGetObjectMacro | ( | OptimizerContainer | , |
ObjectContainerType | |||
) |
elastix::ElastixBase::elxGetObjectMacro | ( | FixedImageContainer | , |
DataObjectContainerType | |||
) |
Set/Get the fixed/moving image containers.
elastix::ElastixBase::elxGetObjectMacro | ( | ResamplerContainer | , |
ObjectContainerType | |||
) |
elastix::ElastixBase::elxGetObjectMacro | ( | MovingImageContainer | , |
DataObjectContainerType | |||
) |
elastix::ElastixBase::elxGetObjectMacro | ( | InitialTransform | , |
ObjectType | |||
) |
elastix::ElastixBase::elxSetObjectMacro | ( | FixedMaskFileNameContainer | , |
FileNameContainerType | |||
) |
elastix::ElastixBase::elxSetObjectMacro | ( | Configuration | , |
ConfigurationType | |||
) |
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.
elastix::ElastixBase::elxSetObjectMacro | ( | MovingMaskContainer | , |
DataObjectContainerType | |||
) |
elastix::ElastixBase::elxSetObjectMacro | ( | MovingImageFileNameContainer | , |
FileNameContainerType | |||
) |
elastix::ElastixBase::elxSetObjectMacro | ( | ResamplerContainer | , |
ObjectContainerType | |||
) |
elastix::ElastixBase::elxSetObjectMacro | ( | TransformContainer | , |
ObjectContainerType | |||
) |
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 | ( | MovingMaskFileNameContainer | , |
FileNameContainerType | |||
) |
elastix::ElastixBase::elxSetObjectMacro | ( | OptimizerContainer | , |
ObjectContainerType | |||
) |
elastix::ElastixBase::elxSetObjectMacro | ( | MetricContainer | , |
ObjectContainerType | |||
) |
elastix::ElastixBase::elxSetObjectMacro | ( | MovingImagePyramidContainer | , |
ObjectContainerType | |||
) |
elastix::ElastixBase::elxSetObjectMacro | ( | InterpolatorContainer | , |
ObjectContainerType | |||
) |
elastix::ElastixBase::elxSetObjectMacro | ( | ImageSamplerContainer | , |
ObjectContainerType | |||
) |
elastix::ElastixBase::elxSetObjectMacro | ( | ComponentDatabase | , |
ComponentDatabaseType | |||
) |
elastix::ElastixBase::elxSetObjectMacro | ( | FixedMaskContainer | , |
DataObjectContainerType | |||
) |
elastix::ElastixBase::elxSetObjectMacro | ( | MovingImageContainer | , |
DataObjectContainerType | |||
) |
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 | ( | FixedImageContainer | , |
DataObjectContainerType | |||
) |
elastix::ElastixBase::elxSetObjectMacro | ( | ResampleInterpolatorContainer | , |
ObjectContainerType | |||
) |
elastix::ElastixBase::elxSetObjectMacro | ( | FixedImageFileNameContainer | , |
FileNameContainerType | |||
) |
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 | ) | [inline, virtual] |
Cast to ITKBaseType.
Definition at line 178 of file elxElastixBase.h.
virtual DBIndexType elastix::ElastixBase::GetDBIndex | ( | void | ) | [inline, virtual] |
Definition at line 189 of file elxElastixBase.h.
virtual int elastix::ElastixBase::GetDefaultOutputPrecision | ( | void | ) | const [inline, virtual] |
Get the default precision of xout. (The value assumed when no DefaultOutputPrecision is given in the parameter file.
Definition at line 321 of file elxElastixBase.h.
virtual const FlatDirectionCosinesType& elastix::ElastixBase::GetOriginalFixedImageDirectionFlat | ( | void | ) | const [virtual] |
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] |
Reimplemented in elastix::ElastixTemplate< TFixedImage, TMovingImage >.
virtual int elastix::ElastixBase::Run | ( | void | ) | [pure virtual] |
Empty Run()-function to be overridden.
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 )
Definition at line 345 of file elxElastixBase.h.
Definition at line 341 of file elxElastixBase.h.
DBIndexType elastix::ElastixBase::m_DBIndex [protected] |
Definition at line 344 of file elxElastixBase.h.
Definition at line 436 of file elxElastixBase.h.
Definition at line 466 of file elxElastixBase.h.
The Image and Mask containers. These are stored as pointers to itk::DataObject.
Definition at line 453 of file elxElastixBase.h.
The image and mask FileNameContainers.
Definition at line 459 of file elxElastixBase.h.
The component containers. These containers contain SmartPointer's to itk::Object.
Definition at line 441 of file elxElastixBase.h.
Definition at line 455 of file elxElastixBase.h.
Definition at line 461 of file elxElastixBase.h.
Definition at line 444 of file elxElastixBase.h.
The initial and final transform.
Definition at line 465 of file elxElastixBase.h.
Definition at line 443 of file elxElastixBase.h.
Definition at line 434 of file elxElastixBase.h.
Definition at line 445 of file elxElastixBase.h.
Definition at line 454 of file elxElastixBase.h.
Definition at line 460 of file elxElastixBase.h.
Definition at line 442 of file elxElastixBase.h.
Definition at line 456 of file elxElastixBase.h.
Definition at line 462 of file elxElastixBase.h.
Definition at line 446 of file elxElastixBase.h.
Definition at line 347 of file elxElastixBase.h.
Definition at line 447 of file elxElastixBase.h.
Definition at line 449 of file elxElastixBase.h.
Definition at line 448 of file elxElastixBase.h.
Definition at line 450 of file elxElastixBase.h.
Use or ignore direction cosines.
Definition at line 469 of file elxElastixBase.h.
Generated on 24-10-2011 for elastix by ![]() |
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