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#include <elxElastixBase.h>
Data Structures | |
class | MultipleImageLoader |
Protected Member Functions | |
ElastixBase () | |
virtual | ~ElastixBase () |
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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 &) |
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: 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:
-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 140 of file elxElastixBase.h.
Definition at line 167 of file elxElastixBase.h.
Other typedef's.
Definition at line 166 of file elxElastixBase.h.
Definition at line 150 of file elxElastixBase.h.
Typedefs used in this class.
Definition at line 149 of file elxElastixBase.h.
typedef DataObjectContainerType::Pointer elastix::ElastixBase::DataObjectContainerPointer |
Definition at line 160 of file elxElastixBase.h.
typedef itk::VectorContainer< unsigned int, DataObjectPointer> elastix::ElastixBase::DataObjectContainerType |
Definition at line 159 of file elxElastixBase.h.
typedef DataObjectType::Pointer elastix::ElastixBase::DataObjectPointer |
Definition at line 154 of file elxElastixBase.h.
typedef itk::DataObject elastix::ElastixBase::DataObjectType |
Definition at line 153 of file elxElastixBase.h.
Definition at line 168 of file elxElastixBase.h.
typedef FileNameContainerType::Pointer elastix::ElastixBase::FileNameContainerPointer |
Definition at line 163 of file elxElastixBase.h.
typedef itk::VectorContainer< unsigned int, std::string > elastix::ElastixBase::FileNameContainerType |
Definition at line 162 of file elxElastixBase.h.
typedef std::vector<double> elastix::ElastixBase::FlatDirectionCosinesType |
Definition at line 169 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 174 of file elxElastixBase.h.
typedef ObjectContainerType::Pointer elastix::ElastixBase::ObjectContainerPointer |
Definition at line 157 of file elxElastixBase.h.
typedef itk::VectorContainer< unsigned int, ObjectPointer> elastix::ElastixBase::ObjectContainerType |
Definition at line 156 of file elxElastixBase.h.
typedef ObjectType::Pointer elastix::ElastixBase::ObjectPointer |
Definition at line 152 of file elxElastixBase.h.
typedef itk::Object elastix::ElastixBase::ObjectType |
Definition at line 151 of file elxElastixBase.h.
Standard typedefs etc.
Definition at line 145 of file elxElastixBase.h.
Definition at line 146 of file elxElastixBase.h.
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inlineprotectedvirtual |
Definition at line 340 of file elxElastixBase.h.
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Reimplemented from elastix::BaseComponent.
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pure virtual |
Empty ApplyTransform()-function to be overridden.
Implemented in elastix::ElastixTemplate< TFixedImage, TMovingImage >.
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Function that is called at the very beginning of ElastixTemplate::Run(). It checks the command line input arguments.
Reimplemented from elastix::BaseComponent.
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Function that is called at the very beginning of ElastixTemplate::ApplyTransform(). It checks the command line input arguments.
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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 | ( | 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 | |||
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elastix::ElastixBase::elxGetObjectMacro | ( | MovingImagePyramidContainer | , |
ObjectContainerType | |||
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elastix::ElastixBase::elxGetObjectMacro | ( | InterpolatorContainer | , |
ObjectContainerType | |||
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elastix::ElastixBase::elxGetObjectMacro | ( | ImageSamplerContainer | , |
ObjectContainerType | |||
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elastix::ElastixBase::elxGetObjectMacro | ( | MetricContainer | , |
ObjectContainerType | |||
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elastix::ElastixBase::elxGetObjectMacro | ( | OptimizerContainer | , |
ObjectContainerType | |||
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elastix::ElastixBase::elxGetObjectMacro | ( | ResamplerContainer | , |
ObjectContainerType | |||
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elastix::ElastixBase::elxGetObjectMacro | ( | ResampleInterpolatorContainer | , |
ObjectContainerType | |||
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elastix::ElastixBase::elxGetObjectMacro | ( | TransformContainer | , |
ObjectContainerType | |||
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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 | |||
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elastix::ElastixBase::elxGetObjectMacro | ( | FixedImageFileNameContainer | , |
FileNameContainerType | |||
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Set/Get The Image FileName containers. Normally, these are filled in the BeforeAllBase function.
elastix::ElastixBase::elxGetObjectMacro | ( | MovingImageFileNameContainer | , |
FileNameContainerType | |||
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elastix::ElastixBase::elxGetObjectMacro | ( | FixedMaskFileNameContainer | , |
FileNameContainerType | |||
) |
Set/Get The Mask FileName containers. Normally, these are filled in the BeforeAllBase function.
elastix::ElastixBase::elxGetObjectMacro | ( | MovingMaskFileNameContainer | , |
FileNameContainerType | |||
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elastix::ElastixBase::elxGetObjectMacro | ( | InitialTransform | , |
ObjectType | |||
) |
elastix::ElastixBase::elxGetObjectMacro | ( | FinalTransform | , |
ObjectType | |||
) |
elastix::ElastixBase::elxSetObjectMacro | ( | Configuration | , |
ConfigurationType | |||
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elastix::ElastixBase::elxSetObjectMacro | ( | ComponentDatabase | , |
ComponentDatabaseType | |||
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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 | |||
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elastix::ElastixBase::elxSetObjectMacro | ( | MovingImagePyramidContainer | , |
ObjectContainerType | |||
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elastix::ElastixBase::elxSetObjectMacro | ( | InterpolatorContainer | , |
ObjectContainerType | |||
) |
elastix::ElastixBase::elxSetObjectMacro | ( | ImageSamplerContainer | , |
ObjectContainerType | |||
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elastix::ElastixBase::elxSetObjectMacro | ( | MetricContainer | , |
ObjectContainerType | |||
) |
elastix::ElastixBase::elxSetObjectMacro | ( | OptimizerContainer | , |
ObjectContainerType | |||
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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 | |||
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elastix::ElastixBase::elxSetObjectMacro | ( | FixedMaskContainer | , |
DataObjectContainerType | |||
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elastix::ElastixBase::elxSetObjectMacro | ( | MovingMaskContainer | , |
DataObjectContainerType | |||
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elastix::ElastixBase::elxSetObjectMacro | ( | FixedImageFileNameContainer | , |
FileNameContainerType | |||
) |
elastix::ElastixBase::elxSetObjectMacro | ( | MovingImageFileNameContainer | , |
FileNameContainerType | |||
) |
elastix::ElastixBase::elxSetObjectMacro | ( | FixedMaskFileNameContainer | , |
FileNameContainerType | |||
) |
elastix::ElastixBase::elxSetObjectMacro | ( | MovingMaskFileNameContainer | , |
FileNameContainerType | |||
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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.
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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.
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Cast to ITKBaseType.
Definition at line 177 of file elxElastixBase.h.
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Definition at line 188 of file elxElastixBase.h.
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Get the default precision of xout. (The value assumed when no DefaultOutputPrecision is given in the parameter file.
Definition at line 320 of file elxElastixBase.h.
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Get whether direction cosines should be taken into account (true) or ignored (false). This depends on the UseDirectionCosines parameter.
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Empty Run()-function to be overridden.
Implemented in elastix::ElastixTemplate< TFixedImage, TMovingImage >.
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Set the database index of the instantiated elastix object.
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Set/Get the original fixed image direction as a flat array (d11 d21 d31 d21 d22 etc )
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Definition at line 344 of file elxElastixBase.h.
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Definition at line 340 of file elxElastixBase.h.
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Definition at line 343 of file elxElastixBase.h.
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Definition at line 435 of file elxElastixBase.h.
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Definition at line 465 of file elxElastixBase.h.
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The Image and Mask containers. These are stored as pointers to itk::DataObject.
Definition at line 452 of file elxElastixBase.h.
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The image and mask FileNameContainers.
Definition at line 458 of file elxElastixBase.h.
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The component containers. These containers contain SmartPointer's to itk::Object.
Definition at line 440 of file elxElastixBase.h.
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Definition at line 454 of file elxElastixBase.h.
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Definition at line 460 of file elxElastixBase.h.
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Definition at line 443 of file elxElastixBase.h.
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The initial and final transform.
Definition at line 464 of file elxElastixBase.h.
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Definition at line 442 of file elxElastixBase.h.
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Definition at line 433 of file elxElastixBase.h.
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Definition at line 444 of file elxElastixBase.h.
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Definition at line 453 of file elxElastixBase.h.
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Definition at line 459 of file elxElastixBase.h.
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Definition at line 441 of file elxElastixBase.h.
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Definition at line 455 of file elxElastixBase.h.
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Definition at line 461 of file elxElastixBase.h.
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Definition at line 445 of file elxElastixBase.h.
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Definition at line 346 of file elxElastixBase.h.
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Definition at line 446 of file elxElastixBase.h.
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Definition at line 448 of file elxElastixBase.h.
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Definition at line 447 of file elxElastixBase.h.
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Definition at line 449 of file elxElastixBase.h.
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Use or ignore direction cosines.
Definition at line 468 of file elxElastixBase.h.
Generated on 05-01-2014 for elastix by ![]() |
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