Public Member Functions |
virtual void | AfterRegistrationBase (void) |
virtual int | ApplyTransform (void)=0 |
virtual int | BeforeAllBase (void) |
virtual int | BeforeAllTransformixBase (void) |
virtual void | BeforeRegistrationBase (void) |
| 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) |
| 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 (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 (FixedImageFileNameContainer, FileNameContainerType) |
| elxSetObjectMacro (MovingImageFileNameContainer, FileNameContainerType) |
| elxSetObjectMacro (FixedMaskFileNameContainer, FileNameContainerType) |
| elxSetObjectMacro (MovingMaskFileNameContainer, FileNameContainerType) |
| elxSetObjectMacro (InitialTransform, ObjectType) |
| elxSetObjectMacro (FinalTransform, ObjectType) |
virtual ITKBaseType * | GetAsITKBaseType (void) |
virtual DBIndexType | GetDBIndex (void) |
virtual int | GetDefaultOutputPrecision (void) const |
virtual const
FlatDirectionCosinesType & | GetOriginalFixedImageDirectionFlat (void) const |
virtual bool | GetUseDirectionCosines (void) const |
virtual int | Run (void)=0 |
virtual void | SetDBIndex (DBIndexType _arg) |
virtual void | SetOriginalFixedImageDirectionFlat (const FlatDirectionCosinesType &arg) |
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) |
virtual const char * | elxGetClassName (void) const |
virtual const char * | GetComponentLabel (void) const |
virtual void | SetComponentLabel (const char *label, unsigned int idx) |
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.
- Parameters:
- 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
- Command line arguments:
- -m: mandatory argument for elastix with the file name of the moving image.
example: -m movingImage.mhd
- Command line arguments:
- -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
- Command line arguments:
- -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.
- Command line arguments:
- -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
- Command line arguments:
- -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
- Command line arguments:
- -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.
- Command line arguments:
- -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".
- Command line arguments:
- -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
- Command line arguments:
- -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 141 of file elxElastixBase.h.