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#include <elxElastixTemplate.h>
The main elastix class, which connects components and invokes the BeforeRegistration(), BeforeEachResolution(), etc. methods.
The ElastixTemplate class ...
WriteTransformParametersEachIteration: Controls whether to save a transform parameter file to disk in every iteration.
example: (WriteTransformParametersEachIteration "true")
This parameter can not be specified for each resolution separately. Default value: "false".
WriteTransformParametersEachResolution: Controls whether to save a transform parameter file to disk in every resolution.
example: (WriteTransformParametersEachResolution "true")
This parameter can not be specified for each resolution separately. Default value: "false".
UseDirectionCosines: Controls whether to use or ignore the direction cosines (world matrix, transform matrix) set in the images. Voxel spacing and image origin are always taken into account, regardless the setting of this parameter.
example: (UseDirectionCosines "true")
Default: false. Recommended: true. The default value is false for backward compatibility reasons. This parameter was introduced in elastix 4.3. Setting it to false means that you choose to ignore important information from the image, which relates voxel coordinates to world coordinates. Ignoring it may easily lead to left/right swaps for example, which could skrew up a (medical) analysis.
Definition at line 113 of file elxElastixTemplate.h.
Static Public Member Functions | |
static Pointer | New () |
Protected Types | |
typedef Superclass2::MultipleImageLoader< FixedImageType > | FixedImageLoaderType |
typedef Superclass2::MultipleImageLoader< FixedMaskType > | FixedMaskLoaderType |
typedef Superclass2::MultipleImageLoader< MovingImageType > | MovingImageLoaderType |
typedef Superclass2::MultipleImageLoader< MovingMaskType > | MovingMaskLoaderType |
Protected Member Functions | |
void | CallInEachComponent (PtrToMemberFunction func) |
int | CallInEachComponentInt (PtrToMemberFunction2 func) |
virtual void | ConfigureComponents (Self *This) |
virtual void | CreateTransformParameterFile (const std::string FileName, const bool ToLog) |
virtual void | CreateTransformParametersMap (void) |
ElastixTemplate () | |
virtual ParameterMapType | GetTransformParametersMap (void) const |
virtual void | OpenIterationInfoFile (void) |
virtual void | SetOriginalFixedImageDirection (const FixedImageDirectionType &arg) |
virtual | ~ElastixTemplate () |
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ElastixBase () | |
virtual | ~ElastixBase () |
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BaseComponent () | |
virtual | ~BaseComponent () |
Private Member Functions | |
ElastixTemplate (const Self &) | |
void | operator= (const Self &) |
typedef AfterEachIterationCommandType::Pointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::AfterEachIterationCommandPointer |
Definition at line 184 of file elxElastixTemplate.h.
typedef itk::SimpleMemberCommand< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::AfterEachIterationCommandType |
Definition at line 181 of file elxElastixTemplate.h.
typedef AfterEachResolutionCommandType::Pointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::AfterEachResolutionCommandPointer |
Definition at line 183 of file elxElastixTemplate.h.
typedef itk::SimpleMemberCommand< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::AfterEachResolutionCommandType |
Definition at line 180 of file elxElastixTemplate.h.
typedef BaseComponent elastix::ElastixTemplate< TFixedImage, TMovingImage >::BaseComponentType |
Definition at line 172 of file elxElastixTemplate.h.
typedef BeforeEachResolutionCommandType::Pointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::BeforeEachResolutionCommandPointer |
Definition at line 182 of file elxElastixTemplate.h.
typedef itk::SimpleMemberCommand< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::BeforeEachResolutionCommandType |
Commands that react on Events and call Self::Function(void).
Definition at line 179 of file elxElastixTemplate.h.
typedef Superclass2::ConfigurationPointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::ConfigurationPointer |
Definition at line 132 of file elxElastixTemplate.h.
typedef Superclass2::ConfigurationType elastix::ElastixTemplate< TFixedImage, TMovingImage >::ConfigurationType |
Typedefs inherited from Superclass2.
Definition at line 128 of file elxElastixTemplate.h.
typedef itk::SmartPointer< const Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::ConstPointer |
Definition at line 122 of file elxElastixTemplate.h.
typedef itk::CostFunction::ParametersValueType elastix::ElastixTemplate< TFixedImage, TMovingImage >::CoordRepType |
Type for representation of the transform coordinates.
Definition at line 169 of file elxElastixTemplate.h.
typedef Superclass2::DataObjectContainerPointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::DataObjectContainerPointer |
Definition at line 141 of file elxElastixTemplate.h.
typedef Superclass2::DataObjectContainerType elastix::ElastixTemplate< TFixedImage, TMovingImage >::DataObjectContainerType |
Definition at line 138 of file elxElastixTemplate.h.
typedef Superclass2::DataObjectPointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::DataObjectPointer |
Definition at line 136 of file elxElastixTemplate.h.
typedef Superclass2::DataObjectType elastix::ElastixTemplate< TFixedImage, TMovingImage >::DataObjectType |
Definition at line 134 of file elxElastixTemplate.h.
typedef Superclass2::FileNameContainerPointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::FileNameContainerPointer |
Definition at line 142 of file elxElastixTemplate.h.
typedef Superclass2::FileNameContainerType elastix::ElastixTemplate< TFixedImage, TMovingImage >::FileNameContainerType |
Definition at line 139 of file elxElastixTemplate.h.
typedef FixedImageType::DirectionType elastix::ElastixTemplate< TFixedImage, TMovingImage >::FixedImageDirectionType |
Typedef for the UseDirectionCosines option.
Definition at line 166 of file elxElastixTemplate.h.
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Classes that contain a function to load multiple images, given a filename container.
Definition at line 329 of file elxElastixTemplate.h.
typedef FixedImageType::Pointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::FixedImagePointer |
Definition at line 147 of file elxElastixTemplate.h.
typedef FixedImagePyramidBase< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::FixedImagePyramidBaseType |
The elastix basecomponent types.
Definition at line 187 of file elxElastixTemplate.h.
typedef TFixedImage elastix::ElastixTemplate< TFixedImage, TMovingImage >::FixedImageType |
Typedef's for this class.
Definition at line 145 of file elxElastixTemplate.h.
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Definition at line 331 of file elxElastixTemplate.h.
typedef FixedMaskType::Pointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::FixedMaskPointer |
Definition at line 162 of file elxElastixTemplate.h.
typedef itk::Image< MaskPixelType, FixedDimension > elastix::ElastixTemplate< TFixedImage, TMovingImage >::FixedMaskType |
Definition at line 160 of file elxElastixTemplate.h.
typedef elx::ImageSamplerBase< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::ImageSamplerBaseType |
Definition at line 190 of file elxElastixTemplate.h.
typedef MovingImageType elastix::ElastixTemplate< TFixedImage, TMovingImage >::InputImageType |
Typedef's for ApplyTransform.
Definition at line 205 of file elxElastixTemplate.h.
typedef InterpolatorBase< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::InterpolatorBaseType |
Definition at line 189 of file elxElastixTemplate.h.
typedef unsigned char elastix::ElastixTemplate< TFixedImage, TMovingImage >::MaskPixelType |
Types for the masks.
Definition at line 159 of file elxElastixTemplate.h.
typedef MetricBase< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::MetricBaseType |
Definition at line 191 of file elxElastixTemplate.h.
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Definition at line 330 of file elxElastixTemplate.h.
typedef MovingImageType::Pointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::MovingImagePointer |
Definition at line 148 of file elxElastixTemplate.h.
typedef MovingImagePyramidBase< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::MovingImagePyramidBaseType |
Definition at line 188 of file elxElastixTemplate.h.
typedef TMovingImage elastix::ElastixTemplate< TFixedImage, TMovingImage >::MovingImageType |
Definition at line 146 of file elxElastixTemplate.h.
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Definition at line 332 of file elxElastixTemplate.h.
typedef MovingMaskType::Pointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::MovingMaskPointer |
Definition at line 163 of file elxElastixTemplate.h.
typedef itk::Image< MaskPixelType, MovingDimension > elastix::ElastixTemplate< TFixedImage, TMovingImage >::MovingMaskType |
Definition at line 161 of file elxElastixTemplate.h.
typedef Superclass2::ObjectContainerPointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::ObjectContainerPointer |
Definition at line 140 of file elxElastixTemplate.h.
typedef Superclass2::ObjectContainerType elastix::ElastixTemplate< TFixedImage, TMovingImage >::ObjectContainerType |
Definition at line 137 of file elxElastixTemplate.h.
typedef Superclass2::ObjectPointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::ObjectPointer |
Definition at line 135 of file elxElastixTemplate.h.
typedef Superclass2::ObjectType elastix::ElastixTemplate< TFixedImage, TMovingImage >::ObjectType |
Definition at line 133 of file elxElastixTemplate.h.
typedef OptimizerBase< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::OptimizerBaseType |
Definition at line 192 of file elxElastixTemplate.h.
typedef MovingImageType elastix::ElastixTemplate< TFixedImage, TMovingImage >::OutputImageType |
Definition at line 206 of file elxElastixTemplate.h.
typedef itk::ParameterMapInterface::ParameterMapType elastix::ElastixTemplate< TFixedImage, TMovingImage >::ParameterMapType |
Typedef that is used in the elastix dll version.
Definition at line 209 of file elxElastixTemplate.h.
typedef itk::SmartPointer< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::Pointer |
Definition at line 121 of file elxElastixTemplate.h.
typedef void(BaseComponentType::* elastix::ElastixTemplate< TFixedImage, TMovingImage >::PtrToMemberFunction) (void) |
A Pointer to a member function of a BaseComponentType.
Definition at line 175 of file elxElastixTemplate.h.
typedef int(BaseComponentType::* elastix::ElastixTemplate< TFixedImage, TMovingImage >::PtrToMemberFunction2) (void) |
Definition at line 176 of file elxElastixTemplate.h.
typedef RegistrationBase< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::RegistrationBaseType |
Definition at line 193 of file elxElastixTemplate.h.
typedef ResampleInterpolatorBase< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::ResampleInterpolatorBaseType |
Definition at line 195 of file elxElastixTemplate.h.
typedef ResamplerBase< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::ResamplerBaseType |
Definition at line 194 of file elxElastixTemplate.h.
typedef itk::DataObject elastix::ElastixTemplate< TFixedImage, TMovingImage >::ResultImageType |
Result image
Definition at line 151 of file elxElastixTemplate.h.
typedef ElastixTemplate elastix::ElastixTemplate< TFixedImage, TMovingImage >::Self |
Standard itk.
Definition at line 118 of file elxElastixTemplate.h.
typedef itk::Object elastix::ElastixTemplate< TFixedImage, TMovingImage >::Superclass1 |
Definition at line 119 of file elxElastixTemplate.h.
typedef ElastixBase elastix::ElastixTemplate< TFixedImage, TMovingImage >::Superclass2 |
Definition at line 120 of file elxElastixTemplate.h.
typedef itk::TimeProbe elastix::ElastixTemplate< TFixedImage, TMovingImage >::TimerType |
Typedef's for Timer class.
Definition at line 199 of file elxElastixTemplate.h.
typedef elx::TransformBase< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::TransformBaseType |
Definition at line 196 of file elxElastixTemplate.h.
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Definition at line 326 of file elxElastixTemplate.h.
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Reimplemented from elastix::BaseComponent.
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Reimplemented from elastix::BaseComponent.
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Reimplemented from elastix::BaseComponent.
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Implements elastix::ElastixBase.
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The Callback functions.
Reimplemented from elastix::BaseComponent.
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Reimplemented from elastix::BaseComponent.
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Reimplemented from elastix::BaseComponent.
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Used by the callback functions, BeforeEachResolution() etc.). This method calls a function in each component, in the following order:
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Call in each component SetElastix(This) and set its ComponentLabel (for example "Metric1"). This makes sure that the component knows its own function in the registration process.
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CreateTransformParameterFile.
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CreateTransformParametersMap.
Implements elastix::ElastixBase.
elastix::ElastixTemplate< TFixedImage, TMovingImage >::elxGetBaseMacro | ( | FixedImagePyramid | , |
FixedImagePyramidBaseType | |||
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Functions to set/get pointers to the elastix components. Get the components as pointers to elxBaseType.
elastix::ElastixTemplate< TFixedImage, TMovingImage >::elxGetBaseMacro | ( | MovingImagePyramid | , |
MovingImagePyramidBaseType | |||
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elastix::ElastixTemplate< TFixedImage, TMovingImage >::elxGetBaseMacro | ( | Interpolator | , |
InterpolatorBaseType | |||
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elastix::ElastixTemplate< TFixedImage, TMovingImage >::elxGetBaseMacro | ( | ImageSampler | , |
ImageSamplerBaseType | |||
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elastix::ElastixTemplate< TFixedImage, TMovingImage >::elxGetBaseMacro | ( | Metric | , |
MetricBaseType | |||
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elastix::ElastixTemplate< TFixedImage, TMovingImage >::elxGetBaseMacro | ( | Optimizer | , |
OptimizerBaseType | |||
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elastix::ElastixTemplate< TFixedImage, TMovingImage >::elxGetBaseMacro | ( | Registration | , |
RegistrationBaseType | |||
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elastix::ElastixTemplate< TFixedImage, TMovingImage >::elxGetBaseMacro | ( | Resampler | , |
ResamplerBaseType | |||
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elastix::ElastixTemplate< TFixedImage, TMovingImage >::elxGetBaseMacro | ( | ResampleInterpolator | , |
ResampleInterpolatorBaseType | |||
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elastix::ElastixTemplate< TFixedImage, TMovingImage >::elxGetBaseMacro | ( | Transform | , |
TransformBaseType | |||
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Run-time type information (and related methods).
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Return configuration from vector of configurations. Library only.
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Definition at line 311 of file elxElastixTemplate.h.
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Get the name of the current transform parameter file.
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Get pointers to the images. They are obtained from the {Fixed,Moving}ImageContainer and casted to the appropriate type.
Definition at line 228 of file elxElastixTemplate.h.
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Get pointers to the masks. They are obtained from the {Fixed,Moving}MaskContainer and casted to the appropriate type.
Definition at line 247 of file elxElastixTemplate.h.
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Get the iteration number.
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Definition at line 236 of file elxElastixTemplate.h.
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Definition at line 255 of file elxElastixTemplate.h.
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Get the original direction cosines of the fixed image. Returns false if it failed to determine the original fixed image direction. In that case the direction var is left unchanged. If no fixed image is present, it tries to read it from the parameter file.
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Get pointers to the result image. They are obtained from the ResultImageContainer and casted to the appropriate type.
Definition at line 266 of file elxElastixTemplate.h.
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GetTransformParametersMap.
Implements elastix::ElastixBase.
elastix::ElastixTemplate< TFixedImage, TMovingImage >::itkStaticConstMacro | ( | Dimension | , |
unsigned | int, | ||
FixedImageType::ImageDimension | |||
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For using the Dimensions.
elastix::ElastixTemplate< TFixedImage, TMovingImage >::itkStaticConstMacro | ( | FixedDimension | , |
unsigned | int, | ||
FixedImageType::ImageDimension | |||
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elastix::ElastixTemplate< TFixedImage, TMovingImage >::itkStaticConstMacro | ( | MovingDimension | , |
unsigned | int, | ||
MovingImageType::ImageDimension | |||
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Method for creation through the object factory.
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Open the IterationInfoFile, where the table with iteration info is written to.
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Main functions: Run() for registration, and ApplyTransform() for just applying a transform to an image.
Implements elastix::ElastixBase.
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Set configuration vector. Library only.
Implements elastix::ElastixBase.
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Set the direction in the superclass' m_OriginalFixedImageDirection variable
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Definition at line 336 of file elxElastixTemplate.h.
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Definition at line 337 of file elxElastixTemplate.h.
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CallBack commands.
Definition at line 335 of file elxElastixTemplate.h.
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A vector of configuration objects, needed when transformix is used as library.
Definition at line 348 of file elxElastixTemplate.h.
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Store the CurrentTransformParameterFileName.
Definition at line 345 of file elxElastixTemplate.h.
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Count the number of iterations.
Definition at line 351 of file elxElastixTemplate.h.
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Definition at line 369 of file elxElastixTemplate.h.
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Definition at line 341 of file elxElastixTemplate.h.
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Definition at line 342 of file elxElastixTemplate.h.
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Timers.
Definition at line 340 of file elxElastixTemplate.h.
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Stores transformation parameters map.
Definition at line 364 of file elxElastixTemplate.h.
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