SimpleITK
2.0.0
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Deformably register two images using a diffeomorphic demons algorithm. More...
#include <sitkDiffeomorphicDemonsRegistrationFilter.h>
Public Types | |
using | PixelIDTypeList = BasicPixelIDTypeList |
using | Self = DiffeomorphicDemonsRegistrationFilter |
enum | UseGradientTypeType { Symmetric, Fixed, WarpedMoving, MappedMoving } |
Public Types inherited from itk::simple::ImageFilter | |
using | Self = ImageFilter |
Public Types inherited from itk::simple::ProcessObject | |
using | Self = ProcessObject |
Public Member Functions | |
DiffeomorphicDemonsRegistrationFilter () | |
Image | Execute (const Image &fixedImage, const Image &movingImage) |
Image | Execute (const Image &fixedImage, const Image &movingImage, const Image &initialDisplacementField) |
uint32_t | GetElapsedIterations () const |
Number of iterations run. More... | |
double | GetIntensityDifferenceThreshold () const |
double | GetMaximumError () const |
unsigned int | GetMaximumKernelWidth () const |
double | GetMaximumRMSError () const |
double | GetMaximumUpdateStepLength () const |
double | GetMetric () const |
std::string | GetName () const |
uint32_t | GetNumberOfIterations () const |
double | GetRMSChange () const |
bool | GetSmoothDisplacementField () const |
bool | GetSmoothUpdateField () const |
std::vector< double > | GetStandardDeviations () const |
std::vector< double > | GetUpdateFieldStandardDeviations () const |
bool | GetUseFirstOrderExp () const |
UseGradientTypeType | GetUseGradientType () const |
bool | GetUseImageSpacing () const |
Self & | SetIntensityDifferenceThreshold (double IntensityDifferenceThreshold) |
Self & | SetMaximumError (double MaximumError) |
Self & | SetMaximumKernelWidth (unsigned int MaximumKernelWidth) |
Self & | SetMaximumRMSError (double MaximumRMSError) |
Self & | SetMaximumUpdateStepLength (double MaximumUpdateStepLength) |
Self & | SetNumberOfIterations (uint32_t NumberOfIterations) |
Self & | SetSmoothDisplacementField (bool SmoothDisplacementField) |
Self & | SetSmoothUpdateField (bool SmoothUpdateField) |
Self & | SetStandardDeviations (double value) |
Self & | SetStandardDeviations (std::vector< double > StandardDeviations) |
Self & | SetUpdateFieldStandardDeviations (double value) |
Self & | SetUpdateFieldStandardDeviations (std::vector< double > UpdateFieldStandardDeviations) |
Self & | SetUseFirstOrderExp (bool UseFirstOrderExp) |
Self & | SetUseGradientType (UseGradientTypeType UseGradientType) |
Self & | SetUseImageSpacing (bool UseImageSpacing) |
Self & | SmoothDisplacementFieldOff () |
Self & | SmoothDisplacementFieldOn () |
Self & | SmoothUpdateFieldOff () |
Self & | SmoothUpdateFieldOn () |
std::string | ToString () const |
Self & | UseFirstOrderExpOff () |
Self & | UseFirstOrderExpOn () |
Self & | UseImageSpacingOff () |
Self & | UseImageSpacingOn () |
virtual | ~DiffeomorphicDemonsRegistrationFilter () |
Public Member Functions inherited from itk::simple::ImageFilter | |
ImageFilter () | |
virtual | ~ImageFilter ()=0 |
Public Member Functions inherited from itk::simple::ProcessObject | |
virtual void | Abort () |
virtual int | AddCommand (itk::simple::EventEnum event, const std::function< void()> &func) |
Directly add a callback to observe an event. More... | |
virtual int | AddCommand (itk::simple::EventEnum event, itk::simple::Command &cmd) |
Add a Command Object to observer the event. More... | |
virtual float | GetProgress () const |
An Active Measurement of the progress of execution. More... | |
virtual bool | HasCommand (itk::simple::EventEnum event) const |
Query of this object has any registered commands for event. More... | |
ProcessObject () | |
virtual void | RemoveAllCommands () |
Remove all registered commands. More... | |
virtual | ~ProcessObject () |
virtual void | DebugOn () |
virtual void | DebugOff () |
virtual bool | GetDebug () const |
virtual void | SetDebug (bool debugFlag) |
virtual void | SetNumberOfThreads (unsigned int n) |
virtual unsigned int | GetNumberOfThreads () const |
virtual void | SetNumberOfWorkUnits (unsigned int n) |
virtual unsigned int | GetNumberOfWorkUnits () const |
Private Types | |
using | MemberFunctionType = Image(Self::*)(const Image *fixedImage, const Image *movingImage, const Image *initialDisplacementField) |
Private Member Functions | |
template<class TImageType > | |
Image | ExecuteInternal (const Image *fixedImage, const Image *movingImage, const Image *initialDisplacementField) |
Private Attributes | |
itk::ProcessObject * | m_Filter {nullptr} |
double | m_IntensityDifferenceThreshold {0.001} |
double | m_MaximumError {0.1} |
unsigned int | m_MaximumKernelWidth {30u} |
double | m_MaximumRMSError {0.02} |
double | m_MaximumUpdateStepLength {0.5} |
std::unique_ptr< detail::MemberFunctionFactory< MemberFunctionType > > | m_MemberFactory |
uint32_t | m_NumberOfIterations {10u} |
std::function< uint32_t()> | m_pfGetElapsedIterations |
std::function< double()> | m_pfGetMetric |
double | m_RMSChange {0.0} |
bool | m_SmoothDisplacementField {true} |
bool | m_SmoothUpdateField {false} |
std::vector< double > | m_StandardDeviations {std::vector<double>(3, 1.0)} |
std::vector< double > | m_UpdateFieldStandardDeviations {std::vector<double>(3, 1.0)} |
bool | m_UseFirstOrderExp {false} |
UseGradientTypeType | m_UseGradientType {itk::simple::DiffeomorphicDemonsRegistrationFilter::Symmetric} |
bool | m_UseImageSpacing {true} |
Friends | |
struct | detail::MemberFunctionAddressor< MemberFunctionType > |
Additional Inherited Members | |
Static Public Member Functions inherited from itk::simple::ProcessObject | |
static bool | GetGlobalDefaultDebug () |
static void | GlobalDefaultDebugOff () |
static void | GlobalDefaultDebugOn () |
static void | SetGlobalDefaultDebug (bool debugFlag) |
static void | GlobalWarningDisplayOn () |
static void | GlobalWarningDisplayOff () |
static void | SetGlobalWarningDisplay (bool flag) |
static bool | GetGlobalWarningDisplay () |
static double | GetGlobalDefaultCoordinateTolerance () |
Access the global tolerance to determine congruent spaces. More... | |
static void | SetGlobalDefaultCoordinateTolerance (double) |
Access the global tolerance to determine congruent spaces. More... | |
static double | GetGlobalDefaultDirectionTolerance () |
Access the global tolerance to determine congruent spaces. More... | |
static void | SetGlobalDefaultDirectionTolerance (double) |
Access the global tolerance to determine congruent spaces. More... | |
static bool | SetGlobalDefaultThreader (const std::string &threader) |
Set/Get the default threader used for process objects. More... | |
static std::string | GetGlobalDefaultThreader () |
Set/Get the default threader used for process objects. More... | |
static void | SetGlobalDefaultNumberOfThreads (unsigned int n) |
static unsigned int | GetGlobalDefaultNumberOfThreads () |
Set/Get the default threader used for process objects. More... | |
Protected Member Functions inherited from itk::simple::ImageFilter | |
void | CheckImageMatchingDimension (const Image &image1, const Image &image2, const std::string &image2Name) |
void | CheckImageMatchingPixelType (const Image &image1, const Image &image2, const std::string &image2Name) |
void | CheckImageMatchingSize (const Image &image1, const Image &image2, const std::string &image2Name) |
Protected Member Functions inherited from itk::simple::ProcessObject | |
virtual unsigned long | AddITKObserver (const itk::EventObject &, itk::Command *) |
virtual itk::ProcessObject * | GetActiveProcess () |
virtual void | OnActiveProcessDelete () |
virtual void | onCommandDelete (const itk::simple::Command *cmd) noexcept |
virtual void | PreUpdate (itk::ProcessObject *p) |
virtual void | RemoveITKObserver (EventCommand &e) |
Protected Member Functions inherited from itk::simple::NonCopyable | |
NonCopyable ()=default | |
NonCopyable (const NonCopyable &)=delete | |
NonCopyable & | operator= (const NonCopyable &)=delete |
Static Protected Member Functions inherited from itk::simple::ImageFilter | |
template<class TImageType > | |
static void | FixNonZeroIndex (TImageType *img) |
Static Protected Member Functions inherited from itk::simple::ProcessObject | |
template<class TImageType > | |
static TImageType::ConstPointer | CastImageToITK (const Image &img) |
template<class TPixelType , unsigned int VImageDimension, unsigned int VLength, template< typename, unsigned int > class TVector> | |
static Image | CastITKToImage (itk::Image< TVector< TPixelType, VLength >, VImageDimension > *img) |
template<class TImageType > | |
static Image | CastITKToImage (TImageType *img) |
static const itk::EventObject & | GetITKEventObject (EventEnum e) |
template<typename T > | |
static std::ostream & | ToStringHelper (std::ostream &os, const T &v) |
static std::ostream & | ToStringHelper (std::ostream &os, const char &v) |
static std::ostream & | ToStringHelper (std::ostream &os, const signed char &v) |
static std::ostream & | ToStringHelper (std::ostream &os, const unsigned char &v) |
Deformably register two images using a diffeomorphic demons algorithm.
This class was contributed by Tom Vercauteren, INRIA & Mauna Kea Technologies, based on a variation of the DemonsRegistrationFilter . The basic modification is to use diffeomorphism exponentials.
See T. Vercauteren, X. Pennec, A. Perchant and N. Ayache, "Non-parametric Diffeomorphic Image Registration with the Demons Algorithm", Proc. of MICCAI 2007.
DiffeomorphicDemonsRegistrationFilter implements the demons deformable algorithm that register two images by computing the deformation field which will map a moving image onto a fixed image.
A deformation field is represented as a image whose pixel type is some vector type with at least N elements, where N is the dimension of the fixed image. The vector type must support element access via operator []. It is assumed that the vector elements behave like floating point scalars.
This class is templated over the fixed image type, moving image type and the deformation field type.
The input fixed and moving images are set via methods SetFixedImage and SetMovingImage respectively. An initial deformation field maybe set via SetInitialDisplacementField or SetInput. If no initial field is set, a zero field is used as the initial condition.
The output deformation field can be obtained via methods GetOutput or GetDisplacementField.
This class make use of the finite difference solver hierarchy. Update for each iteration is computed in DemonsRegistrationFunction .
This implementation was taken from the Insight Journal paper: https://hdl.handle.net/1926/510
Definition at line 69 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Setup for member function dispatching
Definition at line 270 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
Define the pixels types supported by this filter
Definition at line 81 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
using itk::simple::DiffeomorphicDemonsRegistrationFilter::Self = DiffeomorphicDemonsRegistrationFilter |
Definition at line 71 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
Enumerator | |
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Symmetric | |
Fixed | |
WarpedMoving | |
MappedMoving |
Definition at line 113 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Destructor
itk::simple::DiffeomorphicDemonsRegistrationFilter::DiffeomorphicDemonsRegistrationFilter | ( | ) |
Default Constructor that takes no arguments and initializes default parameters
Image itk::simple::DiffeomorphicDemonsRegistrationFilter::Execute | ( | const Image & | fixedImage, |
const Image & | movingImage | ||
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Image itk::simple::DiffeomorphicDemonsRegistrationFilter::Execute | ( | const Image & | fixedImage, |
const Image & | movingImage, | ||
const Image & | initialDisplacementField | ||
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Execute the filter on the input image
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Number of iterations run.
This is an active measurement. It may be accessed while the filter is being executing in command call-backs and can be accessed after execution.
Definition at line 234 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 214 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set/Get the desired maximum error of the Guassian kernel approximate.
Definition at line 205 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set/Get the desired limits of the Gaussian kernel width.
Definition at line 195 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 111 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 144 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Get the metric value. The metric value is the mean square difference in intensity between the fixed image and transforming moving image computed over the the overlapping region between the two images. This value is calculated for the current iteration
This is an active measurement. It may be accessed while the filter is being executing in command call-backs and can be accessed after execution.
Definition at line 251 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Name of this class
Implements itk::simple::ProcessObject.
Definition at line 255 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 103 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set/Get the root mean squared change of the previous iteration. May not be used by all solvers.
This is a measurement. Its value is updated in the Execute methods, so the value will only be valid after an execution.
Definition at line 242 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set/Get whether the displacement field is smoothed (regularized). Smoothing the displacement yields a solution elastic in nature. If SmoothDisplacementField is on, then the displacement field is smoothed with a Gaussian whose standard deviations are specified with SetStandardDeviations()
Definition at line 158 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set/Get whether the update field is smoothed (regularized). Smoothing the update field yields a solution viscous in nature. If SmoothUpdateField is on, then the update field is smoothed with a Gaussian whose standard deviations are specified with SetUpdateFieldStandardDeviations()
Definition at line 172 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set/Get the Gaussian smoothing standard deviations for the displacement field. The values are set with respect to pixel coordinates.
Definition at line 95 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set the Gaussian smoothing standard deviations for the update field. The values are set with respect to pixel coordinates.
Definition at line 185 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Use a first-order approximation of the exponential. This amounts to using an update rule of the type s <- s o (Id + u) instead of s <- s o exp(u)
Definition at line 135 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 121 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 226 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set/Get the threshold below which the absolute difference of intensity yields a match. When the intensities match between a moving and fixed image pixel, the update vector (for that iteration) will be the zero vector. Default is 0.001.
Definition at line 210 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set/Get the desired maximum error of the Guassian kernel approximate.
Definition at line 200 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set/Get the desired limits of the Gaussian kernel width.
Definition at line 190 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 107 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set/Get the maximum length in terms of pixels of the vectors in the update buffer.
Definition at line 140 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 99 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set/Get whether the displacement field is smoothed (regularized). Smoothing the displacement yields a solution elastic in nature. If SmoothDisplacementField is on, then the displacement field is smoothed with a Gaussian whose standard deviations are specified with SetStandardDeviations()
Definition at line 149 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set/Get whether the update field is smoothed (regularized). Smoothing the update field yields a solution viscous in nature. If SmoothUpdateField is on, then the update field is smoothed with a Gaussian whose standard deviations are specified with SetUpdateFieldStandardDeviations()
Definition at line 163 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set the values of the StandardDeviations vector all to value
Definition at line 90 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set/Get the Gaussian smoothing standard deviations for the displacement field. The values are set with respect to pixel coordinates.
Definition at line 87 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set the values of the UpdateFieldStandardDeviations vector all to value
Definition at line 180 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set the Gaussian smoothing standard deviations for the update field. The values are set with respect to pixel coordinates.
Definition at line 177 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Use a first-order approximation of the exponential. This amounts to using an update rule of the type s <- s o (Id + u) instead of s <- s o exp(u)
Definition at line 126 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 117 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 218 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 153 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set the value of SmoothDisplacementField to true or false respectfully.
Definition at line 152 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 167 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set the value of SmoothUpdateField to true or false respectfully.
Definition at line 166 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Print ourselves out
Reimplemented from itk::simple::ProcessObject.
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Definition at line 130 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set the value of UseFirstOrderExp to true or false respectfully.
Definition at line 129 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 222 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set the value of UseImageSpacing to true or false respectfully.
Definition at line 221 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 274 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 315 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 303 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 301 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 299 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 285 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 291 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 276 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 282 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 308 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 312 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 310 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 293 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 295 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 279 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 297 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 289 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 287 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 305 of file sitkDiffeomorphicDemonsRegistrationFilter.h.