itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage > Class Template Reference

FEM Image registration filter. The image registration problem is modeled here with the finite element method. Image registration is, in general, an ill-posed problem. Thus, we use an optimization scheme where the optimization criterion is given by a regularized variational energy. The variational energy arises from modeling the image as a physical body on which external forces act. The body is allowed to deform so as to minimize the applied force. The resistance of the physical body to deformation, determined by the physics associated with the body, serves to regularize the solution. The forces applied to the body are, generally, highly non-linear and so the body is allowed to deform slowly and incrementally. The direction it deforms follows the gradient of the potential energy (the force) we define. The potential energies we may choose from are given by the itk image-to-image metrics. The choices and the associated direction of descent are : Mean Squares (minimize), Normalized Cross-Correlation (maximize) Mutual Information (maximize). Note that we have to set the direction (SetDescentDirection) when we choose a metric. The forces driving the problem may also be given by user-supplied landmarks. The corners of the image, in this example, are always pinned. This example is designed for 2D or 3D images. A rectilinear mesh is generated automatically given the correct element type (Quadrilateral or Hexahedral). Our specific Solver for this example uses trapezoidal time stepping. This is a method for solving a second-order PDE in time. The solution is penalized by the zeroth (mass matrix) and first derivatives (stiffness matrix) of the shape functions. There is an option to perform a line search on the energy after each iteration. Optimal parameter settings require experimentation. The following approach tends to work well : Choose the relative size of density to elasticity (e.g. Rho / E ~= 1.) such that the image deforms locally and slowly. This also affects the stability of the solution. Choose the time step to control the size of the deformation at each step. Choose enough iterations to allow the solution to converge (this may be automated). More...

#include <itkFEMRegistrationFilter.h>

Inheritance diagram for itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >:

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Collaboration diagram for itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >:

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List of all members.

Classes

class FEMOF

Public Types

typedef SmartPointer< const Self > ConstPointer

typedef double CoordRepType

typedef DataObject::Pointer DataObjectPointer

typedef std::vector
< DataObjectPointer > DataObjectPointerArray

typedef
DataObjectPointerArray::size_type DataObjectPointerArraySizeType

typedef
VectorLinearInterpolateImageFunction
< FieldType, CoordRepType > DefaultInterpolatorType

typedef
itk::VectorExpandImageFilter
< FieldType, FieldType > ExpanderType

typedef
ExpanderType::ExpandFactorsType ExpandFactorsType

typedef
itk::ImageRegionIteratorWithIndex
< FieldType > FieldIterator

typedef itk::Image< VectorType,
itkGetStaticConstMacro(ImageDimension)> FieldType

typedef TFixedImage FixedImageType

typedef
itk::RecursiveMultiResolutionPyramidImageFilter
< FixedImageType,
FixedImageType > FixedPyramidType

typedef double Float

typedef
itk::ImageRegionIteratorWithIndex
< FloatImageType > FloatImageIterator

typedef Image< float,
itkGetStaticConstMacro(ImageDimension) > FloatImageType

typedef
itk::ImageRegionIteratorWithIndex
< FixedImageType > ImageIterator

typedef
FiniteDifferenceFunctionLoad
< MovingImageType,
FixedImageType > ImageMetricLoadType

typedef FixedImageType::SizeType ImageSizeType

typedef
itk::VectorIndexSelectionCastImageFilter
< FieldType, FloatImageType > IndexSelectCasterType

typedef
InputImageType::ConstPointer InputImageConstPointer

typedef InputImageType::PixelType InputImagePixelType

typedef InputImageType::Pointer InputImagePointer

typedef InputImageType::RegionType InputImageRegionType

typedef TMovingImage InputImageType

typedef InterpolatorType::Pointer InterpolatorPointer

typedef
VectorInterpolateImageFunction
< FieldType, CoordRepType > InterpolatorType

typedef std::vector< typename
LoadLandmark::Pointer > LandmarkArrayType

typedef LinearSystemWrapperItpack LinearSystemSolverType

typedef Load::ArrayType LoadArray

typedef MaterialLinearElasticity MaterialType

typedef
PDEDeformableRegistrationFunction
< FixedImageType,
MovingImageType, FieldType > MetricBaseType

typedef MetricBaseType::Pointer MetricBaseTypePointer

typedef TMovingImage MovingImageType

Public Member Functions

virtual void AbortGenerateDataOff ()

virtual void AbortGenerateDataOn ()

void ChooseMetric (float whichmetric)

void ComputeJacobian (float sign=1.0, FieldType *field=NULL, float smooth=0.0)

virtual LightObject::Pointer CreateAnother () const

virtual void DebugOff () const

virtual void DebugOn () const

virtual void Delete ()

void DoLineSearch (unsigned int b)

void DoMultiRes (bool b)

void EmployRegridding (unsigned int b)

void EnforceDiffeomorphism (float thresh, SolverType &S, bool onlywriteimages)

virtual void EnlargeOutputRequestedRegion (DataObject *)

virtual const bool & GetAbortGenerateData ()

Command * GetCommand (unsigned long tag)

std::string GetConfigFileName ()

bool GetDebug () const

FieldType * GetDeformationField ()

Float GetElasticity (unsigned int which=0)

std::string GetFixedFile ()

FixedImageType * GetFixedImage ()

ImageSizeType GetImageSize ()

DataObjectPointerArray & GetInputs ()

virtual InterpolatorType * GetInterpolator ()

FloatImageType * GetJacobianImage ()

const MetaDataDictionary & GetMetaDataDictionary (void) const

MetaDataDictionary & GetMetaDataDictionary (void)

std::string GetMovingFile ()

MovingImageType * GetMovingImage ()

virtual unsigned long GetMTime () const

MultiThreader * GetMultiThreader ()

virtual const char * GetNameOfClass () const

DataObjectPointerArraySizeType GetNumberOfInputs () const

virtual
DataObjectPointerArraySizeType GetNumberOfValidRequiredInputs () const

MovingImageType * GetOriginalMovingImage ()

virtual const float & GetProgress ()

virtual int GetReferenceCount () const

std::string GetResultsFileName ()

FixedImageType * GetWarpedImage ()

bool GetWriteDisplacements ()

virtual void GraftNthOutput (unsigned int idx, DataObject *output)

virtual void GraftOutput (DataObject *output)

bool HasObserver (const EventObject &event) const

void InvokeEvent (const EventObject &) const

void InvokeEvent (const EventObject &)

void IterativeSolve (SolverType &S)

itkStaticConstMacro (ImageDimension, unsigned int, FixedImageType::ImageDimension)

virtual DataObjectPointer MakeOutput (unsigned int idx)

virtual void Modified () const

void MultiResSolve ()

virtual void PrepareOutputs ()

void Print (std::ostream &os, Indent indent=0) const

void PrintVectorField (unsigned int modnum=1000)

virtual void PropagateRequestedRegion (DataObject *output)

bool ReadConfigFile (const char *)

virtual void Register () const

void RemoveAllObservers ()

void RemoveObserver (unsigned long tag)

virtual void ResetPipeline ()

void RunRegistration (void)

virtual void SetAbortGenerateData (bool _arg)

void SetAlpha (Float a)

void SetConfigFileName (const char *f)

void SetDebug (bool debugFlag) const

void SetDescentDirectionMaximize ()

void SetDescentDirectionMinimize ()

void SetDisplacementsFile (const char *r)

void SetElasticity (Float i, unsigned int which=0)

void SetElement (Element::Pointer e)

void SetEnergyReductionFactor (Float i)

void SetFixedFile (const char *t)

void SetFixedImage (FixedImageType *T)

void SetGamma (Float r, unsigned int which=0)

virtual void SetInterpolator (InterpolatorType *_arg)

void SetLandmarkFile (const char *l)

void SetLineSearchMaximumIterations (unsigned int f)

void SetMaterial (MaterialType::Pointer m)

void SetMaximumIterations (unsigned int i, unsigned int which)

void SetMaxLevel (unsigned int i)

void SetMetaDataDictionary (const MetaDataDictionary &rhs)

void SetMovingFile (const char *r)

void SetMovingImage (MovingImageType *R)

void SetNumberOfIntegrationPoints (unsigned int i, unsigned int which=0)

void SetNumLevels (unsigned int i)

virtual void SetProgress (float _arg)

virtual void SetReferenceCount (int)

void SetResultsFile (const char *r)

void SetResultsFileName (const char *f)

void SetRho (Float r, unsigned int which=0)

void SetTemp (Float i)

void SetTimeStep (Float i)

void SetWriteDisplacements (bool b)

virtual void UnRegister () const

virtual void Update ()

virtual void UpdateLargestPossibleRegion ()

virtual void UpdateOutputData (DataObject *output)

virtual void UpdateOutputInformation ()

void UpdateProgress (float amount)

void UseLandmarks (bool b)

void WarpImage (const MovingImageType *R)

int WriteDisplacementField (unsigned int index)

int WriteDisplacementFieldMultiComponent ()

void WriteWarpedImage (const char *fn)

unsigned long AddObserver (const EventObject &event, Command *) const

unsigned long AddObserver (const EventObject &event, Command *)

FEMRegistrationFilter ()

~FEMRegistrationFilter ()

const InputImageType * GetInput (unsigned int idx)

const InputImageType * GetInput (void)

virtual void SetInput (unsigned int, const TMovingImage *image)

virtual void SetInput (const InputImageType *image)

MetricBaseTypePointer GetMetric ()

void SetMetric (MetricBaseTypePointer MP)

DataObjectPointerArraySizeType GetNumberOfOutputs () const

DataObjectPointerArray & GetOutputs ()

virtual const int & GetNumberOfThreads ()

virtual void SetNumberOfThreads (int _arg)

OutputImageType * GetOutput (unsigned int idx)

OutputImageType * GetOutput (void)

virtual const bool & GetReleaseDataBeforeUpdateFlag ()

virtual void ReleaseDataBeforeUpdateFlagOff ()

virtual void ReleaseDataBeforeUpdateFlagOn ()

virtual void SetReleaseDataBeforeUpdateFlag (bool _arg)

virtual bool GetReleaseDataFlag () const

void ReleaseDataFlagOff ()

void ReleaseDataFlagOn ()

virtual void SetReleaseDataFlag (bool flag)

unsigned int GetWidthOfMetricRegion (unsigned int which=0)

void SetWidthOfMetricRegion (unsigned int i, unsigned int which=0)

itkStaticConstMacro (OutputImageDimension, unsigned int, TFixedImage::ImageDimension)

itkStaticConstMacro (InputImageDimension, unsigned int, TMovingImage::ImageDimension)

virtual void PopBackInput ()

virtual void PopFrontInput ()

virtual void PushBackInput (const InputImageType *image)

virtual void PushFrontInput (const InputImageType *image)

void SetDeformationField (FieldType *F)

void SetMeshPixelsPerElementAtEachResolution (unsigned int i, unsigned int which=0)

Static Public Member Functions

static void BreakOnError ()

static Pointer New ()

static bool GetGlobalWarningDisplay ()

static void GlobalWarningDisplayOff ()

static void GlobalWarningDisplayOn ()

static void SetGlobalWarningDisplay (bool flag)

Protected Types

typedef
ImageToImageFilterDetail::ImageRegionCopier
< itkGetStaticConstMacro(OutputImageDimension),
itkGetStaticConstMacro(InputImageDimension)> InputToOutputRegionCopierType

typedef
ImageToImageFilterDetail::ImageRegionCopier
< itkGetStaticConstMacro(InputImageDimension),
itkGetStaticConstMacro(OutputImageDimension)> OutputToInputRegionCopierType

typedef int InternalReferenceCountType

Protected Member Functions

virtual void AfterThreadedGenerateData ()

virtual void AllocateOutputs ()

void ApplyImageLoads (SolverType &S, MovingImageType *i1, FixedImageType *i2)

void ApplyLoads (SolverType &S, ImageSizeType Isz, double *spacing=NULL)

virtual void BeforeThreadedGenerateData ()

virtual void CacheInputReleaseDataFlags ()

virtual void CallCopyInputRegionToOutputRegion (OutputImageRegionType &destRegion, const InputImageRegionType &srcRegion)

virtual void CallCopyOutputRegionToInputRegion (InputImageRegionType &destRegion, const OutputImageRegionType &srcRegion)

void CreateLinearSystemSolver ()

void CreateMesh (double ElementsPerSide, Solver &S, ImageSizeType sz)

Float EvaluateEnergy ()

Float EvaluateResidual (SolverType &mySolver, Float t)

void FindBracketingTriplet (SolverType &mySolver, Float *a, Float *b, Float *c)

virtual void GenerateData ()

virtual void GenerateInputRequestedRegion ()

virtual void GenerateOutputInformation ()

virtual void GenerateOutputRequestedRegion (DataObject *output)

FloatImageType * GetMetricImage (FieldType *F)

Float GoldenSection (SolverType &mySolver, Float tol=0.01, unsigned int MaxIters=25)

void InterpolateVectorField (SolverType &S)

bool PrintObservers (std::ostream &os, Indent indent) const

void PrintSelf (std::ostream &os, Indent indent) const

virtual void PropagateResetPipeline ()

virtual void ReleaseInputs ()

virtual void RestoreInputReleaseDataFlags ()

void SampleVectorFieldAtNodes (SolverType &S)

void SetNumberOfInputs (unsigned int num)

void SetNumberOfOutputs (unsigned int num)

virtual int SplitRequestedRegion (int i, int num, OutputImageRegionType &splitRegion)

virtual void ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, int threadId) ITK_NO_RETURN

virtual void AddInput (DataObject *input)

virtual const unsigned int & GetNumberOfRequiredInputs ()

virtual void RemoveInput (DataObject *input)

virtual void SetNthInput (unsigned int num, DataObject *input)

virtual void SetNumberOfRequiredInputs (unsigned int _arg)

virtual void AddOutput (DataObject *output)

virtual const unsigned int & GetNumberOfRequiredOutputs ()

virtual void RemoveOutput (DataObject *output)

virtual void SetNthOutput (unsigned int num, DataObject *output)

virtual void SetNumberOfRequiredOutputs (unsigned int _arg)

const DataObject * GetInput (unsigned int idx) const

virtual ImageMetricLoadType * GetLoad () const

const DataObject * GetOutput (unsigned int idx) const

virtual void PrintHeader (std::ostream &os, Indent indent) const

virtual void PrintTrailer (std::ostream &os, Indent indent) const

void PushBackInput (const DataObject *input)

void PushFrontInput (const DataObject *input)

Static Protected Member Functions

static ITK_THREAD_RETURN_TYPE ThreaderCallback (void *arg)

Protected Attributes

TimeStamp m_OutputInformationMTime

InternalReferenceCountType m_ReferenceCount

SimpleFastMutexLock m_ReferenceCountLock

bool m_Updating

typedef FieldType::Pointer FieldPointer

FieldPointer ExpandVectorField (ExpandFactorsType *expandFactors, FieldType *f)

Detailed Description

template<class TMovingImage, class TFixedImage>
class itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >

FEM Image registration filter. The image registration problem is modeled here with the finite element method. Image registration is, in general, an ill-posed problem. Thus, we use an optimization scheme where the optimization criterion is given by a regularized variational energy. The variational energy arises from modeling the image as a physical body on which external forces act. The body is allowed to deform so as to minimize the applied force. The resistance of the physical body to deformation, determined by the physics associated with the body, serves to regularize the solution. The forces applied to the body are, generally, highly non-linear and so the body is allowed to deform slowly and incrementally. The direction it deforms follows the gradient of the potential energy (the force) we define. The potential energies we may choose from are given by the itk image-to-image metrics. The choices and the associated direction of descent are : Mean Squares (minimize), Normalized Cross-Correlation (maximize) Mutual Information (maximize). Note that we have to set the direction (SetDescentDirection) when we choose a metric. The forces driving the problem may also be given by user-supplied landmarks. The corners of the image, in this example, are always pinned. This example is designed for 2D or 3D images. A rectilinear mesh is generated automatically given the correct element type (Quadrilateral or Hexahedral). Our specific Solver for this example uses trapezoidal time stepping. This is a method for solving a second-order PDE in time. The solution is penalized by the zeroth (mass matrix) and first derivatives (stiffness matrix) of the shape functions. There is an option to perform a line search on the energy after each iteration. Optimal parameter settings require experimentation. The following approach tends to work well : Choose the relative size of density to elasticity (e.g. Rho / E ~= 1.) such that the image deforms locally and slowly. This also affects the stability of the solution. Choose the time step to control the size of the deformation at each step. Choose enough iterations to allow the solution to converge (this may be automated).

Reading images is up to the user. Either set the images using SetMoving/FixedImage or see the ReadImages function.

Note:: This code works for only 2 or 3 dimensions b/c we do not have > 3D elements.
TODO : Keep the full field around (if using re-gridding). Introduce compensation for kinematic non-linearity in time (if using Eulerian frame).

Definition at line 106 of file itkFEMRegistrationFilter.h.

Member Typedef Documentation

template<class TMovingImage , class TFixedImage >

typedef SmartPointer<const Self> itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::ConstPointer

Reimplemented from itk::ImageToImageFilter< TMovingImage, TFixedImage >.

Definition at line 112 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef double itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::CoordRepType

Typedef support for the interpolation function

Definition at line 152 of file itkFEMRegistrationFilter.h.

typedef DataObject::Pointer itk::ImageSource< TFixedImage >::DataObjectPointer [inherited]

Smart Pointer type to a DataObject.

Reimplemented from itk::ProcessObject.

Definition at line 62 of file itkImageSource.h.

typedef std::vector<DataObjectPointer> itk::ProcessObject::DataObjectPointerArray [inherited]

STL Array of SmartPointers to DataObjects

Definition at line 103 of file itkProcessObject.h.

typedef DataObjectPointerArray::size_type itk::ProcessObject::DataObjectPointerArraySizeType [inherited]

Size type of an std::vector

Definition at line 112 of file itkProcessObject.h.

template<class TMovingImage , class TFixedImage >

typedef VectorLinearInterpolateImageFunction<FieldType,CoordRepType> itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::DefaultInterpolatorType

Definition at line 157 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef itk::VectorExpandImageFilter<FieldType,FieldType> itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::ExpanderType

Definition at line 163 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef ExpanderType::ExpandFactorsType itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::ExpandFactorsType

Definition at line 167 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef itk::ImageRegionIteratorWithIndex<FieldType> itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::FieldIterator

Definition at line 147 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef FieldType::Pointer itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::FieldPointer [protected]

Re-size the vector field (smaller to larger).

Definition at line 532 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef itk::Image<VectorType,itkGetStaticConstMacro(ImageDimension)> itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::FieldType

Definition at line 141 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef TFixedImage itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::FixedImageType

Definition at line 121 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef itk::RecursiveMultiResolutionPyramidImageFilter<FixedImageType,FixedImageType> itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::FixedPyramidType

Definition at line 170 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef double itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::Float

Definition at line 133 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef itk::ImageRegionIteratorWithIndex<FloatImageType> itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::FloatImageIterator

Definition at line 146 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef Image< float, itkGetStaticConstMacro(ImageDimension) > itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::FloatImageType

Definition at line 129 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef itk::ImageRegionIteratorWithIndex<FixedImageType> itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::ImageIterator

Definition at line 145 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef FiniteDifferenceFunctionLoad<MovingImageType,FixedImageType> itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::ImageMetricLoadType

Instantiate the load class with the correct image type.

Definition at line 179 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef FixedImageType::SizeType itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::ImageSizeType

Definition at line 123 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef itk::VectorIndexSelectionCastImageFilter<FieldType,FloatImageType> itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::IndexSelectCasterType

Definition at line 149 of file itkFEMRegistrationFilter.h.

typedef InputImageType::ConstPointer itk::ImageToImageFilter< TMovingImage , TFixedImage >::InputImageConstPointer [inherited]

Definition at line 84 of file itkImageToImageFilter.h.

typedef InputImageType::PixelType itk::ImageToImageFilter< TMovingImage , TFixedImage >::InputImagePixelType [inherited]

Definition at line 86 of file itkImageToImageFilter.h.

typedef InputImageType::Pointer itk::ImageToImageFilter< TMovingImage , TFixedImage >::InputImagePointer [inherited]

Definition at line 83 of file itkImageToImageFilter.h.

typedef InputImageType::RegionType itk::ImageToImageFilter< TMovingImage , TFixedImage >::InputImageRegionType [inherited]

Definition at line 85 of file itkImageToImageFilter.h.

typedef TMovingImage itk::ImageToImageFilter< TMovingImage , TFixedImage >::InputImageType [inherited]

Some convenient typedefs.

Definition at line 82 of file itkImageToImageFilter.h.

typedef ImageToImageFilterDetail::ImageRegionCopier<itkGetStaticConstMacro(OutputImageDimension), itkGetStaticConstMacro(InputImageDimension)> itk::ImageToImageFilter< TMovingImage , TFixedImage >::InputToOutputRegionCopierType [protected, inherited]

Typedef for the region copier function object that converts an input region to an output region.

Definition at line 164 of file itkImageToImageFilter.h.

typedef int itk::LightObject::InternalReferenceCountType [protected, inherited]

Define the type of the reference count according to the target. This allows the use of atomic operations

Definition at line 139 of file itkLightObject.h.

template<class TMovingImage , class TFixedImage >

typedef InterpolatorType::Pointer itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::InterpolatorPointer

Definition at line 155 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef VectorInterpolateImageFunction<FieldType,CoordRepType> itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::InterpolatorType

Definition at line 154 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef std::vector<typename LoadLandmark::Pointer> itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::LandmarkArrayType

Definition at line 137 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef LinearSystemWrapperItpack itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::LinearSystemSolverType

Definition at line 130 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef Load::ArrayType itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::LoadArray

Definition at line 134 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef MaterialLinearElasticity itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::MaterialType

Definition at line 144 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef PDEDeformableRegistrationFunction<FixedImageType,MovingImageType,FieldType> itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::MetricBaseType

Definition at line 181 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef MetricBaseType::Pointer itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::MetricBaseTypePointer

Definition at line 183 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef TMovingImage itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::MovingImageType

Definition at line 118 of file itkFEMRegistrationFilter.h.

typedef Superclass::OutputImagePixelType itk::ImageToImageFilter< TMovingImage , TFixedImage >::OutputImagePixelType [inherited]

Reimplemented from itk::ImageSource< TFixedImage >.

Definition at line 79 of file itkImageToImageFilter.h.

typedef OutputImageType::Pointer itk::ImageSource< TFixedImage >::OutputImagePointer [inherited]

Definition at line 69 of file itkImageSource.h.

typedef Superclass::OutputImageRegionType itk::ImageToImageFilter< TMovingImage , TFixedImage >::OutputImageRegionType [inherited]

Superclass typedefs.

Reimplemented from itk::ImageSource< TFixedImage >.

Definition at line 75 of file itkImageToImageFilter.h.

typedef TFixedImage itk::ImageSource< TFixedImage >::OutputImageType [inherited]

Some convenient typedefs.

Definition at line 65 of file itkImageSource.h.

typedef ImageToImageFilterDetail::ImageRegionCopier<itkGetStaticConstMacro(InputImageDimension), itkGetStaticConstMacro(OutputImageDimension)> itk::ImageToImageFilter< TMovingImage , TFixedImage >::OutputToInputRegionCopierType [protected, inherited]

Typedef for the region copier function object that converts an output region to an input region.

Definition at line 169 of file itkImageToImageFilter.h.

template<class TMovingImage , class TFixedImage >

typedef FixedImageType::PixelType itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::PixelType

Definition at line 122 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef SmartPointer<Self> itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::Pointer

Reimplemented from itk::ImageToImageFilter< TMovingImage, TFixedImage >.

Definition at line 111 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef FEMRegistrationFilter itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::Self

Standard class typedefs.

Reimplemented from itk::ImageToImageFilter< TMovingImage, TFixedImage >.

Definition at line 109 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef SolverCrankNicolson itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SolverType

Definition at line 131 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef ImageToImageFilter<TMovingImage, TFixedImage> itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::Superclass

Reimplemented from itk::ImageToImageFilter< TMovingImage, TFixedImage >.

Definition at line 110 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef itk::Vector<float,itkGetStaticConstMacro(ImageDimension)> itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::VectorType

Definition at line 139 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

typedef itk::WarpImageFilter<MovingImageType,FixedImageType, FieldType> itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::WarperType

Definition at line 143 of file itkFEMRegistrationFilter.h.

Member Enumeration Documentation

template<class TMovingImage , class TFixedImage >

enum itk::fem::FEMRegistrationFilter::Sign

Enumerator:

positive
negative

Definition at line 132 of file itkFEMRegistrationFilter.h.

Constructor & Destructor Documentation

template<class TMovingImage , class TFixedImage >

itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::FEMRegistrationFilter ( )

de/constructor

template<class TMovingImage , class TFixedImage >

itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::~FEMRegistrationFilter ( )

de/constructor

Member Function Documentation

virtual void itk::ProcessObject::AbortGenerateDataOff ( ) [virtual, inherited]

virtual void itk::ProcessObject::AbortGenerateDataOn ( ) [virtual, inherited]

Turn on and off the AbortGenerateData flag.

virtual void itk::ProcessObject::AddInput ( DataObject * input ) [protected, virtual, inherited]

Protected methods for setting inputs. Subclasses make use of them for setting input.

unsigned long itk::Object::AddObserver	(	const EventObject &	event,
		Command *
	)			const `[inherited]`

Allow people to add/remove/invoke observers (callbacks) to any ITK object. This is an implementation of the subject/observer design pattern. An observer is added by specifying an event to respond to and an itk::Command to execute. It returns an unsigned long tag which can be used later to remove the event or retrieve the command. The memory for the Command becomes the responsibility of this object, so don't pass the same instance of a command to two different objects

unsigned long itk::Object::AddObserver	(	const EventObject &	event,
		Command *
	)			`[inherited]`

Allow people to add/remove/invoke observers (callbacks) to any ITK object. This is an implementation of the subject/observer design pattern. An observer is added by specifying an event to respond to and an itk::Command to execute. It returns an unsigned long tag which can be used later to remove the event or retrieve the command. The memory for the Command becomes the responsibility of this object, so don't pass the same instance of a command to two different objects

virtual void itk::ProcessObject::AddOutput ( DataObject * output ) [protected, virtual, inherited]

Protected methods for setting outputs. Subclasses make use of them for getting output.

virtual void itk::ImageSource< TFixedImage >::AfterThreadedGenerateData ( void ) [inline, protected, virtual, inherited]

If an imaging filter needs to perform processing after all processing threads have completed, the filter can can provide an implementation for AfterThreadedGenerateData(). The execution flow in the default GenerateData() method will be: 1) Allocate the output buffer 2) Call BeforeThreadedGenerateData() 3) Spawn threads, calling ThreadedGenerateData() in each thread. 4) Call AfterThreadedGenerateData() Note that this flow of control is only available if a filter provides a ThreadedGenerateData() method and NOT a GenerateData() method.

Definition at line 265 of file itkImageSource.h.

virtual void itk::ImageSource< TFixedImage >::AllocateOutputs ( ) [protected, virtual, inherited]

The GenerateData method normally allocates the buffers for all of the outputs of a filter. Some filters may want to override this default behavior. For example, a filter may have multiple outputs with varying resolution. Or a filter may want to process data in place by grafting its input to its output.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::ApplyImageLoads	(	SolverType &	S,
		MovingImageType *	i1,
		FixedImageType *	i2
	)			`[protected]`

The image loads are entered into the solver.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::ApplyLoads	(	SolverType &	S,
		ImageSizeType	Isz,
		double *	spacing = `NULL`
	)			`[protected]`

The non-image loads are entered into the solver.

virtual void itk::ImageSource< TFixedImage >::BeforeThreadedGenerateData ( void ) [inline, protected, virtual, inherited]

If an imaging filter needs to perform processing after the buffer has been allocated but before threads are spawned, the filter can can provide an implementation for BeforeThreadedGenerateData(). The execution flow in the default GenerateData() method will be: 1) Allocate the output buffer 2) Call BeforeThreadedGenerateData() 3) Spawn threads, calling ThreadedGenerateData() in each thread. 4) Call AfterThreadedGenerateData() Note that this flow of control is only available if a filter provides a ThreadedGenerateData() method and NOT a GenerateData() method.

Definition at line 253 of file itkImageSource.h.

static void itk::LightObject::BreakOnError ( ) [static, inherited]

This method is called when itkExceptionMacro executes. It allows the debugger to break on error.

virtual void itk::ProcessObject::CacheInputReleaseDataFlags ( ) [protected, virtual, inherited]

Cache the state of any ReleaseDataFlag's on the inputs. While the filter is executing, we need to set the ReleaseDataFlag's on the inputs to false in case the current filter is implemented using a mini-pipeline (which will try to release the inputs). After the filter finishes, we restore the state of the ReleaseDataFlag's before the call to ReleaseInputs().

virtual void itk::ImageToImageFilter< TMovingImage , TFixedImage >::CallCopyInputRegionToOutputRegion	(	OutputImageRegionType &	destRegion,
		const InputImageRegionType &	srcRegion
	)			`[protected, virtual, inherited]`

This function calls the actual region copier to do the mapping from input image space to output image space. It uses a Function object used for dispatching to various routines to copy an input region (start index and size) to an output region. For most filters, this is a trivial copy because most filters require the input dimension to match the output dimension. However, some filters like itk::UnaryFunctorImageFilter can support output images of a higher dimension that the input.

This function object is used by the default implementation of GenerateOutputInformation(). It can also be used in routines like ThreadedGenerateData() where a filter may need to map an input region to an output region.

The default copier uses a "dispatch pattern" to call one of three overloaded functions depending on whether the input and output images are the same dimension, the input is a higher dimension that the output, or the input is of a lower dimension than the output. The use of an overloaded function is required for proper compilation of the various cases.

For the latter two cases, trivial implementations are used. If the input image is a higher dimension than the output, the first portion of the input region is copied to the output region. If the input region is a lower dimension than the output, the input region information is copied into the first portion of the output region and the rest of the output region is set to zero.

If a filter needs a different default behavior, it can override this method.

virtual void itk::ImageToImageFilter< TMovingImage , TFixedImage >::CallCopyOutputRegionToInputRegion	(	InputImageRegionType &	destRegion,
		const OutputImageRegionType &	srcRegion
	)			`[protected, virtual, inherited]`

This function calls the actual region copier to do the mapping from output image space to input image space. It uses a Function object used for dispatching to various routines to copy an output region (start index and size) to an input region. For most filters, this is a trivial copy because most filters require the input dimension to match the output dimension. However, some filters like itk::ExtractImageFilter can support output images of a lower dimension that the input.

This function object can be used by GenerateOutputInformation() to copy the input LargestPossibleRegion to the output LargestPossibleRegion and can also be used in GenerateData or ThreadedGenerateData() where a filter may need to map an output region to an input region.

The default copier uses a "dispatch pattern" to call one of three overloaded functions depending on whether the input and output images are the same dimension, the input is a higher dimension that the output, or the input is of a lower dimension than the output. The use of an overloaded function is required for proper compilation of the various cases.

For the latter two cases, trivial implementations are used. If the input image is a higher dimension than the output, the output region information is copied into the first portion of the input region and the rest of the input region is set to zero. If the input region is a lower dimension than the output, the first portion of the output region is copied to the input region.

If a filter needs a different default behavior, it can override this method. The ExtractImageFilter overrides this function object so that if the input image is a higher dimension than the output image, the filter can control "where" in the input image the output subimage is extracted (as opposed to mapping to first few dimensions of the input).

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::ChooseMetric ( float whichmetric )

Choose the metric by parameter : 0= mean squares, 1=cross correlation, 2=pattern intensity, 3 = mutual information.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::ComputeJacobian	(	float	sign = `1.0`,
		FieldType *	field = `NULL`,
		float	smooth = `0.0`
	)

Compute the jacobian of the current deformation field.

virtual LightObject::Pointer itk::Object::CreateAnother ( ) const [virtual, inherited]

Create an object from an instance, potentially deferring to a factory. This method allows you to create an instance of an object that is exactly the same type as the referring object. This is useful in cases where an object has been cast back to a base class.

Reimplemented from itk::LightObject.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::CreateLinearSystemSolver ( ) [protected]

Builds the itpack linear system wrapper with appropriate parameters. Currently undefined

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::CreateMesh	(	double	ElementsPerSide,
		Solver &	S,
		ImageSizeType	sz
	)			`[protected]`

This function generates a regular mesh of ElementsPerSide^D size

virtual void itk::Object::DebugOff ( ) const [virtual, inherited]

Turn debugging output off.

virtual void itk::Object::DebugOn ( ) const [virtual, inherited]

Turn debugging output on.

virtual void itk::LightObject::Delete ( ) [virtual, inherited]

Delete an itk object. This method should always be used to delete an object when the new operator was used to create it. Using the C delete method will not work with reference counting.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::DoLineSearch ( unsigned int b ) [inline]

Finds the minimum energy between the current and next solution by linear search.

Definition at line 417 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::DoMultiRes ( bool b ) [inline]

Sets the use of multi-resolution strategy. The control file always uses multi-res.

Definition at line 423 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::EmployRegridding ( unsigned int b ) [inline]

Sets the use of multi-resolution strategy. The control file always uses multi-res.

Definition at line 429 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::EnforceDiffeomorphism	(	float	thresh,
		SolverType &	S,
		bool	onlywriteimages
	)

We check the jacobian of the current deformation field. If it is < threshold, we begin diffeomorphism enforcement: 1) Warp the moving image. 2) Set the vector field to zero. 3) Set the warped moving image as the new moving image, resizing if necessary.

virtual void itk::ProcessObject::EnlargeOutputRequestedRegion ( DataObject * ) [inline, virtual, inherited]

Give the process object a chance to indictate that it will produce more output than it was requested to produce. For example, many imaging filters must compute the entire output at once or can only produce output in complete slices. Such filters cannot handle smaller requested regions. These filters must provide an implementation of this method, setting the output requested region to the size they will produce. By default, a process object does not modify the size of the output requested region.

Definition at line 225 of file itkProcessObject.h.

template<class TMovingImage , class TFixedImage >

Float itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::EvaluateEnergy ( ) [protected]

Evaluates the image similarity energy by calling the image metric

template<class TMovingImage , class TFixedImage >

Float itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::EvaluateResidual	(	SolverType &	mySolver,
		Float	t
	)			`[protected]`

template<class TMovingImage , class TFixedImage >

FieldPointer itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::ExpandVectorField	(	ExpandFactorsType *	expandFactors,
		FieldType *	f
	)			`[protected]`

Re-size the vector field (smaller to larger).

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::FindBracketingTriplet	(	SolverType &	mySolver,
		Float *	a,
		Float *	b,
		Float *	c
	)			`[protected]`

virtual void itk::ImageSource< TFixedImage >::GenerateData ( void ) [protected, virtual, inherited]

A version of GenerateData() specific for image processing filters. This implementation will split the processing across multiple threads. The buffer is allocated by this method. Then the BeforeThreadedGenerateData() method is called (if provided). Then, a series of threads are spawned each calling ThreadedGenerateData(). After all the threads have completed processing, the AfterThreadedGenerateData() method is called (if provided). If an image processing filter cannot be threaded, the filter should provide an implementation of GenerateData(). That implementation is responsible for allocating the output buffer. If a filter an be threaded, it should NOT provide a GenerateData() method but should provide a ThreadedGenerateData() instead.

See also:: ThreadedGenerateData()

Reimplemented from itk::ProcessObject.

virtual void itk::ImageToImageFilter< TMovingImage , TFixedImage >::GenerateInputRequestedRegion ( void ) [protected, virtual, inherited]

What is the input requested region that is required to produce the output requested region? The base assumption for image processing filters is that the input requested region can be set to match the output requested region. If a filter requires more input (for instance a filter that uses neighborhoods needs more input than output to avoid introducing artificial boundary conditions) or less input (for instance a magnify filter) will have to override this method. In doing so, it should call its superclass' implementation as its first step. Note that imaging filters operate differently than the classes to this point in the class hierachy. Up till now, the base assumption has been that the largest possible region will be requested of the input.

This implementation of GenerateInputRequestedRegion() only processes the inputs that are a subclass of the ImageBase<InputImageDimension>. If an input is another type of DataObject (including an Image of a different dimension), they are skipped by this method. The subclasses of ImageToImageFilter are responsible for providing an implementation of GenerateInputRequestedRegion() when there are multiple inputs of different types.

See also:: ProcessObject::GenerateInputRequestedRegion(), ImageSource::GenerateInputRequestedRegion()

Reimplemented from itk::ProcessObject.

virtual void itk::ProcessObject::GenerateOutputInformation ( ) [protected, virtual, inherited]

Generate the information decribing the output data. The default implementation of this method will copy information from the input to the output. A filter may override this method if its output will have different information than its input. For instance, a filter that shrinks an image will need to provide an implementation for this method that changes the spacing of the pixels. Such filters should call their superclass' implementation of this method prior to changing the information values they need (i.e. GenerateOutputInformation() should call Superclass::GenerateOutputInformation() prior to changing the information.

virtual void itk::ProcessObject::GenerateOutputRequestedRegion ( DataObject * output ) [protected, virtual, inherited]

Given one output whose requested region has been set, how should the requested regions for the remaining outputs of the process object be set? By default, all the outputs are set to the same requested region. If a filter needs to produce different requested regions for each output, for instance an image processing filter producing several outputs at different resolutions, then that filter may override this method and set the requested regions appropriatedly.

Note that a filter producing multiple outputs of different types is required to override this method. The default implementation can only correctly handle multiple outputs of the same type.

Reimplemented in itk::MultiResolutionPyramidImageFilter< TInputImage, TOutputImage >, itk::RecursiveMultiResolutionPyramidImageFilter< TInputImage, TOutputImage >, itk::watershed::BoundaryResolver< TPixelType, TDimension >, itk::watershed::EquivalenceRelabeler< TScalarType, TImageDimension >, itk::watershed::Relabeler< TScalarType, TImageDimension >, itk::watershed::Segmenter< TInputImage >, itk::watershed::SegmentTreeGenerator< TScalarType >, itk::watershed::Relabeler< ScalarType, itkGetStaticConstMacro(ImageDimension)>, itk::watershed::Segmenter< InputImageType >, and itk::watershed::SegmentTreeGenerator< ScalarType >.

virtual const bool& itk::ProcessObject::GetAbortGenerateData ( ) [virtual, inherited]

Get the AbortGenerateData flag for the process object. Process objects may handle premature termination of execution in different ways.

Command* itk::Object::GetCommand ( unsigned long tag ) [inherited]

Get the command associated with the given tag. NOTE: This returns a pointer to a Command, but it is safe to asign this to a Command::Pointer. Since Command inherits from LightObject, at this point in the code, only a pointer or a reference to the Command can be used.

template<class TMovingImage , class TFixedImage >

std::string itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::GetConfigFileName ( ) [inline]

Definition at line 456 of file itkFEMRegistrationFilter.h.

bool itk::Object::GetDebug ( ) const [inherited]

Get the value of the debug flag.

template<class TMovingImage , class TFixedImage >

FieldType* itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::GetDeformationField ( ) [inline]

Outputs the FE deformation field interpolated over the entire image domain.

Definition at line 257 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

Float itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::GetElasticity ( unsigned int which = 0 ) [inline]

Gets the stiffness Matrix weight.

Definition at line 386 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

std::string itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::GetFixedFile ( ) [inline]

Definition at line 227 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

FixedImageType* itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::GetFixedImage ( ) [inline]

Definition at line 241 of file itkFEMRegistrationFilter.h.

static bool itk::Object::GetGlobalWarningDisplay ( ) [static, inherited]

This is a global flag that controls whether any debug, warning or error messages are displayed.

template<class TMovingImage , class TFixedImage >

ImageSizeType itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::GetImageSize ( ) [inline]

Definition at line 458 of file itkFEMRegistrationFilter.h.

const DataObject* itk::ProcessObject::GetInput ( unsigned int idx ) const [protected, inherited]

Method used internally for getting an input.

const InputImageType* itk::ImageToImageFilter< TMovingImage , TFixedImage >::GetInput ( unsigned int idx ) [inherited]

Set/Get the image input of this process object.

Reimplemented from itk::ProcessObject.

const InputImageType* itk::ImageToImageFilter< TMovingImage , TFixedImage >::GetInput ( void ) [inherited]

Set/Get the image input of this process object.

DataObjectPointerArray& itk::ProcessObject::GetInputs ( ) [inline, inherited]

Return an array with all the inputs of this process object. This is useful for tracing back in the pipeline to construct graphs etc.

Definition at line 108 of file itkProcessObject.h.

template<class TMovingImage , class TFixedImage >

virtual InterpolatorType* itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::GetInterpolator ( ) [virtual]

Get a pointer to the interpolator function.

template<class TMovingImage , class TFixedImage >

FloatImageType* itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::GetJacobianImage ( ) [inline]

Get the image that gives the jacobian of the deformation field.

Definition at line 252 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

virtual ImageMetricLoadType* itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::GetLoad ( ) const [protected, virtual]

Set the solver's current load.

const MetaDataDictionary& itk::Object::GetMetaDataDictionary ( void ) const [inherited]

Returns:: A constant reference to this objects MetaDataDictionary.

MetaDataDictionary& itk::Object::GetMetaDataDictionary ( void ) [inherited]

Returns:: A reference to this objects MetaDataDictionary.

Warning:: This reference may be changed.

template<class TMovingImage , class TFixedImage >

MetricBaseTypePointer itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::GetMetric ( ) [inline]

Set/Get the Metric.

Definition at line 461 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

FloatImageType* itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::GetMetricImage ( FieldType * F ) [protected]

Calculates the metric over the domain given the vector field.

template<class TMovingImage , class TFixedImage >

std::string itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::GetMovingFile ( ) [inline]

Definition at line 220 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

MovingImageType* itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::GetMovingImage ( ) [inline]

Definition at line 238 of file itkFEMRegistrationFilter.h.

virtual unsigned long itk::Object::GetMTime ( ) const [virtual, inherited]

Return this objects modified time.

Referenced by itk::SpatialObject< ::itk::GetMeshDimension< TMesh >::PointDimension >::GetObjectMTime().

MultiThreader* itk::ProcessObject::GetMultiThreader ( ) [inline, inherited]

Return the multithreader used by this class.

Definition at line 284 of file itkProcessObject.h.

template<class TMovingImage , class TFixedImage >

virtual const char* itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::GetNameOfClass ( ) const [virtual]

Run-time type information (and related methods)

Reimplemented from itk::ImageToImageFilter< TMovingImage, TFixedImage >.

DataObjectPointerArraySizeType itk::ProcessObject::GetNumberOfInputs ( ) const [inline, inherited]

Get the size of the input vector. This is merely the size of the input vector, not the number of inputs that have valid DataObject's assigned. Use GetNumberOfValidRequiredInputs() to determine how many inputs are non-null.

Definition at line 118 of file itkProcessObject.h.

DataObjectPointerArraySizeType itk::ProcessObject::GetNumberOfOutputs ( ) const [inline, inherited]

Return an array with all the outputs of this process object. This is useful for tracing forward in the pipeline to contruct graphs etc.

Definition at line 135 of file itkProcessObject.h.

virtual const unsigned int& itk::ProcessObject::GetNumberOfRequiredInputs ( ) [protected, virtual, inherited]

Protected methods for setting inputs. Subclasses make use of them for setting input.

virtual const unsigned int& itk::ProcessObject::GetNumberOfRequiredOutputs ( ) [protected, virtual, inherited]

Protected methods for setting outputs. Subclasses make use of them for getting output.

virtual const int& itk::ProcessObject::GetNumberOfThreads ( ) [virtual, inherited]

Get/Set the number of threads to create when executing.

virtual DataObjectPointerArraySizeType itk::ProcessObject::GetNumberOfValidRequiredInputs ( ) const [virtual, inherited]

Get the number of valid inputs. This is the number of non-null entries in the input vector in the first NumberOfRequiredInputs slots. This method is used to determine whether the necessary required inputs have been set. Subclasses of ProcessObject may override this implementation if the required inputs are not the first slots in input vector.

Reimplemented in itk::MultiResolutionPDEDeformableRegistration< TFixedImage, TMovingImage, TDeformationField, TRealType >, itk::PDEDeformableRegistrationFilter< TFixedImage, TMovingImage, TDeformationField >, and itk::PDEDeformableRegistrationFilter< TFixedImage, TMovingImage, TDeformationField >.

template<class TMovingImage , class TFixedImage >

MovingImageType* itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::GetOriginalMovingImage ( ) [inline]

Definition at line 239 of file itkFEMRegistrationFilter.h.

const DataObject* itk::ProcessObject::GetOutput ( unsigned int idx ) const [protected, inherited]

Method used internally for getting an output.

OutputImageType* itk::ImageSource< TFixedImage >::GetOutput ( unsigned int idx ) [inherited]

Get the output data of this process object. The output of this function is not valid until an appropriate Update() method has been called, either explicitly or implicitly. Both the filter itself and the data object have Update() methods, and both methods update the data. Here are three ways to use GetOutput() and make sure the data is valid. In these examples, image is a pointer to some Image object, and the particular ProcessObjects involved are filters. The same examples apply to non-image (e.g. Mesh) data as well.

   anotherFilter->SetInput( someFilter->GetOutput() );
   anotherFilter->Update();

In this situation, someFilter and anotherFilter are said to constitute a pipeline.

   image = someFilter->GetOutput();
   image->Update();

   someFilter->Update();
   image = someFilter->GetOutput();

(In the above example, the two lines of code can be in either order.)

Note that Update() is not called automatically except within a pipeline as in the first example. When streaming (using a StreamingImageFilter) is activated, it may be more efficient to use a pipeline than to call Update() once for each filter in turn.

For an image, the data generated is for the requested Region, which can be set using ImageBase::SetRequestedRegion(). By default, the largest possible region is requested.

For Filters which have multiple outputs of different types, the GetOutput() method assumes the output is of OutputImageType. For the GetOutput(unsigned int) method, a dynamic_cast is performed incase the filter has outputs of different types or image types. Derived classes should have names get methods for these outputs.

Reimplemented from itk::ProcessObject.

OutputImageType* itk::ImageSource< TFixedImage >::GetOutput ( void ) [inherited]

Get the output data of this process object. The output of this function is not valid until an appropriate Update() method has been called, either explicitly or implicitly. Both the filter itself and the data object have Update() methods, and both methods update the data. Here are three ways to use GetOutput() and make sure the data is valid. In these examples, image is a pointer to some Image object, and the particular ProcessObjects involved are filters. The same examples apply to non-image (e.g. Mesh) data as well.

   anotherFilter->SetInput( someFilter->GetOutput() );
   anotherFilter->Update();

In this situation, someFilter and anotherFilter are said to constitute a pipeline.

   image = someFilter->GetOutput();
   image->Update();

   someFilter->Update();
   image = someFilter->GetOutput();

(In the above example, the two lines of code can be in either order.)

Note that Update() is not called automatically except within a pipeline as in the first example. When streaming (using a StreamingImageFilter) is activated, it may be more efficient to use a pipeline than to call Update() once for each filter in turn.

For an image, the data generated is for the requested Region, which can be set using ImageBase::SetRequestedRegion(). By default, the largest possible region is requested.

For Filters which have multiple outputs of different types, the GetOutput() method assumes the output is of OutputImageType. For the GetOutput(unsigned int) method, a dynamic_cast is performed incase the filter has outputs of different types or image types. Derived classes should have names get methods for these outputs.

DataObjectPointerArray& itk::ProcessObject::GetOutputs ( ) [inline, inherited]

Return an array with all the outputs of this process object. This is useful for tracing forward in the pipeline to contruct graphs etc.

Definition at line 133 of file itkProcessObject.h.

virtual const float& itk::ProcessObject::GetProgress ( ) [virtual, inherited]

Get the execution progress of a process object. The progress is a floating number in [0,1] with 0 meaning no progress and 1 meaning the filter has completed execution.

Referenced by itk::XMLFilterWatcher::ShowProgress().

virtual int itk::LightObject::GetReferenceCount ( ) const [inline, virtual, inherited]

Gets the reference count on this object.

Definition at line 106 of file itkLightObject.h.

virtual const bool& itk::ProcessObject::GetReleaseDataBeforeUpdateFlag ( ) [virtual, inherited]

Turn on/off the flags to control whether the bulk data belonging to the outputs of this ProcessObject are released/reallocated during an Update(). In limited memory scenarios, a user may want to force the elements of a pipeline to release any bulk data that is going to be regenerated anyway during an Update() in order to control peak memory allocation. Note that this flag is different from the ReleaseDataFlag. ReleaseDataFlag manages the deallocation of a ProcessObject's bulk output data once that data has been consumed by a downstream ProcessObject. The ReleaseDataBeforeUpdateFlag manages the deallocation/reallocation of bulk data during a pipeline update to control peak memory utilization. Default value is on.

virtual bool itk::ProcessObject::GetReleaseDataFlag ( ) const [virtual, inherited]

Turn on/off the flags to control whether the bulk data belonging to the outputs of this ProcessObject are released after being used by a downstream ProcessObject. Default value is off. Another options for controlling memory utilization is the ReleaseDataBeforeUpdateFlag.

template<class TMovingImage , class TFixedImage >

std::string itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::GetResultsFileName ( ) [inline]

Definition at line 304 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

FixedImageType* itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::GetWarpedImage ( ) [inline]

Get the reference image warped to the target image. Must first apply the warp using WarpImage()

Definition at line 246 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

unsigned int itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::GetWidthOfMetricRegion ( unsigned int which = 0 ) [inline]

The metric region allows one to compute the derivative (force) of the similarity metric using a region of size [i,i] in 2D [i,i,i] in 3D.

Parameters:

	i	number of elements
	which	determines the region at a given resolution of the solution process.

Definition at line 344 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

bool itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::GetWriteDisplacements ( ) [inline]

Sets the boolean for writing the displacement field to a file.

Definition at line 447 of file itkFEMRegistrationFilter.h.

static void itk::Object::GlobalWarningDisplayOff ( ) [inline, static, inherited]

This is a global flag that controls whether any debug, warning or error messages are displayed.

Definition at line 100 of file itkObject.h.

References itk::Object::SetGlobalWarningDisplay().

static void itk::Object::GlobalWarningDisplayOn ( ) [inline, static, inherited]

This is a global flag that controls whether any debug, warning or error messages are displayed.

Definition at line 98 of file itkObject.h.

References itk::Object::SetGlobalWarningDisplay().

template<class TMovingImage , class TFixedImage >

Float itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::GoldenSection	(	SolverType &	mySolver,
		Float	tol = `0.01`,
		unsigned int	MaxIters = `25`
	)			`[protected]`

Finds the optimum value between the last two solutions and sets the current solution to that value. Uses Evaluate Residual;

virtual void itk::ImageSource< TFixedImage >::GraftNthOutput	(	unsigned int	idx,
		DataObject *	output
	)			`[virtual, inherited]`

Graft the specified data object onto this ProcessObject's idx'th output. This is similar to the GraftOutput method except it allows you to specify which output is affected. The specified index must be a valid output number (less than ProcessObject::GetNumberOfOutputs()). See the GraftOutput for general usage information.

virtual void itk::ImageSource< TFixedImage >::GraftOutput ( DataObject * output ) [virtual, inherited]

Graft the specified DataObject onto this ProcessObject's output. This method grabs a handle to the specified DataObject's bulk data to used as its output's own bulk data. It also copies the region ivars (RequestedRegion, BufferedRegion, LargestPossibleRegion) and meta-data (Spacing, Origin) from the specified data object into this filter's output data object. Most importantly, however, it leaves the Source ivar untouched so the original pipeline routing is intact. This method is used when a process object is implemented using a mini-pipeline which is defined in its GenerateData() method. The usage is:

    // setup the mini-pipeline to process the input to this filter
    firstFilterInMiniPipeline->SetInput( this->GetInput() );

    // setup the mini-pipeline to calculate the correct regions
    // and write to the appropriate bulk data block
    lastFilterInMiniPipeline->GraftOutput( this->GetOutput() );

    // execute the mini-pipeline
    lastFilterInMiniPipeline->Update();

    // graft the mini-pipeline output back onto this filter's output.
    // this is needed to get the appropriate regions passed back.
    this->GraftOutput( lastFilterInMiniPipeline->GetOutput() );

For proper pipeline execution, a filter using a mini-pipeline must implement the GenerateInputRequestedRegion(), GenerateOutputRequestedRegion(), GenerateOutputInformation() and EnlargeOutputRequestedRegion() methods as necessary to reflect how the mini-pipeline will execute (in other words, the outer filter's pipeline mechanism must be consistent with what the mini-pipeline will do).

bool itk::Object::HasObserver ( const EventObject & event ) const [inherited]

Return true if an observer is registered for this event.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::InterpolateVectorField ( SolverType & S ) [protected]

Interpolates the vector field over the domain. Our convention is to always keep the vector field at the scale of the original images.

void itk::Object::InvokeEvent ( const EventObject & ) const [inherited]

Call Execute on all the Commands observing this event id. The actions triggered by this call doesn't modify this object.

void itk::Object::InvokeEvent ( const EventObject & ) [inherited]

Call Execute on all the Commands observing this event id.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::IterativeSolve ( SolverType & S )

The solution loop

itk::ImageToImageFilter< TMovingImage , TFixedImage >::itkStaticConstMacro	(	OutputImageDimension	,
		unsigned	int,
		TFixedImage ::ImageDimension
	)			`[inherited]`

ImageDimension constants

Reimplemented from itk::ImageSource< TFixedImage >.

itk::ImageToImageFilter< TMovingImage , TFixedImage >::itkStaticConstMacro	(	InputImageDimension	,
		unsigned	int,
		TMovingImage ::ImageDimension
	)			`[inherited]`

ImageDimension constants

template<class TMovingImage , class TFixedImage >

itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::itkStaticConstMacro	(	ImageDimension	,
		unsigned	int,
		FixedImageType::ImageDimension
	)

Dimensionality of input and output data is assumed to be the same.

virtual DataObjectPointer itk::ImageSource< TFixedImage >::MakeOutput ( unsigned int idx ) [virtual, inherited]

Make a DataObject of the correct type to used as the specified output. Every ProcessObject subclass must be able to create a DataObject that can be used as a specified output. This method is automatically called when DataObject::DisconnectPipeline() is called. DataObject::DisconnectPipeline, disconnects a data object from being an output of its current source. When the data object is disconnected, the ProcessObject needs to construct a replacement output data object so that the ProcessObject is in a valid state. So DataObject::DisconnectPipeline eventually calls ProcessObject::MakeOutput. Note that MakeOutput always returns a SmartPointer to a DataObject. If a subclass of ImageSource has multiple outputs of different types, then that class must provide an implementation of MakeOutput().

Reimplemented from itk::ProcessObject.

virtual void itk::Object::Modified ( ) const [virtual, inherited]

Update the modification time for this object. Many filters rely on the modification time to determine if they need to recompute their data.

Referenced by itk::NarrowBandImageFilterBase< TInputImage, TOutputImage >::InsertNarrowBandNode(), itk::MatrixOffsetTransformBase< TScalarType, 3, 3 >::SetCenter(), itk::MatrixOffsetTransformBase< TScalarType, 3, 3 >::SetMatrix(), itk::NarrowBandImageFilterBase< TInputImage, TOutputImage >::SetNarrowBand(), itk::NarrowBandImageFilterBase< TInputImage, TOutputImage >::SetNarrowBandInnerRadius(), itk::NarrowBandImageFilterBase< TInputImage, TOutputImage >::SetNarrowBandTotalRadius(), itk::MatrixOffsetTransformBase< TScalarType, 3, 3 >::SetOffset(), itk::ThresholdLabelerImageFilter< TInputImage, TOutputImage >::SetRealThresholds(), itk::NonUniformBSpline< TDimension >::SetSplineOrder(), itk::ThresholdLabelerImageFilter< TInputImage, TOutputImage >::SetThresholds(), itk::Statistics::GoodnessOfFitFunctionBase< TInputHistogram >::SetTotalObservedScale(), and itk::MatrixOffsetTransformBase< TScalarType, 3, 3 >::SetTranslation().

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::MultiResSolve ( )

The solution loop for a simple multi-resolution strategy.

template<class TMovingImage , class TFixedImage >

static Pointer itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::New ( ) [static]

Method for creation through the object factory.

Reimplemented from itk::Object.

virtual void itk::ImageToImageFilter< TMovingImage , TFixedImage >::PopBackInput ( ) [virtual, inherited]

Push/Pop the input of this process object. These methods allow a filter to model its input vector as a queue or stack. These routines may not be appropriate for all filters, especially filters with different types of inputs. These routines follow the semantics of STL.

The routines are useful for applications that need to process "rolling" sets of images. For instance, if an application has 10 images and they need to run a filter on images 1, 2, 3, 4, then run the filter on images 2, 3, 4, 5, then run the filter on images 3, 4, 5, 6, the application can accomplish this by popping an input off the front of the input list and push a new image onto the back of input list. Again, this only makes sense for filters that single type of input.

Other uses are also possible. For a single input filter, pushing and popping inputs allow the application to temporarily replace an input to a filter.

Reimplemented from itk::ProcessObject.

virtual void itk::ImageToImageFilter< TMovingImage , TFixedImage >::PopFrontInput ( ) [virtual, inherited]

Push/Pop the input of this process object. These methods allow a filter to model its input vector as a queue or stack. These routines may not be appropriate for all filters, especially filters with different types of inputs. These routines follow the semantics of STL.

The routines are useful for applications that need to process "rolling" sets of images. For instance, if an application has 10 images and they need to run a filter on images 1, 2, 3, 4, then run the filter on images 2, 3, 4, 5, then run the filter on images 3, 4, 5, 6, the application can accomplish this by popping an input off the front of the input list and push a new image onto the back of input list. Again, this only makes sense for filters that single type of input.

Other uses are also possible. For a single input filter, pushing and popping inputs allow the application to temporarily replace an input to a filter.

Reimplemented from itk::ProcessObject.

virtual void itk::ProcessObject::PrepareOutputs ( ) [virtual, inherited]

An opportunity to deallocate a ProcessObject's bulk data storage. Some filters may wish to reuse existing bulk data storage to avoid unnecessary deallocation/allocation sequences. The default implementation calls Initialize() on each output. DataObject::Initialize() frees its bulk data by default.

Reimplemented in itk::WatershedImageFilter< TInputImage >.

void itk::LightObject::Print	(	std::ostream &	os,
		Indent	indent = `0`
	)			const `[inherited]`

Cause the object to print itself out.

Referenced by itk::WeakPointer< ProcessObject >::Print().

virtual void itk::LightObject::PrintHeader	(	std::ostream &	os,
		Indent	indent
	)			const `[protected, virtual, inherited]`

Methods invoked by Print() to print information about the object including superclasses. Typically not called by the user (use Print() instead) but used in the hierarchical print process to combine the output of several classes.

bool itk::Object::PrintObservers	(	std::ostream &	os,
		Indent	indent
	)			const `[protected, inherited]`

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::PrintSelf	(	std::ostream &	os,
		Indent	indent
	)			const `[protected, virtual]`

Methods invoked by Print() to print information about the object including superclasses. Typically not called by the user (use Print() instead) but used in the hierarchical print process to combine the output of several classes.

Reimplemented from itk::ImageToImageFilter< TMovingImage, TFixedImage >.

virtual void itk::LightObject::PrintTrailer	(	std::ostream &	os,
		Indent	indent
	)			const `[protected, virtual, inherited]`

Methods invoked by Print() to print information about the object including superclasses. Typically not called by the user (use Print() instead) but used in the hierarchical print process to combine the output of several classes.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::PrintVectorField ( unsigned int modnum = 1000 )

virtual void itk::ProcessObject::PropagateRequestedRegion ( DataObject * output ) [virtual, inherited]

Send the requested region information back up the pipeline (to the filters that preceed this one).

Reimplemented in itk::StreamingImageFilter< TInputImage, TOutputImage >, and itk::VTKImageImport< TOutputImage >.

virtual void itk::ProcessObject::PropagateResetPipeline ( ) [protected, virtual, inherited]

Called to allocate the input array. Copies old inputs. Propagate a call to ResetPipeline() up the pipeline. Called only from DataObject.

void itk::ImageToImageFilter< TMovingImage , TFixedImage >::PushBackInput ( const DataObject * input ) [inline, protected, virtual, inherited]

PushBackInput(), PushFronInput() in the public section force the input to be the type expected by an ImageToImageFilter. However, these methods end of "hiding" the versions from the superclass (ProcessObject) whose arguments are DataObjects. Here, we re-expose the versions from ProcessObject to avoid warnings about hiding methods from the superclass.

Reimplemented from itk::ProcessObject.

Definition at line 251 of file itkImageToImageFilter.h.

virtual void itk::ImageToImageFilter< TMovingImage , TFixedImage >::PushBackInput ( const InputImageType * image ) [virtual, inherited]

Push/Pop the input of this process object. These methods allow a filter to model its input vector as a queue or stack. These routines may not be appropriate for all filters, especially filters with different types of inputs. These routines follow the semantics of STL.

The routines are useful for applications that need to process "rolling" sets of images. For instance, if an application has 10 images and they need to run a filter on images 1, 2, 3, 4, then run the filter on images 2, 3, 4, 5, then run the filter on images 3, 4, 5, 6, the application can accomplish this by popping an input off the front of the input list and push a new image onto the back of input list. Again, this only makes sense for filters that single type of input.

Other uses are also possible. For a single input filter, pushing and popping inputs allow the application to temporarily replace an input to a filter.

void itk::ImageToImageFilter< TMovingImage , TFixedImage >::PushFrontInput ( const DataObject * input ) [inline, protected, virtual, inherited]

PushBackInput(), PushFronInput() in the public section force the input to be the type expected by an ImageToImageFilter. However, these methods end of "hiding" the versions from the superclass (ProcessObject) whose arguments are DataObjects. Here, we re-expose the versions from ProcessObject to avoid warnings about hiding methods from the superclass.

Reimplemented from itk::ProcessObject.

Definition at line 253 of file itkImageToImageFilter.h.

virtual void itk::ImageToImageFilter< TMovingImage , TFixedImage >::PushFrontInput ( const InputImageType * image ) [virtual, inherited]

Push/Pop the input of this process object. These methods allow a filter to model its input vector as a queue or stack. These routines may not be appropriate for all filters, especially filters with different types of inputs. These routines follow the semantics of STL.

The routines are useful for applications that need to process "rolling" sets of images. For instance, if an application has 10 images and they need to run a filter on images 1, 2, 3, 4, then run the filter on images 2, 3, 4, 5, then run the filter on images 3, 4, 5, 6, the application can accomplish this by popping an input off the front of the input list and push a new image onto the back of input list. Again, this only makes sense for filters that single type of input.

Other uses are also possible. For a single input filter, pushing and popping inputs allow the application to temporarily replace an input to a filter.

template<class TMovingImage , class TFixedImage >

bool itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::ReadConfigFile ( const char * )

Read the configuration file to set up the example parameters

virtual void itk::Object::Register ( ) const [virtual, inherited]

Increase the reference count (mark as used by another object).

Reimplemented from itk::LightObject.

virtual void itk::ProcessObject::ReleaseDataBeforeUpdateFlagOff ( ) [virtual, inherited]

Turn on/off the flags to control whether the bulk data belonging to the outputs of this ProcessObject are released/reallocated during an Update(). In limited memory scenarios, a user may want to force the elements of a pipeline to release any bulk data that is going to be regenerated anyway during an Update() in order to control peak memory allocation. Note that this flag is different from the ReleaseDataFlag. ReleaseDataFlag manages the deallocation of a ProcessObject's bulk output data once that data has been consumed by a downstream ProcessObject. The ReleaseDataBeforeUpdateFlag manages the deallocation/reallocation of bulk data during a pipeline update to control peak memory utilization. Default value is on.

virtual void itk::ProcessObject::ReleaseDataBeforeUpdateFlagOn ( ) [virtual, inherited]

Turn on/off the flags to control whether the bulk data belonging to the outputs of this ProcessObject are released/reallocated during an Update(). In limited memory scenarios, a user may want to force the elements of a pipeline to release any bulk data that is going to be regenerated anyway during an Update() in order to control peak memory allocation. Note that this flag is different from the ReleaseDataFlag. ReleaseDataFlag manages the deallocation of a ProcessObject's bulk output data once that data has been consumed by a downstream ProcessObject. The ReleaseDataBeforeUpdateFlag manages the deallocation/reallocation of bulk data during a pipeline update to control peak memory utilization. Default value is on.

void itk::ProcessObject::ReleaseDataFlagOff ( ) [inline, inherited]

Turn on/off the flags to control whether the bulk data belonging to the outputs of this ProcessObject are released after being used by a downstream ProcessObject. Default value is off. Another options for controlling memory utilization is the ReleaseDataBeforeUpdateFlag.

Definition at line 257 of file itkProcessObject.h.

void itk::ProcessObject::ReleaseDataFlagOn ( ) [inline, inherited]

Turn on/off the flags to control whether the bulk data belonging to the outputs of this ProcessObject are released after being used by a downstream ProcessObject. Default value is off. Another options for controlling memory utilization is the ReleaseDataBeforeUpdateFlag.

Definition at line 256 of file itkProcessObject.h.

virtual void itk::ProcessObject::ReleaseInputs ( ) [protected, virtual, inherited]

A filter may need to release its input's bulk data after it has finished calculating a new output. The filter may need to release the inputs because the user has turned on the ReleaseDataFlag or it may need to release the inputs because the filter is an "in place" filter and it has overwritten its input with its output data. The implementation here simply checks the ReleaseDataFlag of the inputs. InPlaceImageFilter overrides this method so release the input it has overwritten.

See also:: InPlaceImageFilter::ReleaseInputs()

void itk::Object::RemoveAllObservers ( ) [inherited]

Remove all observers .

virtual void itk::ProcessObject::RemoveInput ( DataObject * input ) [protected, virtual, inherited]

Protected methods for setting inputs. Subclasses make use of them for setting input.

void itk::Object::RemoveObserver ( unsigned long tag ) [inherited]

Remove the observer with this tag value.

virtual void itk::ProcessObject::RemoveOutput ( DataObject * output ) [protected, virtual, inherited]

Protected methods for setting outputs. Subclasses make use of them for getting output.

virtual void itk::ProcessObject::ResetPipeline ( ) [virtual, inherited]

Reset the pipeline. If an exception is thrown during an Update(), the pipeline may be in an inconsistent state. This method clears the internal state of the pipeline so Update() can be called.

virtual void itk::ProcessObject::RestoreInputReleaseDataFlags ( ) [protected, virtual, inherited]

Restore the cached input ReleaseDataFlags.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::RunRegistration ( void )

Call this to register two images.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SampleVectorFieldAtNodes ( SolverType & S ) [protected]

This is used for changing between mesh resolutions.

virtual void itk::ProcessObject::SetAbortGenerateData ( bool _arg ) [virtual, inherited]

Set the AbortGenerateData flag for the process object. Process objects may handle premature termination of execution in different ways.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetAlpha ( Float a ) [inline]

Set alpha for the trapezoidal rule (usually 1.0 in our experiments).

Definition at line 367 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetConfigFileName ( const char * f ) [inline]

Sets the file name for the FEM multi-resolution registration. One can also set the parameters in code.

Definition at line 454 of file itkFEMRegistrationFilter.h.

void itk::Object::SetDebug ( bool debugFlag ) const [inherited]

Set the value of the debug flag. A non-zero value turns debugging on.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetDeformationField ( FieldType * F ) [inline]

Sets the FE deformation field.

Definition at line 260 of file itkFEMRegistrationFilter.h.

References itk::ImageBase< VImageDimension >::GetLargestPossibleRegion().

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetDescentDirectionMaximize ( ) [inline]

Tries to maximize energy

Definition at line 410 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetDescentDirectionMinimize ( ) [inline]

Tries to minimize energy

Definition at line 404 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetDisplacementsFile ( const char * r ) [inline]

Sets the filename for the vector field component images.

Definition at line 310 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetElasticity	(	Float	i,
		unsigned int	which = `0`
	)			`[inline]`

Sets the stiffness Matrix weight.

Definition at line 380 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetElement ( Element::Pointer e ) [inline]

This function allows one to set the element and its material externally.

Definition at line 470 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetEnergyReductionFactor ( Float i ) [inline]

Sets the energy below which we decide the solution has converged.

Definition at line 374 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetFixedFile ( const char * t ) [inline]

Definition at line 225 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetFixedImage ( FixedImageType * T )

Define the target (fixed) image.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetGamma	(	Float	r,
		unsigned int	which = `0`
	)			`[inline]`

Image similarity energy weight

Definition at line 398 of file itkFEMRegistrationFilter.h.

static void itk::Object::SetGlobalWarningDisplay ( bool flag ) [static, inherited]

This is a global flag that controls whether any debug, warning or error messages are displayed.

Referenced by itk::Object::GlobalWarningDisplayOff(), and itk::Object::GlobalWarningDisplayOn().

virtual void itk::ImageToImageFilter< TMovingImage , TFixedImage >::SetInput	(	unsigned	int,
		const TMovingImage *	image
	)			`[virtual, inherited]`

Set/Get the image input of this process object.

virtual void itk::ImageToImageFilter< TMovingImage , TFixedImage >::SetInput ( const InputImageType * image ) [virtual, inherited]

Set/Get the image input of this process object.

template<class TMovingImage , class TFixedImage >

virtual void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetInterpolator ( InterpolatorType * _arg ) [virtual]

Set the interpolator function.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetLandmarkFile ( const char * l ) [inline]

These functions control the use of landmark constraints. Currently, landmarks must be read in from a file.

Definition at line 269 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetLineSearchMaximumIterations ( unsigned int f ) [inline]

This sets the line search's max iterations.

Definition at line 435 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetMaterial ( MaterialType::Pointer m ) [inline]

This sets the pointer to the material.

Definition at line 473 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetMaximumIterations	(	unsigned int	i,
		unsigned int	which
	)			`[inline]`

Setting the maximum iterations stops the solution after i iterations regardless of energy.

Parameters:

	i	number of elements
	which	determines the resolution of the solution process the call is applied to.

Definition at line 354 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetMaxLevel ( unsigned int i ) [inline]

Definition at line 478 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetMeshPixelsPerElementAtEachResolution	(	unsigned int	i,
		unsigned int	which = `0`
	)			`[inline]`

The FEM filter can generate its own mesh for 2 or 3 dimensions, if none is provided. The mesh is generated for quadrilaterals in 2D and hexahedra in 3D. This function sets the number of elements generated along each dimension at the resolution designated by "which". E.g. to generate 10 pixels per element in each dimension in the 1st resolution, use SetMeshResolution(10,0);.

Definition at line 321 of file itkFEMRegistrationFilter.h.

void itk::Object::SetMetaDataDictionary ( const MetaDataDictionary & rhs ) [inherited]

Returns:: Set the MetaDataDictionary

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetMetric ( MetricBaseTypePointer MP ) [inline]

Set/Get the Metric.

Definition at line 462 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetMovingFile ( const char * r ) [inline]

One can set the reference file names to read images from files

Definition at line 215 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetMovingImage ( MovingImageType * R )

One can set the images directly to input images in an application Define the reference (moving) image.

virtual void itk::ProcessObject::SetNthInput	(	unsigned int	num,
		DataObject *	input
	)			`[protected, virtual, inherited]`

Protected methods for setting inputs. Subclasses make use of them for setting input.

Reimplemented in itk::ImageToVectorImageFilter< TInputImage >.

Referenced by itk::watershed::BoundaryResolver< TPixelType, TDimension >::SetBoundaryA(), itk::watershed::BoundaryResolver< TPixelType, TDimension >::SetBoundaryB(), itk::watershed::EquivalenceRelabeler< TScalarType, TImageDimension >::SetEquivalencyTable(), itk::SegmentationLevelSetImageFilter< TInputImage, TFeatureImage, TOutputPixelType >::SetFeatureImage(), itk::NarrowBandLevelSetImageFilter< TInputImage, TFeatureImage, TOutputPixelType, Image< TOutputPixelType,::itk::GetImageDimension< TInputImage >::ImageDimension > >::SetFeatureImage(), itk::WatershedImageFilter< TInputImage >::SetInput(), itk::watershed::SegmentTreeGenerator< ScalarType >::SetInputEquivalencyTable(), itk::watershed::Segmenter< InputImageType >::SetInputImage(), itk::watershed::Relabeler< ScalarType, itkGetStaticConstMacro(ImageDimension)>::SetInputImage(), itk::watershed::EquivalenceRelabeler< TScalarType, TImageDimension >::SetInputImage(), itk::watershed::SegmentTreeGenerator< ScalarType >::SetInputSegmentTable(), itk::watershed::Relabeler< ScalarType, itkGetStaticConstMacro(ImageDimension)>::SetInputSegmentTree(), itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::SetReferenceImage(), and itk::ChangeInformationImageFilter< TInputImage >::SetReferenceImage().

virtual void itk::ProcessObject::SetNthOutput	(	unsigned int	num,
		DataObject *	output
	)			`[protected, virtual, inherited]`

Protected methods for setting outputs. Subclasses make use of them for getting output.

Referenced by itk::watershed::BoundaryResolver< TPixelType, TDimension >::BoundaryResolver(), itk::watershed::EquivalenceRelabeler< TScalarType, TImageDimension >::EquivalenceRelabeler(), itk::watershed::Segmenter< InputImageType >::SetBoundary(), itk::watershed::BoundaryResolver< TPixelType, TDimension >::SetEquivalencyTable(), itk::watershed::Segmenter< InputImageType >::SetOutputImage(), itk::watershed::Relabeler< ScalarType, itkGetStaticConstMacro(ImageDimension)>::SetOutputImage(), itk::watershed::EquivalenceRelabeler< TScalarType, TImageDimension >::SetOutputImage(), and itk::watershed::Segmenter< InputImageType >::SetSegmentTable().

void itk::ProcessObject::SetNumberOfInputs ( unsigned int num ) [protected, inherited]

Called to allocate the input array. Copies old inputs.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetNumberOfIntegrationPoints	(	unsigned int	i,
		unsigned int	which = `0`
	)			`[inline]`

This determines the number of integration points to use at each resolution. These integration points are used to generate the force. The actual number used will be i^d, where d is the number of parameters in the elements local domain.

Definition at line 330 of file itkFEMRegistrationFilter.h.

void itk::ProcessObject::SetNumberOfOutputs ( unsigned int num ) [protected, inherited]

Called to allocate the output array. Copies old outputs.

virtual void itk::ProcessObject::SetNumberOfRequiredInputs ( unsigned int _arg ) [protected, virtual, inherited]

Protected methods for setting inputs. Subclasses make use of them for setting input.

virtual void itk::ProcessObject::SetNumberOfRequiredOutputs ( unsigned int _arg ) [protected, virtual, inherited]

Protected methods for setting outputs. Subclasses make use of them for getting output.

virtual void itk::ProcessObject::SetNumberOfThreads ( int _arg ) [virtual, inherited]

Get/Set the number of threads to create when executing.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetNumLevels ( unsigned int i ) [inline]

Definition at line 477 of file itkFEMRegistrationFilter.h.

virtual void itk::ProcessObject::SetProgress ( float _arg ) [virtual, inherited]

Set the execution progress of a process object. The progress is a floating number in [0,1] with 0 meaning no progress and 1 meaning the filter has completed execution. The ProgressEvent is NOT invoked.

virtual void itk::Object::SetReferenceCount ( int ) [virtual, inherited]

Sets the reference count (use with care)

Reimplemented from itk::LightObject.

virtual void itk::ProcessObject::SetReleaseDataBeforeUpdateFlag ( bool _arg ) [virtual, inherited]

Turn on/off the flags to control whether the bulk data belonging to the outputs of this ProcessObject are released/reallocated during an Update(). In limited memory scenarios, a user may want to force the elements of a pipeline to release any bulk data that is going to be regenerated anyway during an Update() in order to control peak memory allocation. Note that this flag is different from the ReleaseDataFlag. ReleaseDataFlag manages the deallocation of a ProcessObject's bulk output data once that data has been consumed by a downstream ProcessObject. The ReleaseDataBeforeUpdateFlag manages the deallocation/reallocation of bulk data during a pipeline update to control peak memory utilization. Default value is on.

virtual void itk::ProcessObject::SetReleaseDataFlag ( bool flag ) [virtual, inherited]

Turn on/off the flags to control whether the bulk data belonging to the outputs of this ProcessObject are released after being used by a downstream ProcessObject. Default value is off. Another options for controlling memory utilization is the ReleaseDataBeforeUpdateFlag.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetResultsFile ( const char * r ) [inline]

The warped reference image will be written to this file name with the extension "11.img" appended to it. One can also output the image after every iteration, yielding result11.img, result12.img, etc. by uncommenting the code at the end of IterativeSolve.

Definition at line 294 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetResultsFileName ( const char * f ) [inline]

Definition at line 299 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetRho	(	Float	r,
		unsigned int	which = `0`
	)			`[inline]`

Mass matrix weight

Definition at line 392 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetTemp ( Float i ) [inline]

Definition at line 480 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetTimeStep ( Float i ) [inline]

Setting the time step - usually 1.0. We prefer to use rho to control step sizes.

Definition at line 361 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetWidthOfMetricRegion	(	unsigned int	i,
		unsigned int	which = `0`
	)			`[inline]`

The metric region allows one to compute the derivative (force) of the similarity metric using a region of size [i,i] in 2D [i,i,i] in 3D.

Parameters:

	i	number of elements
	which	determines the region at a given resolution of the solution process.

Definition at line 340 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::SetWriteDisplacements ( bool b ) [inline]

Sets the boolean for writing the displacement field to a file.

Definition at line 441 of file itkFEMRegistrationFilter.h.

virtual int itk::ImageSource< TFixedImage >::SplitRequestedRegion	(	int	i,
		int	num,
		OutputImageRegionType &	splitRegion
	)			`[protected, virtual, inherited]`

Split the output's RequestedRegion into "num" pieces, returning region "i" as "splitRegion". This method is called "num" times. The regions must not overlap. The method returns the number of pieces that the routine is capable of splitting the output RequestedRegion, i.e. return value is less than or equal to "num".

virtual void itk::ImageSource< TFixedImage >::ThreadedGenerateData	(	const OutputImageRegionType &	outputRegionForThread,
		int	threadId
	)			`[protected, virtual, inherited]`

If an imaging filter can be implemented as a multithreaded algorithm, the filter will provide an implementation of ThreadedGenerateData(). This superclass will automatically split the output image into a number of pieces, spawn multiple threads, and call ThreadedGenerateData() in each thread. Prior to spawning threads, the BeforeThreadedGenerateData() method is called. After all the threads have completed, the AfterThreadedGenerateData() method is called. If an image processing filter cannot support threading, that filter should provide an implementation of the GenerateData() method instead of providing an implementation of ThreadedGenerateData(). If a filter provides a GenerateData() method as its implementation, then the filter is responsible for allocating the output data. If a filter provides a ThreadedGenerateData() method as its implementation, then the output memory will allocated automatically by this superclass. The ThreadedGenerateData() method should only produce the output specified by "outputThreadRegion" parameter. ThreadedGenerateData() cannot write to any other portion of the output image (as this is responsibility of a different thread).

See also:: GenerateData(), SplitRequestedRegion()

static ITK_THREAD_RETURN_TYPE itk::ImageSource< TFixedImage >::ThreaderCallback ( void * arg ) [static, protected, inherited]

Static function used as a "callback" by the MultiThreader. The threading library will call this routine for each thread, which will delegate the control to ThreadedGenerateData().

virtual void itk::Object::UnRegister ( ) const [virtual, inherited]

Decrease the reference count (release by another object).

Reimplemented from itk::LightObject.

virtual void itk::ProcessObject::Update ( ) [virtual, inherited]

Bring this filter up-to-date. Update() checks modified times against last execution times, and re-executes objects if necessary. A side effect of this method is that the whole pipeline may execute in order to bring this filter up-to-date. This method updates the currently prescribed requested region. If no requested region has been set on the output, then the requested region will be set to the largest possible region. Once the requested region is set, Update() will make sure the specified requested region is up-to-date. This is a confusing side effect to users who are just calling Update() on a filter. A first call to Update() will cause the largest possible region to be updated. A second call to Update() will update that same region. If a modification to the upstream pipeline cause a filter to have a different largest possible region, this second call to Update() will not cause the output requested region to be reset to the new largest possible region. Instead, the output requested region will be the same as the last time Update() was called. To have a filter always to produce its largest possible region, users should call UpdateLargestPossibleRegion() instead.

Reimplemented in itk::CoreAtomImageToUnaryCorrespondenceMatrixProcess< TSourceImage >, itk::MedialNodePairCorrespondenceProcess< TSourceImage >, itk::MedialNodeTripletCorrespondenceProcess< TSourceImage >, itk::CoreAtomImageToDistanceMatrixProcess< TSourceImage >, itk::ImageFileWriter< TInputImage >, and itk::ImageSeriesWriter< TInputImage, TOutputImage >.

virtual void itk::ProcessObject::UpdateLargestPossibleRegion ( ) [virtual, inherited]

Like Update(), but sets the output requested region to the largest possible region for the output. This is the method users should call if they want the entire dataset to be processed. If a user wants to update the same output region as a previous call to Update() or a previous call to UpdateLargestPossibleRegion(), then they should call the method Update().

virtual void itk::ProcessObject::UpdateOutputData ( DataObject * output ) [virtual, inherited]

Actually generate new output

Reimplemented in itk::StreamingImageFilter< TInputImage, TOutputImage >.

virtual void itk::ProcessObject::UpdateOutputInformation ( ) [virtual, inherited]

Update the information decribing the output data. This method transverses up the pipeline gathering modified time information. On the way back down the pipeline, this method calls GenerateOutputInformation() to set any necessary information about the output data objects. For instance, a filter that shrinks an image will need to provide an implementation for GenerateOutputInformation() that changes the spacing of the pixels. Such filters should call their superclass' implementation of GenerateOutputInformation prior to changing the information values they need (i.e. GenerateOutputInformation() should call Superclass::GenerateOutputInformation() prior to changing the information.

Reimplemented in itk::watershed::Segmenter< TInputImage >, itk::VTKImageImport< TOutputImage >, and itk::watershed::Segmenter< InputImageType >.

void itk::ProcessObject::UpdateProgress ( float amount ) [inherited]

Update the progress of the process object.

Sets the Progress ivar to amount and invokes any observers for the ProgressEvent. The parameter amount should be in [0,1] and is the cumulative (not incremental) progress.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::UseLandmarks ( bool b ) [inline]

This determines if the landmark file will be read

Definition at line 275 of file itkFEMRegistrationFilter.h.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::WarpImage ( const MovingImageType * R )

Applies the warp to the input image.

template<class TMovingImage , class TFixedImage >

int itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::WriteDisplacementField ( unsigned int index )

Writes the displacement field to a file.

template<class TMovingImage , class TFixedImage >

int itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::WriteDisplacementFieldMultiComponent ( )

Writes the displacement field to a file as a single volume with multiple components.

template<class TMovingImage , class TFixedImage >

void itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >::WriteWarpedImage ( const char * fn )

Call this to write out images - a counter is attached to the file name so we can output a numbered sequence tracking the deformation.

Member Data Documentation

TimeStamp itk::ProcessObject::m_OutputInformationMTime [protected, inherited]

Time when GenerateOutputInformation was last called.

Definition at line 431 of file itkProcessObject.h.

InternalReferenceCountType itk::LightObject::m_ReferenceCount [mutable, protected, inherited]

Number of uses of this object by other objects.

Definition at line 144 of file itkLightObject.h.

SimpleFastMutexLock itk::LightObject::m_ReferenceCountLock [mutable, protected, inherited]

Mutex lock to protect modification to the reference count

Definition at line 147 of file itkLightObject.h.

bool itk::ProcessObject::m_Updating [protected, inherited]

These ivars are made protected so filters like itkStreamingImageFilter can access them directly. This flag indicates when the pipeline is executing. It prevents infinite recursion when pipelines have loops.

Definition at line 428 of file itkProcessObject.h.

The documentation for this class was generated from the following file:

itkFEMRegistrationFilter.h


Classes
class	FEMOF
Public Types
typedef SmartPointer< const Self >	ConstPointer
typedef double	CoordRepType
typedef DataObject::Pointer	DataObjectPointer
typedef std::vector < DataObjectPointer >	DataObjectPointerArray
typedef DataObjectPointerArray::size_type	DataObjectPointerArraySizeType
typedef VectorLinearInterpolateImageFunction < FieldType, CoordRepType >	DefaultInterpolatorType
typedef itk::VectorExpandImageFilter < FieldType, FieldType >	ExpanderType
typedef ExpanderType::ExpandFactorsType	ExpandFactorsType
typedef itk::ImageRegionIteratorWithIndex < FieldType >	FieldIterator
typedef itk::Image< VectorType, itkGetStaticConstMacro(ImageDimension)>	FieldType
typedef TFixedImage	FixedImageType
typedef itk::RecursiveMultiResolutionPyramidImageFilter < FixedImageType, FixedImageType >	FixedPyramidType
typedef double	Float
typedef itk::ImageRegionIteratorWithIndex < FloatImageType >	FloatImageIterator
typedef Image< float, itkGetStaticConstMacro(ImageDimension) >	FloatImageType
typedef itk::ImageRegionIteratorWithIndex < FixedImageType >	ImageIterator
typedef FiniteDifferenceFunctionLoad < MovingImageType, FixedImageType >	ImageMetricLoadType
typedef FixedImageType::SizeType	ImageSizeType
typedef itk::VectorIndexSelectionCastImageFilter < FieldType, FloatImageType >	IndexSelectCasterType
typedef InputImageType::ConstPointer	InputImageConstPointer
typedef InputImageType::PixelType	InputImagePixelType
typedef InputImageType::Pointer	InputImagePointer
typedef InputImageType::RegionType	InputImageRegionType
typedef TMovingImage	InputImageType
typedef InterpolatorType::Pointer	InterpolatorPointer
typedef VectorInterpolateImageFunction < FieldType, CoordRepType >	InterpolatorType
typedef std::vector< typename LoadLandmark::Pointer >	LandmarkArrayType
typedef LinearSystemWrapperItpack	LinearSystemSolverType
typedef Load::ArrayType	LoadArray
typedef MaterialLinearElasticity	MaterialType
typedef PDEDeformableRegistrationFunction < FixedImageType, MovingImageType, FieldType >	MetricBaseType
typedef MetricBaseType::Pointer	MetricBaseTypePointer
typedef TMovingImage	MovingImageType
Public Member Functions
virtual void	AbortGenerateDataOff ()
virtual void	AbortGenerateDataOn ()
void	ChooseMetric (float whichmetric)
void	ComputeJacobian (float sign=1.0, FieldType *field=NULL, float smooth=0.0)
virtual LightObject::Pointer	CreateAnother () const
virtual void	DebugOff () const
virtual void	DebugOn () const
virtual void	Delete ()
void	DoLineSearch (unsigned int b)
void	DoMultiRes (bool b)
void	EmployRegridding (unsigned int b)
void	EnforceDiffeomorphism (float thresh, SolverType &S, bool onlywriteimages)
virtual void	EnlargeOutputRequestedRegion (DataObject *)
virtual const bool &	GetAbortGenerateData ()
Command *	GetCommand (unsigned long tag)
std::string	GetConfigFileName ()
bool	GetDebug () const
FieldType *	GetDeformationField ()
Float	GetElasticity (unsigned int which=0)
std::string	GetFixedFile ()
FixedImageType *	GetFixedImage ()
ImageSizeType	GetImageSize ()
DataObjectPointerArray &	GetInputs ()
virtual InterpolatorType *	GetInterpolator ()
FloatImageType *	GetJacobianImage ()
const MetaDataDictionary &	GetMetaDataDictionary (void) const
MetaDataDictionary &	GetMetaDataDictionary (void)
std::string	GetMovingFile ()
MovingImageType *	GetMovingImage ()
virtual unsigned long	GetMTime () const
MultiThreader *	GetMultiThreader ()
virtual const char *	GetNameOfClass () const
DataObjectPointerArraySizeType	GetNumberOfInputs () const
virtual DataObjectPointerArraySizeType	GetNumberOfValidRequiredInputs () const
MovingImageType *	GetOriginalMovingImage ()
virtual const float &	GetProgress ()
virtual int	GetReferenceCount () const
std::string	GetResultsFileName ()
FixedImageType *	GetWarpedImage ()
bool	GetWriteDisplacements ()
virtual void	GraftNthOutput (unsigned int idx, DataObject *output)
virtual void	GraftOutput (DataObject *output)
bool	HasObserver (const EventObject &event) const
void	InvokeEvent (const EventObject &) const
void	InvokeEvent (const EventObject &)
void	IterativeSolve (SolverType &S)
	itkStaticConstMacro (ImageDimension, unsigned int, FixedImageType::ImageDimension)
virtual DataObjectPointer	MakeOutput (unsigned int idx)
virtual void	Modified () const
void	MultiResSolve ()
virtual void	PrepareOutputs ()
void	Print (std::ostream &os, Indent indent=0) const
void	PrintVectorField (unsigned int modnum=1000)
virtual void	PropagateRequestedRegion (DataObject *output)
bool	ReadConfigFile (const char *)
virtual void	Register () const
void	RemoveAllObservers ()
void	RemoveObserver (unsigned long tag)
virtual void	ResetPipeline ()
void	RunRegistration (void)
virtual void	SetAbortGenerateData (bool _arg)
void	SetAlpha (Float a)
void	SetConfigFileName (const char *f)
void	SetDebug (bool debugFlag) const
void	SetDescentDirectionMaximize ()
void	SetDescentDirectionMinimize ()
void	SetDisplacementsFile (const char *r)
void	SetElasticity (Float i, unsigned int which=0)
void	SetElement (Element::Pointer e)
void	SetEnergyReductionFactor (Float i)
void	SetFixedFile (const char *t)
void	SetFixedImage (FixedImageType *T)
void	SetGamma (Float r, unsigned int which=0)
virtual void	SetInterpolator (InterpolatorType *_arg)
void	SetLandmarkFile (const char *l)
void	SetLineSearchMaximumIterations (unsigned int f)
void	SetMaterial (MaterialType::Pointer m)
void	SetMaximumIterations (unsigned int i, unsigned int which)
void	SetMaxLevel (unsigned int i)
void	SetMetaDataDictionary (const MetaDataDictionary &rhs)
void	SetMovingFile (const char *r)
void	SetMovingImage (MovingImageType *R)
void	SetNumberOfIntegrationPoints (unsigned int i, unsigned int which=0)
void	SetNumLevels (unsigned int i)
virtual void	SetProgress (float _arg)
virtual void	SetReferenceCount (int)
void	SetResultsFile (const char *r)
void	SetResultsFileName (const char *f)
void	SetRho (Float r, unsigned int which=0)
void	SetTemp (Float i)
void	SetTimeStep (Float i)
void	SetWriteDisplacements (bool b)
virtual void	UnRegister () const
virtual void	Update ()
virtual void	UpdateLargestPossibleRegion ()
virtual void	UpdateOutputData (DataObject *output)
virtual void	UpdateOutputInformation ()
void	UpdateProgress (float amount)
void	UseLandmarks (bool b)
void	WarpImage (const MovingImageType *R)
int	WriteDisplacementField (unsigned int index)
int	WriteDisplacementFieldMultiComponent ()
void	WriteWarpedImage (const char *fn)

unsigned long	AddObserver (const EventObject &event, Command *) const
unsigned long	AddObserver (const EventObject &event, Command *)

	FEMRegistrationFilter ()
	~FEMRegistrationFilter ()

const InputImageType *	GetInput (unsigned int idx)
const InputImageType *	GetInput (void)
virtual void	SetInput (unsigned int, const TMovingImage *image)
virtual void	SetInput (const InputImageType *image)

MetricBaseTypePointer	GetMetric ()
void	SetMetric (MetricBaseTypePointer MP)

DataObjectPointerArraySizeType	GetNumberOfOutputs () const
DataObjectPointerArray &	GetOutputs ()

virtual const int &	GetNumberOfThreads ()
virtual void	SetNumberOfThreads (int _arg)

OutputImageType *	GetOutput (unsigned int idx)
OutputImageType *	GetOutput (void)

virtual const bool &	GetReleaseDataBeforeUpdateFlag ()
virtual void	ReleaseDataBeforeUpdateFlagOff ()
virtual void	ReleaseDataBeforeUpdateFlagOn ()
virtual void	SetReleaseDataBeforeUpdateFlag (bool _arg)

virtual bool	GetReleaseDataFlag () const
void	ReleaseDataFlagOff ()
void	ReleaseDataFlagOn ()
virtual void	SetReleaseDataFlag (bool flag)

unsigned int	GetWidthOfMetricRegion (unsigned int which=0)
void	SetWidthOfMetricRegion (unsigned int i, unsigned int which=0)

	itkStaticConstMacro (OutputImageDimension, unsigned int, TFixedImage::ImageDimension)
	itkStaticConstMacro (InputImageDimension, unsigned int, TMovingImage::ImageDimension)

virtual void	PopBackInput ()
virtual void	PopFrontInput ()
virtual void	PushBackInput (const InputImageType *image)
virtual void	PushFrontInput (const InputImageType *image)

void	SetDeformationField (FieldType *F)

void	SetMeshPixelsPerElementAtEachResolution (unsigned int i, unsigned int which=0)
Static Public Member Functions
static void	BreakOnError ()
static Pointer	New ()

static bool	GetGlobalWarningDisplay ()
static void	GlobalWarningDisplayOff ()
static void	GlobalWarningDisplayOn ()
static void	SetGlobalWarningDisplay (bool flag)
Protected Types
typedef ImageToImageFilterDetail::ImageRegionCopier < itkGetStaticConstMacro(OutputImageDimension), itkGetStaticConstMacro(InputImageDimension)>	InputToOutputRegionCopierType
typedef ImageToImageFilterDetail::ImageRegionCopier < itkGetStaticConstMacro(InputImageDimension), itkGetStaticConstMacro(OutputImageDimension)>	OutputToInputRegionCopierType

typedef int	InternalReferenceCountType
Protected Member Functions
virtual void	AfterThreadedGenerateData ()
virtual void	AllocateOutputs ()
void	ApplyImageLoads (SolverType &S, MovingImageType i1, FixedImageType i2)
void	ApplyLoads (SolverType &S, ImageSizeType Isz, double *spacing=NULL)
virtual void	BeforeThreadedGenerateData ()
virtual void	CacheInputReleaseDataFlags ()
virtual void	CallCopyInputRegionToOutputRegion (OutputImageRegionType &destRegion, const InputImageRegionType &srcRegion)
virtual void	CallCopyOutputRegionToInputRegion (InputImageRegionType &destRegion, const OutputImageRegionType &srcRegion)
void	CreateLinearSystemSolver ()
void	CreateMesh (double ElementsPerSide, Solver &S, ImageSizeType sz)
Float	EvaluateEnergy ()
Float	EvaluateResidual (SolverType &mySolver, Float t)
void	FindBracketingTriplet (SolverType &mySolver, Float a, Float b, Float *c)
virtual void	GenerateData ()
virtual void	GenerateInputRequestedRegion ()
virtual void	GenerateOutputInformation ()
virtual void	GenerateOutputRequestedRegion (DataObject *output)
FloatImageType *	GetMetricImage (FieldType *F)
Float	GoldenSection (SolverType &mySolver, Float tol=0.01, unsigned int MaxIters=25)
void	InterpolateVectorField (SolverType &S)
bool	PrintObservers (std::ostream &os, Indent indent) const
void	PrintSelf (std::ostream &os, Indent indent) const
virtual void	PropagateResetPipeline ()
virtual void	ReleaseInputs ()
virtual void	RestoreInputReleaseDataFlags ()
void	SampleVectorFieldAtNodes (SolverType &S)
void	SetNumberOfInputs (unsigned int num)
void	SetNumberOfOutputs (unsigned int num)
virtual int	SplitRequestedRegion (int i, int num, OutputImageRegionType &splitRegion)
virtual void	ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, int threadId) ITK_NO_RETURN

virtual void	AddInput (DataObject *input)
virtual const unsigned int &	GetNumberOfRequiredInputs ()
virtual void	RemoveInput (DataObject *input)
virtual void	SetNthInput (unsigned int num, DataObject *input)
virtual void	SetNumberOfRequiredInputs (unsigned int _arg)

virtual void	AddOutput (DataObject *output)
virtual const unsigned int &	GetNumberOfRequiredOutputs ()
virtual void	RemoveOutput (DataObject *output)
virtual void	SetNthOutput (unsigned int num, DataObject *output)
virtual void	SetNumberOfRequiredOutputs (unsigned int _arg)

const DataObject *	GetInput (unsigned int idx) const

virtual ImageMetricLoadType *	GetLoad () const

const DataObject *	GetOutput (unsigned int idx) const

virtual void	PrintHeader (std::ostream &os, Indent indent) const
virtual void	PrintTrailer (std::ostream &os, Indent indent) const

void	PushBackInput (const DataObject *input)
void	PushFrontInput (const DataObject *input)
Static Protected Member Functions
static ITK_THREAD_RETURN_TYPE	ThreaderCallback (void *arg)
Protected Attributes
TimeStamp	m_OutputInformationMTime
InternalReferenceCountType	m_ReferenceCount
SimpleFastMutexLock	m_ReferenceCountLock
bool	m_Updating
typedef FieldType::Pointer	FieldPointer
FieldPointer	ExpandVectorField (ExpandFactorsType expandFactors, FieldType f)

itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage > Class Template Reference

Classes

Public Types

Public Member Functions

Static Public Member Functions

Protected Types

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Detailed Description

template<class TMovingImage, class TFixedImage> class itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<class TMovingImage, class TFixedImage>
class itk::fem::FEMRegistrationFilter< TMovingImage, TFixedImage >