cmtkRegistration Library

This library provides classes related to computing and processing registrations between images. More...

Classes
class	cmtk::HypothesisTests
	Statistical hypothesis testing between groups of images. More...
class	cmtk::AffineMultiChannelRegistrationFunctional< TMultiChannelMetricFunctional >
	Class for affine multi-channel registration functional. More...
class	cmtk::AffineRegistration
	Class for affine multi-resolution voxel registration. More...
class	cmtk::AffineRegistrationCommandLine
	Class for command line-controlled affine registration. More...
class	cmtk::BestDirectionOptimizer
	Optimizer derived from BestNeighbourOptimizer. More...
class	cmtk::BestNeighbourOptimizer
	Best-neighbour-search optimizer. More...
class	cmtk::CongealingFunctional< TXform >
	Functional base class for groupwise congealing registration. More...
class	cmtk::ElasticRegistration
	Generic multiresolution voxel-registration class. More...
class	cmtk::ElasticRegistrationCommandLine
	Class for command line controlled voxel registration. More...
class	cmtk::FunctionalAffine2D
	Functional for the affine registration two 2D images. More...
class	cmtk::GroupwiseRegistrationFunctionalAffineInitializer
	Affine initialization of groupwise registration functionals. More...
class	cmtk::GroupwiseRegistrationFunctionalBase
	Base class for groupwise registration functionals. More...
class	cmtk::GroupwiseRegistrationFunctionalXformTemplate< TXform >
	Trannsformation-dependent class template for groupwise registration functionals. More...
class	cmtk::GroupwiseRegistrationFunctionalXformTemplateBase< TXform >
	Base class template for groupwise registration functionals. More...
class	cmtk::GroupwiseRegistrationOutput
	Class for output of groupwise registration results. More...
class	cmtk::GroupwiseRegistrationRMIFunctional< TXform >
	Functional for groupwise registration. More...
class	cmtk::ImagePairAffineRegistration
	Class for affine multi-resolution voxel registration. More...
class	cmtk::ImagePairAffineRegistrationCommandLine
	Class for command line-controlled affine registration. More...
class	cmtk::ImagePairAffineRegistrationFunctional
	Base-class for affine registration functionals. More...
class	cmtk::ImagePairAffineRegistrationFunctionalTemplate< VM >
	Functional that evaluates a voxel-based similarity measure. More...
class	cmtk::ImagePairNonrigidRegistration
	Generic multiresolution voxel-registration class. More...
class	cmtk::ImagePairNonrigidRegistrationCommandLine
	Class for command line controlled voxel registration. More...
class	cmtk::ImagePairNonrigidRegistrationFunctional
	Common base class for all elastic registration functionals. More...
class	cmtk::ImagePairNonrigidRegistrationFunctionalTemplate< VM >
	Parallel elastic registration functional. More...
class	cmtk::ImagePairRegistration
	Generic multiresolution voxel-registration class. More...
class	cmtk::ImagePairRegistrationFunctional
	Base class for voxel matching functionals. More...
class	cmtk::ImagePairSimilarityJointHistogram
	Base class for voxel metrics with pre-converted image data. More...
class	cmtk::ImagePairSimilarityMeasure
	Base class for voxel metrics with pre-converted image data. More...
class	cmtk::ImagePairSimilarityMeasureCR
	Pairwise image similarity measure "correlation ratio". More...
class	cmtk::ImagePairSimilarityMeasureMI
	Base class for voxel metrics with pre-converted image data. More...
class	cmtk::ImagePairSimilarityMeasureMSD
	Mean squared difference metric. More...
class	cmtk::ImagePairSimilarityMeasureNCC
	Normalized Cross Correlation Metric. More...
class	cmtk::ImagePairSimilarityMeasureNMI
	Base class for voxel metrics with pre-converted image data. More...
class	cmtk::ImagePairSimilarityMeasureRMS
	Mean squared difference metric. More...
class	cmtk::ImagePairSymmetricNonrigidRegistrationFunctional
	Symmtric-consistent elastic registration functional. More...
class	cmtk::ImagePairSymmetricNonrigidRegistrationFunctionalTemplate< VM, W >
	Template for symmtric-consistent elastic registration functional. More...
class	cmtk::ImageSymmetryPlaneCommandLine< TFunctional >
	Class template for symmetry plane computation command line tools. More...
class	cmtk::ImageSymmetryPlaneCommandLineBase
	Base class for symmetry plane computation command line tools. More...
class	cmtk::ImageSymmetryPlaneFunctional
	Functional for finding a symmetry plane in 3-D volumes. More...
class	cmtk::ImageSymmetryPlaneFunctionalBase
	Base class for functionals to find a symmetry plane in 3-D volumes. More...
class	cmtk::ImageXformDB
	Class for image and transformation database. More...
class	cmtk::IterativeDirectionOptimizer
	Iterative direction optimizer. More...
class	cmtk::MakeInitialAffineTransformation
	Class for generating initial affine coordinate transformations between two images. More...
class	cmtk::MultiChannelHistogramRegistrationFunctional< TDataType, TInterpolator, THashKeyType, NBitsPerChannel >
	Base class for multi-channel registration functionals using the Histogram metric. More...
class	cmtk::MultiChannelRegistrationFunctional< TInterpolator >
	Base class for multi-channel registration functionals. More...
class	cmtk::MultiChannelRegistrationFunctionalBase
	Base class for multi-channel registration functionals. More...
class	cmtk::MultiChannelRMIRegistrationFunctional< TRealType, TDataType, TInterpolator >
	Base class for multi-channel registration functionals using the RMI metric. More...
class	cmtk::MultiLevelOptimizer
	Multi-level optimizer. More...
class	cmtk::Optimizer
	Abstract optimizer. More...
class	cmtk::OptimizerBase
	Base class for all optimizers and meta optimizers. More...
class	cmtk::ParallelElasticFunctional< VM >
	Parallel elastic registration functional. More...
class	cmtk::ProtocolCallback
	Callback object with protocol functionality. More...
class	cmtk::ReformatVolume
	Utility class for reformatting volume data. More...
class	cmtk::Registration2d2d
	Class for registration of two 2D images. More...
class	cmtk::RegistrationCallback
	Generic callback class. More...
class	cmtk::RegistrationDatabaseUpdater
	Class for updating the image/transformation database with a newly computed registration. More...
class	cmtk::RegistrationJointHistogram< I >
	2-D histogram for entropy-based image similarity measures. More...
class	cmtk::ScalarImageSimilarityMemory
	Memory for image similarity computation. More...
class	cmtk::ScalarImageSimilarity
	Class with operators to compute various 2-D image similarity measures. More...
class	cmtk::ScaleHistogramValueTrait< T >
	Histogram kernel scaling traits. More...
class	cmtk::ScaleHistogramValueTrait< int >
class	cmtk::ScaleHistogramValueTrait< unsigned int >
class	cmtk::SearchTrace< R >
	Class for traces in the optimization search space. More...
class	cmtk::SplineWarpCongealingFunctional
	Functional for spline warp congealing. More...
class	cmtk::SplineWarpGroupwiseRegistrationRMIFunctional
	Functional for spline warp groupwise registration. More...
class	cmtk::SplineWarpMultiChannelIntensityCorrectionRegistrationFunctional< TMetricFunctional >
	Class for spline warp multi-channel registration functional. More...
class	cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >
	Class for spline warp multi-channel registration functional. More...
class	cmtk::SymmetricElasticFunctional
	Symmtric-consistent elastic registration functional. More...
class	cmtk::SymmetricElasticFunctional_Template< VM >
	Template for symmtric-consistent elastic registration functional. More...
class	cmtk::SymmetryPlaneFunctional
	Functional for finding a symmetry plane in 3-D volumes. More...
class	cmtk::TemplateMultiChannelRegistrationFunctional< TXform, TMetricFunctional >
	Class for transformation-templated multi-channel registration functional. More...
class	cmtk::TypedArraySimilarity
	Class with operators to compute various pixel similarity measures. More...
class	cmtk::TypedArraySimilarityMemory
	Memory for typed array similarity computation. More...
class	cmtk::VoxelMatchingAffineFunctional
	Base-class for affine registration functionals. More...
class	cmtk::VoxelMatchingAffineFunctionalTemplate< VM >
	Functional that evaluates a voxel-based similarity measure. More...
class	cmtk::VoxelMatchingCorrRatio< I >
	Voxel metric "correlation ratio". More...
class	cmtk::VoxelMatchingCrossCorrelation
	Normalized Cross Correlation Metric. More...
class	cmtk::VoxelMatchingElasticFunctional
	Common base class for all elastic registration functionals. More...
class	cmtk::VoxelMatchingElasticFunctional_WarpTemplate< W >
	Template class for elastic registration functional. More...
class	cmtk::VoxelMatchingElasticFunctional_Template< VM >
	Functional that evaluates a voxel-based similarity measure. More...
class	cmtk::VoxelMatchingFunctional
	Base class for voxel matching functionals. More...
class	cmtk::VoxelMatchingFunctional_Template< VM >
	Functional that evaluates a voxel-based similarity measure. More...
class	cmtk::VoxelMatchingMeanSquaredDifference
	Mean squared difference metric. More...
class	cmtk::VoxelMatchingMetric< T, DT, I >
	Base class for voxel metrics with pre-converted image data. More...
class	cmtk::VoxelMatchingMetric_Type< T, DT >
	Base class for voxel metrics with pre-converted image data. More...
class	cmtk::VoxelMatchingMutInf< I >
	Voxel metric "mutual information". More...
class	cmtk::VoxelMatchingNormMutInf< I >
	Voxel metric "normalized mutual information". More...
class	cmtk::VoxelRegistration
	Generic multiresolution voxel-registration class. More...
Typedefs
typedef CongealingFunctional < AffineXform >	cmtk::AffineCongealingFunctional
	Functional for affine congealing.
typedef GroupwiseRegistrationRMIFunctional < AffineXform >	cmtk::AffineGroupwiseRegistrationRMIFunctional
	Functional for affine groupwise registration using "RMI" metric.
typedef ImageSymmetryPlaneCommandLine < TFunctional >	cmtk::ImageSymmetryPlaneCommandLine::Self
	This class.
typedef ImageSymmetryPlaneCommandLineBase	cmtk::ImageSymmetryPlaneCommandLine::Superclass
	Parent class.
typedef SmartPointer< Self >	cmtk::ImageSymmetryPlaneCommandLine::SmartPtr
	Smart pointer.
typedef SmartConstPointer< Self >	cmtk::ImageSymmetryPlaneCommandLine::SmartConstPtr
	Smart pointer to const.
typedef Functional::ReturnType	cmtk::TypedArraySimilarity::ReturnType
	Return type for all similarity measures: match cmtk::Functional's.
typedef VoxelMatchingCorrRatio < Interpolators::LINEAR >	cmtk::VoxelMatchingCorrRatio_Trilinear
	Correlation ratio with trilinear interpolation.
typedef VoxelMatchingCorrRatio < Interpolators::NEAREST_NEIGHBOR >	cmtk::VoxelMatchingCorrRatio_NearestNeighbor
	Correlation ratio with nearest-neighbor interpolation.
typedef SmartPointer< Self >	cmtk::VoxelMatchingElasticFunctional::SmartPtr
	Smart pointer to this class.
typedef VoxelMatchingFunctional	cmtk::VoxelMatchingElasticFunctional::Superclass
	Superclass.
typedef SmartPointer< Self >	cmtk::VoxelMatchingElasticFunctional_WarpTemplate::SmartPtr
	Smart pointer to this class.
typedef VoxelMatchingElasticFunctional	cmtk::VoxelMatchingElasticFunctional_WarpTemplate::Superclass
	Superclass.
typedef VoxelMatchingMetric < short, TYPE_SHORT >	cmtk::VoxelMatchingMetricShort
	Convenience typedef.
typedef VoxelMatchingMetric < byte, TYPE_BYTE >	cmtk::VoxelMatchingMetricByte
	Convenience typedef.
typedef VoxelMatchingMetric < short, TYPE_SHORT, Interpolators::NEAREST_NEIGHBOR >	cmtk::VoxelMatchingMetricShort_NN
	Convenience typedef.
typedef VoxelMatchingMetric < byte, TYPE_BYTE, Interpolators::NEAREST_NEIGHBOR >	cmtk::VoxelMatchingMetricByte_NN
	Convenience typedef.
typedef VoxelMatchingMutInf < Interpolators::LINEAR >	cmtk::VoxelMatchingMutInf_Trilinear
	Mutual information with trilinear interpolation.
typedef VoxelMatchingMutInf < Interpolators::NEAREST_NEIGHBOR >	cmtk::VoxelMatchingMutInf_NearestNeighbor
	Mutual information with nearest-neighbor interpolation.
typedef VoxelMatchingNormMutInf < Interpolators::LINEAR >	cmtk::VoxelMatchingNormMutInf_Trilinear
	Normalized mutual information with trilinear interpolation.
typedef VoxelMatchingNormMutInf < Interpolators::NEAREST_NEIGHBOR >	cmtk::VoxelMatchingNormMutInf_NearestNeighbor
	Normalized mutual information with nearest-neighbor interpolation.
Enumerations
enum	cmtk::ImageSymmetryPlaneCommandLineBase::InitialPlaneEnum { cmtk::ImageSymmetryPlaneCommandLineBase::SYMPL_INIT_XY, cmtk::ImageSymmetryPlaneCommandLineBase::SYMPL_INIT_XZ, cmtk::ImageSymmetryPlaneCommandLineBase::SYMPL_INIT_YZ }
	Constants for initial plane orientation. More...
enum	cmtk::CallbackResult { cmtk::CALLBACK_OK = 0, cmtk::CALLBACK_INTERRUPT = 1, cmtk::CALLBACK_TIMEOUT = 2, cmtk::CALLBACK_FAILED = 3 }
	Status code returned by Execute() methods. More...
Functions
ClassStream &	cmtk::operator<< (ClassStream &stream, const GroupwiseRegistrationFunctionalXformTemplate< AffineXform > &func)
ClassStream &	cmtk::operator>> (ClassStream &stream, GroupwiseRegistrationFunctionalXformTemplate< AffineXform > &func)
ClassStream &	cmtk::operator<< (ClassStream &stream, const GroupwiseRegistrationFunctionalXformTemplate< SplineWarpXform > &func)
ClassStream &	cmtk::operator>> (ClassStream &stream, GroupwiseRegistrationFunctionalXformTemplate< SplineWarpXform > &func)
virtual ImageSymmetryPlaneFunctionalBase::SmartPtr	cmtk::ImageSymmetryPlaneCommandLine::CreateFunctional (UniformVolume::SmartPtr &volume)
	Make a functional of the given template type using an image volume.
virtual ImageSymmetryPlaneFunctionalBase::SmartPtr	cmtk::ImageSymmetryPlaneCommandLine::CreateFunctional (UniformVolume::SmartPtr &volume, const cmtk::Types::DataItemRange &range)
	Make a functional of the given template type using an image volume and a value range.
int	cmtk::ImageSymmetryPlaneCommandLineBase::Run (const int argc, const char *argv[])
	Run the symmetry plane computation based on provided command line arguments.
CommandLine &	cmtk::ImageSymmetryPlaneCommandLineBase::GetCommandLine ()
	Get reference to command line parser object.
virtual ImageSymmetryPlaneFunctionalBase::SmartPtr	cmtk::ImageSymmetryPlaneCommandLineBase::CreateFunctional (UniformVolume::SmartPtr &volume)=0
	Create functional for volume.
virtual ImageSymmetryPlaneFunctionalBase::SmartPtr	cmtk::ImageSymmetryPlaneCommandLineBase::CreateFunctional (UniformVolume::SmartPtr &volume, const Types::DataItemRange &range)=0
	Create functional for volume and value range.
bool	cmtk::ImageSymmetryPlaneCommandLineBase::ParseCommandLine (const int argc, const char *argv[])
	Parse the given command line.
void	cmtk::ImageSymmetryPlaneCommandLineBase::WriteDifference (UniformVolume::SmartConstPtr &originalVolume) const
	Write difference image between original and mirrored image.
void	cmtk::ImageSymmetryPlaneCommandLineBase::WriteMirror (UniformVolume::SmartConstPtr &originalVolume) const
	Write mirrored image.
void	cmtk::ImageSymmetryPlaneCommandLineBase::WriteMarkPlane (UniformVolume::SmartConstPtr &originalVolume) const
	Write original image with marked symmetry plane.
void	cmtk::ImageSymmetryPlaneCommandLineBase::WriteAligned (UniformVolume::SmartConstPtr &originalVolume) const
	Write image aligned w.r.t. the symmetry plane.
SymmetricElasticFunctional *	cmtk::CreateSymmetricElasticFunctional (const int metric, UniformVolume::SmartPtr &refVolume, UniformVolume::SmartPtr &fltVolume)
	Constructor function.
static ReturnType	cmtk::TypedArraySimilarity::GetMutualInformation (const TypedArray *array0, const TypedArray *array1, TypedArraySimilarityMemory *const memory=NULL)
	Compute mutual information between two pixel arrays.
static ReturnType	cmtk::TypedArraySimilarity::GetMutualInformation (const std::vector< const TypedArray * > &data0, const std::vector< const TypedArray * > &data1, const bool normalized=false)
	Compute mutual information between two sets of pixel arrays.
static ReturnType	cmtk::TypedArraySimilarity::GetNormalizedMutualInformation (const std::vector< const TypedArray * > &data0, const std::vector< const TypedArray * > &data1)
	Compute norrmalized mutual information between two sets of pixel arrays.
static ReturnType	cmtk::TypedArraySimilarity::GetCorrelationRatio (const TypedArray *array0, const TypedArray *array1)
	Compute correlation ratio between two pixel arrays.
static ReturnType	cmtk::TypedArraySimilarity::GetNormalizedMutualInformation (const TypedArray *array0, const TypedArray *array1, TypedArraySimilarityMemory *const memory=NULL)
	Compute normalized mutual information between two pixel arrays.
static ReturnType	cmtk::TypedArraySimilarity::GetMinusMeanSquaredDifference (const TypedArray *array0, const TypedArray *array1)
	Compute negated (i.e., sign-switched) mean squared pixel difference between two pixel arrays.
static ReturnType	cmtk::TypedArraySimilarity::GetPeakSignalToNoiseRatio (const TypedArray *data, const TypedArray *signal)
	Compute Peak-Signal-to-Noise-Ratio.
static ReturnType	cmtk::TypedArraySimilarity::GetCrossCorrelation (const TypedArray *array0, const TypedArray *array1)
	Compute normalized cross correlation between two pixel arrays.
static TypedArray::SmartPtr	cmtk::TypedArraySimilarity::GetDifferenceArray (const TypedArray *array0, const TypedArray *array1, Types::DataItem &scaleFactor)
	Compute scaled difference of two images.
static ReturnType	cmtk::TypedArraySimilarity::GetDifferenceArrayEntropy (const TypedArray *array0, const TypedArray *array1, Types::DataItem &scaleFactor)
	Compute entropy of difference of two images.
static bool	cmtk::TypedArraySimilarity::CheckArrayDimensions (const TypedArray *array0, const TypedArray *array1)
	Check whether two pixel arrays have matching pixel dimensions.
static ReturnType	cmtk::TypedArraySimilarity::GetOptimalScale (const TypedArray *array0, const TypedArray *array1)
	Compute the optimal scale factor between two images.
VoxelMatchingElasticFunctional *	cmtk::CreateElasticFunctional (const int metric, UniformVolume::SmartPtr &refVolume, UniformVolume::SmartPtr &fltVolume)
	Create functional from matching template.
virtual void	cmtk::VoxelMatchingElasticFunctional::SetWarpXform (SplineWarpXform::SmartPtr &warp)=0
	Set Warp transformation.
virtual void	cmtk::VoxelMatchingElasticFunctional::SetForceOutside (const bool flag=true, const Types::DataItem value=0)=0
	Set flag and value for forcing pixels outside the floating image.
virtual	cmtk::VoxelMatchingElasticFunctional::~VoxelMatchingElasticFunctional ()
	Destructor.
	cmtk::VoxelMatchingElasticFunctional::VoxelMatchingElasticFunctional (UniformVolume::SmartPtr &reference, UniformVolume::SmartPtr &floating)
	Constructor.
	cmtk::VoxelMatchingElasticFunctional::cmtkGetSetMacroDefault (bool, AdaptiveFixParameters, true)
	Set active and passive warp parameters adaptively.
	cmtk::VoxelMatchingElasticFunctional::cmtkGetSetMacro (double, AdaptiveFixThreshFactor)
	Set threshold factor for selecting passive warp parameters adaptively.
	cmtk::VoxelMatchingElasticFunctional::cmtkGetSetMacroString (ActiveCoordinates)
	Active coordinate directions.
	cmtk::VoxelMatchingElasticFunctional::cmtkGetSetMacroDefault (double, JacobianConstraintWeight, 0)
	Weight of the Jacobian constraint relative to voxel similarity measure.
	cmtk::VoxelMatchingElasticFunctional::cmtkGetSetMacroDefault (double, RigidityConstraintWeight, 0)
	Weight of the rigidity constraint relative to voxel similarity measure.
	cmtk::VoxelMatchingElasticFunctional::cmtkGetSetMacro (DataGrid::SmartPtr, RigidityConstraintMap)
	Map of rigidity weights constraint relative to voxel similarity measure.
	cmtk::VoxelMatchingElasticFunctional::cmtkGetSetMacroDefault (double, GridEnergyWeight, 0)
	Weight of the grid energy relative to voxel similarity measure.
	cmtk::VoxelMatchingElasticFunctional::cmtkGetSetMacroDefault (bool, Regularize, false)
	Regularize the deformation.
void	cmtk::VoxelMatchingElasticFunctional_WarpTemplate::SetInverseTransformation (typename W::SmartPtr &inverseTransformation)
	Set inverse transformation.
void	cmtk::VoxelMatchingElasticFunctional_WarpTemplate::SetInverseConsistencyWeight (const double inverseConsistencyWeight)
	Set inverse consistency weight.
Self::ReturnType	cmtk::VoxelMatchingElasticFunctional_WarpTemplate::WeightedTotal (const typename Self::ReturnType metric, const W *warp) const
	Return weighted combination of voxel similarity and grid energy.
void	cmtk::VoxelMatchingElasticFunctional_WarpTemplate::WeightedDerivative (double &lower, double &upper, W &warp, const int param, const Types::Coordinate step) const
	Return weighted combination of similarity and grid energy derivatives.
virtual Types::Coordinate	cmtk::VoxelMatchingElasticFunctional_WarpTemplate::GetParamStep (const size_t idx, const Types::Coordinate mmStep=1) const
	Get parameter stepping in milimeters.
virtual size_t	cmtk::VoxelMatchingElasticFunctional_WarpTemplate::ParamVectorDim () const
	Return the transformation's parameter vector dimension.
virtual size_t	cmtk::VoxelMatchingElasticFunctional_WarpTemplate::VariableParamVectorDim () const
	Return the number of variable parameters of the transformation.
virtual void	cmtk::VoxelMatchingElasticFunctional_WarpTemplate::SetWarpXform (typename W::SmartPtr &warp)
	Set warp transformation.
virtual void	cmtk::VoxelMatchingElasticFunctional_WarpTemplate::GetParamVector (CoordinateVector &v)
	Return parameter vector.
	cmtk::VoxelMatchingElasticFunctional_WarpTemplate::VoxelMatchingElasticFunctional_WarpTemplate (UniformVolume::SmartPtr &reference, UniformVolume::SmartPtr &floating)
	Constructor.
virtual	cmtk::VoxelMatchingElasticFunctional_WarpTemplate::~VoxelMatchingElasticFunctional_WarpTemplate ()
	Dummy virtual destructor.
	cmtk::VoxelMatchingElasticFunctional_Template::VoxelMatchingElasticFunctional_Template (UniformVolume::SmartPtr &reference, UniformVolume::SmartPtr &floating)
	Constructor.
virtual	cmtk::VoxelMatchingElasticFunctional_Template::~VoxelMatchingElasticFunctional_Template ()
	Virtual destructor.
virtual void	cmtk::VoxelMatchingElasticFunctional_Template::SetForceOutside (const bool flag=true, const Types::DataItem value=0)
	Set flag and value for forcing values outside the floating image.
Self::ReturnType	cmtk::VoxelMatchingElasticFunctional_Template::EvaluateIncremental (const SplineWarpXform *warp, SmartPointer< VM > &localMetric, const DataGrid::RegionType &voi)
	Evaluate functional after change of a single parameter.
void	cmtk::VoxelMatchingElasticFunctional_Template::UpdateWarpFixedParameters ()
	Update set of active and passive parameters.
virtual Self::ReturnType	cmtk::VoxelMatchingElasticFunctional_Template::EvaluateWithGradient (CoordinateVector &v, CoordinateVector &g, const Types::Coordinate step=1)
	Compute functional value and gradient.
virtual Self::ReturnType	cmtk::VoxelMatchingElasticFunctional_Template::EvaluateAt (CoordinateVector &v)
	Evaluate functional.
virtual Self::ReturnType	cmtk::VoxelMatchingElasticFunctional_Template::Evaluate ()
	Evaluate functional.
static TypedArray::SmartPtr	cmtk::HypothesisTests::GetUnpairedTwoTailedTTest (std::vector< TypedArray::SmartPtr > &dataX, std::vector< TypedArray::SmartPtr > &dataY, TypedArray::SmartPtr *tstatData, TypedArray::SmartPtr *avgXData, TypedArray::SmartPtr *avgYData, const TypedArray *mask=NULL)
	Test Jacobian maps of two populations for statistical independence.
static TypedArray::SmartPtr	cmtk::HypothesisTests::GetPairedTwoTailedTTest (std::vector< TypedArray::SmartPtr > &dataX, std::vector< TypedArray::SmartPtr > &dataY, TypedArray::SmartPtr *tstatData, TypedArray::SmartPtr *avgXData, TypedArray::SmartPtr *avgYData, const TypedArray *mask=NULL)
	Test parameter maps of two populations for statistical independence.
static TypedArray::SmartPtr	cmtk::HypothesisTests::GetPairedCorrelation (std::vector< TypedArray::SmartPtr > &dataX, std::vector< TypedArray::SmartPtr > &dataY, TypedArray::SmartPtr *pData=NULL, const TypedArray *mask=NULL)
	Get pixel-wise correlation between two sets of input images.
static TypedArray::SmartPtr	cmtk::HypothesisTests::GetOneSampleTTest (std::vector< TypedArray::SmartPtr > &dataX, TypedArray::SmartPtr *tstatData, TypedArray::SmartPtr *avgXData, const TypedArray *mask=NULL)
	Test mean of Jacobian map of a single population for difference from zero.
static TypedArray::SmartPtr	cmtk::HypothesisTests::GetHeritability (std::vector< TypedArray::SmartPtr > &dataX, std::vector< TypedArray::SmartPtr > &dataY, const TypedArray *mask=NULL)
	Get pixelwise heritability of two populations.
static TypedArray::SmartPtr	cmtk::HypothesisTests::GetZScores (std::vector< TypedArray::SmartPtr > &dataX, std::vector< TypedArray::SmartPtr > &dataY, const TypedArray *mask=NULL)
	Get pixelwise z-scores.
static TypedArray::SmartPtr	cmtk::HypothesisTests::GetGeneticCovariance (std::vector< TypedArray::SmartPtr > &dataMZ, std::vector< TypedArray::SmartPtr > &dataDZ, const TypedArray *mask=NULL)
	Get pixelwise genetic covariance from MZ and DZ twin data.
	cmtk::ImagePairAffineRegistrationFunctionalDevice::ImagePairAffineRegistrationFunctionalDevice (UniformVolume::SmartConstPtr &fixedVolume, UniformVolume::SmartConstPtr &movingVolume)
	Constructor.
virtual Self::ReturnType	cmtk::ImagePairAffineRegistrationFunctionalDevice::Evaluate ()
	Compute functional value.
	cmtk::ImageSymmetryPlaneFunctionalDevice::ImageSymmetryPlaneFunctionalDevice (UniformVolume::SmartConstPtr &volume)
	Constructor.
	cmtk::ImageSymmetryPlaneFunctionalDevice::ImageSymmetryPlaneFunctionalDevice (UniformVolume::SmartConstPtr &volume, const Types::DataItemRange &valueRange)
	Constructor with value range limits.
virtual Self::ReturnType	cmtk::ImageSymmetryPlaneFunctionalDevice::Evaluate ()
	Compute functional value.
	cmtk::VolumeInjectionReconstruction::VolumeInjectionReconstruction (const UniformVolume *originalImage, const int numberOfPasses, const int interleaveAxis)
	Constructor from single interleaved image.
	cmtk::VolumeInjectionReconstruction::VolumeInjectionReconstruction (const UniformVolume *reconstructionGrid, std::vector< UniformVolume::SmartPtr > &images)
	Constructor for general volume reconstruction from multiple acquired images.
static int	cmtk::VolumeInjectionReconstruction::GuessInterleaveAxis (const UniformVolume *image, const int defaultAxis=2)
	Static helper function: guess interleaved axis.
void	cmtk::VolumeInjectionReconstruction::SetupHistogramKernels (const TypedArray *originalData)
	Setup kernels and histograms for image entropy estimation.
void	cmtk::VolumeInjectionReconstruction::ComputeTransformationsToPassImages (const int registrationMetric=0)
	Compute transformations between the reference image grid and the original pass images.
void	cmtk::VolumeInjectionReconstruction::VolumeInjectionAnisotropic (const Types::Coordinate kernelSigmaFactor, const Types::Coordinate kernelRadiusFactor)
	Create initial approximation using anisotropic volume injection.
void	cmtk::VolumeInjectionReconstruction::VolumeInjectionIsotropic (const Types::Coordinate kernelSigma, const Types::Coordinate kernelRadius)
	Create initial approximation using isotropic volume injection.
UniformVolume::SmartPtr &	cmtk::VolumeInjectionReconstruction::GetCorrectedImage ()
	Returns the corrected image.
void	cmtk::VolumeInjectionReconstruction::SetReferenceImage (UniformVolume::SmartPtr &referenceImage)
	Set optional separate reference image for motion parameter estimation.
ap::real_value_type	cmtk::VolumeInjectionReconstruction::GetOriginalToCorrectedImageKLD (const ap::real_1d_array &x)
	Get Kullback-Leibler Divergence between intensity distributions in original and corrected image.
ap::real_value_type	cmtk::VolumeInjectionReconstruction::ComputeCorrectedImageLaplacianNorm (const ap::real_1d_array &correctedImagePixels)
	Compute norm of the corrected image Laplacian.
void	cmtk::VolumeInjectionReconstruction::AddLaplacianGradientImage (ap::real_1d_array &g, const ap::real_1d_array &correctedImagePixels, const ap::real_value_type weight) const
	Add weighted gradient image of Laplacian to already computed cost function gradient.
void	cmtk::AffineMultiChannelRegistrationFunctional::InitTransformation (const bool alignCenters)
	Initialize transformation.
virtual Self::ReturnType	cmtk::AffineMultiChannelRegistrationFunctional::Evaluate ()
	Compute functional value with volume clipping using multi-threading.
static void	cmtk::AffineMultiChannelRegistrationFunctional::EvaluateThreadFunction (void *args, const size_t taskIdx, const size_t taskCnt, const size_t threadIdx, const size_t)
	Thread function for metric computation.
bool	cmtk::AffineMultiChannelRegistrationFunctional::ClipZ (const VolumeClipping &clipper, const Vector3D &origin, int &start, int &end) const
	Perform clipping/cropping in z-direction.
bool	cmtk::AffineMultiChannelRegistrationFunctional::ClipX (const VolumeClipping &clipper, const Vector3D &origin, int &start, int &end) const
	Perform clipping/cropping in x-direction.
bool	cmtk::AffineMultiChannelRegistrationFunctional::ClipY (const VolumeClipping &clipper, const Vector3D &origin, int &start, int &end) const
	Perform clipping/cropping in y-direction.
	cmtk::AffineRegistration::AffineRegistration ()
	Default constructor.
virtual	cmtk::AffineRegistration::~AffineRegistration ()
	Destructor.
virtual CallbackResult	cmtk::AffineRegistration::InitRegistration ()
	Initialize registration.
virtual void	cmtk::AffineRegistration::EnterResolution (CoordinateVector::SmartPtr &v, Functional::SmartPtr &f, const int level, const int total)
	Enter a resolution level.
virtual int	cmtk::AffineRegistration::DoneResolution (CoordinateVector::SmartPtr &v, Functional::SmartPtr &f, const int level, const int total)
	Finish resolution level.
AffineXform::SmartPtr	cmtk::AffineRegistration::GetTransformation () const
	Return final transformation.
const UniformVolume::SmartPtr	cmtk::AffineRegistration::GetReformattedFloatingImage (Interpolators::InterpolationEnum interpolator=Interpolators::LINEAR) const
	Get reformatted floating image.
	cmtk::AffineRegistrationCommandLine::AffineRegistrationCommandLine (const int argc, const char *argv[])
	Constructor.
virtual CallbackResult	cmtk::AffineRegistrationCommandLine::InitRegistration ()
	Initialize registration.
void	cmtk::AffineRegistrationCommandLine::OutputResultMatrix (const char *matrixName) const
	Output result as matrix (text) file.
void	cmtk::AffineRegistrationCommandLine::OutputResultParameters (const char *paramsName, const CoordinateVector &v) const
	Output result (and statistics) as studylist archive.
void	cmtk::AffineRegistrationCommandLine::OutputResultList (const char *studyList) const
	Output result (and statistics) as studylist archive.
virtual void	cmtk::AffineRegistrationCommandLine::OutputResult (const CoordinateVector *)
	Output registration result.
virtual void	cmtk::AffineRegistrationCommandLine::EnterResolution (CoordinateVector::SmartPtr &, Functional::SmartPtr &, const int, const int)
	Enter resolution level.
virtual CallbackResult	cmtk::AffineRegistrationCommandLine::Register ()
	Perform registration.
virtual CallbackResult	cmtk::BestDirectionOptimizer::Optimize (CoordinateVector &, const Self::ParameterType=1, const Self::ParameterType=0)
	Optimize functional.
virtual CallbackResult	cmtk::BestNeighbourOptimizer::Optimize (CoordinateVector &, const Self::ParameterType=1, const Self::ParameterType=0)
	Perform the optimization.
	cmtk::CongealingFunctional::CongealingFunctional ()
	Constructor.
virtual	cmtk::CongealingFunctional::~CongealingFunctional ()
	Destructor.
virtual void	cmtk::CongealingFunctional::SetNumberOfHistogramBins (const size_t numberOfHistogramBins)
	Set number of histogram bins.
void	cmtk::CongealingFunctional::CreateGaussianKernels ()
	Create Gaussian kernels for samples in histogram.
virtual void	cmtk::CongealingFunctional::SetTemplateGrid (UniformVolume::SmartPtr &templateGrid, const int downsample=1, const bool useTemplateData=false)
	Set template grid.
virtual Self::ReturnType	cmtk::CongealingFunctional::Evaluate ()
	Evaluate functional with currently set parameters.
static void	cmtk::CongealingFunctional::EvaluateThread (void *const args, const size_t taskIdx, const size_t taskCnt, const size_t threadIdx, const size_t threadCnt)
	Evaluate functional with currently set parameters.
static void	cmtk::CongealingFunctional::EvaluateProbabilisticThread (void *const args, const size_t taskIdx, const size_t taskCnt, const size_t threadIdx, const size_t threadCnt)
	Evaluate functional with currently set parameters with probabilistic sampling.
virtual bool	cmtk::CongealingFunctional::Wiggle ()
	Update probabilistic sample table..
virtual void	cmtk::CongealingFunctional::UpdateStandardDeviationByPixel ()
	Update standard deviation by pixel.
static void	cmtk::CongealingFunctional::UpdateStandardDeviationByPixelThreadFunc (void *const args, const size_t taskIdx, const size_t taskCnt, const size_t, const size_t)
	Thread function to update standard dedviations by pixel.
	cmtk::ElasticRegistration::ElasticRegistration ()
	Default constructor.
const SplineWarpXform::SmartPtr	cmtk::ElasticRegistration::MakeWarpXform (const Vector3D &size, const AffineXform *initialAffine) const
	Create warp transformation with current settings.
Functional *	cmtk::ElasticRegistration::MakeFunctional (UniformVolume::SmartPtr &refVolume, UniformVolume::SmartPtr &fltVolume, UniformVolume::SmartPtr &rigidityMap) const
	Create functional with all settings and two given volume objects.
const UniformVolume::SmartPtr	cmtk::ElasticRegistration::GetReformattedFloatingImage (Interpolators::InterpolationEnum interpolator=Interpolators::LINEAR)
	Get reformatted floating image.
	cmtk::ElasticRegistrationCommandLine::ElasticRegistrationCommandLine (const int argc, const char *argv[])
	Constructor.
	cmtk::ElasticRegistrationCommandLine::~ElasticRegistrationCommandLine ()
	Destructor.
virtual CallbackResult	cmtk::ElasticRegistrationCommandLine::InitRegistration ()
	Initialize registration.
virtual void	cmtk::ElasticRegistrationCommandLine::OutputResult (const CoordinateVector *)
	Output registration result.
virtual void	cmtk::ElasticRegistrationCommandLine::EnterResolution (CoordinateVector::SmartPtr &, Functional::SmartPtr &, const int, const int)
	Enter resolution level.
virtual int	cmtk::ElasticRegistrationCommandLine::DoneResolution (CoordinateVector::SmartPtr &, Functional::SmartPtr &, const int, const int)
	Leave resolution level.
void	cmtk::ElasticRegistrationCommandLine::OutputWarp (const char *) const
	Write deformation to studylist archive.
void	cmtk::ElasticRegistrationCommandLine::OutputIntermediate (const bool incrementCount=true)
	Write intermediate deformation file.
virtual CallbackResult	cmtk::ElasticRegistrationCommandLine::Register ()
	Perform registration.
	cmtk::FunctionalAffine2D::FunctionalAffine2D (ScalarImage::SmartPtr &refImage, ScalarImage::SmartPtr &fltImage, const ScalarImage::RegionType *fltROI=NULL)
	Contructor.
	cmtk::FunctionalAffine2D::FunctionalAffine2D (std::vector< ScalarImage::SmartPtr > &refImage, std::vector< ScalarImage::SmartPtr > &fltImage, const ScalarImage::RegionType *fltROI=NULL)
	Contructor.
void	cmtk::FunctionalAffine2D::SetNumberOfBins (const size_t minBins, const size_t maxBins=0)
	Set minimum and maximum number of bins for histogram-based similarity.
virtual Types::Coordinate	cmtk::FunctionalAffine2D::GetParamStep (const size_t idx, const Types::Coordinate mmStep=1) const
	Return parameter stepping.
virtual void	cmtk::FunctionalAffine2D::SetParamVector (CoordinateVector &v)
	Set parameter vector without evaluating the functional.
virtual void	cmtk::FunctionalAffine2D::GetParamVector (CoordinateVector &v)
	Return current parameter vector.
virtual Self::ReturnType	cmtk::FunctionalAffine2D::EvaluateAt (CoordinateVector &v)
	Compute functional value.
virtual Self::ReturnType	cmtk::FunctionalAffine2D::Evaluate ()
	Compute functional value.
Self::ReturnType	cmtk::FunctionalAffine2D::GetSimilarity (const ScalarImage *img0, const ScalarImage *img1) const
	Compute appropriate similarity measure for a single image pair.
Self::ReturnType	cmtk::FunctionalAffine2D::GetSimilarity (std::vector< const ScalarImage * > &imgs0, std::vector< const ScalarImage * > &imgs1) const
	Compute appropriate similarity measure for multiple images.
static void	cmtk::GroupwiseRegistrationFunctionalAffineInitializer::InitializeXforms (GroupwiseRegistrationFunctionalBase &functional, const bool alignCenters=true, const bool alignCenterOfMass=false, const bool initScales=false)
	Initialize affine transformations.
	cmtk::GroupwiseRegistrationFunctionalBase::GroupwiseRegistrationFunctionalBase ()
	Constructor.
virtual	cmtk::GroupwiseRegistrationFunctionalBase::~GroupwiseRegistrationFunctionalBase ()
	Destructor.
virtual void	cmtk::GroupwiseRegistrationFunctionalBase::CreateTemplateGridFromTargets (const std::vector< UniformVolume::SmartPtr > &targets, const int downsample=0)
	Create template grid based on target images.
virtual void	cmtk::GroupwiseRegistrationFunctionalBase::CreateTemplateGrid (const DataGrid::IndexType &dims, const UniformVolume::CoordinateVectorType &deltas)
	Create template grid based on geometry.
virtual void	cmtk::GroupwiseRegistrationFunctionalBase::SetTemplateGrid (UniformVolume::SmartPtr &templateGrid, const int downsample=1, const bool useTemplateData=false)
	Set template grid.
virtual void	cmtk::GroupwiseRegistrationFunctionalBase::AllocateStorage ()
	Allocate storage for reformatted images etc.
virtual void	cmtk::GroupwiseRegistrationFunctionalBase::SetTargetImages (std::vector< UniformVolume::SmartPtr > &tImages)
	Set target images.
virtual UniformVolume::SmartPtr	cmtk::GroupwiseRegistrationFunctionalBase::PrepareSingleImage (UniformVolume::SmartPtr &image)
	Prepare data for one image.
virtual void	cmtk::GroupwiseRegistrationFunctionalBase::PrepareTargetImages ()
	Smooth and pre-scale target images.
virtual void	cmtk::GroupwiseRegistrationFunctionalBase::GetParamVector (CoordinateVector &v)
	Get parameter vector.
virtual void	cmtk::GroupwiseRegistrationFunctionalBase::SetParamVector (CoordinateVector &v)
	Set parameter vector.
virtual void	cmtk::GroupwiseRegistrationFunctionalBase::SetParamVector (CoordinateVector &v, const size_t xformIdx)
	Set parameter vector for a given transformation.
virtual void	cmtk::GroupwiseRegistrationFunctionalBase::SetParameter (const size_t param, const Types::Coordinate value)
	Set single parameter value.
virtual void	cmtk::GroupwiseRegistrationFunctionalBase::SetParameter (const size_t xform, const size_t param, const Types::Coordinate value)
	Set single parameter value with separate xform and parameter index.
virtual Self::ReturnType	cmtk::GroupwiseRegistrationFunctionalBase::EvaluateAt (CoordinateVector &v)
	Evaluate functional with given parameter vector.
virtual Self::ReturnType	cmtk::GroupwiseRegistrationFunctionalBase::EvaluateWithGradient (CoordinateVector &v, CoordinateVector &g, const Types::Coordinate step=1)
	Compute functional value and gradient.
virtual void	cmtk::GroupwiseRegistrationFunctionalBase::UpdateProbabilisticSamples ()
	Update probablistic samples.
virtual void	cmtk::GroupwiseRegistrationFunctionalBase::InterpolateAllImages ()
	Interpolate all moving images.
virtual void	cmtk::GroupwiseRegistrationFunctionalBase::ForceZeroSumGradient (CoordinateVector &g) const
	Enforce gradient to be zero-sum over all images.
virtual bool	cmtk::GroupwiseRegistrationFunctionalBase::Wiggle ()
	Update probabilistic sample table..
void	cmtk::GroupwiseRegistrationFunctionalBase::CopyTemplateData ()
	Copy template data from TypedArray to byte vector.
void	cmtk::GroupwiseRegistrationFunctionalBase::DebugWriteImages ()
	Write all images for debug purposes.
virtual const UniformVolume::SmartPtr	cmtk::GroupwiseRegistrationFunctionalBase::GetReformattedImage (const UniformVolume::SmartPtr &targetGrid, const size_t idx) const
	Reformat one image to a given target grid.
	cmtk::GroupwiseRegistrationFunctionalXformTemplate::GroupwiseRegistrationFunctionalXformTemplate ()
	Constructor.
virtual void	cmtk::GroupwiseRegistrationFunctionalXformTemplate::InterpolateImage (const size_t idx, byte *const destination)
	Interpolate given moving image to template.
static void	cmtk::GroupwiseRegistrationFunctionalXformTemplate::InterpolateImageThread (void *const args, const size_t taskIdx, const size_t taskCnt, const size_t threadIdx, const size_t threadCont)
	Image interpolation thread function.
static void	cmtk::GroupwiseRegistrationFunctionalXformTemplate::InterpolateImageProbabilisticThread (void *const args, const size_t taskIdx, const size_t taskCnt, const size_t threadIdx, const size_t threadCont)
	Image interpolation thread function with probabilistic sampling.
	cmtk::GroupwiseRegistrationFunctionalXformTemplateBase::GroupwiseRegistrationFunctionalXformTemplateBase ()
	Constructor.
virtual	cmtk::GroupwiseRegistrationFunctionalXformTemplateBase::~GroupwiseRegistrationFunctionalXformTemplateBase ()
	Destructor.
virtual void	cmtk::GroupwiseRegistrationFunctionalXformTemplateBase::SetNumberOfHistogramBins (const size_t numberOfHistogramBins)
	Set number of histogram bins.
virtual UniformVolume::SmartPtr	cmtk::GroupwiseRegistrationFunctionalXformTemplateBase::PrepareSingleImage (UniformVolume::SmartPtr &image)
	Prepare data for one image.
virtual void	cmtk::GroupwiseRegistrationFunctionalXformTemplateBase::PrepareTargetImages ()
	Smooth and pre-scale target images.
bool	cmtk::GroupwiseRegistrationOutput::WriteGroupwiseArchive (const char *path) const
	Write template specifications and transformations to a single file.
bool	cmtk::GroupwiseRegistrationOutput::WriteXformsSeparateArchives (const char *path, const char *templatePath)
	Write each transformations to a different typedstream archive.
bool	cmtk::GroupwiseRegistrationOutput::WriteAverageImage (const char *path, const cmtk::Interpolators::InterpolationEnum interp=cmtk::Interpolators::LINEAR, const bool useTemplateData=false)
	Reformat and write average image.
	cmtk::GroupwiseRegistrationRMIFunctional::GroupwiseRegistrationRMIFunctional ()
	Constructor.
virtual	cmtk::GroupwiseRegistrationRMIFunctional::~GroupwiseRegistrationRMIFunctional ()
	Destructor.
virtual void	cmtk::GroupwiseRegistrationRMIFunctional::SetTemplateGrid (UniformVolume::SmartPtr &templateGrid, const int downsample=1, const bool useTemplateData=false)
	Set template grid.
virtual Self::ReturnType	cmtk::GroupwiseRegistrationRMIFunctional::Evaluate ()
	Evaluate functional with currently set parameters.
static void	cmtk::GroupwiseRegistrationRMIFunctional::EvaluateThread (void *const threadParameters, const size_t taskIdx, const size_t taskCnt, const size_t threadIdx, const size_t)
	Evaluate functional with currently set parameters.
static void	cmtk::GroupwiseRegistrationRMIFunctional::EvaluateProbabilisticThread (void *const threadParameters, const size_t taskIdx, const size_t taskCnt, const size_t threadIdx, const size_t)
	Evaluate functional with currently set parameters with probabilistic sampling.
virtual Self::ReturnType	cmtk::GroupwiseRegistrationRMIFunctional::EvaluateWithGradient (CoordinateVector &v, CoordinateVector &g, const Types::Coordinate step=1)
	Compute functional value and gradient.
virtual bool	cmtk::GroupwiseRegistrationRMIFunctional::Wiggle ()
	Update probabilistic sample table..
	cmtk::ImagePairAffineRegistration::ImagePairAffineRegistration ()
	Default constructor.
virtual	cmtk::ImagePairAffineRegistration::~ImagePairAffineRegistration ()
	Destructor.
virtual CallbackResult	cmtk::ImagePairAffineRegistration::InitRegistration ()
	Initialize registration.
virtual Functional *	cmtk::ImagePairAffineRegistration::MakeFunctional (const int level, const Superclass::LevelParameters *)
	Create functional with all settings for next level.
virtual void	cmtk::ImagePairAffineRegistration::EnterResolution (CoordinateVector::SmartPtr &v, Functional::SmartPtr &f, const int level, const int total)
	Enter a resolution level.
virtual int	cmtk::ImagePairAffineRegistration::DoneResolution (CoordinateVector::SmartPtr &v, Functional::SmartPtr &f, const int level, const int total)
	Finish resolution level.
AffineXform::SmartPtr	cmtk::ImagePairAffineRegistration::GetTransformation () const
	Return final transformation.
const UniformVolume::SmartPtr	cmtk::ImagePairAffineRegistration::GetReformattedFloatingImage (Interpolators::InterpolationEnum interpolator=Interpolators::LINEAR) const
	Get reformatted floating image.
	cmtk::ImagePairAffineRegistrationCommandLine::ImagePairAffineRegistrationCommandLine (const int argc, const char *argv[])
	Constructor.
virtual CallbackResult	cmtk::ImagePairAffineRegistrationCommandLine::InitRegistration ()
	Initialize registration.
void	cmtk::ImagePairAffineRegistrationCommandLine::OutputResultMatrix (const char *matrixName) const
	Output result as matrix (text) file.
void	cmtk::ImagePairAffineRegistrationCommandLine::OutputResultParameters (const char *paramsName, const CoordinateVector &v) const
	Output result (and statistics) as studylist archive.
void	cmtk::ImagePairAffineRegistrationCommandLine::OutputResultList (const char *studyList) const
	Output result (and statistics) as studylist archive.
virtual void	cmtk::ImagePairAffineRegistrationCommandLine::OutputResult (const CoordinateVector *)
	Output registration result.
virtual void	cmtk::ImagePairAffineRegistrationCommandLine::EnterResolution (CoordinateVector::SmartPtr &, Functional::SmartPtr &, const int, const int)
	Enter resolution level.
virtual CallbackResult	cmtk::ImagePairAffineRegistrationCommandLine::Register ()
	Perform registration.
static ImagePairAffineRegistrationFunctional *	cmtk::ImagePairAffineRegistrationFunctional::Create (const int metric, UniformVolume::SmartPtr &refVolume, UniformVolume::SmartPtr &fltVolume, const Interpolators::InterpolationEnum interpolation, AffineXform::SmartPtr &affineXform)
	Constructor function for affine voxel registration functionals.
	cmtk::ImagePairNonrigidRegistration::ImagePairNonrigidRegistration ()
	Default constructor.
SplineWarpXform::SmartPtr	cmtk::ImagePairNonrigidRegistration::MakeWarpXform (const UniformVolume::CoordinateVectorType &size, const AffineXform *initialAffine) const
	Create warp transformation with current settings.
virtual Functional *	cmtk::ImagePairNonrigidRegistration::MakeFunctional (const int level, const Superclass::LevelParameters *levelParameters)
	Create functional with current level settings.
const UniformVolume::SmartPtr	cmtk::ImagePairNonrigidRegistration::GetReformattedFloatingImage (Interpolators::InterpolationEnum interpolator=Interpolators::LINEAR) const
	Get reformatted floating image.
	cmtk::ImagePairNonrigidRegistrationCommandLine::ImagePairNonrigidRegistrationCommandLine (const int argc, const char *argv[])
	Constructor.
	cmtk::ImagePairNonrigidRegistrationCommandLine::~ImagePairNonrigidRegistrationCommandLine ()
	Destructor.
virtual CallbackResult	cmtk::ImagePairNonrigidRegistrationCommandLine::InitRegistration ()
	Initialize registration.
virtual void	cmtk::ImagePairNonrigidRegistrationCommandLine::OutputResult (const CoordinateVector *)
	Output registration result.
virtual void	cmtk::ImagePairNonrigidRegistrationCommandLine::EnterResolution (CoordinateVector::SmartPtr &, Functional::SmartPtr &, const int, const int)
	Enter resolution level.
virtual int	cmtk::ImagePairNonrigidRegistrationCommandLine::DoneResolution (CoordinateVector::SmartPtr &, Functional::SmartPtr &, const int, const int)
	Leave resolution level.
void	cmtk::ImagePairNonrigidRegistrationCommandLine::OutputWarp (const char *) const
	Write deformation to studylist archive.
void	cmtk::ImagePairNonrigidRegistrationCommandLine::OutputIntermediate (const bool incrementCount=true)
	Write intermediate deformation file.
virtual CallbackResult	cmtk::ImagePairNonrigidRegistrationCommandLine::Register ()
	Perform registration.
	cmtk::ImagePairNonrigidRegistrationFunctional::ImagePairNonrigidRegistrationFunctional (UniformVolume::SmartPtr &reference, UniformVolume::SmartPtr &floating)
	Constructor.
virtual	cmtk::ImagePairNonrigidRegistrationFunctional::~ImagePairNonrigidRegistrationFunctional ()
	Virtual destructor.
void	cmtk::ImagePairNonrigidRegistrationFunctional::WeightedDerivative (double &lower, double &upper, SplineWarpXform &warp, const int param, const Types::Coordinate step) const
	Return weighted combination of similarity and grid energy derivatives.
virtual void	cmtk::ImagePairNonrigidRegistrationFunctional::SetWarpXform (SplineWarpXform::SmartPtr &warp)=0
	Set Warp transformation.
static ImagePairNonrigidRegistrationFunctional *	cmtk::ImagePairNonrigidRegistrationFunctional::Create (const int metric, UniformVolume::SmartPtr &refVolume, UniformVolume::SmartPtr &fltVolume, const Interpolators::InterpolationEnum interpolation)
	Constructor function.
	cmtk::ImagePairRegistration::ImagePairRegistration ()
	Default constructor.
virtual CallbackResult	cmtk::ImagePairRegistration::Register ()
	Do registration.
void	cmtk::ImagePairRegistrationFunctional::InitFloating (UniformVolume::SmartConstPtr &floating)
	Initialize internal data structures for floating image.
void	cmtk::ImagePairRegistrationFunctional::InitReference (UniformVolume::SmartConstPtr &reference)
	Initialize internal data structures for reference image.
const DataGrid::RegionType	cmtk::ImagePairRegistrationFunctional::GetReferenceGridRange (const Vector3D &fromVOI, const Vector3D &toVOI)
	Find rectilinear area in original reference grid.
	cmtk::ImagePairSimilarityJointHistogram::ImagePairSimilarityJointHistogram (UniformVolume::SmartConstPtr &refVolume, UniformVolume::SmartConstPtr &fltVolume, const Interpolators::InterpolationEnum interpolation=Interpolators::DEFAULT)
	Constructor.
virtual void	cmtk::ImagePairSimilarityJointHistogram::SetReferenceVolume (const UniformVolume::SmartConstPtr &refVolume)
	Set reference volume.
virtual void	cmtk::ImagePairSimilarityJointHistogram::SetFloatingVolume (const UniformVolume::SmartConstPtr &fltVolume)
	Set floating volume.
UniformVolume::SmartPtr	cmtk::ImagePairSimilarityJointHistogram::PrescaleData (const UniformVolume::SmartConstPtr &volume, size_t *numberOfBins, Types::DataItem *scaleFactor, Types::DataItem *scaleOffset)
	Duplicate and pre-scale image data so that we have the histogram bin numbers readily available.
	cmtk::ImagePairSimilarityMeasure::ImagePairSimilarityMeasure (const UniformVolume::SmartConstPtr &refVolume, const UniformVolume::SmartConstPtr &fltVolume, const Interpolators::InterpolationEnum interpolation=Interpolators::DEFAULT)
	Constructor.
virtual void	cmtk::ImagePairSimilarityMeasure::SetReferenceVolume (const UniformVolume::SmartConstPtr &refVolume)
	Set reference volume.
virtual void	cmtk::ImagePairSimilarityMeasure::SetFloatingVolume (const UniformVolume::SmartConstPtr &fltVolume)
	Set floating volume.
	cmtk::ImagePairSimilarityMeasureCR::ImagePairSimilarityMeasureCR (const UniformVolume::SmartPtr &refVolume, const UniformVolume::SmartPtr &fltVolume, const Interpolators::InterpolationEnum interpolation=Interpolators::DEFAULT)
	Constructor.
virtual Self::ReturnType	cmtk::ImagePairSimilarityMeasureCR::Get () const
	Return correlation ratio.
	cmtk::ImagePairSimilarityMeasureMSD::ImagePairSimilarityMeasureMSD (const UniformVolume::SmartConstPtr &refVolume, const UniformVolume::SmartConstPtr &fltVolume, const Interpolators::InterpolationEnum interpolation=Interpolators::DEFAULT)
	Constructor.
	cmtk::ImagePairSimilarityMeasureNCC::ImagePairSimilarityMeasureNCC (const UniformVolume::SmartPtr &refVolume, const UniformVolume::SmartPtr &fltVolume, const Interpolators::InterpolationEnum interpolation=Interpolators::DEFAULT)
	Constructor.
	cmtk::ImagePairSimilarityMeasureNCC::ImagePairSimilarityMeasureNCC (const Self &other)
	Constant copy constructor.
virtual Self::ReturnType	cmtk::ImagePairSimilarityMeasureNCC::Get () const
	Compute cross correlation.
	cmtk::ImagePairSimilarityMeasureRMS::ImagePairSimilarityMeasureRMS (const UniformVolume::SmartConstPtr &refVolume, const UniformVolume::SmartConstPtr &fltVolume, const Interpolators::InterpolationEnum interpolation=Interpolators::DEFAULT)
	Constructor.
virtual void	cmtk::ImagePairSymmetricNonrigidRegistrationFunctionalTemplate::SetWarpXform (SplineWarpXform::SmartPtr &warpFwd, SplineWarpXform::SmartPtr &warpBwd)
	Set warp for forward and backward functional.
virtual Self::ReturnType	cmtk::ImagePairSymmetricNonrigidRegistrationFunctionalTemplate::EvaluateWithGradient (CoordinateVector &v, CoordinateVector &g, const Types::Coordinate step=1)
	Evaluate functional value and gradient.
static ImagePairSymmetricNonrigidRegistrationFunctional *	cmtk::ImagePairSymmetricNonrigidRegistrationFunctional::Create (const int metric, UniformVolume::SmartPtr &refVolume, UniformVolume::SmartPtr &fltVolume, const Interpolators::InterpolationEnum interpolation)
	Constructor function.
	cmtk::ImageSymmetryPlaneFunctional::ImageSymmetryPlaneFunctional (UniformVolume::SmartConstPtr &volume)
	Constructor.
	cmtk::ImageSymmetryPlaneFunctional::ImageSymmetryPlaneFunctional (UniformVolume::SmartConstPtr &volume, const Types::DataItemRange &valueRange)
	Constructor with value range limits.
virtual Self::ReturnType	cmtk::ImageSymmetryPlaneFunctional::Evaluate ()
	Compute functional value.
	cmtk::ImageSymmetryPlaneFunctionalBase::ImageSymmetryPlaneFunctionalBase (UniformVolume::SmartConstPtr &volume)
	Constructor.
	cmtk::ImageSymmetryPlaneFunctionalBase::ImageSymmetryPlaneFunctionalBase (UniformVolume::SmartConstPtr &volume, const Types::DataItemRange &valueRange)
	Constructor with value range limits.
virtual Types::Coordinate	cmtk::ImageSymmetryPlaneFunctionalBase::GetParamStep (const size_t idx, const Types::Coordinate mmStep=1) const
	Return the parameter stepping for 1 mm optimization steps.
static UniformVolume::SmartPtr	cmtk::ImageSymmetryPlaneFunctionalBase::ApplyThresholds (const UniformVolume &volume, const Types::DataItemRange &valueRange)
	Apply thresholding to volume data.
virtual CallbackResult	cmtk::IterativeDirectionOptimizer::Optimize (CoordinateVector &, const Types::Coordinate=1, const Types::Coordinate=0)
	Perform the optimization.
static const std::string	cmtk::MakeInitialAffineTransformation::GetModeName (const Self::Mode mode)
	Return a name for each initialization mode.
static AffineXform *	cmtk::MakeInitialAffineTransformation::Create (const UniformVolume &referenceImage, const UniformVolume &floatingImage, const Self::Mode mode)
	Create an initial affine transformation for two images based on a selected mode.
static AffineXform *	cmtk::MakeInitialAffineTransformation::AlignDirectionVectors (const UniformVolume &referenceImage, const UniformVolume &floatingImage, const bool centerXform=false)
	Align images based on their direction vectors.
static AffineXform *	cmtk::MakeInitialAffineTransformation::AlignFieldsOfView (const UniformVolume &referenceImage, const UniformVolume &floatingImage)
	Align images based on fields of view.
static AffineXform *	cmtk::MakeInitialAffineTransformation::AlignCentersOfMass (const UniformVolume &referenceImage, const UniformVolume &floatingImage)
	Align images based on center of mass.
static AffineXform *	cmtk::MakeInitialAffineTransformation::AlignPrincipalAxes (const UniformVolume &referenceImage, const UniformVolume &floatingImage)
	Rigidly align images based on principal axes.
virtual void	cmtk::MultiChannelHistogramRegistrationFunctional::ClearAllChannels ()
	Reset channels, clear all images.
virtual void	cmtk::MultiChannelHistogramRegistrationFunctional::AddReferenceChannel (UniformVolume::SmartPtr &channel)
	Add reference channel.
virtual void	cmtk::MultiChannelHistogramRegistrationFunctional::AddFloatingChannel (UniformVolume::SmartPtr &channel)
	Add floating channel.
virtual void	cmtk::MultiChannelHistogramRegistrationFunctional::ContinueMetric (MetricData &metricData, const size_t rindex, const Vector3D &fvector)
	Continue metric computation.
virtual Functional::ReturnType	cmtk::MultiChannelHistogramRegistrationFunctional::GetMetric (const MetricData &metricData) const
	Get metric value.
void	cmtk::MultiChannelHistogramRegistrationFunctional::MetricData::Init (Parent *const parent)
	Initialize metric object and local storage.
void	cmtk::MultiChannelHistogramRegistrationFunctional::MetricData::operator+= (const Types::DataItem *values)
	In-place single sample addition operator.
void	cmtk::MultiChannelHistogramRegistrationFunctional::MetricData::operator-= (const Types::DataItem *values)
	In-place single sample subtraction operator.
virtual void	cmtk::MultiChannelRegistrationFunctional::AddFloatingChannel (UniformVolume::SmartPtr &channel)
	Add floating channel.
virtual void	cmtk::MultiChannelRegistrationFunctionalBase::ClearAllChannels ()
	Reset channels, clear all images.
virtual void	cmtk::MultiChannelRegistrationFunctionalBase::AddReferenceChannel (UniformVolume::SmartPtr &channel)
	Add reference channel.
virtual void	cmtk::MultiChannelRegistrationFunctionalBase::AddFloatingChannel (UniformVolume::SmartPtr &channel)
	Add floating channel.
void	cmtk::MultiChannelRegistrationFunctionalBase::VerifyImageSize (const UniformVolume *imgA, const UniformVolume *imgB)
	Verify size and geometry of newly added image channels against already added channels.
virtual void	cmtk::MultiChannelRMIRegistrationFunctional::ContinueMetric (MetricData &metricData, const size_t rindex, const Vector3D &fvector)
	Continue metric computation.
virtual RealType	cmtk::MultiChannelRMIRegistrationFunctional::GetMetric (const MetricData &metricData) const
	Get metric value.
void	cmtk::MultiChannelRMIRegistrationFunctional::MetricData::Init (Parent *const parent)
	Initialize metric object and local storage.
void	cmtk::MultiChannelRMIRegistrationFunctional::MetricData::operator+= (const Types::DataItem *values)
	In-place single sample addition operator.
void	cmtk::MultiChannelRMIRegistrationFunctional::MetricData::operator-= (const Types::DataItem *values)
	In-place single sample subtraction operator.
virtual CallbackResult	cmtk::MultiLevelOptimizer::Optimize (CoordinateVector &, const Types::Coordinate=1, const Types::Coordinate=0)
	Perform the optimization.
	cmtk::ProtocolCallback::ProtocolCallback (const char *filename=NULL, const bool debug=false)
	Open protocol stream if filename is given.
virtual	cmtk::ProtocolCallback::~ProtocolCallback ()
	Destructor.
virtual CallbackResult	cmtk::ProtocolCallback::ExecuteWithData (const CoordinateVector &v, const double metric)
	Execute callback action.
virtual void	cmtk::ProtocolCallback::Comment (const char *comment=NULL)
	Write comment to protocol file.
	cmtk::ReformatVolume::ReformatVolume ()
	Default constructor.
void	cmtk::ReformatVolume::SetReferenceVolume (const UniformVolume::SmartConstPtr &referenceVolume)
	Set the reference volume for reformatting.
void	cmtk::ReformatVolume::SetFloatingVolume (const UniformVolume::SmartConstPtr &floatingVolume)
	Set the floating (transformed) volume for reformatting.
void	cmtk::ReformatVolume::SetAffineXform (const AffineXform::SmartPtr &affineXform)
	Set affine transformation to be applied to the floating volume.
void	cmtk::ReformatVolume::SetWarpXform (const WarpXform::SmartPtr &warpXform)
	Set the local deformation to be applied to the reference grid.
const UniformVolume::SmartPtr	cmtk::ReformatVolume::MakeTargetVolume () const
	Make target volume matching (reoriented) reference volume.
const UniformVolume::SmartPtr	cmtk::ReformatVolume::PlainReformat ()
	Plain reformatting.
TypedArray::SmartPtr	cmtk::ReformatVolume::PlainReformat (const int plane, TypedArray::SmartPtr &target=TypedArray::SmartPtr::Null, const size_t targetOffset=0)
	Plain reformatting of a single plane.
UniformVolume *	cmtk::ReformatVolume::GetTransformedReference (Types::Coordinate *const volumeOffset=NULL)
	Apply forward warp transformation to reference volume.
static CMTK_THREAD_RETURN_TYPE	cmtk::ReformatVolume::GetTransformedReferenceGrey (void *const arg)
	Apply forward warp transformation to grey-level reference volume.
static CMTK_THREAD_RETURN_TYPE	cmtk::ReformatVolume::GetTransformedReferenceLabel (void *const arg)
	Apply forward warp transformation to label reference volume.
UniformVolume *	cmtk::ReformatVolume::GetTransformedReferenceJacobianAvg (const std::vector< SplineWarpXform::SmartPtr > *xformList, Types::Coordinate *const volumeOffset=NULL, const bool includeReferenceData=true)
	Average Jacobians into deformed reference coordinate system.
static CMTK_THREAD_RETURN_TYPE	cmtk::ReformatVolume::GetTransformedReferenceJacobianAvgThread (void *const arg)
	Thread function: average Jacobians into deformed reference system.
UniformVolume *	cmtk::ReformatVolume::CreateTransformedReference (Types::Coordinate *const bbFrom, Types::Coordinate *const delta, Types::Coordinate *const volumeOffset=NULL)
	Create uniform volume with correct dimensions for reformatted reference.
static UniformVolumeInterpolatorBase::SmartPtr	cmtk::ReformatVolume::CreateInterpolator (const cmtk::Interpolators::InterpolationEnum interpolation, const UniformVolume::SmartConstPtr &volume)
	Create interpolator object for given volume according to interpolation mode set in this object.
UniformVolumeInterpolatorBase::SmartPtr	cmtk::ReformatVolume::CreateInterpolator (const UniformVolume::SmartConstPtr &volume)
	Create interpolator object for given volume according to interpolation mode set in this object.
UniformVolume *	cmtk::ReformatVolume::GetTransformedReference (const std::vector< SplineWarpXform::SmartPtr > *xformList, std::vector< UniformVolume::SmartPtr > *volumeList, Types::Coordinate *const volumeOffset=NULL, const bool includeReferenceData=true)
	Apply forward warp transformation to reference volume.
static CMTK_THREAD_RETURN_TYPE	cmtk::ReformatVolume::GetTransformedReferenceGreyAvg (void *const arg)
	Apply forward warp transformation to average grey-level reference volume.
template<class TInterpolator >
bool	cmtk::ReformatVolume::Jacobian::operator() (Types::DataItem &value, const Vector3D &inRef, const XformList &refToFloat, TInterpolator &)
template<class TInterpolator >
bool	cmtk::ReformatVolume::Plain::operator() (Types::DataItem &value, const Vector3D &inRef, const XformList &refToFloat, TInterpolator &interpolator)
template<class TInterpolator , class Fct >
static TypedArray::SmartPtr	cmtk::ReformatVolume::ReformatMasked (const UniformVolume *target, const cmtk::XformList &targetToRef, const cmtk::XformList &refToFloat, Fct &fct, const UniformVolume *floating=NULL, TInterpolator &interpolator=TInterpolator::Null)
	Complex reformat using target data as the mask.
template<class TInterpolator , class Fct >
static TypedArray::SmartPtr	cmtk::ReformatVolume::ReformatUnmasked (const UniformVolume *target, const cmtk::XformList &targetToRef, const cmtk::XformList &refToFloat, Fct &fct, const UniformVolume *floating=NULL, TInterpolator &interpolator=TInterpolator::Null)
	Complex reformat without mask.
static void	cmtk::Registration2d2d::Register (CoordinateMatrix3x3 &matrix, ScalarImage::SmartPtr &refImage, ScalarImage::SmartPtr &fltImage, const ScalarImage::RegionType *fltROI)
	Register two 2D images, where the second is cropped to a given ROI.
static void	cmtk::Registration2d2d::Register (CoordinateMatrix3x3 &matrix, ScalarImage::SmartPtr &refImage, ScalarImage::SmartPtr &fltImage)
	Register two 2D images.
	cmtk::RegistrationCallback::RegistrationCallback ()
	Default constructor.
virtual	cmtk::RegistrationCallback::~RegistrationCallback ()
	Virtual destructor.
virtual CallbackResult	cmtk::RegistrationCallback::ExecuteWithData (const CoordinateVector &v, const double metric)
	Interface: Execute callback action.
virtual CallbackResult	cmtk::RegistrationCallback::Execute ()
	Execute callback action without interim result.
virtual void	cmtk::RegistrationCallback::Comment (const char *comment=NULL)
	Notify callback of an annotation.
virtual void	cmtk::RegistrationCallback::FormatComment (const char *format,...)
	Notify callback of an annotation with variable parameters.
	cmtk::RegistrationJointHistogram::RegistrationJointHistogram (const UniformVolume *refVolume, const UniformVolume *fltVolume, const unsigned int numBinsX=CMTK_HISTOGRAM_AUTOBINS, const unsigned int numBinsY=CMTK_HISTOGRAM_AUTOBINS, const Types::DataItemRange &boundsX=Types::DataItemRange(-HUGE_VAL, HUGE_VAL), const Types::DataItemRange &boundsY=Types::DataItemRange(-HUGE_VAL, HUGE_VAL))
	Constructor.
static ReturnType	cmtk::ScalarImageSimilarity::GetMutualInformation (const ScalarImage *image0, const ScalarImage *image1, ScalarImageSimilarityMemory *const memory=NULL)
	Compute mutual information between two images.
static ReturnType	cmtk::ScalarImageSimilarity::GetNormalizedMutualInformation (const ScalarImage *image0, const ScalarImage *image1, ScalarImageSimilarityMemory *const memory=NULL)
	Compute normalized mutual information between two images.
static ReturnType	cmtk::ScalarImageSimilarity::GetMinusMeanSquaredDifference (const ScalarImage *image0, const ScalarImage *image1)
	Compute negated (i.e., sign-switched) mean squared pixel difference between two images.
static ReturnType	cmtk::ScalarImageSimilarity::GetCrossCorrelation (const ScalarImage *image0, const ScalarImage *image1)
	Compute normalized cross correlation between two images.
static ReturnType	cmtk::ScalarImageSimilarity::GetGradientCorrelation (const ScalarImage *image0, const ScalarImage *image1)
	Compute gradient correlation between two images.
static ReturnType	cmtk::ScalarImageSimilarity::GetGradientDifference (const ScalarImage *image0, const ScalarImage *image1, const ReturnType Ax=1, const ReturnType Ay=1)
	Compute gradient difference between two images.
static ReturnType	cmtk::ScalarImageSimilarity::GetPatternIntensity (const ScalarImage *image0, const ScalarImage *image1, const ReturnType sigma=10, const int radius=3)
	Compute pattern intensity between two images.
static ReturnType	cmtk::ScalarImageSimilarity::GetDifferenceImageEntropy (const ScalarImage *image0, const ScalarImage *image1)
	Compute entropy of difference of two images.
static ReturnType	cmtk::ScalarImageSimilarity::GetDifferenceImageEntropy (const ScalarImage *image0, const ScalarImage *image1, Types::DataItem &scaleFactor)
	Compute entropy of difference of two images.
static ReturnType	cmtk::ScalarImageSimilarity::GetCorrelationRatio (const ScalarImage *image0, const ScalarImage *image1)
	Compute correlation ratio between two pixel arrays.
static bool	cmtk::ScalarImageSimilarity::CheckImageDimensions (const ScalarImage *image0, const ScalarImage *image1)
	Check whether two images are valid and have matching pixel dimensions.
static ReturnType	cmtk::ScalarImageSimilarity::GetRegionalMutualInformation (const ScalarImage *image0, const ScalarImage *image1, const int radius=2)
	Compute regional mutual information between two images.
virtual void	cmtk::SplineWarpCongealingFunctional::SetTemplateGrid (UniformVolume::SmartPtr &templateGrid, const int downsample=1, const bool useTemplateData=false)
	Call inherited function and allocate local storage.
virtual void	cmtk::SplineWarpCongealingFunctional::InitializeXformsFromAffine (const Types::Coordinate gridSpacing, std::vector< AffineXform::SmartPtr > initialAffineXformsVector, const bool exactSpacing=true)
	Initialize spline warp transformations.
virtual void	cmtk::SplineWarpCongealingFunctional::RefineTransformationGrids ()
	Refine transformation control point grids.
virtual void	cmtk::SplineWarpCongealingFunctional::UpdateStandardDeviationByPixel ()
	Update standard deviation by pixel.
virtual void	cmtk::SplineWarpCongealingFunctional::UpdateActiveControlPoints ()
	Update deactivated control points.
virtual Self::ReturnType	cmtk::SplineWarpCongealingFunctional::Evaluate ()
	Evaluate functional with currently set parameters.
static void	cmtk::SplineWarpCongealingFunctional::EvaluateThread (void *args, const size_t taskIdx, const size_t taskCnt, const size_t threadIdx, const size_t)
	Evaluate functional with currently set parameters.
virtual Self::ReturnType	cmtk::SplineWarpCongealingFunctional::EvaluateWithGradient (CoordinateVector &v, CoordinateVector &g, const Types::Coordinate step=1)
	Compute functional value and gradient.
static CMTK_THREAD_RETURN_TYPE	cmtk::SplineWarpCongealingFunctional::EvaluateLocalGradientThreadFunc (void *args)
	Thread function: Compute local gradient of the cost function for gradient approximation.
void	cmtk::SplineWarpCongealingFunctional::StaticThreadStorage::Initialize (const Self *This)
	Initialize thread storage based on parent functional ("This").
virtual void	cmtk::SplineWarpGroupwiseRegistrationRMIFunctional::UpdateInformationByControlPoint ()
	Update local information by control point.
virtual void	cmtk::SplineWarpGroupwiseRegistrationRMIFunctional::UpdateControlPointSchedule ()
	Update control point schedule for gradient approximation.
virtual void	cmtk::SplineWarpGroupwiseRegistrationRMIFunctional::UpdateActiveControlPoints ()
	Update deactivated control points.
virtual Self::ReturnType	cmtk::SplineWarpGroupwiseRegistrationRMIFunctional::Evaluate ()
	Evaluate functional with currently set parameters.
virtual Self::ReturnType	cmtk::SplineWarpGroupwiseRegistrationRMIFunctional::EvaluateWithGradient (CoordinateVector &v, CoordinateVector &g, const Types::Coordinate step=1)
	Compute functional value and gradient.
static CMTK_THREAD_RETURN_TYPE	cmtk::SplineWarpGroupwiseRegistrationRMIFunctional::EvaluateLocalGradientThreadFunc (void *args)
	Thread function: Compute local gradient of the cost function for gradient approximation.
virtual void	cmtk::SplineWarpMultiChannelIntensityCorrectionRegistrationFunctional::ContinueMetric (MetricData &metricData, const size_t rindex, const Vector3D &fvector)
	Continue metric computation and store reformatted floating channels for local recomputation.
virtual void	cmtk::SplineWarpMultiChannelIntensityCorrectionRegistrationFunctional::ContinueMetricStoreReformatted (MetricData &metricData, const size_t rindex, const Vector3D &fvector)
	Continue metric computation and store reformatted floating channels for local recomputation.
	cmtk::SplineWarpMultiChannelRegistrationFunctional::SplineWarpMultiChannelRegistrationFunctional ()
	Default constructor.
template<class TAffineMetricFunctional >
	cmtk::SplineWarpMultiChannelRegistrationFunctional::SplineWarpMultiChannelRegistrationFunctional (AffineMultiChannelRegistrationFunctional< TAffineMetricFunctional > &affineFunctional)
	Constructor from affine multi-channel functional.
virtual void	cmtk::SplineWarpMultiChannelRegistrationFunctional::InitTransformation (const Vector3D &domain, const Types::Coordinate gridSpacing, const bool exact)
	Initialize transformation.
virtual void	cmtk::SplineWarpMultiChannelRegistrationFunctional::RefineTransformation ()
	Refine transformation control point grid by factor 2.
virtual void	cmtk::SplineWarpMultiChannelRegistrationFunctional::UpdateTransformationData ()
	Update all transformation-related data after init, refine, or image change.
virtual void	cmtk::SplineWarpMultiChannelRegistrationFunctional::UpdateTransformationFixedControlPoints ()
	Update fixed and active control points in transformation.
virtual void	cmtk::SplineWarpMultiChannelRegistrationFunctional::ContinueMetricStoreReformatted (MetricData &metricData, const size_t rindex, const Vector3D &fvector)
	Continue metric computation and store reformatted floating channels for local recomputation.
virtual void	cmtk::SplineWarpMultiChannelRegistrationFunctional::BacktraceMetric (MetricData &metricData, const DataGrid::RegionType &voi)
	Locally undo metric computation.
virtual Self::ReturnType	cmtk::SplineWarpMultiChannelRegistrationFunctional::Evaluate ()
	Compute functional value.
Self::ReturnType	cmtk::SplineWarpMultiChannelRegistrationFunctional::EvaluateIncremental (const SplineWarpXform *warp, MetricData &metricData, const DataGrid::RegionType &region)
	Evaluate metric after a local transformation change.
virtual Self::ReturnType	cmtk::SplineWarpMultiChannelRegistrationFunctional::EvaluateWithGradient (CoordinateVector &v, CoordinateVector &g, const Types::Coordinate step=1)
	Compute functional value and gradient.
virtual void	cmtk::SplineWarpMultiChannelRegistrationFunctional::AllocateReformattedFloatingChannels ()
	Allocate reformatted floating channel memory.
virtual void	cmtk::SplineWarpMultiChannelRegistrationFunctional::ClearReformattedFloatingChannels ()
	Clear and free reformatted floating channel memory.
static void	cmtk::SplineWarpMultiChannelRegistrationFunctional::EvaluateThreadFunction (void *args, const size_t taskIdx, const size_t taskCnt, const size_t threadIdx, const size_t)
	Thread function for gradient computation.
static void	cmtk::SplineWarpMultiChannelRegistrationFunctional::EvaluateWithGradientThreadFunction (void *args, const size_t taskIdx, const size_t taskCnt, const size_t threadIdx, const size_t)
	Thread function for gradient computation.
virtual void	cmtk::SymmetricElasticFunctional_Template::SetWarpXform (SplineWarpXform::SmartPtr &warpFwd, SplineWarpXform::SmartPtr &warpBwd)
	Set warp for forward and backward functional.
virtual Self::ReturnType	cmtk::SymmetricElasticFunctional_Template::EvaluateWithGradient (CoordinateVector &v, CoordinateVector &g, const Types::Coordinate step=1)
	Evaluate functional value and gradient.
	cmtk::SymmetryPlaneFunctional::SymmetryPlaneFunctional (UniformVolume::SmartPtr &volume)
	Constructor.
	cmtk::SymmetryPlaneFunctional::SymmetryPlaneFunctional (UniformVolume::SmartPtr &volume, const Types::DataItemRange &valueRange)
	Constructor with value range limits.
virtual Types::Coordinate	cmtk::SymmetryPlaneFunctional::GetParamStep (const size_t idx, const Types::Coordinate mmStep=1) const
	Return the parameter stepping for 1 mm optimization steps.
virtual Self::ReturnType	cmtk::SymmetryPlaneFunctional::Evaluate ()
	Compute functional value.
const Types::DataItemRange	cmtk::TypedArraySimilarityMemory::GetRangeX (const TypedArray *array, const size_t numBins)
	Get range of X distribution.
const Types::DataItemRange	cmtk::TypedArraySimilarityMemory::GetRangeY (const TypedArray *array, const size_t numBins)
	Get range of Y distribution.
JointHistogram< unsigned int > ::SmartPtr	cmtk::TypedArraySimilarityMemory::CreateHistogram (const TypedArray *array0, const TypedArray *array1)
	Create histogram based on memorized settings.
static VoxelMatchingAffineFunctional *	cmtk::VoxelMatchingAffineFunctional::Create (const int metric, UniformVolume::SmartPtr &refVolume, UniformVolume::SmartPtr &modVolume, AffineXform::SmartPtr &affineXform)
	Constructor function for affine voxel registration functionals.
Self::ReturnType	cmtk::VoxelMatchingCorrRatio::Get () const
	Return correlation ratio.
	cmtk::VoxelMatchingCrossCorrelation::VoxelMatchingCrossCorrelation (const UniformVolume *refVolume, const UniformVolume *fltVolume)
	Constructor.
Self::ReturnType	cmtk::VoxelMatchingCrossCorrelation::Get () const
	Compute cross correlation.
void	cmtk::VoxelMatchingFunctional::InitFloating (UniformVolume::SmartPtr &floating)
	Initialize internal data structures for floating image.
void	cmtk::VoxelMatchingFunctional::InitReference (UniformVolume::SmartPtr &reference)
	Initialize internal data structures for reference image.
const DataGrid::RegionType	cmtk::VoxelMatchingFunctional::GetReferenceGridRange (const Vector3D &fromVOI, const Vector3D &toVOI)
	Find rectilinear area in original reference grid.
	cmtk::VoxelMatchingMeanSquaredDifference::VoxelMatchingMeanSquaredDifference (const UniformVolume *refVolume, const UniformVolume *fltVolume)
	Constructor.
	cmtk::VoxelMatchingMetric::VoxelMatchingMetric (const UniformVolume *refVolume, const UniformVolume *fltVolume, const bool initData=true)
	Constructor.
T	cmtk::VoxelMatchingMetric::GetSampleY (const size_t baseIndex, const Types::Coordinate *frac) const
	Interpolate a value from the Y distribution (floating image).
void	cmtk::VoxelMatchingMetric_Type::ImageData::Init (const UniformVolume *volume)
	Initialize internal storage for one (reference of model) volume.
size_t	cmtk::VoxelMatchingMetric_Type::ImageData::Init (const UniformVolume *volume, const size_t defNumBins, const Types::DataItemRange &bounds=Types::DataItemRange(-HUGE_VAL, HUGE_VAL))
	Initialize internal storage for one volume.
void	cmtk::VoxelMatchingMetric_Type::ImageData::AllocDataArray (const TypedArray *templateArray)
	Allocate internal data array and create wrapper for reference counting.
void	cmtk::VoxelMatchingMetric_Type::ImageData::PrecomputeIncrements (const UniformVolume *volume)
	Precompute grid increments.
	cmtk::VoxelRegistration::VoxelRegistration ()
	Default constructor.
virtual	cmtk::VoxelRegistration::~VoxelRegistration ()
	Destructor.
virtual CallbackResult	cmtk::VoxelRegistration::Register ()
	Do registration.
Variables
ParametricPlane	cmtk::ImageSymmetryPlaneCommandLineBase::m_SymmetryPlane
	The symmetry plane object.
bool	cmtk::ImageSymmetryPlaneCommandLineBase::m_Verbose
	Verbosity flag.
float	cmtk::ImageSymmetryPlaneCommandLineBase::m_MinValue
	Minimum data value (lower threshold).
bool	cmtk::ImageSymmetryPlaneCommandLineBase::m_MinValueSet
	Flag for valid (user-set) minimum data value.
float	cmtk::ImageSymmetryPlaneCommandLineBase::m_MaxValue
	Minimum data value (lower threshold).
bool	cmtk::ImageSymmetryPlaneCommandLineBase::m_MaxValueSet
	Flag for valid (user-set) maximum data value.
Types::Coordinate	cmtk::ImageSymmetryPlaneCommandLineBase::m_Sampling
	Image sampling (highest resampled resolution).
Types::Coordinate	cmtk::ImageSymmetryPlaneCommandLineBase::m_Accuracy
	Optimization "accuracy" (really, precision)
Interpolators::InterpolationEnum	cmtk::ImageSymmetryPlaneCommandLineBase::m_Interpolation
	Interpolation method for reformatted image generation.
int	cmtk::ImageSymmetryPlaneCommandLineBase::m_Levels
	Number of multi-resolution levels.
bool	cmtk::ImageSymmetryPlaneCommandLineBase::m_DisableOptimization
	Flag to disable optimization.
Types::Coordinate	cmtk::ImageSymmetryPlaneCommandLineBase::m_Rho
	Symmetry plane "Rho" parameter (offset).
Units::Degrees	cmtk::ImageSymmetryPlaneCommandLineBase::m_Theta
	Symmetry plane "Theta" angle parameter.
Units::Degrees	cmtk::ImageSymmetryPlaneCommandLineBase::m_Phi
	Symmetry plane "Phi" angle parameter.
bool	cmtk::ImageSymmetryPlaneCommandLineBase::m_FixOffset
	Flag to fix symmetry plane offset parameter (i.e., do not optimize "Rho")
const char *	cmtk::ImageSymmetryPlaneCommandLineBase::m_MirrorOutFile
	Optional output path for mirrored file.
const char *	cmtk::ImageSymmetryPlaneCommandLineBase::m_AlignedOutFile
	Optional output path for aligned file.
bool	cmtk::ImageSymmetryPlaneCommandLineBase::m_MarkPlaneAligned
	Flag for marking the symmetry plane in the aligned file.
const char *	cmtk::ImageSymmetryPlaneCommandLineBase::m_MarkedOutFile
	Optional output path for file with marked symmetry plane.
const char *	cmtk::ImageSymmetryPlaneCommandLineBase::m_DifferenceOutFile
	Optional output path for file with subtraction between input and mirrored input.
const char *	cmtk::ImageSymmetryPlaneCommandLineBase::m_WriteXformPath
	Optional output path for the alignment transformation.
Types::DataItem	cmtk::ImageSymmetryPlaneCommandLineBase::m_MarkPlaneValue
	Data value used for marking the symmetry plane in output images.
bool	cmtk::ImageSymmetryPlaneCommandLineBase::m_PadOutValueSet
	Flag for user-provided padding value.
Types::DataItem	cmtk::ImageSymmetryPlaneCommandLineBase::m_PadOutValue
	User-provided padding value.
const char *	cmtk::ImageSymmetryPlaneCommandLineBase::m_SymmetryOutFileName
	Optional output path for symmetry plane.
const char *	cmtk::ImageSymmetryPlaneCommandLineBase::m_SymmetryParameters
	Optional output path for symmetry plane parameters.
const char *	cmtk::ImageSymmetryPlaneCommandLineBase::m_SymmetryParametersFile
	Optional input path for previously computed symmetry plane parameters.
const char *	cmtk::ImageSymmetryPlaneCommandLineBase::m_InFileName
	Input image file path.
InitialPlaneEnum	cmtk::ImageSymmetryPlaneCommandLineBase::m_InitialPlane
	Initial plane orientation: default to sagittal for human images.
CommandLine	cmtk::ImageSymmetryPlaneCommandLineBase::m_CommandLine
static bool	cmtk::InterruptSignalReceived
	Flag that is set upon SIGINT signal.
bool	cmtk::VoxelMatchingElasticFunctional::WarpNeedsFixUpdate
	Warp's fixed parameters need to be updated.
JointHistogram< unsigned int > ::SmartPtr	cmtk::VoxelMatchingElasticFunctional::ConsistencyHistogram
	Histogram used for consistency computation.
size_t	cmtk::VoxelMatchingElasticFunctional::Dim
	Dimension of warp parameter vector.
std::vector< Types::Coordinate >	cmtk::VoxelMatchingElasticFunctional::StepScaleVector
	Parameter scaling vector.
DataGrid::RegionType *	cmtk::VoxelMatchingElasticFunctional::VolumeOfInfluence
	Volume of influence table.
Vector3D	cmtk::VoxelMatchingElasticFunctional::ReferenceFrom
	Coordinate of the beginning of the reference colume crop area.
Vector3D	cmtk::VoxelMatchingElasticFunctional::ReferenceTo
	Coordinate of the end of the reference colume crop area.
Vector3D *	cmtk::VoxelMatchingElasticFunctional::VectorCache
	Storage for simultaneously retrieving multiple deformed vectors.
W::SmartPtr	cmtk::VoxelMatchingElasticFunctional_WarpTemplate::Warp
	Pointer to the local warp transformation.
W::SmartPtr	cmtk::VoxelMatchingElasticFunctional_WarpTemplate::InverseTransformation
	Optional inverse transformation for inverse-consistent deformation.
double	cmtk::VoxelMatchingElasticFunctional_WarpTemplate::InverseConsistencyWeight
	Weight for inverse consistency constraint.
VM::Exchange *	cmtk::VoxelMatchingElasticFunctional_Template::WarpedVolume
	Ground transformed volume.
bool	cmtk::VoxelMatchingElasticFunctional_Template::m_ForceOutsideFlag
	Flag for forcing pixel values outside the floating image.
VM::Exchange	cmtk::VoxelMatchingElasticFunctional_Template::m_ForceOutsideValueRescaled
	Rescaled byte value for forcing pixel values outside the floating image.
SmartPointer< VM >	cmtk::VoxelMatchingElasticFunctional_Template::IncrementalMetric
	Metric object for incremental computation.
DataGrid::IndexType::ValueType	cmtk::VoxelMatchingElasticFunctional_Template::DimsX
	Shortcut variables for x, y, z dimension of the reference image.
DataGrid::IndexType::ValueType	cmtk::VoxelMatchingElasticFunctional_Template::DimsY
DataGrid::IndexType::ValueType	cmtk::VoxelMatchingElasticFunctional_Template::DimsZ
DataGrid::IndexType::ValueType	cmtk::VoxelMatchingElasticFunctional_Template::FltDimsX
	Shorcut variables for x and y dimensions of the floating image.
DataGrid::IndexType::ValueType	cmtk::VoxelMatchingElasticFunctional_Template::FltDimsY
static Self *	cmtk::ElasticRegistrationCommandLine::StaticThis = NULL
	Static pointer to this object.
static Self *	cmtk::ImagePairNonrigidRegistrationCommandLine::StaticThis = NULL
	Static pointer to this object.
Member functions to be overwritten.
virtual CallbackResult	cmtk::ElasticRegistration::InitRegistration ()
	Initialize registration.
virtual void	cmtk::ElasticRegistration::EnterResolution (CoordinateVector::SmartPtr &, Functional::SmartPtr &, const int, const int)
	Enter resolution level.
virtual int	cmtk::ElasticRegistration::DoneResolution (CoordinateVector::SmartPtr &, Functional::SmartPtr &, const int, const int)
	Finish resolution level.
Member functions to be overwritten.
virtual CallbackResult	cmtk::ImagePairNonrigidRegistration::InitRegistration ()
	Initialize registration.
virtual void	cmtk::ImagePairNonrigidRegistration::EnterResolution (CoordinateVector::SmartPtr &, Functional::SmartPtr &, const int, const int)
	Enter resolution level.
virtual int	cmtk::ImagePairNonrigidRegistration::DoneResolution (CoordinateVector::SmartPtr &, Functional::SmartPtr &, const int, const int)
	Finish resolution level.
Member functions to be overwritten.
virtual CallbackResult	cmtk::ImagePairRegistration::InitRegistration ()
	Initialize registration.
virtual void	cmtk::ImagePairRegistration::DoneRegistration (const CoordinateVector *v=NULL)
	Finalize registration.
virtual void	cmtk::ImagePairRegistration::EnterResolution (CoordinateVector::SmartPtr &v, Functional::SmartPtr &f, const int idx, const int total)
	Enter resolution level.
virtual void	cmtk::ImagePairRegistration::OutputResult (const CoordinateVector *v)
	Output registration result.
virtual int	cmtk::ImagePairRegistration::DoneResolution (CoordinateVector::SmartPtr &, Functional::SmartPtr &, const int, const int)
	Finish resolution level.
Member functions to be overwritten.
virtual CallbackResult	cmtk::VoxelRegistration::InitRegistration ()
	Initialize registration.
virtual void	cmtk::VoxelRegistration::DoneRegistration (const CoordinateVector *v=NULL)
	Finalize registration.
virtual void	cmtk::VoxelRegistration::EnterResolution (CoordinateVector::SmartPtr &v, Functional::SmartPtr &f, const int idx, const int total)
	Enter resolution level.
virtual void	cmtk::VoxelRegistration::OutputResult (const CoordinateVector *v)
	Output registration result.
virtual int	cmtk::VoxelRegistration::DoneResolution (CoordinateVector::SmartPtr &, Functional::SmartPtr &, const int, const int)
	Finish resolution level.

---

Detailed Description

This library provides classes related to computing and processing registrations between images.

---

Typedef Documentation

typedef CongealingFunctional<AffineXform> cmtk::AffineCongealingFunctional

Functional for affine congealing.

This functional evaluates Lilla Zollei's entropy criterion for massively groupwise image registration.

References

[1] L . Zöllei, E. Learned-Miller, E. Grimson, W.M. Wells III: "Efficient Population Registration of 3D Data", ICCV 2005, Computer Vision for Biomedical Image Applications; Beijing, China

Definition at line 59 of file cmtkAffineCongealingFunctional.h.

typedef GroupwiseRegistrationRMIFunctional<AffineXform> cmtk::AffineGroupwiseRegistrationRMIFunctional

Functional for affine groupwise registration using "RMI" metric.

Definition at line 50 of file cmtkAffineGroupwiseRegistrationRMIFunctional.h.

typedef Functional::ReturnType cmtk::TypedArraySimilarity::ReturnType [inherited]

Return type for all similarity measures: match cmtk::Functional's.

Definition at line 75 of file cmtkTypedArraySimilarity.h.

template<class TFunctional >

typedef ImageSymmetryPlaneCommandLine<TFunctional> cmtk::ImageSymmetryPlaneCommandLine< TFunctional >::Self [inherited]

This class.

Definition at line 61 of file cmtkImageSymmetryPlaneCommandLine.h.

template<class TFunctional >

typedef SmartConstPointer<Self> cmtk::ImageSymmetryPlaneCommandLine< TFunctional >::SmartConstPtr [inherited]

Smart pointer to const.

Definition at line 70 of file cmtkImageSymmetryPlaneCommandLine.h.

template<class TFunctional >

typedef SmartPointer<Self> cmtk::ImageSymmetryPlaneCommandLine< TFunctional >::SmartPtr [inherited]

Smart pointer.

Definition at line 67 of file cmtkImageSymmetryPlaneCommandLine.h.

typedef SmartPointer<Self> cmtk::VoxelMatchingElasticFunctional::SmartPtr [inherited]

Smart pointer to this class.

Reimplemented from cmtk::Functional.

Reimplemented in cmtk::VoxelMatchingElasticFunctional_WarpTemplate< W >, and cmtk::VoxelMatchingElasticFunctional_WarpTemplate< SplineWarpXform >.

Definition at line 80 of file cmtkVoxelMatchingElasticFunctional.h.

template<class W>

typedef SmartPointer<Self> cmtk::VoxelMatchingElasticFunctional_WarpTemplate< W >::SmartPtr [inherited]

Smart pointer to this class.

Reimplemented from cmtk::VoxelMatchingElasticFunctional.

Definition at line 215 of file cmtkVoxelMatchingElasticFunctional.h.

template<class TFunctional >

typedef ImageSymmetryPlaneCommandLineBase cmtk::ImageSymmetryPlaneCommandLine< TFunctional >::Superclass [inherited]

Parent class.

Definition at line 64 of file cmtkImageSymmetryPlaneCommandLine.h.

typedef VoxelMatchingFunctional cmtk::VoxelMatchingElasticFunctional::Superclass [inherited]

Superclass.

Reimplemented from cmtk::VoxelMatchingFunctional.

Reimplemented in cmtk::ParallelElasticFunctional< VM >, cmtk::VoxelMatchingElasticFunctional_WarpTemplate< W >, and cmtk::VoxelMatchingElasticFunctional_WarpTemplate< SplineWarpXform >.

Definition at line 83 of file cmtkVoxelMatchingElasticFunctional.h.

template<class W>

typedef VoxelMatchingElasticFunctional cmtk::VoxelMatchingElasticFunctional_WarpTemplate< W >::Superclass [inherited]

Superclass.

Reimplemented from cmtk::VoxelMatchingElasticFunctional.

Reimplemented in cmtk::ParallelElasticFunctional< VM >.

Definition at line 218 of file cmtkVoxelMatchingElasticFunctional.h.

typedef VoxelMatchingCorrRatio<Interpolators::NEAREST_NEIGHBOR> cmtk::VoxelMatchingCorrRatio_NearestNeighbor

Correlation ratio with nearest-neighbor interpolation.

Definition at line 233 of file cmtkVoxelMatchingCorrRatio.h.

typedef VoxelMatchingCorrRatio<Interpolators::LINEAR> cmtk::VoxelMatchingCorrRatio_Trilinear

Correlation ratio with trilinear interpolation.

Definition at line 230 of file cmtkVoxelMatchingCorrRatio.h.

typedef VoxelMatchingMetric<byte,TYPE_BYTE> cmtk::VoxelMatchingMetricByte

Convenience typedef.

Definition at line 108 of file cmtkVoxelMatchingMetric.h.

typedef VoxelMatchingMetric<byte,TYPE_BYTE,Interpolators::NEAREST_NEIGHBOR> cmtk::VoxelMatchingMetricByte_NN

Convenience typedef.

Definition at line 114 of file cmtkVoxelMatchingMetric.h.

typedef VoxelMatchingMetric<short,TYPE_SHORT> cmtk::VoxelMatchingMetricShort

Convenience typedef.

Definition at line 105 of file cmtkVoxelMatchingMetric.h.

typedef VoxelMatchingMetric<short,TYPE_SHORT,Interpolators::NEAREST_NEIGHBOR> cmtk::VoxelMatchingMetricShort_NN

Convenience typedef.

Definition at line 111 of file cmtkVoxelMatchingMetric.h.

typedef VoxelMatchingMutInf<Interpolators::NEAREST_NEIGHBOR> cmtk::VoxelMatchingMutInf_NearestNeighbor

Mutual information with nearest-neighbor interpolation.

Definition at line 96 of file cmtkVoxelMatchingMutInf.h.

typedef VoxelMatchingMutInf<Interpolators::LINEAR> cmtk::VoxelMatchingMutInf_Trilinear

Mutual information with trilinear interpolation.

Definition at line 93 of file cmtkVoxelMatchingMutInf.h.

typedef VoxelMatchingNormMutInf<Interpolators::NEAREST_NEIGHBOR> cmtk::VoxelMatchingNormMutInf_NearestNeighbor

Normalized mutual information with nearest-neighbor interpolation.

Definition at line 107 of file cmtkVoxelMatchingNormMutInf.h.

typedef VoxelMatchingNormMutInf<Interpolators::LINEAR> cmtk::VoxelMatchingNormMutInf_Trilinear

Normalized mutual information with trilinear interpolation.

Definition at line 104 of file cmtkVoxelMatchingNormMutInf.h.

---

Enumeration Type Documentation

enum cmtk::CallbackResult

Status code returned by Execute() methods.

Enumerator:

CALLBACK_OK	Everything okay; continue as usual.
CALLBACK_INTERRUPT	User requests interrupt of operation.
CALLBACK_TIMEOUT	Interrupt generated by timeout.
CALLBACK_FAILED	Something went wrong.

Definition at line 51 of file cmtkRegistrationCallback.h.

enum cmtk::ImageSymmetryPlaneCommandLineBase::InitialPlaneEnum [private, inherited]

Constants for initial plane orientation.

Enumerator:

SYMPL_INIT_XY	XY plane (axial)
SYMPL_INIT_XZ	XZ plane (coronal)
SYMPL_INIT_YZ	YZ plane (sagittal)

Definition at line 167 of file cmtkImageSymmetryPlaneCommandLineBase.h.

---

Function Documentation

template<class TDataType , class TInterpolator , class THashKeyType , char NBitsPerChannel>

void cmtk::MultiChannelHistogramRegistrationFunctional< TDataType, TInterpolator, THashKeyType, NBitsPerChannel >::AddFloatingChannel

(

UniformVolume::SmartPtr &

channel )

[virtual, inherited]

Add floating channel.

Reimplemented from cmtk::MultiChannelRegistrationFunctional< TInterpolator >.

Definition at line 93 of file cmtkMultiChannelHistogramRegistrationFunctional.txx.

References cmtk::Types::Range< T >::m_LowerBound, cmtk::StdErr, and cmtk::Types::Range< T >::Width().

template<class TInterpolator >

void cmtk::MultiChannelRegistrationFunctional< TInterpolator >::AddFloatingChannel

(

UniformVolume::SmartPtr &

channel )

[virtual, inherited]

Add floating channel.

Reimplemented from cmtk::MultiChannelRegistrationFunctionalBase.

Reimplemented in cmtk::MultiChannelHistogramRegistrationFunctional< TDataType, TInterpolator, THashKeyType, NBitsPerChannel >.

Definition at line 50 of file cmtkMultiChannelRegistrationFunctional.txx.

void cmtk::MultiChannelRegistrationFunctionalBase::AddFloatingChannel

(

UniformVolume::SmartPtr &

channel )

[virtual, inherited]

Add floating channel.

Reimplemented in cmtk::MultiChannelHistogramRegistrationFunctional< TDataType, TInterpolator, THashKeyType, NBitsPerChannel >, and cmtk::MultiChannelRegistrationFunctional< TInterpolator >.

Definition at line 81 of file cmtkMultiChannelRegistrationFunctionalBase.cxx.

void cmtk::VolumeInjectionReconstruction::AddLaplacianGradientImage	(	ap::real_1d_array &	g,
		const ap::real_1d_array &	correctedImagePixels,
		const ap::real_value_type	weight
	)		const [protected, inherited]

Add weighted gradient image of Laplacian to already computed cost function gradient.

Definition at line 511 of file cmtkVolumeInjectionReconstruction.cxx.

References cmtk::DataGrid::GetDims(), cmtk::DataGrid::GetIndexFromOffset(), and cmtk::DataGrid::GetNumberOfPixels().

template<class TDataType , class TInterpolator , class THashKeyType , char NBitsPerChannel>

void cmtk::MultiChannelHistogramRegistrationFunctional< TDataType, TInterpolator, THashKeyType, NBitsPerChannel >::AddReferenceChannel

(

UniformVolume::SmartPtr &

channel )

[virtual, inherited]

Add reference channel.

Reimplemented from cmtk::MultiChannelRegistrationFunctionalBase.

Definition at line 64 of file cmtkMultiChannelHistogramRegistrationFunctional.txx.

References cmtk::Types::Range< T >::m_LowerBound, cmtk::StdErr, and cmtk::Types::Range< T >::Width().

void cmtk::MultiChannelRegistrationFunctionalBase::AddReferenceChannel

(

UniformVolume::SmartPtr &

channel )

[virtual, inherited]

Add reference channel.

Reimplemented in cmtk::MultiChannelHistogramRegistrationFunctional< TDataType, TInterpolator, THashKeyType, NBitsPerChannel >.

Definition at line 58 of file cmtkMultiChannelRegistrationFunctionalBase.cxx.

cmtk::AffineRegistration::AffineRegistration

(

)

[inherited]

Default constructor.

Definition at line 62 of file cmtkAffineRegistration.cxx.

cmtk::AffineRegistrationCommandLine::AffineRegistrationCommandLine	(	const int	argc,
		const char *	argv[]
	)		[inherited]

Constructor.

Parameters:

argc	Number of command line arguments; this should be the argc parameter of the main() function.
argv	Array of command line arguments; this should be the argv parameter of the main() function.

Exceptions:

ConstructorFailed

This exception is thrown if there where invalid or unknown options or missing required parameters. In all these cases, an information text describing the known options will have been written to the standard error stream before throwing the exception.

Definition at line 90 of file cmtkAffineRegistrationCommandLine.cxx.

References cmtk::CommandLine::AddEnum(), cmtk::CommandLine::AddOption(), cmtk::CommandLine::AddParameter(), cmtk::CommandLine::AddSwitch(), cmtk::CommandLine::AddVector(), cmtk::CommandLine::BeginGroup(), cmtk::TypedStream::Close(), cmtk::SmartPointer< Self >::DynamicCastFrom(), cmtk::CommandLine::EndGroup(), cmtk::TransformChangeFromSpaceAffine::GetTransformation(), cmtk::TypedStream::IsValid(), cmtk::META_SPACE, NULL, cmtk::AnatomicalOrientationBase::ORIENTATION_STANDARD, cmtk::CommandLine::Parse(), cmtk::CommandLine::PRG_CATEG, cmtk::CommandLine::PRG_DESCR, cmtk::CommandLine::PRG_TITLE, cmtk::CommandLine::PROPS_IMAGE, cmtk::CommandLine::PROPS_NOXML, cmtk::CommandLine::PROPS_OPTIONAL, cmtk::CommandLine::PROPS_OUTPUT, cmtk::CommandLine::PROPS_XFORM, cmtk::CommandLine::PROPS_XML, cmtk::XformIO::Read(), cmtk::ClassStream::READ, cmtk::VolumeIO::ReadOriented(), cmtk::TypedStream::ReadString(), cmtk::TypedStream::Seek(), cmtk::CommandLine::SetProgramInfo(), cmtk::StdErr, and cmtk::MountPoints::Translate().

AffineXform * cmtk::MakeInitialAffineTransformation::AlignCentersOfMass	(	const UniformVolume &	referenceImage,
		const UniformVolume &	floatingImage
	)		[static, inherited]

Align images based on center of mass.

Returns:

This function returns a transformation with three degrees of freedom for a translation only.

Definition at line 136 of file cmtkMakeInitialAffineTransformation.cxx.

References cmtk::FixedVector< NDIM, T >::begin(), cmtk::UniformVolume::GetCenterOfMass(), and cmtk::AffineXform::SetXlate().

AffineXform * cmtk::MakeInitialAffineTransformation::AlignDirectionVectors	(	const UniformVolume &	referenceImage,
		const UniformVolume &	floatingImage,
		const bool	centerXform = false
	)		[static, inherited]

Align images based on their direction vectors.

The direction vectors are encoded in each volume's "AffineXform" field.

Parameters:

referenceImage	The reference (fixed) image
floatingImage	The floating (moving) image
centerXform	If this flag is set, the rotation center of the transformation is set to the center of the reference image.

Definition at line 88 of file cmtkMakeInitialAffineTransformation.cxx.

References cmtk::AffineXform::ChangeCenter(), cmtk::AffineXform::Concat(), cmtk::UniformVolume::GetCenterCropRegion(), cmtk::UniformVolume::GetImageToPhysicalMatrix(), cmtk::AffineXform::GetInverse(), cmtk::MetaInformationObject::m_MetaInformation, cmtk::META_EXTERNAL_SPACE_ID, cmtk::META_SPACE, NULL, and cmtk::StdErr.

AffineXform * cmtk::MakeInitialAffineTransformation::AlignFieldsOfView	(	const UniformVolume &	referenceImage,
		const UniformVolume &	floatingImage
	)		[static, inherited]

Align images based on fields of view.

Returns:

This function returns a transformation with three degrees of freedom for a translation only, which aligns the centers of field of view for the two input images. If a crop region is defined in an image, the crop region center is used, otherwise the bounding box center.

Definition at line 124 of file cmtkMakeInitialAffineTransformation.cxx.

References cmtk::FixedVector< NDIM, T >::begin(), cmtk::UniformVolume::GetCenterCropRegion(), and cmtk::AffineXform::SetXlate().

AffineXform * cmtk::MakeInitialAffineTransformation::AlignPrincipalAxes	(	const UniformVolume &	referenceImage,
		const UniformVolume &	floatingImage
	)		[static, inherited]

Rigidly align images based on principal axes.

This function implies alignment by translation according to the centers of mass.

Definition at line 148 of file cmtkMakeInitialAffineTransformation.cxx.

References cmtk::AffineXform::ChangeCenter(), cmtk::UniformVolume::GetPrincipalAxes(), cmtk::Matrix3x3< T >::GetTranspose(), cmtk::Matrix3x3< T >::Invert3x3(), cmtk::Matrix3x3< T >::Multiply(), cmtk::AffineXform::RetAngles(), and cmtk::AffineXform::SetAngles().

template<class TMetricFunctional >

void cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::AllocateReformattedFloatingChannels

(

)

[private, virtual, inherited]

Allocate reformatted floating channel memory.

Definition at line 536 of file cmtkSplineWarpMultiChannelRegistrationFunctional.txx.

void cmtk::GroupwiseRegistrationFunctionalBase::AllocateStorage

(

)

[virtual, inherited]

Allocate storage for reformatted images etc.

This function must be called AFTER setting template grid and target images, but BEFORE any calls to Evaluate, EvaluateAt, or EvaluateWithGradient.

Definition at line 193 of file cmtkGroupwiseRegistrationFunctionalBase.cxx.

References cmtk::Memory::DeleteArray(), and cmtk::StdErr.

template<class T , ScalarDataType DT>

void cmtk::VoxelMatchingMetric_Type< T, DT >::ImageData::AllocDataArray

(

const TypedArray *

templateArray )

[inherited]

Allocate internal data array and create wrapper for reference counting.

Definition at line 184 of file cmtkVoxelMatchingMetric_Type.cxx.

References cmtk::TypedArray::GetDataSize().

UniformVolume::SmartPtr cmtk::ImageSymmetryPlaneFunctionalBase::ApplyThresholds	(	const UniformVolume &	volume,
		const Types::DataItemRange &	valueRange
	)		[static, protected, inherited]

Apply thresholding to volume data.

Definition at line 79 of file cmtkImageSymmetryPlaneFunctionalBase.cxx.

References cmtk::UniformVolume::Clone().

template<class TMetricFunctional >

void cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::BacktraceMetric	(	MetricData &	metricData,
		const DataGrid::RegionType &	voi
	)		[private, virtual, inherited]

Locally undo metric computation.

Definition at line 402 of file cmtkSplineWarpMultiChannelRegistrationFunctional.txx.

References cmtk::Region< NDIM, T >::From(), and cmtk::Region< NDIM, T >::To().

Referenced by cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::EvaluateWithGradientThreadFunction().

bool cmtk::TypedArraySimilarity::CheckArrayDimensions	(	const TypedArray *	array0,
		const TypedArray *	array1
	)		[static, inherited]

Check whether two pixel arrays have matching pixel dimensions.

Definition at line 304 of file cmtkTypedArraySimilarity.cxx.

References cmtk::TypedArray::GetDataSize().

bool cmtk::ScalarImageSimilarity::CheckImageDimensions	(	const ScalarImage *	image0,
		const ScalarImage *	image1
	)		[static, inherited]

Check whether two images are valid and have matching pixel dimensions.

Definition at line 277 of file cmtkScalarImageSimilarity.cxx.

References cmtk::ScalarImage::GetDims().

template<class TDataType , class TInterpolator , class THashKeyType , char NBitsPerChannel>

void cmtk::MultiChannelHistogramRegistrationFunctional< TDataType, TInterpolator, THashKeyType, NBitsPerChannel >::ClearAllChannels

(

)

[virtual, inherited]

Reset channels, clear all images.

Reimplemented from cmtk::MultiChannelRegistrationFunctionalBase.

Definition at line 50 of file cmtkMultiChannelHistogramRegistrationFunctional.txx.

void cmtk::MultiChannelRegistrationFunctionalBase::ClearAllChannels

(

)

[virtual, inherited]

Reset channels, clear all images.

Reimplemented in cmtk::MultiChannelHistogramRegistrationFunctional< TDataType, TInterpolator, THashKeyType, NBitsPerChannel >.

Definition at line 50 of file cmtkMultiChannelRegistrationFunctionalBase.cxx.

template<class TMetricFunctional >

void cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::ClearReformattedFloatingChannels

(

)

[private, virtual, inherited]

Clear and free reformatted floating channel memory.

Definition at line 548 of file cmtkSplineWarpMultiChannelRegistrationFunctional.txx.

template<class TMultiChannelMetricFunctional >

bool cmtk::AffineMultiChannelRegistrationFunctional< TMultiChannelMetricFunctional >::ClipX	(	const VolumeClipping &	clipper,
		const Vector3D &	origin,
		int &	start,
		int &	end
	)		const [private, inherited]

Perform clipping/cropping in x-direction.

This function computes the intersection of reference and floating data in x-direction. It determines the range of indices of those voxels in the current reference row that intersect the floating image. This is the range over which to for-loop during metric computation.

Compared to ClipZ and ClipY, this step has to operate very exact as there is no further level that would reduce remaining invalid voxels. Therefore, clipper.ClipX() is called with an extended initial range of indices and an explicitly open upper bound.

This is necessary to discriminate inside-boundary from on-boundary voxels. For the right, upper and back boundary, on-boundary voxels are already outside the allowed range as the upper boundaries of the volume are open in terms of interpolation.

Parameters:

clipper	A volume clipping object with clipping boundaries and grid orientation set.
origin	Starting point of the current row in the reference volume.
start	Upon return, this reference is set to the index of first voxel in the reference that intersects the floating image.
end	Upon return, this reference is set to one plus the index of the last voxel in the reference that intersects the floating image.

Returns:

true if there is an intersection of the current reference row and the floating, false if there isn't. The range of indices returned in "start" and "end" is only guaranteed to be valid if true is the return value.

Definition at line 212 of file cmtkAffineMultiChannelRegistrationFunctional.txx.

References cmtk::VolumeClipping::ClipX().

Referenced by cmtk::AffineMultiChannelRegistrationFunctional< TMultiChannelMetricFunctional >::EvaluateThreadFunction().

template<class TMultiChannelMetricFunctional >

bool cmtk::AffineMultiChannelRegistrationFunctional< TMultiChannelMetricFunctional >::ClipY	(	const VolumeClipping &	clipper,
		const Vector3D &	origin,
		int &	start,
		int &	end
	)		const [private, inherited]

Perform clipping/cropping in y-direction.

This function computes the intersection of reference and floating data in y-direction. It determines the range of indices of those rows in the current reference plane that intersect the floating image. This is the range over which to for-loop during metric computation.

Parameters:

clipper	A volume clipping object with clipping boundaries and grid orientation set.
origin	Starting point of the current plane in the reference volume.
start	Upon return, this reference is set to the index of first row in the reference that intersects the floating image.
end	Upon return, this reference is set to one plus the index of the last row in the reference that intersects the floating image.

Returns:

true if there is an intersection of the current reference plane and the floating, false if there isn't. The range of indices returned in "start" and "end" is only guaranteed to be valid if true is the return value.

Definition at line 249 of file cmtkAffineMultiChannelRegistrationFunctional.txx.

References cmtk::VolumeClipping::ClipY().

Referenced by cmtk::AffineMultiChannelRegistrationFunctional< TMultiChannelMetricFunctional >::EvaluateThreadFunction().

template<class TMultiChannelMetricFunctional >

bool cmtk::AffineMultiChannelRegistrationFunctional< TMultiChannelMetricFunctional >::ClipZ	(	const VolumeClipping &	clipper,
		const Vector3D &	origin,
		int &	start,
		int &	end
	)		const [private, inherited]

Perform clipping/cropping in z-direction.

This function computes the intersection of reference and floating data in z-direction. It determines the range of indices of those planes in the reference that intersect the floating. This is the range over which to for-loop during metric computation.

Parameters:

clipper	A volume clipping object with clipping boundaries and grid orientation set.
origin	Starting point of the reference volume.
start	Upon return, this reference is set to the index of first plane in the reference that intersects the floating.
end	Upon return, this reference is set to one plus the index of the last plane in the reference that intersects the floating.

Returns:

true if there is an intersection of reference and floating, false if there isn't. The range of indices returned in "start" and "end" is only guaranteed to be valid if 1 is the return value.

Definition at line 190 of file cmtkAffineMultiChannelRegistrationFunctional.txx.

References cmtk::VolumeClipping::ClipZ().

cmtk::VoxelMatchingElasticFunctional::cmtkGetSetMacro	(	DataGrid::SmartPtr	,
		RigidityConstraintMap
	)		[protected, inherited]

Map of rigidity weights constraint relative to voxel similarity measure.

cmtk::VoxelMatchingElasticFunctional::cmtkGetSetMacro	(	double	,
		AdaptiveFixThreshFactor
	)		[protected, inherited]

Set threshold factor for selecting passive warp parameters adaptively.

If the flag AdaptiveFixParameters is set, this value determines the threshold by which active vs. passive parameters are selected. All control points are set to passive for which the local region entropy is below this factor times sum of min and max region entropy. The default value is 0.5.

cmtk::VoxelMatchingElasticFunctional::cmtkGetSetMacroDefault	(	bool	,
		AdaptiveFixParameters	,
		true
	)		[protected, inherited]

Set active and passive warp parameters adaptively.

If this flag is set, the functional will adaptively determine active and passive parameters of the warp transformation prior to gradient computation.

cmtk::VoxelMatchingElasticFunctional::cmtkGetSetMacroDefault	(	double	,
		JacobianConstraintWeight	,
		0
	)		[protected, inherited]

Weight of the Jacobian constraint relative to voxel similarity measure.

If this is zero, only the voxel-based similarity will be computed.

cmtk::VoxelMatchingElasticFunctional::cmtkGetSetMacroDefault	(	double	,
		RigidityConstraintWeight	,
		0
	)		[protected, inherited]

Weight of the rigidity constraint relative to voxel similarity measure.

cmtk::VoxelMatchingElasticFunctional::cmtkGetSetMacroDefault	(	double	,
		GridEnergyWeight	,
		0
	)		[protected, inherited]

Weight of the grid energy relative to voxel similarity measure.

If this is zero, only the voxel-based similarity will be computed. If equal to one, only the grid energy will be computed.

cmtk::VoxelMatchingElasticFunctional::cmtkGetSetMacroDefault	(	bool	,
		Regularize	,
		false
	)		[protected, inherited]

Regularize the deformation.

cmtk::VoxelMatchingElasticFunctional::cmtkGetSetMacroString

(

ActiveCoordinates

)

[protected, inherited]

Active coordinate directions.

void cmtk::ProtocolCallback::Comment

(

const char *

comment = NULL )

[virtual, inherited]

Write comment to protocol file.

Reimplemented from cmtk::RegistrationCallback.

Definition at line 93 of file cmtkProtocolCallback.cxx.

void cmtk::RegistrationCallback::Comment

(

const char *

comment = NULL )

[virtual, inherited]

Notify callback of an annotation.

Reimplemented in cmtk::ProtocolCallback.

Definition at line 83 of file cmtkRegistrationCallback.cxx.

ap::real_value_type cmtk::VolumeInjectionReconstruction::ComputeCorrectedImageLaplacianNorm

(

const ap::real_1d_array &

correctedImagePixels )

[protected, inherited]

Compute norm of the corrected image Laplacian.

Side effect: this function first computes the Laplacian image, which is stored in m_CorrectedImageLaplacian for use in the AddLaplacianGradientImage function.

Parameters:

correctedImagePixels

Current vector of corrected image pixels.

Definition at line 471 of file cmtkVolumeInjectionReconstruction.cxx.

References cmtk::DataGrid::GetDims(), cmtk::DataGrid::GetIndexFromOffset(), and cmtk::DataGrid::GetNumberOfPixels().

void cmtk::VolumeInjectionReconstruction::ComputeTransformationsToPassImages

(

const int

registrationMetric = 0 )

[inherited]

Compute transformations between the reference image grid and the original pass images.

The resulting transformations are stored in the m_TransformationsToPassImages vector. If a high-resolution reference image is set in m_ReferenceImage, then all subimages are registered to it. Otherwise, the 0th subimage is used as the reference and the remaining subimages are registered to it. In this case, the transformation for the 0th subimage is set as the identity transformation.

Parameters:

registrationMetric

Similarity metric for registration of the passes to the reference image.

Definition at line 179 of file cmtkVolumeInjectionReconstruction.cxx.

References cmtk::AffineRegistration::AddNumberDOFs(), cmtk::AffineRegistration::GetTransformation(), and cmtk::VoxelRegistration::Register().

template<class TXform >

cmtk::CongealingFunctional< TXform >::CongealingFunctional

(

)

[inherited]

Constructor.

Definition at line 46 of file cmtkCongealingFunctional.cxx.

References cmtk::GroupwiseRegistrationFunctionalXformTemplateBase< TXform >::m_HistogramBins, and cmtk::CongealingFunctional< TXform >::SetNumberOfHistogramBins().

template<class TDataType , class TInterpolator , class THashKeyType , char NBitsPerChannel>

void cmtk::MultiChannelHistogramRegistrationFunctional< TDataType, TInterpolator, THashKeyType, NBitsPerChannel >::ContinueMetric	(	MetricData &	metricData,
		const size_t	rindex,
		const Vector3D &	fvector
	)		[protected, virtual, inherited]

Continue metric computation.

Definition at line 121 of file cmtkMultiChannelHistogramRegistrationFunctional.txx.

template<class TRealType , class TDataType , class TInterpolator >

void cmtk::MultiChannelRMIRegistrationFunctional< TRealType, TDataType, TInterpolator >::ContinueMetric	(	MetricData &	metricData,
		const size_t	rindex,
		const Vector3D &	fvector
	)		[protected, virtual, inherited]

Continue metric computation.

Definition at line 51 of file cmtkMultiChannelRMIRegistrationFunctional.txx.

template<class TMetricFunctional >

void cmtk::SplineWarpMultiChannelIntensityCorrectionRegistrationFunctional< TMetricFunctional >::ContinueMetric	(	MetricData &	metricData,
		const size_t	rindex,
		const Vector3D &	fvector
	)		[private, virtual, inherited]

Continue metric computation and store reformatted floating channels for local recomputation.

Definition at line 44 of file cmtkSplineWarpMultiChannelIntensityCorrectionRegistrationFunctional.txx.

template<class TMetricFunctional >

void cmtk::SplineWarpMultiChannelIntensityCorrectionRegistrationFunctional< TMetricFunctional >::ContinueMetricStoreReformatted	(	MetricData &	metricData,
		const size_t	rindex,
		const Vector3D &	fvector
	)		[private, virtual, inherited]

Continue metric computation and store reformatted floating channels for local recomputation.

Definition at line 81 of file cmtkSplineWarpMultiChannelIntensityCorrectionRegistrationFunctional.txx.

template<class TMetricFunctional >

void cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::ContinueMetricStoreReformatted	(	MetricData &	metricData,
		const size_t	rindex,
		const Vector3D &	fvector
	)		[private, virtual, inherited]

Continue metric computation and store reformatted floating channels for local recomputation.

Definition at line 369 of file cmtkSplineWarpMultiChannelRegistrationFunctional.txx.

void cmtk::GroupwiseRegistrationFunctionalBase::CopyTemplateData

(

)

[private, inherited]

Copy template data from TypedArray to byte vector.

Definition at line 555 of file cmtkGroupwiseRegistrationFunctionalBase.cxx.

References cmtk::TypedArray::Get(), cmtk::TypedArray::GetData(), and cmtk::TypedArray::GetDataSize().

AffineXform * cmtk::MakeInitialAffineTransformation::Create	(	const UniformVolume &	referenceImage,
		const UniformVolume &	floatingImage,
		const Self::Mode	mode
	)		[static, inherited]

Create an initial affine transformation for two images based on a selected mode.

Parameters:

referenceImage	The reference (fixed) image
floatingImage	The floating (moving) image
mode	Selected initialization method.

Definition at line 67 of file cmtkMakeInitialAffineTransformation.cxx.

Referenced by cmtk::ImagePairAffineRegistration::InitRegistration().

VoxelMatchingAffineFunctional * cmtk::VoxelMatchingAffineFunctional::Create	(	const int	metric,
		UniformVolume::SmartPtr &	refVolume,
		UniformVolume::SmartPtr &	modVolume,
		AffineXform::SmartPtr &	affineXform
	)		[static, inherited]

Constructor function for affine voxel registration functionals.

This function takes the index of a metric in the list of available voxel similarity measures plus all required objects. It the creates an appropriate instance of VoxelMatchingAffineFunctional with the correct metric class as template parameter.

Definition at line 56 of file cmtkVoxelMatchingAffineFunctional.cxx.

References cmtk::DATACLASS_GREY, cmtk::DATACLASS_LABEL, cmtk::DATACLASS_UNKNOWN, and NULL.

Referenced by cmtk::AffineRegistration::InitRegistration().

ImagePairAffineRegistrationFunctional * cmtk::ImagePairAffineRegistrationFunctional::Create	(	const int	metric,
		UniformVolume::SmartPtr &	refVolume,
		UniformVolume::SmartPtr &	fltVolume,
		const Interpolators::InterpolationEnum	interpolation,
		AffineXform::SmartPtr &	affineXform
	)		[static, inherited]

Constructor function for affine voxel registration functionals.

This function takes the index of a metric in the list of available voxel similarity measures plus all required objects. It the creates an appropriate instance of ImagePairAffineRegistrationFunctional with the correct metric class as template parameter.

Parameters:

metric	Index of image similarity measure.
refVolume	Reference volume.
fltVolume	Floating volume
interpolation	Floating volume interpolation.
affineXform	Use this affine transformation.

Definition at line 53 of file cmtkImagePairAffineRegistrationFunctional.cxx.

References NULL.

Referenced by cmtk::ImagePairAffineRegistration::MakeFunctional().

ImagePairNonrigidRegistrationFunctional * cmtk::ImagePairNonrigidRegistrationFunctional::Create	(	const int	metric,
		UniformVolume::SmartPtr &	refVolume,
		UniformVolume::SmartPtr &	fltVolume,
		const Interpolators::InterpolationEnum	interpolation
	)		[static, inherited]

Constructor function.

Definition at line 182 of file cmtkImagePairNonrigidRegistrationFunctional.cxx.

References NULL.

Referenced by cmtk::ImagePairNonrigidRegistration::MakeFunctional().

ImagePairSymmetricNonrigidRegistrationFunctional * cmtk::ImagePairSymmetricNonrigidRegistrationFunctional::Create	(	const int	metric,
		UniformVolume::SmartPtr &	refVolume,
		UniformVolume::SmartPtr &	fltVolume,
		const Interpolators::InterpolationEnum	interpolation
	)		[static, inherited]

Constructor function.

Definition at line 83 of file cmtkImagePairSymmetricNonrigidRegistrationFunctional.cxx.

References NULL.

Referenced by cmtk::ImagePairNonrigidRegistration::MakeFunctional().

VoxelMatchingElasticFunctional * cmtk::CreateElasticFunctional	(	const int	metric,
		UniformVolume::SmartPtr &	refVolume,
		UniformVolume::SmartPtr &	fltVolume
	)

Create functional from matching template.

This constructor function returns a pointer to a newly created elastic matching functional. The functional is created from the template corresponding to the given parameters.

Returns:

A pointer to the newly created functional of NULL if creation failed.

Parameters:

metric	Index of the voxel similarity measure to be used.
refVolume	Reference volume data.
fltVolume	Floating volume data. template.

Definition at line 340 of file cmtkVoxelMatchingElasticFunctional.cxx.

References cmtk::DATACLASS_GREY, cmtk::DATACLASS_LABEL, cmtk::DATACLASS_UNKNOWN, and NULL.

Referenced by cmtk::ElasticRegistration::MakeFunctional().

virtual ImageSymmetryPlaneFunctionalBase::SmartPtr cmtk::ImageSymmetryPlaneCommandLineBase::CreateFunctional

(

UniformVolume::SmartPtr &

volume )

[protected, pure virtual, inherited]

Create functional for volume.

virtual ImageSymmetryPlaneFunctionalBase::SmartPtr cmtk::ImageSymmetryPlaneCommandLineBase::CreateFunctional	(	UniformVolume::SmartPtr &	volume,
		const Types::DataItemRange &	range
	)		[protected, pure virtual, inherited]

Create functional for volume and value range.

template<class TFunctional >

virtual ImageSymmetryPlaneFunctionalBase::SmartPtr cmtk::ImageSymmetryPlaneCommandLine< TFunctional >::CreateFunctional	(	UniformVolume::SmartPtr &	volume,
		const cmtk::Types::DataItemRange &	range
	)		[inline, protected, virtual, inherited]

Make a functional of the given template type using an image volume and a value range.

Definition at line 80 of file cmtkImageSymmetryPlaneCommandLine.h.

template<class TFunctional >

virtual ImageSymmetryPlaneFunctionalBase::SmartPtr cmtk::ImageSymmetryPlaneCommandLine< TFunctional >::CreateFunctional

(

UniformVolume::SmartPtr &

volume )

[inline, protected, virtual, inherited]

Make a functional of the given template type using an image volume.

Definition at line 74 of file cmtkImageSymmetryPlaneCommandLine.h.

template<class TXform >

void cmtk::CongealingFunctional< TXform >::CreateGaussianKernels

(

)

[protected, inherited]

Create Gaussian kernels for samples in histogram.

Definition at line 75 of file cmtkCongealingFunctional.cxx.

References cmtk::Memory::DeleteArray(), M_PI, and cmtk::MathUtil::Square().

JointHistogram< unsigned int >::SmartPtr cmtk::TypedArraySimilarityMemory::CreateHistogram	(	const TypedArray *	array0,
		const TypedArray *	array1
	)		[inherited]

Create histogram based on memorized settings.

Definition at line 122 of file cmtkTypedArraySimilarityMemory.cxx.

References cmtk::TypedArray::GetDataSize(), cmtk::JointHistogram< T >::SetRangeX(), and cmtk::JointHistogram< T >::SetRangeY().

Referenced by cmtk::TypedArraySimilarity::GetMutualInformation(), and cmtk::TypedArraySimilarity::GetNormalizedMutualInformation().

UniformVolumeInterpolatorBase::SmartPtr cmtk::ReformatVolume::CreateInterpolator	(	const cmtk::Interpolators::InterpolationEnum	interpolation,
		const UniformVolume::SmartConstPtr &	volume
	)		[static, inherited]

Create interpolator object for given volume according to interpolation mode set in this object.

Definition at line 641 of file cmtkReformatVolume.cxx.

References cmtk::Interpolators::COSINE_SINC, cmtk::Interpolators::CUBIC, cmtk::Interpolators::LINEAR, cmtk::Interpolators::NEAREST_NEIGHBOR, NULL, and cmtk::Interpolators::PARTIALVOLUME.

UniformVolumeInterpolatorBase::SmartPtr cmtk::ReformatVolume::CreateInterpolator

(

const UniformVolume::SmartConstPtr &

volume )

[inherited]

Create interpolator object for given volume according to interpolation mode set in this object.

Definition at line 677 of file cmtkReformatVolume.cxx.

Referenced by cmtk::ReformatVolume::PlainReformat(), cmtk::ImageSymmetryPlaneCommandLineBase::WriteAligned(), cmtk::ImageSymmetryPlaneCommandLineBase::WriteDifference(), and cmtk::ImageSymmetryPlaneCommandLineBase::WriteMirror().

SymmetricElasticFunctional * cmtk::CreateSymmetricElasticFunctional	(	const int	metric,
		UniformVolume::SmartPtr &	refVolume,
		UniformVolume::SmartPtr &	fltVolume
	)

Constructor function.

Definition at line 79 of file cmtkSymmetricElasticFunctional.cxx.

References cmtk::DATACLASS_GREY, cmtk::DATACLASS_LABEL, cmtk::DATACLASS_UNKNOWN, and NULL.

Referenced by cmtk::ElasticRegistration::MakeFunctional().

void cmtk::GroupwiseRegistrationFunctionalBase::CreateTemplateGrid	(	const DataGrid::IndexType &	dims,
		const UniformVolume::CoordinateVectorType &	deltas
	)		[virtual, inherited]

Create template grid based on geometry.

Parameters:

dims	Template grid dimensions
deltas	Template grid deltas (i.e., pixel size).

Definition at line 133 of file cmtkGroupwiseRegistrationFunctionalBase.cxx.

void cmtk::GroupwiseRegistrationFunctionalBase::CreateTemplateGridFromTargets	(	const std::vector< UniformVolume::SmartPtr > &	targets,
		const int	downsample = 0
	)		[virtual, inherited]

Create template grid based on target images.

The template image is constructed so that is has the maximum number of pixels of all targets in each dimension, and the minimum isotropic pixel size.

Parameters:

targets	The vector of target images for this groupwise registration.
downsample	Downsampling factor. The voxel size in the template image is increased by this factor.

Definition at line 106 of file cmtkGroupwiseRegistrationFunctionalBase.cxx.

UniformVolume * cmtk::ReformatVolume::CreateTransformedReference	(	Types::Coordinate *const	bbFrom,
		Types::Coordinate *const	delta,
		Types::Coordinate *const	volumeOffset = NULL
	)		[private, inherited]

Create uniform volume with correct dimensions for reformatted reference.

Definition at line 578 of file cmtkReformatVolume.cxx.

References cmtk::AXIS_X, cmtk::AXIS_Y, and cmtk::AXIS_Z.

void cmtk::GroupwiseRegistrationFunctionalBase::DebugWriteImages

(

)

[inherited]

Write all images for debug purposes.

Definition at line 577 of file cmtkGroupwiseRegistrationFunctionalBase.cxx.

References cmtk::TYPE_BYTE.

void cmtk::VoxelRegistration::DoneRegistration

(

const CoordinateVector *

v = NULL )

[protected, virtual, inherited]

Finalize registration.

This function is called after registration has been terminated. It can be used to destroy progress dialog windows, free memory etc. Its last operation should be a call to the respective parent class' implementation.

Definition at line 163 of file cmtkVoxelRegistration.cxx.

References cmtk::VoxelRegistration::m_Xform.

Referenced by cmtk::VoxelRegistration::Register().

void cmtk::ImagePairRegistration::DoneRegistration

(

const CoordinateVector *

v = NULL )

[protected, virtual, inherited]

Finalize registration.

This function is called after registration has been terminated. It can be used to destroy progress dialog windows, free memory etc. Its last operation should be a call to the respective parent class' implementation.

Definition at line 175 of file cmtkImagePairRegistration.cxx.

References cmtk::ImagePairRegistration::m_Xform.

Referenced by cmtk::ImagePairRegistration::Register().

int cmtk::ElasticRegistrationCommandLine::DoneResolution	(	CoordinateVector::SmartPtr &	v,
		Functional::SmartPtr &	f,
		const int	index,
		const int	total
	)		[protected, virtual, inherited]

Leave resolution level.

The transformation found so far is written to a file if desired.

Reimplemented from cmtk::ElasticRegistration.

Definition at line 445 of file cmtkElasticRegistrationCommandLine.cxx.

int cmtk::AffineRegistration::DoneResolution	(	CoordinateVector::SmartPtr &	v,
		Functional::SmartPtr &	f,
		const int	level,
		const int	total
	)		[protected, virtual, inherited]

Finish resolution level.

This function determines whether there are any remaining numbers in the effective NumberDOFs list. If so, the list iterator is advanced and 0 is returned, indicating that the current resolution level is to be repeated. With no number left, 1 is returned indicating that the current level has been completed.

Reimplemented from cmtk::VoxelRegistration.

Definition at line 197 of file cmtkAffineRegistration.cxx.

int cmtk::ImagePairAffineRegistration::DoneResolution	(	CoordinateVector::SmartPtr &	v,
		Functional::SmartPtr &	f,
		const int	level,
		const int	total
	)		[protected, virtual, inherited]

Finish resolution level.

This function determines whether there are any remaining numbers in the effective NumberDOFs list. If so, the list iterator is advanced and 0 is returned, indicating that the current resolution level is to be repeated. With no number left, 1 is returned indicating that the current level has been completed.

Reimplemented from cmtk::ImagePairRegistration.

Definition at line 199 of file cmtkImagePairAffineRegistration.cxx.

virtual int cmtk::ImagePairRegistration::DoneResolution	(	CoordinateVector::SmartPtr &	,
		Functional::SmartPtr &	,
		const	int,
		const	int
	)		[inline, protected, virtual, inherited]

Finish resolution level.

This function is called after every resolution level. It should do any necessary cleanups resulting from the previous call to EnterRegistration.

Returns:

If the current level is finished, 1 is returned. Otherwise, ie. if the derived class requests another run of the same level, 0 may be returned. This is used for example by the affine registration in order to make repeated runs of the same level with different numbers of degrees of freedom. Be careful not to create any inifinite loops.

Reimplemented in cmtk::ImagePairAffineRegistration, cmtk::ImagePairNonrigidRegistration, and cmtk::ImagePairNonrigidRegistrationCommandLine.

Definition at line 323 of file cmtkImagePairRegistration.h.

Referenced by cmtk::ImagePairRegistration::Register().

virtual int cmtk::VoxelRegistration::DoneResolution	(	CoordinateVector::SmartPtr &	,
		Functional::SmartPtr &	,
		const	int,
		const	int
	)		[inline, protected, virtual, inherited]

Finish resolution level.

This function is called after every resolution level. It should do any necessary cleanups resulting from the previous call to EnterRegistration.

Returns:

If the current level is finished, 1 is returned. Otherwise, ie. if the derived class requests another run of the same level, 0 may be returned. This is used for example by the affine registration in order to make repeated runs of the same level with different numbers of degrees of freedom. Be careful not to create any inifinite loops.

Reimplemented in cmtk::AffineRegistration, cmtk::ElasticRegistration, and cmtk::ElasticRegistrationCommandLine.

Definition at line 276 of file cmtkVoxelRegistration.h.

Referenced by cmtk::VoxelRegistration::Register().

int cmtk::ImagePairNonrigidRegistration::DoneResolution	(	CoordinateVector::SmartPtr &	v,
		Functional::SmartPtr &	functional,
		const int	idx,
		const int	total
	)		[protected, virtual, inherited]

Finish resolution level.

In addition to operations necessary for general registration, we have to make some additional modifications. In particular the sampling of the warp transformations' control point mesh has to be refined before entering the next resolution.

Reimplemented from cmtk::ImagePairRegistration.

Reimplemented in cmtk::ImagePairNonrigidRegistrationCommandLine.

Definition at line 322 of file cmtkImagePairNonrigidRegistration.cxx.

References cmtk::SmartPointer< Self >::DynamicCastFrom().

int cmtk::ImagePairNonrigidRegistrationCommandLine::DoneResolution	(	CoordinateVector::SmartPtr &	v,
		Functional::SmartPtr &	f,
		const int	index,
		const int	total
	)		[protected, virtual, inherited]

Leave resolution level.

The transformation found so far is written to a file if desired.

Reimplemented from cmtk::ImagePairNonrigidRegistration.

Definition at line 377 of file cmtkImagePairNonrigidRegistrationCommandLine.cxx.

int cmtk::ElasticRegistration::DoneResolution	(	CoordinateVector::SmartPtr &	v,
		Functional::SmartPtr &	functional,
		const int	idx,
		const int	total
	)		[protected, virtual, inherited]

Finish resolution level.

In addition to operations necessary for general registration, we have to make some additional modifications. In particular the sampling of the warp transformations' control point mesh has to be refined before entering the next resolution.

Reimplemented from cmtk::VoxelRegistration.

Reimplemented in cmtk::ElasticRegistrationCommandLine.

Definition at line 321 of file cmtkElasticRegistration.cxx.

References cmtk::SmartPointer< Self >::DynamicCastFrom().

cmtk::ElasticRegistration::ElasticRegistration

(

)

[protected, inherited]

Default constructor.

Set initial values for some flags.

Definition at line 57 of file cmtkElasticRegistration.cxx.

References cmtk::ElasticRegistration::IgnoreEdge, NULL, cmtk::ElasticRegistration::RefineDelayed, cmtk::ElasticRegistration::RefinedGridAtLevel, cmtk::ElasticRegistration::RefineGridCount, cmtk::ElasticRegistration::RelaxationStep, and cmtk::ElasticRegistration::RestrictToAxes.

cmtk::ElasticRegistrationCommandLine::ElasticRegistrationCommandLine	(	const int	argc,
		const char *	argv[]
	)		[inherited]

Constructor.

Parameters:

argc	Number of command line arguments; this should be the argc parameter of the main() function.
argv	Array of command line arguments; this should be the argv parameter of the main() function.

Was an initial studylist given? If so, get warp

Definition at line 94 of file cmtkElasticRegistrationCommandLine.cxx.

References cmtk::CommandLine::AddEnum(), cmtk::CommandLine::AddOption(), cmtk::CommandLine::AddParameter(), cmtk::CommandLine::AddSwitch(), cmtk::CommandLine::BeginGroup(), cmtk::TypedStream::Close(), cmtk::CommandLine::EndGroup(), cmtk::TypedStream::IsValid(), cmtk::META_SPACE, NULL, cmtk::CommandLine::Parse(), cmtk::TypedStream::ReadString(), cmtk::TypedStream::Seek(), cmtk::CommandLine::SetProgramInfo(), and cmtk::StdErr.

void cmtk::ElasticRegistrationCommandLine::EnterResolution	(	CoordinateVector::SmartPtr &	v,
		Functional::SmartPtr &	f,
		const int	index,
		const int	total
	)		[protected, virtual, inherited]

Enter resolution level.

An information is printed to stderr and to the protocol file if one is written.

Reimplemented from cmtk::ElasticRegistration.

Definition at line 434 of file cmtkElasticRegistrationCommandLine.cxx.

void cmtk::AffineRegistration::EnterResolution	(	CoordinateVector::SmartPtr &	v,
		Functional::SmartPtr &	f,
		const int	level,
		const int	total
	)		[protected, virtual, inherited]

Enter a resolution level.

This function mainly determines the next effective number of degrees of freedom of the optimization. It sets the transformation object accordingly and writes a comment to the "Callback" object. Afterwards, the inherited EnterResolution() function is called.

Reimplemented from cmtk::VoxelRegistration.

Reimplemented in cmtk::AffineRegistrationCommandLine.

Definition at line 170 of file cmtkAffineRegistration.cxx.

References cmtk::SmartPointer< Self >::DynamicCastFrom().

void cmtk::ImagePairAffineRegistration::EnterResolution	(	CoordinateVector::SmartPtr &	v,
		Functional::SmartPtr &	f,
		const int	level,
		const int	total
	)		[protected, virtual, inherited]

Enter a resolution level.

This function mainly determines the next effective number of degrees of freedom of the optimization. It sets the transformation object accordingly and writes a comment to the "Callback" object. Afterwards, the inherited EnterResolution() function is called.

Reimplemented from cmtk::ImagePairRegistration.

Reimplemented in cmtk::ImagePairAffineRegistrationCommandLine.

Definition at line 173 of file cmtkImagePairAffineRegistration.cxx.

References cmtk::SmartPointer< Self >::DynamicCastFrom().

void cmtk::VoxelRegistration::EnterResolution	(	CoordinateVector::SmartPtr &	v,
		Functional::SmartPtr &	f,
		const int	idx,
		const int	total
	)		[protected, virtual, inherited]

Enter resolution level.

This function is called before entering each resolution level. It can be used to update status displays etc.

Parameters:

v	Current parameter vector.
f	Functional for next level.
idx	Index of the current resolution level. 0 is first (coarsest), subsequent (finer) resolutions have increasing numbers.
total	Total number of resolution levels.

Reimplemented in cmtk::AffineRegistration, cmtk::AffineRegistrationCommandLine, cmtk::ElasticRegistration, and cmtk::ElasticRegistrationCommandLine.

Definition at line 171 of file cmtkVoxelRegistration.cxx.

References cmtk::Timers::GetTimeProcess(), cmtk::Timers::GetTimeThread(), and cmtk::Timers::GetWalltime().

Referenced by cmtk::VoxelRegistration::Register().

void cmtk::ImagePairAffineRegistrationCommandLine::EnterResolution	(	CoordinateVector::SmartPtr &	v,
		Functional::SmartPtr &	f,
		const int	index,
		const int	total
	)		[protected, virtual, inherited]

Enter resolution level.

An information is printed to stderr and to the protocol file if one is written.

Reimplemented from cmtk::ImagePairAffineRegistration.

Definition at line 519 of file cmtkImagePairAffineRegistrationCommandLine.cxx.

void cmtk::ImagePairNonrigidRegistration::EnterResolution	(	CoordinateVector::SmartPtr &	v,
		Functional::SmartPtr &	functional,
		const int	idx,
		const int	total
	)		[protected, virtual, inherited]

Enter resolution level.

Reimplemented from cmtk::ImagePairRegistration.

Reimplemented in cmtk::ImagePairNonrigidRegistrationCommandLine.

Definition at line 266 of file cmtkImagePairNonrigidRegistration.cxx.

References cmtk::SmartPointer< Self >::DynamicCastFrom(), and cmtk::StdErr.

void cmtk::ImagePairNonrigidRegistrationCommandLine::EnterResolution	(	CoordinateVector::SmartPtr &	v,
		Functional::SmartPtr &	f,
		const int	index,
		const int	total
	)		[protected, virtual, inherited]

Enter resolution level.

An information is printed to stderr and to the protocol file if one is written.

Reimplemented from cmtk::ImagePairNonrigidRegistration.

Definition at line 366 of file cmtkImagePairNonrigidRegistrationCommandLine.cxx.

void cmtk::AffineRegistrationCommandLine::EnterResolution	(	CoordinateVector::SmartPtr &	v,
		Functional::SmartPtr &	f,
		const int	index,
		const int	total
	)		[protected, virtual, inherited]

Enter resolution level.

An information is printed to stderr and to the protocol file if one is written.

Reimplemented from cmtk::AffineRegistration.

Definition at line 510 of file cmtkAffineRegistrationCommandLine.cxx.

void cmtk::ImagePairRegistration::EnterResolution	(	CoordinateVector::SmartPtr &	v,
		Functional::SmartPtr &	f,
		const int	idx,
		const int	total
	)		[protected, virtual, inherited]

Enter resolution level.

This function is called before entering each resolution level. It can be used to update status displays etc.

Parameters:

v	Current parameter vector.
f	Functional for next level.
idx	Index of the current resolution level. 0 is first (coarsest), subsequent (finer) resolutions have increasing numbers.
total	Total number of resolution levels.

Reimplemented in cmtk::ImagePairAffineRegistration, cmtk::ImagePairAffineRegistrationCommandLine, cmtk::ImagePairNonrigidRegistration, and cmtk::ImagePairNonrigidRegistrationCommandLine.

Definition at line 183 of file cmtkImagePairRegistration.cxx.

References cmtk::Timers::GetTimeProcess(), cmtk::Timers::GetTimeThread(), and cmtk::Timers::GetWalltime().

Referenced by cmtk::ImagePairRegistration::Register().

void cmtk::ElasticRegistration::EnterResolution	(	CoordinateVector::SmartPtr &	v,
		Functional::SmartPtr &	functional,
		const int	idx,
		const int	total
	)		[protected, virtual, inherited]

Enter resolution level.

Reimplemented from cmtk::VoxelRegistration.

Reimplemented in cmtk::ElasticRegistrationCommandLine.

Definition at line 257 of file cmtkElasticRegistration.cxx.

References cmtk::SmartPointer< Self >::DynamicCastFrom(), and cmtk::StdErr.

ImagePairAffineRegistrationFunctionalDevice::ReturnType cmtk::ImagePairAffineRegistrationFunctionalDevice::Evaluate

(

)

[virtual, inherited]

Compute functional value.

Reimplemented from cmtk::Functional.

Definition at line 53 of file cmtkImagePairAffineRegistrationFunctionalDevice.cxx.

References cmtk::ImagePairAffineRegistrationFunctionalDeviceEvaluateMSD().

FunctionalAffine2D::ReturnType cmtk::FunctionalAffine2D::Evaluate

(

)

[virtual, inherited]

Compute functional value.

Reimplemented from cmtk::Functional.

Definition at line 211 of file cmtkFunctionalAffine2D.cxx.

ImageSymmetryPlaneFunctionalDevice::ReturnType cmtk::ImageSymmetryPlaneFunctionalDevice::Evaluate

(

)

[virtual, inherited]

Compute functional value.

Implements cmtk::ImageSymmetryPlaneFunctionalBase.

Definition at line 60 of file cmtkImageSymmetryPlaneFunctionalDevice.cxx.

References cmtk::ImagePairAffineRegistrationFunctionalDeviceEvaluateMSD().

SplineWarpCongealingFunctional::ReturnType cmtk::SplineWarpCongealingFunctional::Evaluate

(

)

[virtual, inherited]

Evaluate functional with currently set parameters.

Reimplemented from cmtk::CongealingFunctional< SplineWarpXform >.

Definition at line 141 of file cmtkSplineWarpCongealingFunctional.cxx.

References cmtk::ThreadPool::GetNumberOfThreads(), and cmtk::ThreadPool::Run().

SplineWarpGroupwiseRegistrationRMIFunctional::ReturnType cmtk::SplineWarpGroupwiseRegistrationRMIFunctional::Evaluate

(

)

[virtual, inherited]

Evaluate functional with currently set parameters.

Reimplemented from cmtk::GroupwiseRegistrationRMIFunctional< SplineWarpXform >.

Definition at line 191 of file cmtkSplineWarpGroupwiseRegistrationRMIFunctional.cxx.

template<class TMultiChannelMetricFunctional >

AffineMultiChannelRegistrationFunctional< TMultiChannelMetricFunctional >::ReturnType cmtk::AffineMultiChannelRegistrationFunctional< TMultiChannelMetricFunctional >::Evaluate

(

)

[virtual, inherited]

Compute functional value with volume clipping using multi-threading.

This function iterates over all voxels of the reference image that - after applying the current coordinate transformation - are located inside the mode image. This set of voxels is determined on-the-fly by an extension of Liang and Barsky's "Parameterized Line-Clipping" technique.

From the resulting sequence of reference/floating voxel pairs, the selected voxel-based similarity measure (metric) is computed.

Returns:

The computed similarity measure as returned by the "Metric" subobject.

See also:

VolumeClipping

Definition at line 68 of file cmtkAffineMultiChannelRegistrationFunctional.txx.

template<class TMetricFunctional >

SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::ReturnType cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::Evaluate

(

)

[virtual, inherited]

Compute functional value.

Definition at line 445 of file cmtkSplineWarpMultiChannelRegistrationFunctional.txx.

References cmtk::ThreadPool::GetNumberOfThreads(), and cmtk::ThreadPool::Run().

SymmetryPlaneFunctional::ReturnType cmtk::SymmetryPlaneFunctional::Evaluate

(

)

[virtual, inherited]

Compute functional value.

Reimplemented from cmtk::Functional.

Definition at line 81 of file cmtkSymmetryPlaneFunctional.cxx.

template<class TXform >

GroupwiseRegistrationRMIFunctional< TXform >::ReturnType cmtk::GroupwiseRegistrationRMIFunctional< TXform >::Evaluate

(

)

[virtual, inherited]

Evaluate functional with currently set parameters.

Reimplemented from cmtk::Functional.

Reimplemented in cmtk::SplineWarpGroupwiseRegistrationRMIFunctional.

Definition at line 74 of file cmtkGroupwiseRegistrationRMIFunctional.cxx.

References cmtk::ThreadPool::Run().

template<class TXform >

CongealingFunctional< TXform >::ReturnType cmtk::CongealingFunctional< TXform >::Evaluate

(

)

[virtual, inherited]

Evaluate functional with currently set parameters.

Reimplemented from cmtk::Functional.

Reimplemented in cmtk::SplineWarpCongealingFunctional.

Definition at line 121 of file cmtkCongealingFunctional.cxx.

References cmtk::ThreadPool::GetGlobalThreadPool(), and cmtk::ThreadPool::Run().

template<class VM>

virtual Self::ReturnType cmtk::VoxelMatchingElasticFunctional_Template< VM >::Evaluate

(

)

[inline, virtual, inherited]

Evaluate functional.

Reimplemented from cmtk::Functional.

Reimplemented in cmtk::ParallelElasticFunctional< VM >.

Definition at line 516 of file cmtkVoxelMatchingElasticFunctional.h.

ImageSymmetryPlaneFunctional::ReturnType cmtk::ImageSymmetryPlaneFunctional::Evaluate

(

)

[virtual, inherited]

Compute functional value.

Implements cmtk::ImageSymmetryPlaneFunctionalBase.

Definition at line 60 of file cmtkImageSymmetryPlaneFunctional.cxx.

FunctionalAffine2D::ReturnType cmtk::FunctionalAffine2D::EvaluateAt

(

CoordinateVector &

v )

[virtual, inherited]

Compute functional value.

Definition at line 204 of file cmtkFunctionalAffine2D.cxx.

GroupwiseRegistrationFunctionalBase::ReturnType cmtk::GroupwiseRegistrationFunctionalBase::EvaluateAt

(

CoordinateVector &

v )

[virtual, inherited]

Evaluate functional with given parameter vector.

This function sets the current parameter vector, reformats all image data into template space according to the current transformations, and calls Evaluate() to compute the entropy-based functional value.

Parameters:

v	Parameter vector.

Returns:

Const function value for given parameters.

Reimplemented in cmtk::SplineWarpCongealingFunctional, and cmtk::SplineWarpGroupwiseRegistrationRMIFunctional.

Definition at line 341 of file cmtkGroupwiseRegistrationFunctionalBase.cxx.

template<class VM>

virtual Self::ReturnType cmtk::VoxelMatchingElasticFunctional_Template< VM >::EvaluateAt

(

CoordinateVector &

v )

[inline, virtual, inherited]

Evaluate functional.

Reimplemented in cmtk::ParallelElasticFunctional< VM >.

Definition at line 509 of file cmtkVoxelMatchingElasticFunctional.h.

template<class TMetricFunctional >

SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::ReturnType cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::EvaluateIncremental	(	const SplineWarpXform *	warp,
		MetricData &	metricData,
		const DataGrid::RegionType &	region
	)		[private, inherited]

Evaluate metric after a local transformation change.

Definition at line 477 of file cmtkSplineWarpMultiChannelRegistrationFunctional.txx.

References cmtk::Region< NDIM, T >::From(), cmtk::SplineWarpXform::GetTransformedGridRow(), and cmtk::Region< NDIM, T >::To().

Referenced by cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::EvaluateWithGradientThreadFunction().

template<class VM>

Self::ReturnType cmtk::VoxelMatchingElasticFunctional_Template< VM >::EvaluateIncremental	(	const SplineWarpXform *	warp,
		SmartPointer< VM > &	localMetric,
		const DataGrid::RegionType &	voi
	)		[inline, inherited]

Evaluate functional after change of a single parameter.

Parameters:

warp	The current deformation.
localMetric	Metric object for local recomputation.
voi	Volume-of-Influence for the parameter under consideration.

Returns:

The metric after recomputation over the given volume-of-influence.

Definition at line 396 of file cmtkVoxelMatchingElasticFunctional.h.

References cmtk::Region< NDIM, T >::From(), cmtk::SplineWarpXform::GetTransformedGridRow(), and cmtk::Region< NDIM, T >::To().

CMTK_THREAD_RETURN_TYPE cmtk::SplineWarpCongealingFunctional::EvaluateLocalGradientThreadFunc

(

void *

args )

[static, private, inherited]

Thread function: Compute local gradient of the cost function for gradient approximation.

This function takes into consideration that in a spline warp, each control point effects only a local neighborhood. It also groups the parameters by control point and works over all images and x,y,z to speed things up substantially.

Definition at line 99 of file cmtkSplineWarpCongealingFunctional.txx.

References CMTK_THREAD_RETURN_VALUE, cmtk::SplineWarpXform::GetGridEnergyDerivative(), cmtk::SplineWarpXform::GetJacobianConstraintDerivative(), cmtk::DataGrid::GetOffsetFromIndex(), cmtk::SplineWarpCongealingFunctional::EvaluateLocalGradientThreadParameters::m_Gradient, cmtk::SplineWarpCongealingFunctional::EvaluateLocalGradientThreadParameters::m_Step, cmtk::Functional::ParamVectorDim(), cmtk::UniformVolume::ProbeData(), cmtk::ThreadParameters< T >::thisObject, and cmtk::ThreadParameters< T >::ThisThreadIndex.

CMTK_THREAD_RETURN_TYPE cmtk::SplineWarpGroupwiseRegistrationRMIFunctional::EvaluateLocalGradientThreadFunc

(

void *

args )

[static, private, inherited]

Thread function: Compute local gradient of the cost function for gradient approximation.

This function takes into consideration that in a spline warp, each control point effects only a local neighborhood. It also groups the parameters by control point and works over all images and x,y,z to speed things up substantially.

Definition at line 97 of file cmtkSplineWarpGroupwiseRegistrationRMIFunctional.txx.

References CMTK_THREAD_RETURN_VALUE, cmtk::DataGrid::GetOffsetFromIndex(), cmtk::SplineWarpGroupwiseRegistrationRMIFunctional::EvaluateLocalGradientThreadParameters::m_Gradient, cmtk::SplineWarpGroupwiseRegistrationRMIFunctional::EvaluateLocalGradientThreadParameters::m_MetricBaseValue, cmtk::SplineWarpGroupwiseRegistrationRMIFunctional::EvaluateLocalGradientThreadParameters::m_Step, cmtk::SplineWarpGroupwiseRegistrationRMIFunctional::EvaluateLocalGradientThreadParameters::m_ThreadStorageIndex, cmtk::Functional::ParamVectorDim(), cmtk::UniformVolume::ProbeData(), cmtk::ThreadParameters< T >::thisObject, and cmtk::ThreadParameters< T >::ThisThreadIndex.

template<class TXform >

void cmtk::GroupwiseRegistrationRMIFunctional< TXform >::EvaluateProbabilisticThread	(	void *const	threadParameters,
		const size_t	taskIdx,
		const size_t	taskCnt,
		const size_t	threadIdx,
		const	size_t
	)		[static, private, inherited]

Evaluate functional with currently set parameters with probabilistic sampling.

Definition at line 249 of file cmtkGroupwiseRegistrationRMIFunctional.cxx.

References cmtk::ThreadParameters< T >::thisObject.

template<class TXform >

void cmtk::CongealingFunctional< TXform >::EvaluateProbabilisticThread	(	void *const	args,
		const size_t	taskIdx,
		const size_t	taskCnt,
		const size_t	threadIdx,
		const size_t	threadCnt
	)		[static, private, inherited]

Evaluate functional with currently set parameters with probabilistic sampling.

Definition at line 237 of file cmtkCongealingFunctional.cxx.

References cmtk::Histogram< T >::AddWeightedSymmetricKernel(), cmtk::Histogram< T >::GetEntropy(), cmtk::CongealingFunctional< TXform >::EvaluateThreadParameters::m_Count, cmtk::CongealingFunctional< TXform >::EvaluateThreadParameters::m_Entropy, cmtk::Histogram< T >::Reset(), cmtk::Histogram< T >::Resize(), and cmtk::ThreadParameters< T >::thisObject.

void cmtk::SplineWarpCongealingFunctional::EvaluateThread	(	void *	args,
		const size_t	taskIdx,
		const size_t	taskCnt,
		const size_t	threadIdx,
		const	size_t
	)		[static, private, inherited]

Evaluate functional with currently set parameters.

Reimplemented from cmtk::CongealingFunctional< SplineWarpXform >.

Definition at line 207 of file cmtkSplineWarpCongealingFunctional.cxx.

References cmtk::SplineWarpCongealingFunctional::EvaluateThreadParameters::m_Count, cmtk::SplineWarpCongealingFunctional::EvaluateThreadParameters::m_Entropy, and cmtk::ThreadParameters< T >::thisObject.

template<class TXform >

void cmtk::GroupwiseRegistrationRMIFunctional< TXform >::EvaluateThread	(	void *const	threadParameters,
		const size_t	taskIdx,
		const size_t	taskCnt,
		const size_t	threadIdx,
		const	size_t
	)		[static, private, inherited]

Evaluate functional with currently set parameters.

Definition at line 169 of file cmtkGroupwiseRegistrationRMIFunctional.cxx.

References cmtk::ThreadParameters< T >::thisObject.

template<class TXform >

void cmtk::CongealingFunctional< TXform >::EvaluateThread	(	void *const	args,
		const size_t	taskIdx,
		const size_t	taskCnt,
		const size_t	threadIdx,
		const size_t	threadCnt
	)		[static, private, inherited]

Evaluate functional with currently set parameters.

Reimplemented in cmtk::SplineWarpCongealingFunctional.

Definition at line 165 of file cmtkCongealingFunctional.cxx.

References cmtk::Histogram< T >::AddWeightedSymmetricKernel(), cmtk::Histogram< T >::GetEntropy(), cmtk::CongealingFunctional< TXform >::EvaluateThreadParameters::m_Count, cmtk::CongealingFunctional< TXform >::EvaluateThreadParameters::m_Entropy, cmtk::Histogram< T >::Reset(), cmtk::Histogram< T >::Resize(), and cmtk::ThreadParameters< T >::thisObject.

template<class TMultiChannelMetricFunctional >

void cmtk::AffineMultiChannelRegistrationFunctional< TMultiChannelMetricFunctional >::EvaluateThreadFunction	(	void *	args,
		const size_t	taskIdx,
		const size_t	taskCnt,
		const size_t	threadIdx,
		const	size_t
	)		[static, private, inherited]

Thread function for metric computation.

Definition at line 109 of file cmtkAffineMultiChannelRegistrationFunctional.txx.

References cmtk::AffineMultiChannelRegistrationFunctional< TMultiChannelMetricFunctional >::ClipX(), cmtk::AffineMultiChannelRegistrationFunctional< TMultiChannelMetricFunctional >::ClipY(), cmtk::AffineMultiChannelRegistrationFunctional< TMultiChannelMetricFunctional >::EvaluateThreadParameters::m_StartZ, cmtk::AffineMultiChannelRegistrationFunctional< TMultiChannelMetricFunctional >::EvaluateThreadParameters::m_TransformedAxes, cmtk::AffineMultiChannelRegistrationFunctional< TMultiChannelMetricFunctional >::m_VolumeClipper, and cmtk::ThreadParameters< T >::thisObject.

template<class TMetricFunctional >

void cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::EvaluateThreadFunction	(	void *	args,
		const size_t	taskIdx,
		const size_t	taskCnt,
		const size_t	threadIdx,
		const	size_t
	)		[static, private, inherited]

Thread function for gradient computation.

Definition at line 43 of file cmtkSplineWarpMultiChannelRegistrationFunctionalThreadFunctions.txx.

References cmtk::SplineWarpXform::GetTransformedGridRow(), cmtk::TemplateMultiChannelRegistrationFunctional< TXform, TMetricFunctional >::m_Transformation, and cmtk::ThreadParameters< T >::thisObject.

template<class TXform >

GroupwiseRegistrationRMIFunctional< TXform >::ReturnType cmtk::GroupwiseRegistrationRMIFunctional< TXform >::EvaluateWithGradient	(	CoordinateVector &	v,
		CoordinateVector &	g,
		const Types::Coordinate	step = 1
	)		[virtual, inherited]

Compute functional value and gradient.

Parameters:

v	Parameter vector.
g	The extimated gradient of the functional is stored in this vector.
step	Step size for finite difference gradient approximation. Default is 1 mm.

Returns:

Const function value for given parameters.

Reimplemented from cmtk::GroupwiseRegistrationFunctionalBase.

Reimplemented in cmtk::SplineWarpGroupwiseRegistrationRMIFunctional.

Definition at line 327 of file cmtkGroupwiseRegistrationRMIFunctional.cxx.

GroupwiseRegistrationFunctionalBase::ReturnType cmtk::GroupwiseRegistrationFunctionalBase::EvaluateWithGradient	(	CoordinateVector &	v,
		CoordinateVector &	g,
		const Types::Coordinate	step = 1
	)		[virtual, inherited]

Compute functional value and gradient.

Parameters:

v	Parameter vector.
g	The extimated gradient of the functional is stored in this vector.
step	Step size for finite difference gradient approximation. Default is 1 mm.

Returns:

Const function value for given parameters.

Reimplemented in cmtk::GroupwiseRegistrationRMIFunctional< TXform >, cmtk::SplineWarpCongealingFunctional, cmtk::SplineWarpGroupwiseRegistrationRMIFunctional, and cmtk::GroupwiseRegistrationRMIFunctional< SplineWarpXform >.

Definition at line 358 of file cmtkGroupwiseRegistrationFunctionalBase.cxx.

SplineWarpCongealingFunctional::ReturnType cmtk::SplineWarpCongealingFunctional::EvaluateWithGradient	(	CoordinateVector &	v,
		CoordinateVector &	g,
		const Types::Coordinate	step = 1
	)		[virtual, inherited]

Compute functional value and gradient.

Parameters:

v	Parameter vector.
g	The extimated gradient of the functional is stored in this vector.
step	Step size for finite difference gradient approximation. Default is 1 mm.

Returns:

Const function value for given parameters.

Reimplemented from cmtk::GroupwiseRegistrationFunctionalBase.

Definition at line 43 of file cmtkSplineWarpCongealingFunctional.txx.

References cmtk::Vector< T >::Dim, cmtk::Vector< T >::Elements, cmtk::Threads::GetNumberOfThreads(), cmtk::Vector< T >::MaxNorm(), and cmtk::ThreadParameterArray< TClass, TParam >::RunInParallel().

SplineWarpGroupwiseRegistrationRMIFunctional::ReturnType cmtk::SplineWarpGroupwiseRegistrationRMIFunctional::EvaluateWithGradient	(	CoordinateVector &	v,
		CoordinateVector &	g,
		const Types::Coordinate	step = 1
	)		[virtual, inherited]

Compute functional value and gradient.

Parameters:

v	Parameter vector.
g	The extimated gradient of the functional is stored in this vector.
step	Step size for finite difference gradient approximation. Default is 1 mm.

Returns:

Const function value for given parameters.

Reimplemented from cmtk::GroupwiseRegistrationRMIFunctional< SplineWarpXform >.

Definition at line 42 of file cmtkSplineWarpGroupwiseRegistrationRMIFunctional.txx.

References cmtk::Vector< T >::Dim, cmtk::Vector< T >::Elements, cmtk::Threads::GetNumberOfThreads(), cmtk::Vector< T >::MaxNorm(), and cmtk::ThreadParameterArray< TClass, TParam >::RunInParallelFIFO().

template<class TMetricFunctional >

SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::ReturnType cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::EvaluateWithGradient	(	CoordinateVector &	v,
		CoordinateVector &	g,
		const Types::Coordinate	step = 1
	)		[virtual, inherited]

Compute functional value and gradient.

Definition at line 507 of file cmtkSplineWarpMultiChannelRegistrationFunctional.txx.

References cmtk::Vector< T >::Elements, cmtk::ThreadPool::GetNumberOfThreads(), and cmtk::ThreadPool::Run().

template<class VM >

SymmetricElasticFunctional_Template< VM >::ReturnType cmtk::SymmetricElasticFunctional_Template< VM >::EvaluateWithGradient	(	CoordinateVector &	v,
		CoordinateVector &	g,
		const Types::Coordinate	step = 1
	)		[virtual, inherited]

Evaluate functional value and gradient.

Definition at line 67 of file cmtkSymmetricElasticFunctional.cxx.

References cmtk::Vector< T >::Elements.

template<class VM>

virtual Self::ReturnType cmtk::VoxelMatchingElasticFunctional_Template< VM >::EvaluateWithGradient	(	CoordinateVector &	v,
		CoordinateVector &	g,
		const Types::Coordinate	step = 1
	)		[inline, virtual, inherited]

Compute functional value and gradient.

Definition at line 459 of file cmtkVoxelMatchingElasticFunctional.h.

template<class VM , class W >

ImagePairSymmetricNonrigidRegistrationFunctionalTemplate< VM, W >::ReturnType cmtk::ImagePairSymmetricNonrigidRegistrationFunctionalTemplate< VM, W >::EvaluateWithGradient	(	CoordinateVector &	v,
		CoordinateVector &	g,
		const Types::Coordinate	step = 1
	)		[virtual, inherited]

Evaluate functional value and gradient.

Definition at line 68 of file cmtkImagePairSymmetricNonrigidRegistrationFunctional.cxx.

References cmtk::Vector< T >::Elements.

template<class TMetricFunctional >

void cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::EvaluateWithGradientThreadFunction	(	void *	args,
		const size_t	taskIdx,
		const size_t	taskCnt,
		const size_t	threadIdx,
		const	size_t
	)		[static, private, inherited]

Thread function for gradient computation.

Definition at line 80 of file cmtkSplineWarpMultiChannelRegistrationFunctionalThreadFunctions.txx.

References cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::BacktraceMetric(), cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::EvaluateIncremental(), cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::EvaluateGradientThreadParameters::m_Gradient, cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::m_JacobianConstraintWeight, cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::EvaluateGradientThreadParameters::m_MetricBaseValue, cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::EvaluateGradientThreadParameters::m_ParameterVector, cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::EvaluateGradientThreadParameters::m_Step, cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::m_StepScaleVector, cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::m_ThreadTransformations, cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::m_VolumeOfInfluenceVector, cmtk::ThreadParameters< T >::thisObject, and cmtk::TemplateMultiChannelRegistrationFunctional< TXform, TMetricFunctional >::VariableParamVectorDim().

CallbackResult cmtk::RegistrationCallback::Execute

(

)

[virtual, inherited]

Execute callback action without interim result.

Definition at line 77 of file cmtkRegistrationCallback.cxx.

References cmtk::CALLBACK_INTERRUPT, and cmtk::CALLBACK_OK.

CallbackResult cmtk::ProtocolCallback::ExecuteWithData	(	const CoordinateVector &	v,
		const double	metric
	)		[virtual, inherited]

Execute callback action.

Reimplemented from cmtk::RegistrationCallback.

Definition at line 67 of file cmtkProtocolCallback.cxx.

References cmtk::Vector< T >::Dim.

CallbackResult cmtk::RegistrationCallback::ExecuteWithData	(	const CoordinateVector &	v,
		const double	metric
	)		[virtual, inherited]

Interface: Execute callback action.

Reimplemented in cmtk::ProtocolCallback.

Definition at line 71 of file cmtkRegistrationCallback.cxx.

References cmtk::CALLBACK_INTERRUPT, and cmtk::CALLBACK_OK.

void cmtk::GroupwiseRegistrationFunctionalBase::ForceZeroSumGradient

(

CoordinateVector &

g )

const [protected, virtual, inherited]

Enforce gradient to be zero-sum over all images.

Reimplemented in cmtk::GroupwiseRegistrationFunctionalXformTemplate< SplineWarpXform >.

Definition at line 471 of file cmtkGroupwiseRegistrationFunctionalBase.cxx.

References cmtk::Vector< T >::Clear(), and cmtk::Vector< T >::MaxNorm().

void cmtk::RegistrationCallback::FormatComment	(	const char *	format,
			...
	)		[virtual, inherited]

Notify callback of an annotation with variable parameters.

Definition at line 89 of file cmtkRegistrationCallback.cxx.

cmtk::FunctionalAffine2D::FunctionalAffine2D	(	ScalarImage::SmartPtr &	refImage,
		ScalarImage::SmartPtr &	fltImage,
		const ScalarImage::RegionType *	fltROI = NULL
	)		[inherited]

Contructor.

Definition at line 53 of file cmtkFunctionalAffine2D.cxx.

References cmtk::Region< NDIM, T >::From().

cmtk::FunctionalAffine2D::FunctionalAffine2D	(	std::vector< ScalarImage::SmartPtr > &	refImage,
		std::vector< ScalarImage::SmartPtr > &	fltImage,
		const ScalarImage::RegionType *	fltROI = NULL
	)		[inherited]

Contructor.

Definition at line 92 of file cmtkFunctionalAffine2D.cxx.

References cmtk::Region< NDIM, T >::From().

template<Interpolators::InterpolationEnum I>

VoxelMatchingCorrRatio< I >::ReturnType cmtk::VoxelMatchingCorrRatio< I >::Get

(

)

const [inherited]

Return correlation ratio.

Definition at line 44 of file cmtkVoxelMatchingCorrRatio.cxx.

VoxelMatchingCrossCorrelation::ReturnType cmtk::VoxelMatchingCrossCorrelation::Get

(

)

const [inherited]

Compute cross correlation.

Definition at line 49 of file cmtkVoxelMatchingCrossCorrelation.cxx.

ImagePairSimilarityMeasureCR::ReturnType cmtk::ImagePairSimilarityMeasureCR::Get

(

)

const [virtual, inherited]

Return correlation ratio.

Implements cmtk::ImagePairSimilarityMeasure.

Definition at line 68 of file cmtkImagePairSimilarityMeasureCR.cxx.

ImagePairSimilarityMeasureNCC::ReturnType cmtk::ImagePairSimilarityMeasureNCC::Get

(

)

const [virtual, inherited]

Compute cross correlation.

Implements cmtk::ImagePairSimilarityMeasure.

Definition at line 61 of file cmtkImagePairSimilarityMeasureNCC.cxx.

CommandLine& cmtk::ImageSymmetryPlaneCommandLineBase::GetCommandLine

(

)

[inline, inherited]

Get reference to command line parser object.

Definition at line 66 of file cmtkImageSymmetryPlaneCommandLineBase.h.

UniformVolume::SmartPtr & cmtk::VolumeInjectionReconstruction::GetCorrectedImage

(

)

[inherited]

Returns the corrected image.

Definition at line 444 of file cmtkVolumeInjectionReconstruction.cxx.

ScalarImageSimilarity::ReturnType cmtk::ScalarImageSimilarity::GetCorrelationRatio	(	const ScalarImage *	image0,
		const ScalarImage *	image1
	)		[static, inherited]

Compute correlation ratio between two pixel arrays.

This function is implemented using a 1-D histogram.

Definition at line 264 of file cmtkScalarImageSimilarity.cxx.

TypedArraySimilarity::ReturnType cmtk::TypedArraySimilarity::GetCorrelationRatio	(	const TypedArray *	array0,
		const TypedArray *	array1
	)		[static, inherited]

Compute correlation ratio between two pixel arrays.

This function is implemented using a 1-D histogram.

Definition at line 84 of file cmtkTypedArraySimilarity.cxx.

References cmtk::Memory::DeleteArray(), cmtk::TypedArray::Get(), cmtk::TypedArray::GetDataSize(), cmtk::TypedArray::GetRange(), cmtk::TypedArray::GetStatistics(), cmtk::TypedArray::GetType(), cmtk::Histogram< T >::Increment(), cmtk::Histogram< T >::SampleCount(), cmtk::HistogramBase::SetRange(), cmtk::TYPE_DOUBLE, cmtk::TYPE_FLOAT, cmtk::HistogramBase::ValueToBin(), and cmtk::Types::Range< T >::Width().

ScalarImageSimilarity::ReturnType cmtk::ScalarImageSimilarity::GetCrossCorrelation	(	const ScalarImage *	image0,
		const ScalarImage *	image1
	)		[static, inherited]

Compute normalized cross correlation between two images.

See Penney et al. III-A.

Definition at line 88 of file cmtkScalarImageSimilarity.cxx.

TypedArraySimilarity::ReturnType cmtk::TypedArraySimilarity::GetCrossCorrelation	(	const TypedArray *	array0,
		const TypedArray *	array1
	)		[static, inherited]

Compute normalized cross correlation between two pixel arrays.

Definition at line 232 of file cmtkTypedArraySimilarity.cxx.

References cmtk::TypedArray::Get(), cmtk::TypedArray::GetDataSize(), and cmtk::TypedArray::GetStatistics().

TypedArray::SmartPtr cmtk::TypedArraySimilarity::GetDifferenceArray	(	const TypedArray *	array0,
		const TypedArray *	array1,
		Types::DataItem &	scaleFactor
	)		[static, inherited]

Compute scaled difference of two images.

The values of the second array are scaled with a comon factor so that the entropy of the difference array is minimized. The resulting scale factor is returned via a reference argument.

Definition at line 260 of file cmtkTypedArraySimilarity.cxx.

References cmtk::TypedArray::Get(), cmtk::TypedArray::GetDataSize(), cmtk::GetSignedDataType(), and cmtk::TypedArray::GetType().

TypedArraySimilarity::ReturnType cmtk::TypedArraySimilarity::GetDifferenceArrayEntropy	(	const TypedArray *	array0,
		const TypedArray *	array1,
		Types::DataItem &	scaleFactor
	)		[static, inherited]

Compute entropy of difference of two images.

Definition at line 294 of file cmtkTypedArraySimilarity.cxx.

ScalarImageSimilarity::ReturnType cmtk::ScalarImageSimilarity::GetDifferenceImageEntropy	(	const ScalarImage *	image0,
		const ScalarImage *	image1
	)		[static, inherited]

Compute entropy of difference of two images.

See Penney et al. III-B.

Definition at line 243 of file cmtkScalarImageSimilarity.cxx.

ScalarImageSimilarity::ReturnType cmtk::ScalarImageSimilarity::GetDifferenceImageEntropy	(	const ScalarImage *	image0,
		const ScalarImage *	image1,
		Types::DataItem &	scaleFactor
	)		[static, inherited]

Compute entropy of difference of two images.

See Penney et al. III-B. This function returns the actual scaling factor used for intensity normalization via a reference parameter.

Definition at line 251 of file cmtkScalarImageSimilarity.cxx.

TypedArray::SmartPtr cmtk::HypothesisTests::GetGeneticCovariance	(	std::vector< TypedArray::SmartPtr > &	dataMZ,
		std::vector< TypedArray::SmartPtr > &	dataDZ,
		const TypedArray *	mask = NULL
	)		[static, inherited]

Get pixelwise genetic covariance from MZ and DZ twin data.

Definition at line 409 of file cmtkHypothesisTests.cxx.

References cmtk::TypedArray::Get(), and cmtk::TYPE_FLOAT.

ScalarImageSimilarity::ReturnType cmtk::ScalarImageSimilarity::GetGradientCorrelation	(	const ScalarImage *	image0,
		const ScalarImage *	image1
	)		[static, inherited]

Compute gradient correlation between two images.

See Penney et al. III-D.

Definition at line 101 of file cmtkScalarImageSimilarity.cxx.

References CMTK_SCALARIMAGE_HORIZONTAL, CMTK_SCALARIMAGE_VERTICAL, and cmtk::ScalarImage::GetSobelFiltered().

ScalarImageSimilarity::ReturnType cmtk::ScalarImageSimilarity::GetGradientDifference	(	const ScalarImage *	image0,
		const ScalarImage *	image1,
		const ReturnType	Ax = 1,
		const ReturnType	Ay = 1
	)		[static, inherited]

Compute gradient difference between two images.

See Penney et al. III-F.

Definition at line 117 of file cmtkScalarImageSimilarity.cxx.

References CMTK_SCALARIMAGE_HORIZONTAL, CMTK_SCALARIMAGE_VERTICAL, cmtk::ScalarImage::GetNumberOfPixels(), and cmtk::ScalarImage::GetSobelFiltered().

TypedArray::SmartPtr cmtk::HypothesisTests::GetHeritability	(	std::vector< TypedArray::SmartPtr > &	dataX,
		std::vector< TypedArray::SmartPtr > &	dataY,
		const TypedArray *	mask = NULL
	)		[static, inherited]

Get pixelwise heritability of two populations.

Definition at line 327 of file cmtkHypothesisTests.cxx.

References cmtk::TypedArray::Get(), and cmtk::TYPE_FLOAT.

template<class TDataType , class TInterpolator , class THashKeyType , char NBitsPerChannel>

Functional::ReturnType cmtk::MultiChannelHistogramRegistrationFunctional< TDataType, TInterpolator, THashKeyType, NBitsPerChannel >::GetMetric

(

const MetricData &

metricData )

const [protected, virtual, inherited]

Get metric value.

Definition at line 146 of file cmtkMultiChannelHistogramRegistrationFunctional.txx.

References cmtk::MultiChannelHistogramRegistrationFunctional< TDataType, TInterpolator, THashKeyType, NBitsPerChannel >::MetricData::m_FloatingHash, cmtk::MultiChannelHistogramRegistrationFunctional< TDataType, TInterpolator, THashKeyType, NBitsPerChannel >::MetricData::m_JointHash, cmtk::MultiChannelHistogramRegistrationFunctional< TDataType, TInterpolator, THashKeyType, NBitsPerChannel >::MetricData::m_ReferenceHash, and cmtk::MultiChannelHistogramRegistrationFunctional< TDataType, TInterpolator, THashKeyType, NBitsPerChannel >::MetricData::m_TotalNumberOfSamples.

template<class TRealType , class TDataType , class TInterpolator >

TRealType cmtk::MultiChannelRMIRegistrationFunctional< TRealType, TDataType, TInterpolator >::GetMetric

(

const MetricData &

metricData )

const [protected, virtual, inherited]

Get metric value.

Definition at line 76 of file cmtkMultiChannelRMIRegistrationFunctional.txx.

References cmtk::MultiChannelRMIRegistrationFunctional< TRealType, TDataType, TInterpolator >::MetricData::m_CovarianceMatrix, cmtk::MultiChannelRMIRegistrationFunctional< TRealType, TDataType, TInterpolator >::MetricData::m_CovarianceMatrixFlt, cmtk::MultiChannelRMIRegistrationFunctional< TRealType, TDataType, TInterpolator >::MetricData::m_CovarianceMatrixRef, cmtk::MultiChannelRMIRegistrationFunctional< TRealType, TDataType, TInterpolator >::MetricData::m_Products, cmtk::MultiChannelRMIRegistrationFunctional< TRealType, TDataType, TInterpolator >::MetricData::m_Sums, and cmtk::MultiChannelRMIRegistrationFunctional< TRealType, TDataType, TInterpolator >::MetricData::m_TotalNumberOfSamples.

ScalarImageSimilarity::ReturnType cmtk::ScalarImageSimilarity::GetMinusMeanSquaredDifference	(	const ScalarImage *	image0,
		const ScalarImage *	image1
	)		[static, inherited]

Compute negated (i.e., sign-switched) mean squared pixel difference between two images.

Definition at line 75 of file cmtkScalarImageSimilarity.cxx.

TypedArraySimilarity::ReturnType cmtk::TypedArraySimilarity::GetMinusMeanSquaredDifference	(	const TypedArray *	array0,
		const TypedArray *	array1
	)		[static, inherited]

Compute negated (i.e., sign-switched) mean squared pixel difference between two pixel arrays.

Definition at line 199 of file cmtkTypedArraySimilarity.cxx.

References cmtk::TypedArray::Get(), and cmtk::TypedArray::GetDataSize().

const std::string cmtk::MakeInitialAffineTransformation::GetModeName

(

const Self::Mode

mode )

[static, inherited]

Return a name for each initialization mode.

Definition at line 46 of file cmtkMakeInitialAffineTransformation.cxx.

Referenced by cmtk::ImagePairAffineRegistrationCommandLine::OutputResultList().

TypedArraySimilarity::ReturnType cmtk::TypedArraySimilarity::GetMutualInformation	(	const TypedArray *	array0,
		const TypedArray *	array1,
		TypedArraySimilarityMemory *const	memory = NULL
	)		[static, inherited]

Compute mutual information between two pixel arrays.

Definition at line 47 of file cmtkTypedArraySimilarity.cxx.

References cmtk::TypedArraySimilarityMemory::CreateHistogram(), cmtk::TypedArray::Get(), cmtk::TypedArray::GetDataSize(), cmtk::JointHistogram< T >::GetMutualInformation(), cmtk::TypedArray::GetRange(), cmtk::JointHistogram< T >::Increment(), cmtk::JointHistogram< T >::ValueToBinX(), and cmtk::JointHistogram< T >::ValueToBinY().

TypedArraySimilarity::ReturnType cmtk::TypedArraySimilarity::GetMutualInformation	(	const std::vector< const TypedArray * > &	data0,
		const std::vector< const TypedArray * > &	data1,
		const bool	normalized = false
	)		[static, inherited]

Compute mutual information between two sets of pixel arrays.

Definition at line 45 of file cmtkTypedArraySimilarityRMI.cxx.

ScalarImageSimilarity::ReturnType cmtk::ScalarImageSimilarity::GetMutualInformation	(	const ScalarImage *	image0,
		const ScalarImage *	image1,
		ScalarImageSimilarityMemory *const	memory = NULL
	)		[static, inherited]

Compute mutual information between two images.

This is the standard mutual information similarity measure. See Penney et al. III-C.

Definition at line 48 of file cmtkScalarImageSimilarity.cxx.

TypedArraySimilarity::ReturnType cmtk::TypedArraySimilarity::GetNormalizedMutualInformation	(	const TypedArray *	array0,
		const TypedArray *	array1,
		TypedArraySimilarityMemory *const	memory = NULL
	)		[static, inherited]

Compute normalized mutual information between two pixel arrays.

Definition at line 166 of file cmtkTypedArraySimilarity.cxx.

References cmtk::TypedArraySimilarityMemory::CreateHistogram(), cmtk::TypedArray::Get(), cmtk::TypedArray::GetDataSize(), cmtk::JointHistogram< T >::GetMutualInformation(), cmtk::TypedArray::GetRange(), cmtk::JointHistogram< T >::Increment(), cmtk::JointHistogram< T >::ValueToBinX(), and cmtk::JointHistogram< T >::ValueToBinY().

static ReturnType cmtk::TypedArraySimilarity::GetNormalizedMutualInformation	(	const std::vector< const TypedArray * > &	data0,
		const std::vector< const TypedArray * > &	data1
	)		[inline, static, inherited]

Compute norrmalized mutual information between two sets of pixel arrays.

Definition at line 86 of file cmtkTypedArraySimilarity.h.

ScalarImageSimilarity::ReturnType cmtk::ScalarImageSimilarity::GetNormalizedMutualInformation	(	const ScalarImage *	image0,
		const ScalarImage *	image1,
		ScalarImageSimilarityMemory *const	memory = NULL
	)		[static, inherited]

Compute normalized mutual information between two images.

This is the normalized mutual information measure as described by Studholme et al. [Studholme, Hill, Hawkes, Pattern Analysis, 1999].

Definition at line 62 of file cmtkScalarImageSimilarity.cxx.

TypedArray::SmartPtr cmtk::HypothesisTests::GetOneSampleTTest	(	std::vector< TypedArray::SmartPtr > &	dataX,
		TypedArray::SmartPtr *	tstatData,
		TypedArray::SmartPtr *	avgXData,
		const TypedArray *	mask = NULL
	)		[static, inherited]

Test mean of Jacobian map of a single population for difference from zero.

Definition at line 263 of file cmtkHypothesisTests.cxx.

References cmtk::TypedArray::Get(), and cmtk::TYPE_FLOAT.

TypedArraySimilarity::ReturnType cmtk::TypedArraySimilarity::GetOptimalScale	(	const TypedArray *	array0,
		const TypedArray *	array1
	)		[static, inherited]

Compute the optimal scale factor between two images.

This implementation uses least squares fitting

Definition at line 314 of file cmtkTypedArraySimilarity.cxx.

References cmtk::TypedArray::Get(), and cmtk::TypedArray::GetDataSize().

ap::real_value_type cmtk::VolumeInjectionReconstruction::GetOriginalToCorrectedImageKLD

(

const ap::real_1d_array &

x )

[inherited]

Get Kullback-Leibler Divergence between intensity distributions in original and corrected image.

Definition at line 458 of file cmtkVolumeInjectionReconstruction.cxx.

TypedArray::SmartPtr cmtk::HypothesisTests::GetPairedCorrelation	(	std::vector< TypedArray::SmartPtr > &	dataX,
		std::vector< TypedArray::SmartPtr > &	dataY,
		TypedArray::SmartPtr *	pData = NULL,
		const TypedArray *	mask = NULL
	)		[static, inherited]

Get pixel-wise correlation between two sets of input images.

Definition at line 210 of file cmtkHypothesisTests.cxx.

References cmtk::TypedArray::Get(), and cmtk::TYPE_FLOAT.

TypedArray::SmartPtr cmtk::HypothesisTests::GetPairedTwoTailedTTest	(	std::vector< TypedArray::SmartPtr > &	dataX,
		std::vector< TypedArray::SmartPtr > &	dataY,
		TypedArray::SmartPtr *	tstatData,
		TypedArray::SmartPtr *	avgXData,
		TypedArray::SmartPtr *	avgYData,
		const TypedArray *	mask = NULL
	)		[static, inherited]

Test parameter maps of two populations for statistical independence.

Definition at line 125 of file cmtkHypothesisTests.cxx.

References cmtk::TypedArray::Get(), and cmtk::TYPE_FLOAT.

Types::Coordinate cmtk::ImageSymmetryPlaneFunctionalBase::GetParamStep	(	const size_t	idx,
		const Types::Coordinate	mmStep = 1
	)		const [virtual, inherited]

Return the parameter stepping for 1 mm optimization steps.

Reimplemented from cmtk::Functional.

Definition at line 59 of file cmtkImageSymmetryPlaneFunctionalBase.cxx.

References M_PI.

Types::Coordinate cmtk::FunctionalAffine2D::GetParamStep	(	const size_t	idx,
		const Types::Coordinate	mmStep = 1
	)		const [virtual, inherited]

Return parameter stepping.

Reimplemented from cmtk::Functional.

Definition at line 151 of file cmtkFunctionalAffine2D.cxx.

References cmtk::AXIS_X, cmtk::AXIS_Y, and cmtk::Units::UnitBase::Value().

Types::Coordinate cmtk::SymmetryPlaneFunctional::GetParamStep	(	const size_t	idx,
		const Types::Coordinate	mmStep = 1
	)		const [virtual, inherited]

Return the parameter stepping for 1 mm optimization steps.

Reimplemented from cmtk::Functional.

Definition at line 64 of file cmtkSymmetryPlaneFunctional.cxx.

References M_PI.

template<class W>

virtual Types::Coordinate cmtk::VoxelMatchingElasticFunctional_WarpTemplate< W >::GetParamStep	(	const size_t	idx,
		const Types::Coordinate	mmStep = 1
	)		const [inline, virtual, inherited]

Get parameter stepping in milimeters.

Reimplemented from cmtk::Functional.

Definition at line 292 of file cmtkVoxelMatchingElasticFunctional.h.

void cmtk::FunctionalAffine2D::GetParamVector

(

CoordinateVector &

v )

[virtual, inherited]

Return current parameter vector.

This is useful to retrieve the intial parameter values set by this class upon initialization.

Definition at line 198 of file cmtkFunctionalAffine2D.cxx.

void cmtk::GroupwiseRegistrationFunctionalBase::GetParamVector

(

CoordinateVector &

v )

[virtual, inherited]

Get parameter vector.

Definition at line 295 of file cmtkGroupwiseRegistrationFunctionalBase.cxx.

References cmtk::Vector< T >::SetDim().

template<class W>

virtual void cmtk::VoxelMatchingElasticFunctional_WarpTemplate< W >::GetParamVector

(

CoordinateVector &

v )

[inline, virtual, inherited]

Return parameter vector.

Definition at line 317 of file cmtkVoxelMatchingElasticFunctional.h.

ScalarImageSimilarity::ReturnType cmtk::ScalarImageSimilarity::GetPatternIntensity	(	const ScalarImage *	image0,
		const ScalarImage *	image1,
		const ReturnType	sigma = 10,
		const int	radius = 3
	)		[static, inherited]

Compute pattern intensity between two images.

See Penney et al. III-E.

Definition at line 156 of file cmtkScalarImageSimilarity.cxx.

References cmtk::AXIS_X, cmtk::AXIS_Y, and cmtk::ScalarImage::GetDims().

TypedArraySimilarity::ReturnType cmtk::TypedArraySimilarity::GetPeakSignalToNoiseRatio	(	const TypedArray *	data,
		const TypedArray *	signal
	)		[static, inherited]

Compute Peak-Signal-to-Noise-Ratio.

Parameters:

data	Measured data.
signal	Pure signal without noise.

Definition at line 225 of file cmtkTypedArraySimilarity.cxx.

References cmtk::TypedArray::GetRange(), and cmtk::Types::Range< T >::Width().

const Types::DataItemRange cmtk::TypedArraySimilarityMemory::GetRangeX	(	const TypedArray *	array,
		const size_t	numBins
	)		[inherited]

Get range of X distribution.

If this object is not yet initialized, the given array is queried for its value range, and this object is initialized accordingly.

Definition at line 42 of file cmtkTypedArraySimilarityMemory.cxx.

References cmtk::TypedArray::GetRange(), cmtk::Types::Range< T >::m_LowerBound, and cmtk::Types::Range< T >::m_UpperBound.

const Types::DataItemRange cmtk::TypedArraySimilarityMemory::GetRangeY	(	const TypedArray *	array,
		const size_t	numBins
	)		[inherited]

Get range of Y distribution.

If this object is not yet initialized, the given array is queried for its value range, and this object is initialized accordingly.

Definition at line 82 of file cmtkTypedArraySimilarityMemory.cxx.

References cmtk::TypedArray::GetRange(), cmtk::Types::Range< T >::m_LowerBound, and cmtk::Types::Range< T >::m_UpperBound.

const DataGrid::RegionType cmtk::VoxelMatchingFunctional::GetReferenceGridRange	(	const Vector3D &	fromVOI,
		const Vector3D &	toVOI
	)		[protected, inherited]

Find rectilinear area in original reference grid.

Parameters:

fromVOI	Lower corner of area to find.
toVOI	Upper corner of area to find.

Returns:

The smallest box of reference grid voxels that contains the given coordinate range.

Definition at line 82 of file cmtkVoxelMatchingFunctional.cxx.

const DataGrid::RegionType cmtk::ImagePairRegistrationFunctional::GetReferenceGridRange	(	const Vector3D &	fromVOI,
		const Vector3D &	toVOI
	)		[protected, inherited]

Find rectilinear area in original reference grid.

Parameters:

fromVOI	Lower corner of area to find.
toVOI	Upper corner of area to find.

Returns:

The smallest region of reference grid voxels that contains the given coordinate range.

Definition at line 81 of file cmtkImagePairRegistrationFunctional.cxx.

const UniformVolume::SmartPtr cmtk::ImagePairAffineRegistration::GetReformattedFloatingImage

(

Interpolators::InterpolationEnum

interpolator = Interpolators::LINEAR )

const [inherited]

Get reformatted floating image.

Definition at line 216 of file cmtkImagePairAffineRegistration.cxx.

References cmtk::ImagePairAffineRegistration::GetTransformation(), cmtk::ReformatVolume::PlainReformat(), cmtk::ReformatVolume::SetAffineXform(), cmtk::ReformatVolume::SetFloatingVolume(), cmtk::ReformatVolume::SetInterpolation(), and cmtk::ReformatVolume::SetReferenceVolume().

Referenced by cmtk::ImagePairAffineRegistrationCommandLine::OutputResult().

const UniformVolume::SmartPtr cmtk::AffineRegistration::GetReformattedFloatingImage

(

Interpolators::InterpolationEnum

interpolator = Interpolators::LINEAR )

const [inherited]

Get reformatted floating image.

Definition at line 221 of file cmtkAffineRegistration.cxx.

References cmtk::AffineRegistration::GetTransformation(), cmtk::ReformatVolume::PlainReformat(), cmtk::ReformatVolume::SetAffineXform(), cmtk::ReformatVolume::SetFloatingVolume(), cmtk::ReformatVolume::SetInterpolation(), cmtk::ReformatVolume::SetReferenceVolume(), and cmtk::VoxelRegistration::SwitchVolumes.

Referenced by cmtk::AffineRegistrationCommandLine::OutputResult().

const UniformVolume::SmartPtr cmtk::ImagePairNonrigidRegistration::GetReformattedFloatingImage

(

Interpolators::InterpolationEnum

interpolator = Interpolators::LINEAR )

const [protected, inherited]

Get reformatted floating image.

Definition at line 374 of file cmtkImagePairNonrigidRegistration.cxx.

References cmtk::ImagePairNonrigidRegistration::GetTransformation(), cmtk::ImagePairRegistration::m_ForceOutsideFlag, cmtk::ImagePairRegistration::m_ForceOutsideValue, cmtk::ReformatVolume::PlainReformat(), cmtk::ReformatVolume::SetFloatingVolume(), cmtk::ReformatVolume::SetInterpolation(), cmtk::ReformatVolume::SetReferenceVolume(), and cmtk::ReformatVolume::SetWarpXform().

const UniformVolume::SmartPtr cmtk::ElasticRegistration::GetReformattedFloatingImage

(

Interpolators::InterpolationEnum

interpolator = Interpolators::LINEAR )

[protected, inherited]

Get reformatted floating image.

Definition at line 373 of file cmtkElasticRegistration.cxx.

References cmtk::ElasticRegistration::GetTransformation(), cmtk::ReformatVolume::PlainReformat(), cmtk::ReformatVolume::SetFloatingVolume(), cmtk::ReformatVolume::SetInterpolation(), cmtk::ReformatVolume::SetReferenceVolume(), and cmtk::ReformatVolume::SetWarpXform().

const UniformVolume::SmartPtr cmtk::GroupwiseRegistrationFunctionalBase::GetReformattedImage	(	const UniformVolume::SmartPtr &	targetGrid,
		const size_t	idx
	)		const [protected, virtual, inherited]

Reformat one image to a given target grid.

Definition at line 604 of file cmtkGroupwiseRegistrationFunctionalBase.cxx.

References cmtk::Interpolators::LINEAR, cmtk::ReformatVolume::PlainReformat(), cmtk::ReformatVolume::SetAffineXform(), cmtk::ReformatVolume::SetFloatingVolume(), cmtk::ReformatVolume::SetInterpolation(), cmtk::ReformatVolume::SetReferenceVolume(), and cmtk::ReformatVolume::SetWarpXform().

ScalarImageSimilarity::ReturnType cmtk::ScalarImageSimilarity::GetRegionalMutualInformation	(	const ScalarImage *	image0,
		const ScalarImage *	image1,
		const int	radius = 2
	)		[static, inherited]

Compute regional mutual information between two images.

Definition at line 47 of file cmtkScalarImageSimilarityRMI.cxx.

References cmtk::TypedArray::Get(), and cmtk::ScalarImage::GetDims().

template<class T , ScalarDataType DT, cmtk::Interpolators::InterpolationEnum I>

T cmtk::VoxelMatchingMetric< T, DT, I >::GetSampleY	(	const size_t	baseIndex,
		const Types::Coordinate *	frac
	)		const [inline, inherited]

Interpolate a value from the Y distribution (floating image).

Definition at line 41 of file cmtkVoxelMatchingMetric.txx.

FunctionalAffine2D::ReturnType cmtk::FunctionalAffine2D::GetSimilarity	(	const ScalarImage *	img0,
		const ScalarImage *	img1
	)		const [private, inherited]

Compute appropriate similarity measure for a single image pair.

Definition at line 239 of file cmtkFunctionalAffine2D.cxx.

FunctionalAffine2D::ReturnType cmtk::FunctionalAffine2D::GetSimilarity	(	std::vector< const ScalarImage * > &	imgs0,
		std::vector< const ScalarImage * > &	imgs1
	)		const [private, inherited]

Compute appropriate similarity measure for multiple images.

Definition at line 270 of file cmtkFunctionalAffine2D.cxx.

AffineXform::SmartPtr cmtk::AffineRegistration::GetTransformation

(

)

const [inherited]

Return final transformation.

Definition at line 207 of file cmtkAffineRegistration.cxx.

References cmtk::SmartPointer< Self >::DynamicCastFrom(), cmtk::VoxelRegistration::m_Xform, and cmtk::VoxelRegistration::SwitchVolumes.

Referenced by cmtk::VolumeInjectionReconstruction::ComputeTransformationsToPassImages(), cmtk::AffineRegistration::GetReformattedFloatingImage(), cmtk::AffineRegistrationCommandLine::OutputResult(), cmtk::AffineRegistrationCommandLine::OutputResultList(), cmtk::AffineRegistrationCommandLine::OutputResultMatrix(), and cmtk::AtlasSegmentation::RegisterAffine().

AffineXform::SmartPtr cmtk::ImagePairAffineRegistration::GetTransformation

(

)

const [inherited]

Return final transformation.

Definition at line 209 of file cmtkImagePairAffineRegistration.cxx.

References cmtk::SmartPointer< Self >::DynamicCastFrom(), and cmtk::ImagePairRegistration::m_Xform.

Referenced by cmtk::ImagePairAffineRegistration::GetReformattedFloatingImage(), cmtk::ImagePairAffineRegistrationCommandLine::OutputResult(), cmtk::ImagePairAffineRegistrationCommandLine::OutputResultList(), and cmtk::ImagePairAffineRegistrationCommandLine::OutputResultMatrix().

UniformVolume * cmtk::ReformatVolume::GetTransformedReference

(

Types::Coordinate *const

volumeOffset = NULL )

[inherited]

Apply forward warp transformation to reference volume.

Definition at line 243 of file cmtkReformatVolume.cxx.

References cmtk::ReformatVolume::GetTransformedReferenceTP::bbFrom, cmtk::TypedArray::Create(), cmtk::ReformatVolume::GetTransformedReferenceTP::dataArray, cmtk::DATACLASS_GREY, cmtk::DATACLASS_LABEL, cmtk::ReformatVolume::GetTransformedReferenceTP::delta, cmtk::ReformatVolume::GetTransformedReferenceTP::dims, cmtk::DataGrid::GetDims(), cmtk::DataGrid::GetNumberOfPixels(), NULL, cmtk::ThreadParameters< T >::NumberOfThreads, cmtk::ReformatVolume::GetTransformedReferenceTP::referenceInterpolator, cmtk::ReformatVolume::GetTransformedReferenceTP::splineXform, cmtk::StdErr, cmtk::ThreadParameters< T >::thisObject, and cmtk::ThreadParameters< T >::ThisThreadIndex.

UniformVolume * cmtk::ReformatVolume::GetTransformedReference	(	const std::vector< SplineWarpXform::SmartPtr > *	xformList,
		std::vector< UniformVolume::SmartPtr > *	volumeList,
		Types::Coordinate *const	volumeOffset = NULL,
		const bool	includeReferenceData = true
	)		[inherited]

Apply forward warp transformation to reference volume.

Definition at line 42 of file cmtkReformatVolume.txx.

References cmtk::DATACLASS_GREY, cmtk::DATACLASS_LABEL, cmtk::DataGrid::GetDims(), cmtk::DataGrid::GetNumberOfPixels(), cmtk::Threads::GetNumberOfThreads(), cmtk::Types::Range< T >::m_UpperBound, NULL, cmtk::Threads::RunThreads(), cmtk::StdErr, and cmtk::TYPE_NONE.

CMTK_THREAD_RETURN_TYPE cmtk::ReformatVolume::GetTransformedReferenceGrey

(

void *const

arg )

[static, private, inherited]

Apply forward warp transformation to grey-level reference volume.

Definition at line 298 of file cmtkReformatVolume.cxx.

References cmtk::SplineWarpXform::ApplyInverseInPlace(), cmtk::ReformatVolume::GetTransformedReferenceTP::bbFrom, CMTK_THREAD_RETURN_VALUE, cmtk::ReformatVolume::GetTransformedReferenceTP::dataArray, cmtk::ReformatVolume::GetTransformedReferenceTP::delta, cmtk::ReformatVolume::GetTransformedReferenceTP::dims, cmtk::UniformVolumeInterpolatorBase::GetDataAt(), cmtk::MathUtil::Min(), cmtk::ReformatVolume::GetTransformedReferenceTP::referenceInterpolator, cmtk::Progress::SetProgress(), cmtk::ReformatVolume::GetTransformedReferenceTP::splineXform, and cmtk::ThreadParameters< T >::ThisThreadIndex.

CMTK_THREAD_RETURN_TYPE cmtk::ReformatVolume::GetTransformedReferenceGreyAvg

(

void *const

arg )

[static, private, inherited]

Apply forward warp transformation to average grey-level reference volume.

Definition at line 135 of file cmtkReformatVolume.txx.

References cmtk::SplineWarpXform::ApplyInverseInPlace(), cmtk::ReformatVolume::GetTransformedReferenceTP::bbFrom, CMTK_THREAD_RETURN_VALUE, cmtk::ReformatVolume::GetTransformedReferenceTP::dataArray, cmtk::ReformatVolume::GetTransformedReferenceTP::delta, cmtk::ReformatVolume::GetTransformedReferenceTP::dims, cmtk::ReformatVolume::GetTransformedReferenceTP::IncludeReferenceData, cmtk::ReformatVolume::GetTransformedReferenceTP::interpolatorList, cmtk::ReformatVolume::GetTransformedReferenceTP::numberOfImages, cmtk::ThreadParameters< T >::NumberOfThreads, cmtk::Threads::NumberOfThreads, cmtk::ReformatVolume::GetTransformedReferenceTP::splineXform, cmtk::ThreadParameters< T >::ThisThreadIndex, and cmtk::ReformatVolume::GetTransformedReferenceTP::xformList.

UniformVolume * cmtk::ReformatVolume::GetTransformedReferenceJacobianAvg	(	const std::vector< SplineWarpXform::SmartPtr > *	xformList,
		Types::Coordinate *const	volumeOffset = NULL,
		const bool	includeReferenceData = true
	)		[inherited]

Average Jacobians into deformed reference coordinate system.

Definition at line 430 of file cmtkReformatVolume.cxx.

References cmtk::TypedArray::Create(), cmtk::DataGrid::GetDims(), cmtk::DataGrid::GetNumberOfPixels(), cmtk::Threads::GetNumberOfThreads(), NULL, cmtk::Threads::RunThreads(), cmtk::StdErr, and cmtk::TYPE_FLOAT.

CMTK_THREAD_RETURN_TYPE cmtk::ReformatVolume::GetTransformedReferenceJacobianAvgThread

(

void *const

arg )

[static, private, inherited]

Thread function: average Jacobians into deformed reference system.

Definition at line 477 of file cmtkReformatVolume.cxx.

References cmtk::SplineWarpXform::ApplyInverseInPlace(), cmtk::ReformatVolume::GetTransformedReferenceTP::avgMode, cmtk::ReformatVolume::GetTransformedReferenceTP::bbFrom, CMTK_THREAD_RETURN_VALUE, cmtk::ReformatVolume::GetTransformedReferenceTP::dataArray, cmtk::ReformatVolume::GetTransformedReferenceTP::delta, cmtk::ReformatVolume::GetTransformedReferenceTP::dims, cmtk::WarpXform::GetGlobalScaling(), cmtk::SplineWarpXform::GetJacobianDeterminant(), cmtk::ReformatVolume::GetTransformedReferenceTP::IncludeReferenceData, cmtk::MathUtil::Min(), cmtk::ThreadParameters< T >::NumberOfThreads, cmtk::Progress::SetProgress(), cmtk::Vector< T >::Sort(), cmtk::ReformatVolume::GetTransformedReferenceTP::splineXform, cmtk::ThreadParameters< T >::ThisThreadIndex, and cmtk::ReformatVolume::GetTransformedReferenceTP::xformList.

CMTK_THREAD_RETURN_TYPE cmtk::ReformatVolume::GetTransformedReferenceLabel

(

void *const

arg )

[static, private, inherited]

Apply forward warp transformation to label reference volume.

Definition at line 343 of file cmtkReformatVolume.cxx.

References cmtk::SplineWarpXform::ApplyInverseInPlace(), cmtk::ReformatVolume::GetTransformedReferenceTP::bbFrom, CMTK_THREAD_RETURN_VALUE, cmtk::ReformatVolume::GetTransformedReferenceTP::dataArray, cmtk::ReformatVolume::GetTransformedReferenceTP::delta, cmtk::ReformatVolume::GetTransformedReferenceTP::dims, cmtk::ReformatVolume::GetTransformedReferenceTP::IncludeReferenceData, cmtk::ReformatVolume::GetTransformedReferenceTP::maxLabel, cmtk::MathUtil::Min(), cmtk::ReformatVolume::GetTransformedReferenceTP::numberOfImages, cmtk::ReformatVolume::ReferenceVolume, cmtk::Progress::SetProgress(), cmtk::ReformatVolume::GetTransformedReferenceTP::splineXform, cmtk::ThreadParameters< T >::thisObject, cmtk::ThreadParameters< T >::ThisThreadIndex, cmtk::ReformatVolume::GetTransformedReferenceTP::volumeList, and cmtk::ReformatVolume::GetTransformedReferenceTP::xformList.

TypedArray::SmartPtr cmtk::HypothesisTests::GetUnpairedTwoTailedTTest	(	std::vector< TypedArray::SmartPtr > &	dataX,
		std::vector< TypedArray::SmartPtr > &	dataY,
		TypedArray::SmartPtr *	tstatData,
		TypedArray::SmartPtr *	avgXData,
		TypedArray::SmartPtr *	avgYData,
		const TypedArray *	mask = NULL
	)		[static, inherited]

Test Jacobian maps of two populations for statistical independence.

Definition at line 50 of file cmtkHypothesisTests.cxx.

References cmtk::TypedArray::Get(), and cmtk::TYPE_FLOAT.

TypedArray::SmartPtr cmtk::HypothesisTests::GetZScores	(	std::vector< TypedArray::SmartPtr > &	dataX,
		std::vector< TypedArray::SmartPtr > &	dataY,
		const TypedArray *	mask = NULL
	)		[static, inherited]

Get pixelwise z-scores.

The X distribution is taken as the "true" or "reference" distribution. The Y distribution is taken as the "test" or "sample" distribution.

Definition at line 352 of file cmtkHypothesisTests.cxx.

References cmtk::TypedArray::Get(), and cmtk::TYPE_FLOAT.

cmtk::GroupwiseRegistrationFunctionalBase::GroupwiseRegistrationFunctionalBase

(

)

[inherited]

Constructor.

Definition at line 63 of file cmtkGroupwiseRegistrationFunctionalBase.cxx.

template<class TXform >

cmtk::GroupwiseRegistrationFunctionalXformTemplate< TXform >::GroupwiseRegistrationFunctionalXformTemplate

(

)

[inherited]

Constructor.

Definition at line 53 of file cmtkGroupwiseRegistrationFunctionalXformTemplate.cxx.

References cmtk::Threads::GetNumberOfThreads().

template<class TXform >

cmtk::GroupwiseRegistrationFunctionalXformTemplateBase< TXform >::GroupwiseRegistrationFunctionalXformTemplateBase

(

)

[inherited]

Constructor.

Definition at line 53 of file cmtkGroupwiseRegistrationFunctionalXformTemplateBase.cxx.

template<class TXform >

cmtk::GroupwiseRegistrationRMIFunctional< TXform >::GroupwiseRegistrationRMIFunctional

(

)

[inherited]

Constructor.

Definition at line 49 of file cmtkGroupwiseRegistrationRMIFunctional.cxx.

int cmtk::VolumeInjectionReconstruction::GuessInterleaveAxis	(	const UniformVolume *	image,
		const int	defaultAxis = 2
	)		[static, inherited]

Static helper function: guess interleaved axis.

Basically, we assume that images are acquired as interleaved stacks of square 2D images with pixel size different from inter-slice spacing. So we guess that the interleaved axis is the one that does not match the other two axes' image dimensions, and if all three are the same, the one that doesn't match their spacing (delta).

Parameters:

image	The interleaved image.
defaultAxis	In case all guessing fails, this is the default axis we return.

Definition at line 110 of file cmtkVolumeInjectionReconstruction.cxx.

References cmtk::UniformVolume::m_Delta, and cmtk::DataGrid::m_Dims.

cmtk::ImagePairAffineRegistration::ImagePairAffineRegistration

(

)

[inherited]

Default constructor.

Definition at line 57 of file cmtkImagePairAffineRegistration.cxx.

cmtk::ImagePairAffineRegistrationCommandLine::ImagePairAffineRegistrationCommandLine	(	const int	argc,
		const char *	argv[]
	)		[inherited]

Constructor.

Parameters:

argc	Number of command line arguments; this should be the argc parameter of the main() function.
argv	Array of command line arguments; this should be the argv parameter of the main() function.

Exceptions:

ConstructorFailed

This exception is thrown if there where invalid or unknown options or missing required parameters. In all these cases, an information text describing the known options will have been written to the standard error stream before throwing the exception.

Definition at line 91 of file cmtkImagePairAffineRegistrationCommandLine.cxx.

References cmtk::CommandLine::AddEnum(), cmtk::CommandLine::AddOption(), cmtk::CommandLine::AddParameter(), cmtk::CommandLine::AddSwitch(), cmtk::CommandLine::AddVector(), cmtk::CommandLine::BeginGroup(), cmtk::TypedStream::Close(), cmtk::MakeInitialAffineTransformation::COM, cmtk::Interpolators::COSINE_SINC, cmtk::Interpolators::CUBIC, cmtk::Interpolators::DEFAULT, cmtk::SmartPointer< Self >::DynamicCastFrom(), cmtk::CommandLine::EndGroup(), cmtk::MakeInitialAffineTransformation::FOV, cmtk::TransformChangeFromSpaceAffine::GetTransformation(), cmtk::TypedStream::IsValid(), cmtk::Interpolators::LINEAR, cmtk::META_SPACE, cmtk::Interpolators::NEAREST_NEIGHBOR, cmtk::MakeInitialAffineTransformation::NONE, NULL, cmtk::AnatomicalOrientationBase::ORIENTATION_STANDARD, cmtk::CommandLine::Parse(), cmtk::Interpolators::PARTIALVOLUME, cmtk::MakeInitialAffineTransformation::PAX, cmtk::MakeInitialAffineTransformation::PHYS, cmtk::CommandLine::PRG_CATEG, cmtk::CommandLine::PRG_DESCR, cmtk::CommandLine::PRG_TITLE, cmtk::CommandLine::PROPS_IMAGE, cmtk::CommandLine::PROPS_NOXML, cmtk::CommandLine::PROPS_OPTIONAL, cmtk::CommandLine::PROPS_OUTPUT, cmtk::CommandLine::PROPS_XFORM, cmtk::CommandLine::PROPS_XML, cmtk::XformIO::Read(), cmtk::ClassStream::READ, cmtk::VolumeIO::ReadOriented(), cmtk::TypedStream::ReadString(), cmtk::TypedStream::Seek(), cmtk::CommandLine::SetProgramInfo(), cmtk::StdErr, and cmtk::MountPoints::Translate().

cmtk::ImagePairAffineRegistrationFunctionalDevice::ImagePairAffineRegistrationFunctionalDevice	(	UniformVolume::SmartConstPtr &	fixedVolume,
		UniformVolume::SmartConstPtr &	movingVolume
	)		[inherited]

Constructor.

Definition at line 45 of file cmtkImagePairAffineRegistrationFunctionalDevice.cxx.

cmtk::ImagePairNonrigidRegistration::ImagePairNonrigidRegistration

(

)

[protected, inherited]

Default constructor.

Set initial values for some flags.

Definition at line 57 of file cmtkImagePairNonrigidRegistration.cxx.

References cmtk::ImagePairNonrigidRegistration::IgnoreEdge, cmtk::ImagePairRegistration::m_Metric, NULL, cmtk::ImagePairNonrigidRegistration::RefineDelayed, cmtk::ImagePairNonrigidRegistration::RefinedGridAtLevel, cmtk::ImagePairNonrigidRegistration::RefineGridCount, cmtk::ImagePairNonrigidRegistration::RelaxationStep, and cmtk::ImagePairNonrigidRegistration::RestrictToAxes.

cmtk::ImagePairNonrigidRegistrationCommandLine::ImagePairNonrigidRegistrationCommandLine	(	const int	argc,
		const char *	argv[]
	)		[inherited]

Constructor.

Parameters:

argc	Number of command line arguments; this should be the argc parameter of the main() function.
argv	Array of command line arguments; this should be the argv parameter of the main() function.

Was an initial studylist given? If so, get warp

Definition at line 87 of file cmtkImagePairNonrigidRegistrationCommandLine.cxx.

References cmtk::CommandLine::AddEnum(), cmtk::CommandLine::AddOption(), cmtk::CommandLine::AddParameter(), cmtk::CommandLine::AddSwitch(), cmtk::CommandLine::BeginGroup(), cmtk::TypedStream::Close(), cmtk::Interpolators::COSINE_SINC, cmtk::Interpolators::CUBIC, cmtk::Interpolators::DEFAULT, cmtk::CommandLine::EndGroup(), cmtk::TypedStream::IsValid(), cmtk::Interpolators::LINEAR, cmtk::META_SPACE, cmtk::Interpolators::NEAREST_NEIGHBOR, NULL, cmtk::CommandLine::Parse(), cmtk::Interpolators::PARTIALVOLUME, cmtk::TypedStream::ReadString(), cmtk::TypedStream::Seek(), cmtk::CommandLine::SetProgramInfo(), and cmtk::StdErr.

cmtk::ImagePairNonrigidRegistrationFunctional::ImagePairNonrigidRegistrationFunctional	(	UniformVolume::SmartPtr &	reference,
		UniformVolume::SmartPtr &	floating
	)		[protected, inherited]

Constructor.

Definition at line 55 of file cmtkImagePairNonrigidRegistrationFunctional.cxx.

References NULL.

cmtk::ImagePairRegistration::ImagePairRegistration

(

)

[inherited]

Default constructor.

Definition at line 54 of file cmtkImagePairRegistration.cxx.

References cmtk::ImagePairRegistration::m_CoarsestResolution, cmtk::ImagePairRegistration::m_OptimizerStepFactor, cmtk::ImagePairRegistration::m_Sampling, cmtk::ImagePairRegistration::m_UseMaxNorm, and cmtk::ImagePairRegistration::m_UseOriginalData.

cmtk::ImagePairSimilarityJointHistogram::ImagePairSimilarityJointHistogram	(	UniformVolume::SmartConstPtr &	refVolume,
		UniformVolume::SmartConstPtr &	fltVolume,
		const Interpolators::InterpolationEnum	interpolation = Interpolators::DEFAULT
	)		[inherited]

Constructor.

For reference and model volume, InitDataset is called.

Parameters:

refVolume	The reference (fixed) volume.
fltVolume	The floating (moving, transformed) volume.
interpolation	ID of the interpolator to use for the floating image.

Definition at line 43 of file cmtkImagePairSimilarityJointHistogram.cxx.

cmtk::ImagePairSimilarityMeasure::ImagePairSimilarityMeasure	(	const UniformVolume::SmartConstPtr &	refVolume,
		const UniformVolume::SmartConstPtr &	fltVolume,
		const Interpolators::InterpolationEnum	interpolation = Interpolators::DEFAULT
	)		[inherited]

Constructor.

Parameters:

refVolume	The reference image.
fltVolume	The floating image.
interpolation	User-selected interpolation kernel

Definition at line 49 of file cmtkImagePairSimilarityMeasure.cxx.

cmtk::ImagePairSimilarityMeasureCR::ImagePairSimilarityMeasureCR	(	const UniformVolume::SmartPtr &	refVolume,
		const UniformVolume::SmartPtr &	fltVolume,
		const Interpolators::InterpolationEnum	interpolation = Interpolators::DEFAULT
	)		[inherited]

Constructor.

The inherited constructor is called to initialize the given datasets. Afterwards, the original (untransformed) probability distribution functions of model and reference are calculated.

Definition at line 43 of file cmtkImagePairSimilarityMeasureCR.cxx.

cmtk::ImagePairSimilarityMeasureMSD::ImagePairSimilarityMeasureMSD	(	const UniformVolume::SmartConstPtr &	refVolume,
		const UniformVolume::SmartConstPtr &	fltVolume,
		const Interpolators::InterpolationEnum	interpolation = Interpolators::DEFAULT
	)		[inherited]

Constructor.

For reference and model volume, InitDataset is called.

Parameters:

refVolume	The reference (fixed) volume.
fltVolume	The floating (moving) volume.
interpolation	ID of the interpolator to use for the floating image.

Definition at line 43 of file cmtkImagePairSimilarityMeasureMSD.cxx.

cmtk::ImagePairSimilarityMeasureNCC::ImagePairSimilarityMeasureNCC	(	const UniformVolume::SmartPtr &	refVolume,
		const UniformVolume::SmartPtr &	fltVolume,
		const Interpolators::InterpolationEnum	interpolation = Interpolators::DEFAULT
	)		[inherited]

Constructor.

For reference and floating volume, InitDataset is called.

Parameters:

refVolume	The reference (fixed) volume.
fltVolume	The floating (moving) volume.
interpolation	ID of the interpolation algorithm to use for the floating image.

Definition at line 43 of file cmtkImagePairSimilarityMeasureNCC.cxx.

cmtk::ImagePairSimilarityMeasureNCC::ImagePairSimilarityMeasureNCC

(

const Self &

other )

[inherited]

Constant copy constructor.

Definition at line 48 of file cmtkImagePairSimilarityMeasureNCC.cxx.

cmtk::ImagePairSimilarityMeasureRMS::ImagePairSimilarityMeasureRMS	(	const UniformVolume::SmartConstPtr &	refVolume,
		const UniformVolume::SmartConstPtr &	fltVolume,
		const Interpolators::InterpolationEnum	interpolation = Interpolators::DEFAULT
	)		[inherited]

Constructor.

For reference and model volume, InitDataset is called.

Parameters:

refVolume	The reference (fixed) volume.
fltVolume	The floating (moving) volume.
interpolation	ID of the interpolation algorithm to use for the floating image.

Definition at line 43 of file cmtkImagePairSimilarityMeasureRMS.cxx.

cmtk::ImageSymmetryPlaneFunctional::ImageSymmetryPlaneFunctional

(

UniformVolume::SmartConstPtr &

volume )

[inherited]

Constructor.

Definition at line 45 of file cmtkImageSymmetryPlaneFunctional.cxx.

cmtk::ImageSymmetryPlaneFunctional::ImageSymmetryPlaneFunctional	(	UniformVolume::SmartConstPtr &	volume,
		const Types::DataItemRange &	valueRange
	)		[inherited]

Constructor with value range limits.

Definition at line 52 of file cmtkImageSymmetryPlaneFunctional.cxx.

cmtk::ImageSymmetryPlaneFunctionalBase::ImageSymmetryPlaneFunctionalBase	(	UniformVolume::SmartConstPtr &	volume,
		const Types::DataItemRange &	valueRange
	)		[inherited]

Constructor with value range limits.

Definition at line 50 of file cmtkImageSymmetryPlaneFunctionalBase.cxx.

cmtk::ImageSymmetryPlaneFunctionalBase::ImageSymmetryPlaneFunctionalBase

(

UniformVolume::SmartConstPtr &

volume )

[inherited]

Constructor.

Definition at line 43 of file cmtkImageSymmetryPlaneFunctionalBase.cxx.

cmtk::ImageSymmetryPlaneFunctionalDevice::ImageSymmetryPlaneFunctionalDevice

(

UniformVolume::SmartConstPtr &

volume )

[inherited]

Constructor.

Definition at line 45 of file cmtkImageSymmetryPlaneFunctionalDevice.cxx.

cmtk::ImageSymmetryPlaneFunctionalDevice::ImageSymmetryPlaneFunctionalDevice	(	UniformVolume::SmartConstPtr &	volume,
		const Types::DataItemRange &	valueRange
	)		[inherited]

Constructor with value range limits.

Definition at line 52 of file cmtkImageSymmetryPlaneFunctionalDevice.cxx.

template<class TRealType , class TDataType , class TInterpolator >

void cmtk::MultiChannelRMIRegistrationFunctional< TRealType, TDataType, TInterpolator >::MetricData::Init

(

Parent *const

parent )

[inherited]

Initialize metric object and local storage.

Definition at line 47 of file cmtkMultiChannelRMIRegistrationFunctionalMetricData.txx.

References cmtk::MultiChannelRegistrationFunctionalBase::m_FloatingChannels, and cmtk::MultiChannelRegistrationFunctionalBase::m_ReferenceChannels.

template<class T , ScalarDataType DT>

size_t cmtk::VoxelMatchingMetric_Type< T, DT >::ImageData::Init	(	const UniformVolume *	volume,
		const size_t	defNumBins,
		const Types::DataItemRange &	bounds = Types::DataItemRange( -HUGE_VAL, HUGE_VAL )
	)		[inherited]

Initialize internal storage for one volume.

The volume's data is converted into an array of byte values that directly represent the bin to sort the respective sample into. In addition, the number of bins is determined and the bins array allocated.

Parameters:

volume	The original volume data.
defNumBins	The desired number of bins. If this parameter is zero, a suitable number is automatically determined.
bounds	User-specified bounds for data values. All values outside this range will be set to the upper or lower limit and sorted into the first or last histogram bin, respectively.

Returns:

The number of bins required to hold the data. Note that there will be an extra bin allocated to hold non-existing data values.

Definition at line 71 of file cmtkVoxelMatchingMetric_Type.cxx.

References CMTK_HISTOGRAM_AUTOBINS, cmtk::DataGrid::CropRegion(), cmtk::DATACLASS_GREY, cmtk::DATACLASS_LABEL, cmtk::TypedArray::Get(), cmtk::DataGrid::GetCropRegionIncrements(), cmtk::Types::Range< T >::m_LowerBound, and cmtk::Types::Range< T >::m_UpperBound.

template<class TDataType , class TInterpolator , class THashKeyType , char NBitsPerChannel>

void cmtk::MultiChannelHistogramRegistrationFunctional< TDataType, TInterpolator, THashKeyType, NBitsPerChannel >::MetricData::Init

(

Parent *const

parent )

[inherited]

Initialize metric object and local storage.

Definition at line 47 of file cmtkMultiChannelHistogramRegistrationFunctionalMetricData.txx.

template<class T , ScalarDataType DT>

void cmtk::VoxelMatchingMetric_Type< T, DT >::ImageData::Init

(

const UniformVolume *

volume )

[inherited]

Initialize internal storage for one (reference of model) volume.

The volume's data is converted into an array of byte values that directly represent the bin to sort the respective sample into. In addition, the number of bins is determined and the bins array allocated. This function can distinguish between different kinds of data (grey-level, binary, and labels) and handle these accordingly.

Parameters:

volume

The original volume data.

Definition at line 47 of file cmtkVoxelMatchingMetric_Type.cxx.

References cmtk::TypedArray::Convert(), cmtk::TypedArray::GetPaddingFlag(), and cmtk::TypedArray::GetPaddingValue().

void cmtk::VoxelMatchingFunctional::InitFloating

(

UniformVolume::SmartPtr &

floating )

[private, inherited]

Initialize internal data structures for floating image.

Definition at line 47 of file cmtkVoxelMatchingFunctional.cxx.

void cmtk::ImagePairRegistrationFunctional::InitFloating

(

UniformVolume::SmartConstPtr &

floating )

[private, inherited]

Initialize internal data structures for floating image.

Definition at line 47 of file cmtkImagePairRegistrationFunctional.cxx.

void cmtk::SplineWarpCongealingFunctional::StaticThreadStorage::Initialize

(

const Self *

This )

[inherited]

Initialize thread storage based on parent functional ("This").

Definition at line 43 of file cmtkSplineWarpCongealingFunctionalStaticThreadStorage.cxx.

void cmtk::GroupwiseRegistrationFunctionalAffineInitializer::InitializeXforms	(	GroupwiseRegistrationFunctionalBase &	functional,
		const bool	alignCenters = true,
		const bool	alignCenterOfMass = false,
		const bool	initScales = false
	)		[static, inherited]

Initialize affine transformations.

Parameters:

functional	The functional to initialize.
alignCenters	If set, the centers of all target images will be aligned with the center of the template grid via translations.
initScales	!< If set, target images will be aligned via translations according to their centers of mass. If set, approximate initial scaling factors will be computed based on image centers of mass and moments.

Definition at line 46 of file cmtkGroupwiseRegistrationFunctionalAffineInitializer.cxx.

References cmtk::FixedVector< NDIM, T >::begin(), cmtk::FixedVector< NDIM, T >::end(), cmtk::GroupwiseRegistrationFunctionalBase::m_ImageVector, cmtk::GroupwiseRegistrationFunctionalBase::m_TemplateGrid, and cmtk::GroupwiseRegistrationFunctionalBase::m_XformVector.

void cmtk::SplineWarpCongealingFunctional::InitializeXformsFromAffine	(	const Types::Coordinate	gridSpacing,
		std::vector< AffineXform::SmartPtr >	initialAffineXformsVector,
		const bool	exactSpacing = true
	)		[virtual, inherited]

Initialize spline warp transformations.

Parameters:

gridSpacing	Control point grid spacing in real-world units
initialAffineXformsVector	Vector of initial affine coordinate transformations
exactSpacing	If set, the control point spacing will be exactly as given in the first parameter

Reimplemented from cmtk::GroupwiseRegistrationFunctionalXformTemplate< SplineWarpXform >.

Definition at line 65 of file cmtkSplineWarpCongealingFunctional.cxx.

void cmtk::ImagePairRegistrationFunctional::InitReference

(

UniformVolume::SmartConstPtr &

reference )

[private, inherited]

Initialize internal data structures for reference image.

Definition at line 65 of file cmtkImagePairRegistrationFunctional.cxx.

void cmtk::VoxelMatchingFunctional::InitReference

(

UniformVolume::SmartPtr &

reference )

[private, inherited]

Initialize internal data structures for reference image.

Definition at line 66 of file cmtkVoxelMatchingFunctional.cxx.

CallbackResult cmtk::VoxelRegistration::InitRegistration

(

)

[protected, virtual, inherited]

Initialize registration.

This function is called by Register before any other operations. It can be overloaded to open status dialog windows, etc. Derived implementations should call their base class' InitRegistration first.

Returns:

Reimplemented in cmtk::AffineRegistration, cmtk::AffineRegistrationCommandLine, cmtk::ElasticRegistration, and cmtk::ElasticRegistrationCommandLine.

Definition at line 85 of file cmtkVoxelRegistration.cxx.

References cmtk::CALLBACK_OK, cmtk::Timers::GetTimeProcess(), cmtk::Timers::GetTimeThread(), cmtk::Timers::GetWalltime(), cmtk::VoxelRegistration::ThreadTimeStartLevel, cmtk::VoxelRegistration::ThreadTimeStartRegistration, cmtk::VoxelRegistration::TimeStartLevel, cmtk::VoxelRegistration::TimeStartRegistration, cmtk::VoxelRegistration::WalltimeStartLevel, and cmtk::VoxelRegistration::WalltimeStartRegistration.

Referenced by cmtk::ElasticRegistration::InitRegistration(), cmtk::AffineRegistration::InitRegistration(), and cmtk::VoxelRegistration::Register().

CallbackResult cmtk::ImagePairAffineRegistrationCommandLine::InitRegistration

(

)

[protected, virtual, inherited]

Initialize registration.

So far, this function has no effect other than calling the equivalent inherited function.

Reimplemented from cmtk::ImagePairAffineRegistration.

Definition at line 350 of file cmtkImagePairAffineRegistrationCommandLine.cxx.

References cmtk::ImagePairAffineRegistration::InitRegistration().

CallbackResult cmtk::AffineRegistration::InitRegistration

(

)

[protected, virtual, inherited]

Initialize registration.

This function is called by Register before any other operations. It can be overloaded to open status dialog windows, etc. Derived implementations should call their base class' InitRegistration first.

Returns:

Overriding functions should return a value other than CALLBACK_OK if the registration is to be interrupted.

Reimplemented from cmtk::VoxelRegistration.

Reimplemented in cmtk::AffineRegistrationCommandLine.

Definition at line 74 of file cmtkAffineRegistration.cxx.

References cmtk::FixedVector< NDIM, T >::begin(), cmtk::CALLBACK_OK, cmtk::VoxelRegistration::CoarsestResolution, cmtk::VoxelMatchingAffineFunctional::Create(), cmtk::VoxelRegistration::FunctionalStack, cmtk::VoxelRegistration::InitRegistration(), cmtk::VoxelRegistration::m_Optimizer, cmtk::VoxelRegistration::m_Xform, cmtk::AffineRegistration::NumberDOFs, cmtk::AffineRegistration::NumberDOFsFinal, cmtk::AffineRegistration::NumberDOFsIterator, cmtk::VoxelRegistration::OptimizerStepFactor, and cmtk::VoxelRegistration::SwitchVolumes.

CallbackResult cmtk::ElasticRegistrationCommandLine::InitRegistration

(

)

[protected, virtual, inherited]

Initialize registration.

So far, this function has no effect other than calling the equivalent inherited function.

Reimplemented from cmtk::ElasticRegistration.

Definition at line 363 of file cmtkElasticRegistrationCommandLine.cxx.

References cmtk::CALLBACK_OK, and cmtkElasticRegistrationCommandLineDispatchSIGUSR1().

CallbackResult cmtk::ImagePairAffineRegistration::InitRegistration

(

)

[protected, virtual, inherited]

Initialize registration.

This function is called by Register before any other operations. It can be overloaded to open status dialog windows, etc. Derived implementations should call their base class' InitRegistration first.

Returns:

Overriding functions should return a value other than CALLBACK_OK if the registration is to be interrupted.

Reimplemented from cmtk::ImagePairRegistration.

Reimplemented in cmtk::ImagePairAffineRegistrationCommandLine.

Definition at line 68 of file cmtkImagePairAffineRegistration.cxx.

References cmtk::CALLBACK_OK, cmtk::MakeInitialAffineTransformation::Create(), cmtk::ImagePairRegistration::InitRegistration(), cmtk::ImagePairRegistration::m_CoarsestResolution, cmtk::ImagePairRegistration::m_MaxStepSize, cmtk::ImagePairRegistration::m_Optimizer, cmtk::ImagePairRegistration::m_OptimizerStepFactor, cmtk::ImagePairRegistration::m_ParameterStack, cmtk::ImagePairRegistration::m_Sampling, cmtk::ImagePairRegistration::m_UseOriginalData, cmtk::ImagePairRegistration::m_Xform, cmtk::ImagePairAffineRegistration::NumberDOFs, cmtk::ImagePairAffineRegistration::NumberDOFsFinal, and cmtk::ImagePairAffineRegistration::NumberDOFsIterator.

Referenced by cmtk::ImagePairAffineRegistrationCommandLine::InitRegistration().

CallbackResult cmtk::AffineRegistrationCommandLine::InitRegistration

(

)

[protected, virtual, inherited]

Initialize registration.

So far, this function has no effect other than calling the equivalent inherited function.

Reimplemented from cmtk::AffineRegistration.

Definition at line 341 of file cmtkAffineRegistrationCommandLine.cxx.

CallbackResult cmtk::ImagePairNonrigidRegistration::InitRegistration

(

)

[protected, virtual, inherited]

Initialize registration.

This function is called by Register before any other operations. It can be overloaded to open status dialog windows, etc. Derived implementations should call their base class' InitRegistration first.

Returns:

Reimplemented from cmtk::ImagePairRegistration.

Reimplemented in cmtk::ImagePairNonrigidRegistrationCommandLine.

Definition at line 90 of file cmtkImagePairNonrigidRegistration.cxx.

References cmtk::SmartPointer< Self >::DynamicCastFrom(), cmtk::ImagePairNonrigidRegistration::IgnoreEdge, cmtk::ImagePairNonrigidRegistration::InitialWarpXform, cmtk::ImagePairRegistration::InitRegistration(), cmtk::ImagePairNonrigidRegistration::InverseWarpXform, cmtk::ImagePairRegistration::m_CoarsestResolution, cmtk::ImagePairNonrigidRegistration::m_MatchedLandmarks, cmtk::ImagePairRegistration::m_MaxStepSize, cmtk::ImagePairRegistration::m_Optimizer, cmtk::ImagePairRegistration::m_OptimizerStepFactor, cmtk::ImagePairRegistration::m_ParameterStack, cmtk::ImagePairRegistration::m_Sampling, cmtk::ImagePairRegistration::m_UseMaxNorm, cmtk::ImagePairRegistration::m_UseOriginalData, cmtk::ImagePairRegistration::m_Xform, cmtk::ImagePairNonrigidRegistration::MakeWarpXform(), NULL, and cmtk::WarpXform::Spacing.

CallbackResult cmtk::ImagePairNonrigidRegistrationCommandLine::InitRegistration

(

)

[protected, virtual, inherited]

Initialize registration.

So far, this function has no effect other than calling the equivalent inherited function.

Reimplemented from cmtk::ImagePairNonrigidRegistration.

Definition at line 326 of file cmtkImagePairNonrigidRegistrationCommandLine.cxx.

References cmtk::CALLBACK_OK, and cmtkImagePairNonrigidRegistrationCommandLineDispatchSIGUSR1().

CallbackResult cmtk::ImagePairRegistration::InitRegistration

(

)

[protected, virtual, inherited]

Initialize registration.

This function is called by Register before any other operations. It can be overloaded to open status dialog windows, etc. Derived implementations should call their base class' InitRegistration first.

Returns:

Reimplemented in cmtk::ImagePairAffineRegistration, cmtk::ImagePairAffineRegistrationCommandLine, cmtk::ImagePairNonrigidRegistration, and cmtk::ImagePairNonrigidRegistrationCommandLine.

Definition at line 83 of file cmtkImagePairRegistration.cxx.

References cmtk::CALLBACK_OK, cmtk::Timers::GetTimeProcess(), cmtk::Timers::GetTimeThread(), cmtk::Timers::GetWalltime(), cmtk::ImagePairRegistration::m_AutoMultiLevels, cmtk::ImagePairRegistration::m_MaxStepSize, cmtk::ImagePairRegistration::m_MinStepSize, cmtk::ImagePairRegistration::m_Sampling, cmtk::ImagePairRegistration::m_ThreadTimeStartLevel, cmtk::ImagePairRegistration::m_ThreadTimeStartRegistration, cmtk::ImagePairRegistration::m_TimeStartLevel, cmtk::ImagePairRegistration::m_TimeStartRegistration, cmtk::ImagePairRegistration::m_WalltimeStartLevel, and cmtk::ImagePairRegistration::m_WalltimeStartRegistration.

Referenced by cmtk::ImagePairNonrigidRegistration::InitRegistration(), cmtk::ImagePairAffineRegistration::InitRegistration(), and cmtk::ImagePairRegistration::Register().

CallbackResult cmtk::ElasticRegistration::InitRegistration

(

)

[protected, virtual, inherited]

Initialize registration.

This function is called by Register before any other operations. It can be overloaded to open status dialog windows, etc. Derived implementations should call their base class' InitRegistration first.

Returns:

Reimplemented from cmtk::VoxelRegistration.

Reimplemented in cmtk::ElasticRegistrationCommandLine.

Definition at line 90 of file cmtkElasticRegistration.cxx.

References cmtk::VoxelRegistration::CoarsestResolution, cmtk::SmartPointer< Self >::DynamicCastFrom(), cmtk::VoxelRegistration::FunctionalStack, cmtk::ElasticRegistration::IgnoreEdge, cmtk::ElasticRegistration::InitialWarpXform, cmtk::VoxelRegistration::InitRegistration(), cmtk::ElasticRegistration::InverseWarpXform, cmtk::VoxelRegistration::m_Optimizer, cmtk::VoxelRegistration::m_Xform, cmtk::ElasticRegistration::MakeFunctional(), cmtk::ElasticRegistration::MakeWarpXform(), NULL, cmtk::VoxelRegistration::OptimizerStepFactor, cmtk::WarpXform::Spacing, and cmtk::VoxelRegistration::UseMaxNorm.

template<class TMultiChannelMetricFunctional >

void cmtk::AffineMultiChannelRegistrationFunctional< TMultiChannelMetricFunctional >::InitTransformation

(

const bool

alignCenters )

[inherited]

Initialize transformation.

Definition at line 45 of file cmtkAffineMultiChannelRegistrationFunctional.txx.

References cmtk::FixedVector< NDIM, T >::begin(), and cmtk::StdErr.

template<class TMetricFunctional >

void cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::InitTransformation	(	const Vector3D &	domain,
		const Types::Coordinate	gridSpacing,
		const bool	exact
	)		[virtual, inherited]

Initialize transformation.

Definition at line 78 of file cmtkSplineWarpMultiChannelRegistrationFunctional.txx.

References cmtk::StdErr.

void cmtk::GroupwiseRegistrationFunctionalBase::InterpolateAllImages

(

)

[protected, virtual, inherited]

Interpolate all moving images.

By default, this only calls InterpolateImage() for each image. However, this functionality can be overriden for better efficiency, for example in the distributed MPI implementation.

Definition at line 444 of file cmtkGroupwiseRegistrationFunctionalBase.cxx.

template<class TXform >

void cmtk::GroupwiseRegistrationFunctionalXformTemplate< TXform >::InterpolateImage	(	const size_t	idx,
		byte *const	destination
	)		[protected, virtual, inherited]

Interpolate given moving image to template.

Parameters:

idx	Index of of to reformat to template. This also determines which transformation is used.
destination	The reformatted pixel data is stored in this array. Sufficient memory (for as many pixels as there are in the template grid) must be allocated there.

Reimplemented from cmtk::GroupwiseRegistrationFunctionalBase.

Definition at line 63 of file cmtkGroupwiseRegistrationFunctionalXformTemplate.cxx.

References cmtk::ThreadPool::Run().

template<class TXform >

void cmtk::GroupwiseRegistrationFunctionalXformTemplate< TXform >::InterpolateImageProbabilisticThread	(	void *const	args,
		const size_t	taskIdx,
		const size_t	taskCnt,
		const size_t	threadIdx,
		const size_t	threadCont
	)		[static, private, inherited]

Image interpolation thread function with probabilistic sampling.

Definition at line 147 of file cmtkGroupwiseRegistrationFunctionalXformTemplate.cxx.

References cmtk::GroupwiseRegistrationFunctionalXformTemplate< TXform >::InterpolateImageThreadParameters::m_Destination, cmtk::GroupwiseRegistrationFunctionalXformTemplate< TXform >::InterpolateImageThreadParameters::m_Idx, cmtk::GroupwiseRegistrationFunctionalXformTemplate< TXform >::InterpolateImageThreadParameters::m_NumberOfOutsidePixels, cmtk::UniformVolume::ProbeData(), and cmtk::ThreadParameters< T >::thisObject.

template<class TXform >

void cmtk::GroupwiseRegistrationFunctionalXformTemplate< TXform >::InterpolateImageThread	(	void *const	args,
		const size_t	taskIdx,
		const size_t	taskCnt,
		const size_t	threadIdx,
		const size_t	threadCont
	)		[static, private, inherited]

Image interpolation thread function.

Definition at line 95 of file cmtkGroupwiseRegistrationFunctionalXformTemplate.cxx.

References cmtk::AXIS_X, cmtk::AXIS_Y, cmtk::AXIS_Z, cmtk::GroupwiseRegistrationFunctionalXformTemplate< TXform >::InterpolateImageThreadParameters::m_Destination, cmtk::GroupwiseRegistrationFunctionalXformTemplate< TXform >::InterpolateImageThreadParameters::m_Idx, cmtk::GroupwiseRegistrationFunctionalXformTemplate< TXform >::InterpolateImageThreadParameters::m_NumberOfOutsidePixels, cmtk::UniformVolume::ProbeData(), and cmtk::ThreadParameters< T >::thisObject.

Functional * cmtk::ImagePairAffineRegistration::MakeFunctional	(	const int	level,
		const Superclass::LevelParameters *	parameters
	)		[private, virtual, inherited]

Create functional with all settings for next level.

Implements cmtk::ImagePairRegistration.

Definition at line 137 of file cmtkImagePairAffineRegistration.cxx.

References cmtk::ImagePairAffineRegistrationFunctional::Create(), cmtk::SmartPointer< Self >::DynamicCastFrom(), cmtk::ImagePairAffineRegistration::LevelParameters::m_Resolution, cmtk::ImagePairRegistrationFunctional::SetForceOutside(), and cmtk::StdErr.

Functional * cmtk::ElasticRegistration::MakeFunctional	(	UniformVolume::SmartPtr &	refVolume,
		UniformVolume::SmartPtr &	fltVolume,
		UniformVolume::SmartPtr &	rigidityMap
	)		const [private, inherited]

Create functional with all settings and two given volume objects.

Todo:

Currently, if a tissue property map is used for local constraint weights, this cannot be used with edge volumes. This is because this function has access to the resampled edge data in such a case, but not to the actual image intensities of the resmpled image. The latter is required for the tissue property map. Potentially, we could create the entire map outside this function and give it as an additional optional parameter. But since we're using neither edge images nor tissue maps much, it doesn't seem worth the effort.

Definition at line 216 of file cmtkElasticRegistration.cxx.

References cmtk::CreateElasticFunctional(), cmtk::CreateSymmetricElasticFunctional(), cmtk::SymmetricElasticFunctional::SetAdaptiveFixParameters(), cmtk::SymmetricElasticFunctional::SetAdaptiveFixThreshFactor(), cmtk::VoxelMatchingElasticFunctional::SetForceOutside(), cmtk::SymmetricElasticFunctional::SetGridEnergyWeight(), cmtk::SymmetricElasticFunctional::SetInverseConsistencyWeight(), cmtk::SymmetricElasticFunctional::SetJacobianConstraintWeight(), and cmtk::SymmetricElasticFunctional::SetRigidityConstraintWeight().

Referenced by cmtk::ElasticRegistration::InitRegistration().

Functional * cmtk::ImagePairNonrigidRegistration::MakeFunctional	(	const int	level,
		const Superclass::LevelParameters *	levelParameters
	)		[private, virtual, inherited]

Create functional with current level settings.

Implements cmtk::ImagePairRegistration.

Definition at line 192 of file cmtkImagePairNonrigidRegistration.cxx.

References cmtk::ImagePairNonrigidRegistrationFunctional::Create(), cmtk::ImagePairSymmetricNonrigidRegistrationFunctional::Create(), cmtk::SmartPointer< Self >::DynamicCastFrom(), cmtk::ImagePairNonrigidRegistration::LevelParameters::m_Resolution, cmtk::Interpolators::NEAREST_NEIGHBOR, cmtk::ImagePairSymmetricNonrigidRegistrationFunctional::SetAdaptiveFixParameters(), cmtk::ImagePairSymmetricNonrigidRegistrationFunctional::SetAdaptiveFixThreshFactor(), cmtk::ImagePairRegistrationFunctional::SetForceOutside(), cmtk::ImagePairSymmetricNonrigidRegistrationFunctional::SetGridEnergyWeight(), cmtk::ImagePairSymmetricNonrigidRegistrationFunctional::SetInverseConsistencyWeight(), cmtk::ImagePairSymmetricNonrigidRegistrationFunctional::SetJacobianConstraintWeight(), and cmtk::StdErr.

const UniformVolume::SmartPtr cmtk::ReformatVolume::MakeTargetVolume

(

)

const [private, inherited]

Make target volume matching (reoriented) reference volume.

Definition at line 103 of file cmtkReformatVolume.cxx.

References cmtk::ReformatVolume::ReferenceVolume.

Referenced by cmtk::ReformatVolume::PlainReformat().

const SplineWarpXform::SmartPtr cmtk::ElasticRegistration::MakeWarpXform	(	const Vector3D &	size,
		const AffineXform *	initialAffine
	)		const [private, inherited]

Create warp transformation with current settings.

This function is used to create the standard warp, as well as the approximated inverse warp for the optional inverse-consistent registration.

Parameters:

size	Reference volume size.
initialAffine	Initial affine transformation for the warp.

Definition at line 203 of file cmtkElasticRegistration.cxx.

Referenced by cmtk::ElasticRegistration::InitRegistration().

SplineWarpXform::SmartPtr cmtk::ImagePairNonrigidRegistration::MakeWarpXform	(	const UniformVolume::CoordinateVectorType &	size,
		const AffineXform *	initialAffine
	)		const [private, inherited]

Create warp transformation with current settings.

This function is used to create the standard warp, as well as the approximated inverse warp for the optional inverse-consistent registration.

Parameters:

size	Reference volume size.
initialAffine	Initial affine transformation for the warp.

Definition at line 180 of file cmtkImagePairNonrigidRegistration.cxx.

Referenced by cmtk::ImagePairNonrigidRegistration::InitRegistration().

template<class TInterpolator >

bool cmtk::ReformatVolume::Plain::operator()	(	Types::DataItem &	value,
		const Vector3D &	inRef,
		const XformList &	refToFloat,
		TInterpolator &	interpolator
	)		[inherited]

Reimplemented in cmtk::ReformatVolume::Jacobian.

Definition at line 46 of file cmtkReformatVolumePlain.txx.

template<class TInterpolator >

bool cmtk::ReformatVolume::Jacobian::operator()	(	Types::DataItem &	value,
		const Vector3D &	inRef,
		const XformList &	refToFloat,
		TInterpolator &
	)		[inherited]

Reimplemented from cmtk::ReformatVolume::Plain.

Definition at line 45 of file cmtkReformatVolumeJacobian.txx.

References cmtk::XformList::GetJacobian().

template<class TDataType , class TInterpolator , class THashKeyType , char NBitsPerChannel>

void cmtk::MultiChannelHistogramRegistrationFunctional< TDataType, TInterpolator, THashKeyType, NBitsPerChannel >::MetricData::operator+=

(

const Types::DataItem *

values )

[inherited]

In-place single sample addition operator.

Definition at line 121 of file cmtkMultiChannelHistogramRegistrationFunctionalMetricData.txx.

template<class TRealType , class TDataType , class TInterpolator >

void cmtk::MultiChannelRMIRegistrationFunctional< TRealType, TDataType, TInterpolator >::MetricData::operator+=

(

const Types::DataItem *

values )

[inherited]

In-place single sample addition operator.

Definition at line 128 of file cmtkMultiChannelRMIRegistrationFunctionalMetricData.txx.

template<class TDataType , class TInterpolator , class THashKeyType , char NBitsPerChannel>

void cmtk::MultiChannelHistogramRegistrationFunctional< TDataType, TInterpolator, THashKeyType, NBitsPerChannel >::MetricData::operator-=

(

const Types::DataItem *

values )

[inherited]

In-place single sample subtraction operator.

Definition at line 146 of file cmtkMultiChannelHistogramRegistrationFunctionalMetricData.txx.

template<class TRealType , class TDataType , class TInterpolator >

void cmtk::MultiChannelRMIRegistrationFunctional< TRealType, TDataType, TInterpolator >::MetricData::operator-=

(

const Types::DataItem *

values )

[inherited]

In-place single sample subtraction operator.

Definition at line 151 of file cmtkMultiChannelRMIRegistrationFunctionalMetricData.txx.

ClassStream & cmtk::operator<<	(	ClassStream &	stream,
		const GroupwiseRegistrationFunctionalXformTemplate< AffineXform > &	func
	)

Definition at line 47 of file cmtkGroupwiseRegistrationFunctionalXformTemplate_Affine_IO.cxx.

References cmtk::TypedStream::Begin(), cmtk::TypedStream::End(), cmtk::META_FS_PATH, cmtk::TypedStream::WriteCoordinateArray(), cmtk::TypedStream::WriteIntArray(), and cmtk::TypedStream::WriteString().

ClassStream & cmtk::operator<<	(	ClassStream &	stream,
		const GroupwiseRegistrationFunctionalXformTemplate< SplineWarpXform > &	func
	)

Definition at line 48 of file cmtkGroupwiseRegistrationFunctionalXformTemplate_SplineWarp_IO.cxx.

References cmtk::TypedStream::Begin(), cmtk::TypedStream::End(), cmtk::META_FS_PATH, cmtk::TypedStream::WriteCoordinateArray(), cmtk::TypedStream::WriteIntArray(), and cmtk::TypedStream::WriteString().

ClassStream & cmtk::operator>>	(	ClassStream &	stream,
		GroupwiseRegistrationFunctionalXformTemplate< SplineWarpXform > &	func
	)

Definition at line 68 of file cmtkGroupwiseRegistrationFunctionalXformTemplate_SplineWarp_IO.cxx.

References cmtk::TypedStream::End(), NULL, cmtk::TypedStream::ReadCoordinateArray(), cmtk::TypedStream::ReadIntArray(), cmtk::TypedStream::ReadString(), cmtk::TypedStream::Seek(), and cmtk::StdErr.

ClassStream & cmtk::operator>>	(	ClassStream &	stream,
		GroupwiseRegistrationFunctionalXformTemplate< AffineXform > &	func
	)

Definition at line 67 of file cmtkGroupwiseRegistrationFunctionalXformTemplate_Affine_IO.cxx.

References cmtk::TypedStream::End(), NULL, cmtk::TypedStream::ReadCoordinateArray(), cmtk::TypedStream::ReadIntArray(), cmtk::TypedStream::ReadString(), cmtk::TypedStream::Seek(), and cmtk::StdErr.

CallbackResult cmtk::IterativeDirectionOptimizer::Optimize	(	CoordinateVector &	v,
		const Types::Coordinate	exploration = 1,
		const Types::Coordinate	accuracy = 0
	)		[virtual, inherited]

Perform the optimization.

Definition at line 48 of file cmtkIterativeDirectionOptimizer.cxx.

References cmtk::CALLBACK_OK.

CallbackResult cmtk::MultiLevelOptimizer::Optimize	(	CoordinateVector &	v,
		const Types::Coordinate	= 1,
		const Types::Coordinate	= 0
	)		[virtual, inherited]

Perform the optimization.

Definition at line 45 of file cmtkMultiLevelOptimizer.cxx.

References cmtk::CALLBACK_OK.

CallbackResult cmtk::BestDirectionOptimizer::Optimize	(	CoordinateVector &	v,
		const Self::ParameterType	exploration = 1,
		const Self::ParameterType	accuracy = 0
	)		[virtual, inherited]

Optimize functional.

Implements cmtk::Optimizer.

Definition at line 50 of file cmtkBestDirectionOptimizer.cxx.

References cmtk::CALLBACK_OK, cmtk::Vector< T >::Dim, cmtk::Vector< T >::EuclidNorm(), cmtk::Vector< T >::MaxNorm(), cmtk::Console::printf(), and cmtk::StdErr.

CallbackResult cmtk::BestNeighbourOptimizer::Optimize	(	CoordinateVector &	v,
		const Self::ParameterType	exploration = 1,
		const Self::ParameterType	accuracy = 0
	)		[virtual, inherited]

Perform the optimization.

Implements cmtk::Optimizer.

Definition at line 51 of file cmtkBestNeighbourOptimizer.cxx.

References cmtk::CALLBACK_OK, cmtk::SearchTrace< R >::Get(), and cmtk::SearchTrace< R >::Move().

Referenced by cmtk::Registration2d2d::Register(), and cmtk::ImageSymmetryPlaneCommandLineBase::Run().

void cmtk::ElasticRegistrationCommandLine::OutputIntermediate

(

const bool

incrementCount = true )

[inherited]

Write intermediate deformation file.

Definition at line 552 of file cmtkElasticRegistrationCommandLine.cxx.

void cmtk::ImagePairNonrigidRegistrationCommandLine::OutputIntermediate

(

const bool

incrementCount = true )

[inherited]

Write intermediate deformation file.

Definition at line 478 of file cmtkImagePairNonrigidRegistrationCommandLine.cxx.

void cmtk::ElasticRegistrationCommandLine::OutputResult

(

const CoordinateVector *

)

[protected, virtual, inherited]

Output registration result.

This function write the transformation that was found to a studylist archive with the name provided by command line arguments. The result is also printed to stderr in parameter list form.

Reimplemented from cmtk::VoxelRegistration.

Definition at line 384 of file cmtkElasticRegistrationCommandLine.cxx.

References cmtk::ImageXformDB::AddImage(), cmtk::ImageXformDB::AddImagePairXform(), cmtk::ImageXformDB::AddRefinedXform(), cmtk::META_FS_PATH, cmtk::StdErr, and cmtk::Exception::what().

virtual void cmtk::ImagePairRegistration::OutputResult

(

const CoordinateVector *

v )

[inline, protected, virtual, inherited]

Output registration result.

This function is called after finishing registration. It can overloaded to report the resulting transformation, export it to an encapsulating application, etc...

Parameters:

v	The vector of resulting transformation parameters.

Reimplemented in cmtk::ImagePairAffineRegistrationCommandLine, and cmtk::ImagePairNonrigidRegistrationCommandLine.

Definition at line 294 of file cmtkImagePairRegistration.h.

Referenced by cmtk::ImagePairRegistration::Register().

virtual void cmtk::VoxelRegistration::OutputResult

(

const CoordinateVector *

v )

[inline, protected, virtual, inherited]

Output registration result.

This function is called after finishing registration. It can overloaded to report the resulting transformation, export it to an encapsulating application, etc...

Parameters:

v	The vector of resulting transformation parameters.

Reimplemented in cmtk::AffineRegistrationCommandLine, and cmtk::ElasticRegistrationCommandLine.

Definition at line 247 of file cmtkVoxelRegistration.h.

Referenced by cmtk::VoxelRegistration::Register().

void cmtk::ImagePairAffineRegistrationCommandLine::OutputResult

(

const CoordinateVector *

v )

[protected, virtual, inherited]

Output registration result.

This function write the transformation that was found to a studylist archive with the name provided by command line arguments. The result is also printed to stderr in parameter list form.

Reimplemented from cmtk::ImagePairRegistration.

Definition at line 450 of file cmtkImagePairAffineRegistrationCommandLine.cxx.

References cmtk::ImageXformDB::AddImage(), cmtk::ImageXformDB::AddImagePairXform(), cmtk::ImageXformDB::AddRefinedXform(), cmtk::Vector< T >::Dim, cmtk::Vector< T >::Elements, cmtk::ImagePairAffineRegistration::GetReformattedFloatingImage(), cmtk::TransformChangeToSpaceAffine::GetTransformation(), cmtk::ImagePairAffineRegistration::GetTransformation(), cmtk::ImagePairAffineRegistrationCommandLine::m_InitialXformPath, cmtk::ImagePairAffineRegistrationCommandLine::m_OutputPathITK, cmtk::ImagePairAffineRegistrationCommandLine::m_ReformattedImagePath, cmtk::META_FS_PATH, cmtk::ImagePairAffineRegistrationCommandLine::OutMatrixName, cmtk::ImagePairAffineRegistrationCommandLine::OutParametersName, cmtk::ImagePairAffineRegistrationCommandLine::OutputResultList(), cmtk::ImagePairAffineRegistrationCommandLine::OutputResultMatrix(), cmtk::ImagePairAffineRegistrationCommandLine::OutputResultParameters(), cmtk::AnatomicalOrientationBase::SPACE_ITK, cmtk::StdErr, cmtk::ImagePairAffineRegistrationCommandLine::Studylist, cmtk::ImagePairAffineRegistrationCommandLine::Verbose, cmtk::Exception::what(), cmtk::VolumeIO::Write(), and cmtk::AffineXformITKIO::Write().

void cmtk::AffineRegistrationCommandLine::OutputResult

(

const CoordinateVector *

v )

[protected, virtual, inherited]

Output registration result.

This function write the transformation that was found to a studylist archive with the name provided by command line arguments. The result is also printed to stderr in parameter list form.

Reimplemented from cmtk::VoxelRegistration.

Definition at line 441 of file cmtkAffineRegistrationCommandLine.cxx.

References cmtk::ImageXformDB::AddImage(), cmtk::ImageXformDB::AddImagePairXform(), cmtk::ImageXformDB::AddRefinedXform(), cmtk::Vector< T >::Dim, cmtk::Vector< T >::Elements, cmtk::AffineRegistration::GetReformattedFloatingImage(), cmtk::TransformChangeToSpaceAffine::GetTransformation(), cmtk::AffineRegistration::GetTransformation(), cmtk::AffineRegistrationCommandLine::m_InitialXformPath, cmtk::AffineRegistrationCommandLine::m_OutputPathITK, cmtk::AffineRegistrationCommandLine::m_ReformattedImagePath, cmtk::META_FS_PATH, cmtk::AffineRegistrationCommandLine::OutMatrixName, cmtk::AffineRegistrationCommandLine::OutParametersName, cmtk::AffineRegistrationCommandLine::OutputResultList(), cmtk::AffineRegistrationCommandLine::OutputResultMatrix(), cmtk::AffineRegistrationCommandLine::OutputResultParameters(), cmtk::AnatomicalOrientationBase::SPACE_ITK, cmtk::StdErr, cmtk::AffineRegistrationCommandLine::Studylist, cmtk::AffineRegistrationCommandLine::Verbose, cmtk::Exception::what(), cmtk::VolumeIO::Write(), and cmtk::AffineXformITKIO::Write().

void cmtk::ImagePairNonrigidRegistrationCommandLine::OutputResult

(

const CoordinateVector *

)

[protected, virtual, inherited]

Output registration result.

This function write the transformation that was found to a studylist archive with the name provided by command line arguments. The result is also printed to stderr in parameter list form.

Reimplemented from cmtk::ImagePairRegistration.

Definition at line 347 of file cmtkImagePairNonrigidRegistrationCommandLine.cxx.

void cmtk::ImagePairAffineRegistrationCommandLine::OutputResultList

(

const char *

studyList )

const [private, inherited]

Output result (and statistics) as studylist archive.

Definition at line 387 of file cmtkImagePairAffineRegistrationCommandLine.cxx.

References cmtk::TypedStream::Begin(), cmtk::TypedStream::Close(), cmtk::TypedStream::End(), cmtk::CompressedStream::GetBaseName(), cmtk::MakeInitialAffineTransformation::GetModeName(), cmtk::ImagePairRegistration::GetThreadTotalElapsedTime(), cmtk::ImagePairRegistration::GetTotalElapsedTime(), cmtk::ImagePairRegistration::GetTotalElapsedWalltime(), cmtk::ImagePairAffineRegistration::GetTransformation(), cmtk::TypedStream::IsValid(), cmtk::ImagePairRegistration::m_CoarsestResolution, cmtk::ImagePairRegistration::m_MaxStepSize, cmtk::ImagePairRegistration::m_Metric, cmtk::ImagePairRegistration::m_MinStepSize, cmtk::ImagePairRegistration::m_OptimizerStepFactor, cmtk::ImagePairRegistration::m_PreprocessorFlt, cmtk::ImagePairRegistration::m_PreprocessorRef, cmtk::ImagePairRegistration::m_Sampling, cmtk::ClassStream::Open(), cmtk::ImagePairAffineRegistrationCommandLine::Study1, cmtk::ImagePairAffineRegistrationCommandLine::Study2, cmtk::ClassStream::WRITE, cmtk::TypedStream::WriteDouble(), cmtk::TypedStream::WriteInt(), cmtk::ImagePairRegistration::ImagePreprocessor::WriteSettings(), and cmtk::TypedStream::WriteString().

Referenced by cmtk::ImagePairAffineRegistrationCommandLine::OutputResult().

void cmtk::AffineRegistrationCommandLine::OutputResultList

(

const char *

studyList )

const [private, inherited]

Output result (and statistics) as studylist archive.

Definition at line 378 of file cmtkAffineRegistrationCommandLine.cxx.

References cmtk::TypedStream::Begin(), cmtk::TypedStream::Close(), cmtk::VoxelRegistration::CoarsestResolution, cmtk::TypedStream::End(), cmtk::CompressedStream::GetBaseName(), cmtk::VoxelRegistration::GetThreadTotalElapsedTime(), cmtk::VoxelRegistration::GetTotalElapsedTime(), cmtk::VoxelRegistration::GetTotalElapsedWalltime(), cmtk::AffineRegistration::GetTransformation(), cmtk::TypedStream::IsValid(), cmtk::VoxelRegistration::m_PreprocessorFlt, cmtk::VoxelRegistration::m_PreprocessorRef, cmtk::ClassStream::Open(), cmtk::VoxelRegistration::OptimizerStepFactor, cmtk::AffineRegistrationCommandLine::Study1, cmtk::AffineRegistrationCommandLine::Study2, cmtk::ClassStream::WRITE, cmtk::TypedStream::WriteBool(), cmtk::TypedStream::WriteDouble(), cmtk::TypedStream::WriteInt(), cmtk::VoxelRegistration::ImagePreprocessor::WriteSettings(), and cmtk::TypedStream::WriteString().

Referenced by cmtk::AffineRegistrationCommandLine::OutputResult().

void cmtk::AffineRegistrationCommandLine::OutputResultMatrix

(

const char *

matrixName )

const [private, inherited]

Output result as matrix (text) file.

Definition at line 348 of file cmtkAffineRegistrationCommandLine.cxx.

References cmtk::AffineRegistration::GetTransformation().

Referenced by cmtk::AffineRegistrationCommandLine::OutputResult().

void cmtk::ImagePairAffineRegistrationCommandLine::OutputResultMatrix

(

const char *

matrixName )

const [private, inherited]

Output result as matrix (text) file.

Definition at line 357 of file cmtkImagePairAffineRegistrationCommandLine.cxx.

References cmtk::ImagePairAffineRegistration::GetTransformation().

Referenced by cmtk::ImagePairAffineRegistrationCommandLine::OutputResult().

void cmtk::ImagePairAffineRegistrationCommandLine::OutputResultParameters	(	const char *	paramsName,
		const CoordinateVector &	v
	)		const [private, inherited]

Output result (and statistics) as studylist archive.

Definition at line 375 of file cmtkImagePairAffineRegistrationCommandLine.cxx.

References cmtk::Vector< T >::Dim, and cmtk::Vector< T >::Elements.

Referenced by cmtk::ImagePairAffineRegistrationCommandLine::OutputResult().

void cmtk::AffineRegistrationCommandLine::OutputResultParameters	(	const char *	paramsName,
		const CoordinateVector &	v
	)		const [private, inherited]

Output result (and statistics) as studylist archive.

Definition at line 366 of file cmtkAffineRegistrationCommandLine.cxx.

References cmtk::Vector< T >::Dim, and cmtk::Vector< T >::Elements.

Referenced by cmtk::AffineRegistrationCommandLine::OutputResult().

void cmtk::ElasticRegistrationCommandLine::OutputWarp

(

const char *

path )

const [private, inherited]

Write deformation to studylist archive.

Definition at line 453 of file cmtkElasticRegistrationCommandLine.cxx.

References cmtk::TypedStream::Begin(), cmtk::TypedStream::Close(), cmtk::TypedStream::End(), cmtk::Threads::GetNumberOfProcessors(), cmtk::TypedStream::IsValid(), cmtk::Threads::NumberOfThreads, cmtk::ClassStream::Open(), cmtk::TypedStream::WriteBool(), cmtk::TypedStream::WriteDouble(), cmtk::TypedStream::WriteInt(), and cmtk::TypedStream::WriteString().

void cmtk::ImagePairNonrigidRegistrationCommandLine::OutputWarp

(

const char *

path )

const [private, inherited]

Write deformation to studylist archive.

Definition at line 385 of file cmtkImagePairNonrigidRegistrationCommandLine.cxx.

References cmtk::TypedStream::Begin(), cmtk::TypedStream::Close(), cmtk::TypedStream::End(), cmtk::Threads::GetNumberOfProcessors(), cmtk::TypedStream::IsValid(), cmtk::Threads::NumberOfThreads, cmtk::ClassStream::Open(), cmtk::TypedStream::WriteBool(), cmtk::TypedStream::WriteDouble(), cmtk::TypedStream::WriteInt(), and cmtk::TypedStream::WriteString().

template<class W>

virtual size_t cmtk::VoxelMatchingElasticFunctional_WarpTemplate< W >::ParamVectorDim

(

)

const [inline, virtual, inherited]

Return the transformation's parameter vector dimension.

Implements cmtk::Functional.

Definition at line 298 of file cmtkVoxelMatchingElasticFunctional.h.

bool cmtk::ImageSymmetryPlaneCommandLineBase::ParseCommandLine	(	const int	argc,
		const char *	argv[]
	)		[private, inherited]

Parse the given command line.

Definition at line 269 of file cmtkImageSymmetryPlaneCommandLineBase.cxx.

References cmtk::ParametricPlane::GetRho(), cmtk::TypedStream::IsValid(), NULL, cmtk::Console::printf(), cmtk::ClassStream::READ, and cmtk::StdErr.

TypedArray::SmartPtr cmtk::ReformatVolume::PlainReformat	(	const int	plane,
		TypedArray::SmartPtr &	target = TypedArray::SmartPtr::Null,
		const size_t	targetOffset = 0
	)		[inherited]

Plain reformatting of a single plane.

This function reformats the floating data to a plane spatially identical to the given plane in the reference image. This is useful for interactive reformatting, where we want a single plane reformatted as fast as possible.

Definition at line 177 of file cmtkReformatVolume.cxx.

References cmtk::TypedArray::Create(), cmtk::SmartConstPointer< Self >::DynamicCastFrom(), and cmtk::SplineWarpXformUniformVolume::GetTransformedGrid().

const UniformVolume::SmartPtr cmtk::ReformatVolume::PlainReformat

(

)

[inherited]

Plain reformatting.

Definition at line 109 of file cmtkReformatVolume.cxx.

References cmtk::AXIS_Z, cmtk::Progress::Begin(), cmtk::TypedArray::Create(), cmtk::ReformatVolume::CreateInterpolator(), cmtk::SmartConstPointer< Self >::DynamicCastFrom(), cmtk::ReformatVolume::FloatingVolume, cmtk::SplineWarpXformUniformVolume::GetTransformedGrid(), cmtk::ReformatVolume::m_AffineXform, cmtk::ReformatVolume::m_WarpXform, cmtk::ReformatVolume::MakeTargetVolume(), cmtk::ReformatVolume::ReferenceVolume, and cmtk::Progress::SetProgress().

Referenced by cmtk::ImagePairNonrigidRegistration::GetReformattedFloatingImage(), cmtk::ImagePairAffineRegistration::GetReformattedFloatingImage(), cmtk::ElasticRegistration::GetReformattedFloatingImage(), cmtk::AffineRegistration::GetReformattedFloatingImage(), cmtk::GroupwiseRegistrationFunctionalBase::GetReformattedImage(), cmtk::AtlasSegmentation::ReformatLabels(), and cmtk::GroupwiseRegistrationOutput::WriteAverageImage().

template<class T , ScalarDataType DT>

void cmtk::VoxelMatchingMetric_Type< T, DT >::ImageData::PrecomputeIncrements

(

const UniformVolume *

volume )

[inherited]

Precompute grid increments.

Definition at line 194 of file cmtkVoxelMatchingMetric_Type.cxx.

References cmtk::DataGrid::GetDims().

Referenced by cmtk::VoxelMatchingMetric_Type< byte, DT >::SetDataX().

UniformVolume::SmartPtr cmtk::GroupwiseRegistrationFunctionalBase::PrepareSingleImage

(

UniformVolume::SmartPtr &

image )

[protected, virtual, inherited]

Prepare data for one image.

Reimplemented in cmtk::GroupwiseRegistrationFunctionalXformTemplateBase< TXform >, cmtk::GroupwiseRegistrationFunctionalXformTemplateBase< SplineWarpXform >, and cmtk::GroupwiseRegistrationFunctionalXformTemplateBase< AffineXform >.

Definition at line 247 of file cmtkGroupwiseRegistrationFunctionalBase.cxx.

References cmtk::UniformVolumeFilter::GetDataGaussFiltered(), and cmtk::META_FS_PATH.

template<class TXform >

UniformVolume::SmartPtr cmtk::GroupwiseRegistrationFunctionalXformTemplateBase< TXform >::PrepareSingleImage

(

UniformVolume::SmartPtr &

image )

[private, virtual, inherited]

Prepare data for one image.

Reimplemented from cmtk::GroupwiseRegistrationFunctionalBase.

Definition at line 83 of file cmtkGroupwiseRegistrationFunctionalXformTemplateBase.cxx.

References cmtk::TYPE_BYTE.

template<class TXform >

void cmtk::GroupwiseRegistrationFunctionalXformTemplateBase< TXform >::PrepareTargetImages

(

)

[private, virtual, inherited]

Smooth and pre-scale target images.

Reimplemented from cmtk::GroupwiseRegistrationFunctionalBase.

Definition at line 102 of file cmtkGroupwiseRegistrationFunctionalXformTemplateBase.cxx.

void cmtk::GroupwiseRegistrationFunctionalBase::PrepareTargetImages

(

)

[protected, virtual, inherited]

Smooth and pre-scale target images.

Reimplemented in cmtk::GroupwiseRegistrationFunctionalXformTemplateBase< TXform >, cmtk::GroupwiseRegistrationFunctionalXformTemplateBase< SplineWarpXform >, and cmtk::GroupwiseRegistrationFunctionalXformTemplateBase< AffineXform >.

Definition at line 285 of file cmtkGroupwiseRegistrationFunctionalBase.cxx.

UniformVolume::SmartPtr cmtk::ImagePairSimilarityJointHistogram::PrescaleData	(	const UniformVolume::SmartConstPtr &	volume,
		size_t *	numberOfBins,
		Types::DataItem *	scaleFactor,
		Types::DataItem *	scaleOffset
	)		[private, inherited]

Duplicate and pre-scale image data so that we have the histogram bin numbers readily available.

Returns:

A new volume with the same geometry as the input volume, but for DATACLASS_GREY, all pixel values will have been rescaled to represent histogram bin indexes directly.

Parameters:

volume	Input volume.
numberOfBins	Output: number of bins that the histogram should allocate for the output volume.
scaleFactor	Data scaling factor.
scaleOffset	Data scaling offset.

Definition at line 66 of file cmtkImagePairSimilarityJointHistogram.cxx.

References cmtk::DATACLASS_GREY, cmtk::DATACLASS_LABEL, cmtk::StdErr, and cmtk::TYPE_ITEM.

cmtk::ProtocolCallback::ProtocolCallback	(	const char *	filename = NULL,
		const bool	debug = false
	)		[inherited]

Open protocol stream if filename is given.

Definition at line 44 of file cmtkProtocolCallback.cxx.

References NULL.

template<class TMetricFunctional >

void cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::RefineTransformation

(

)

[virtual, inherited]

Refine transformation control point grid by factor 2.

Definition at line 98 of file cmtkSplineWarpMultiChannelRegistrationFunctional.txx.

void cmtk::SplineWarpCongealingFunctional::RefineTransformationGrids

(

)

[virtual, inherited]

Refine transformation control point grids.

Reimplemented from cmtk::GroupwiseRegistrationFunctionalXformTemplate< SplineWarpXform >.

Definition at line 75 of file cmtkSplineWarpCongealingFunctional.cxx.

template<class TInterpolator , class Fct >

TypedArray::SmartPtr cmtk::ReformatVolume::ReformatMasked	(	const UniformVolume *	target,
		const cmtk::XformList &	targetToRef,
		const cmtk::XformList &	refToFloat,
		Fct &	fct,
		const UniformVolume *	floating = NULL,
		TInterpolator &	interpolator = TInterpolator::Null
	)		[static, inherited]

Complex reformat using target data as the mask.

Definition at line 43 of file cmtkReformatVolumeReformat.txx.

References cmtk::XformList::ApplyInPlace(), cmtk::TypedArray::Get(), cmtk::DataGrid::GetDims(), cmtk::UniformVolume::GetGridLocation(), and cmtk::DataGrid::GetNumberOfPixels().

template<class TInterpolator , class Fct >

TypedArray::SmartPtr cmtk::ReformatVolume::ReformatUnmasked	(	const UniformVolume *	target,
		const cmtk::XformList &	targetToRef,
		const cmtk::XformList &	refToFloat,
		Fct &	fct,
		const UniformVolume *	floating = NULL,
		TInterpolator &	interpolator = TInterpolator::Null
	)		[static, inherited]

Complex reformat without mask.

Definition at line 97 of file cmtkReformatVolumeReformat.txx.

References cmtk::XformList::ApplyInPlace(), cmtk::DataGrid::GetDims(), cmtk::UniformVolume::GetGridLocation(), and cmtk::DataGrid::GetNumberOfPixels().

cmtk::ReformatVolume::ReformatVolume

(

)

[inherited]

Default constructor.

Definition at line 65 of file cmtkReformatVolume.cxx.

References cmtk::ReformatVolume::Interpolation, and cmtk::Interpolators::LINEAR.

CallbackResult cmtk::ImagePairAffineRegistrationCommandLine::Register

(

)

[virtual, inherited]

Perform registration.

Reimplemented from cmtk::ImagePairRegistration.

Definition at line 528 of file cmtkImagePairAffineRegistrationCommandLine.cxx.

References cmtk::Timers::GetTimeProcess(), cmtk::ImagePairRegistration::Register(), and cmtk::ImagePairAffineRegistrationCommandLine::Time.

void cmtk::Registration2d2d::Register	(	CoordinateMatrix3x3 &	matrix,
		ScalarImage::SmartPtr &	refImage,
		ScalarImage::SmartPtr &	fltImage
	)		[static, inherited]

Register two 2D images.

Definition at line 74 of file cmtkRegistration2d2d.cxx.

References cmtk::Matrix3x3< T >::Compose(), cmtk::Matrix3x3< T >::Decompose(), cmtk::Vector< T >::Elements, and cmtk::BestNeighbourOptimizer::Optimize().

CallbackResult cmtk::AffineRegistrationCommandLine::Register

(

)

[virtual, inherited]

Perform registration.

Reimplemented from cmtk::VoxelRegistration.

Definition at line 519 of file cmtkAffineRegistrationCommandLine.cxx.

References cmtk::Timers::GetTimeProcess(), cmtk::VoxelRegistration::Register(), and cmtk::AffineRegistrationCommandLine::Time.

CallbackResult cmtk::ElasticRegistrationCommandLine::Register

(

)

[virtual, inherited]

Perform registration.

Reimplemented from cmtk::VoxelRegistration.

Definition at line 569 of file cmtkElasticRegistrationCommandLine.cxx.

References cmtk::Timers::GetTimeProcess().

CallbackResult cmtk::VoxelRegistration::Register

(

)

[virtual, inherited]

Do registration.

This function must be called to start the multiresolution optimization using the specified parameters.

Returns:

1 if registration was terminated by a user interrupt, 0 if registration was finished.

Reimplemented in cmtk::AffineRegistrationCommandLine, and cmtk::ElasticRegistrationCommandLine.

Definition at line 104 of file cmtkVoxelRegistration.cxx.

References cmtk::Progress::Begin(), cmtk::CALLBACK_OK, cmtk::Progress::Done(), cmtk::VoxelRegistration::DoneRegistration(), cmtk::VoxelRegistration::DoneResolution(), cmtk::VoxelRegistration::EnterResolution(), cmtk::VoxelRegistration::FunctionalStack, cmtk::VoxelRegistration::InitRegistration(), cmtk::VoxelRegistration::m_DeltaFThreshold, cmtk::VoxelRegistration::m_Optimizer, cmtk::VoxelRegistration::m_Xform, cmtk::SmartPointer< Self >::Null, cmtk::VoxelRegistration::OutputResult(), and cmtk::Progress::SetProgress().

Referenced by cmtk::VolumeInjectionReconstruction::ComputeTransformationsToPassImages(), cmtk::AffineRegistrationCommandLine::Register(), cmtk::AtlasSegmentation::RegisterAffine(), and cmtk::AtlasSegmentation::RegisterSpline().

void cmtk::Registration2d2d::Register	(	CoordinateMatrix3x3 &	matrix,
		ScalarImage::SmartPtr &	refImage,
		ScalarImage::SmartPtr &	fltImage,
		const ScalarImage::RegionType *	fltROI
	)		[static, inherited]

Register two 2D images, where the second is cropped to a given ROI.

Definition at line 54 of file cmtkRegistration2d2d.cxx.

References cmtk::AXIS_X, cmtk::AXIS_Y, cmtk::Matrix3x3< T >::Compose(), cmtk::Matrix3x3< T >::Decompose(), and cmtk::Region< NDIM, T >::From().

CallbackResult cmtk::ImagePairNonrigidRegistrationCommandLine::Register

(

)

[virtual, inherited]

Perform registration.

Reimplemented from cmtk::ImagePairRegistration.

Definition at line 496 of file cmtkImagePairNonrigidRegistrationCommandLine.cxx.

References cmtk::Timers::GetTimeProcess().

CallbackResult cmtk::ImagePairRegistration::Register

(

)

[virtual, inherited]

Do registration.

This function must be called to start the multiresolution optimization using the specified parameters.

Returns:

1 if registration was terminated by a user interrupt, 0 if registration was finished.

Reimplemented in cmtk::ImagePairAffineRegistrationCommandLine, and cmtk::ImagePairNonrigidRegistrationCommandLine.

Definition at line 112 of file cmtkImagePairRegistration.cxx.

References cmtk::Progress::Begin(), cmtk::CALLBACK_OK, cmtk::Progress::Done(), cmtk::ImagePairRegistration::DoneRegistration(), cmtk::ImagePairRegistration::DoneResolution(), cmtk::ImagePairRegistration::EnterResolution(), cmtk::ImagePairRegistration::InitRegistration(), cmtk::ImagePairRegistration::m_DeltaFThreshold, cmtk::ImagePairRegistration::m_MaxStepSize, cmtk::ImagePairRegistration::m_MinStepSize, cmtk::ImagePairRegistration::m_Optimizer, cmtk::ImagePairRegistration::m_ParameterStack, cmtk::ImagePairRegistration::m_Xform, cmtk::ImagePairRegistration::MakeFunctional(), cmtk::SmartPointer< Self >::Null, cmtk::ImagePairRegistration::OutputResult(), and cmtk::Progress::SetProgress().

Referenced by cmtk::ImagePairAffineRegistrationCommandLine::Register().

cmtk::RegistrationCallback::RegistrationCallback

(

)

[inherited]

Default constructor.

Definition at line 50 of file cmtkRegistrationCallback.cxx.

References cmtkRegistrationCallbackDispatchSIGINT().

template<cmtk::Interpolators::InterpolationEnum I>

cmtk::RegistrationJointHistogram< I >::RegistrationJointHistogram	(	const UniformVolume *	refVolume,
		const UniformVolume *	fltVolume,
		const unsigned int	numBinsX = CMTK_HISTOGRAM_AUTOBINS,
		const unsigned int	numBinsY = CMTK_HISTOGRAM_AUTOBINS,
		const Types::DataItemRange &	boundsX = Types::DataItemRange( -HUGE_VAL, HUGE_VAL ),
		const Types::DataItemRange &	boundsY = Types::DataItemRange( -HUGE_VAL, HUGE_VAL )
	)		[inherited]

Constructor.

Parameters:

refVolume	The reference (fixed) volume.
fltVolume	The floating (transformed) volume.
numBinsX	The desired number of bins to classify the reference data. If this parameter is zero (default), a suitable value is automatically determined.
numBinsY	The desired number of bins to classify the floating data. If this parameter is zero (default), a suitable value is automatically determined.
boundsX	Value range for the X data distribution. Values outside this range will be assigned to the first and last histogram bins, respectively.
boundsY	Value range for the Y data distribution. Values outside this range will be assigned to the first and last histogram bins, respectively.

Definition at line 44 of file cmtkRegistrationJointHistogram.cxx.

int cmtk::ImageSymmetryPlaneCommandLineBase::Run	(	const int	argc,
		const char *	argv[]
	)		[inherited]

Run the symmetry plane computation based on provided command line arguments.

Returns:

The return code for the symmetry plane program. This should be returned from main() via either "return" or "exit()".

Definition at line 136 of file cmtkImageSymmetryPlaneCommandLineBase.cxx.

References cmtk::Progress::Begin(), cmtk::TypedStream::Close(), cmtk::Progress::Done(), cmtk::Types::Range< T >::m_LowerBound, cmtk::Types::Range< T >::m_UpperBound, cmtk::BestNeighbourOptimizer::Optimize(), cmtk::Console::printf(), cmtk::VolumeIO::ReadOriented(), cmtk::Progress::SetProgress(), cmtk::StdErr, cmtk::XformIO::Write(), and cmtk::ClassStream::WRITE.

void cmtk::ReformatVolume::SetAffineXform

(

const AffineXform::SmartPtr &

affineXform )

[inherited]

Set affine transformation to be applied to the floating volume.

Definition at line 91 of file cmtkReformatVolume.cxx.

References cmtk::ReformatVolume::m_AffineXform.

Referenced by cmtk::ImagePairAffineRegistration::GetReformattedFloatingImage(), cmtk::AffineRegistration::GetReformattedFloatingImage(), cmtk::GroupwiseRegistrationFunctionalBase::GetReformattedImage(), and cmtk::GroupwiseRegistrationOutput::WriteAverageImage().

void cmtk::ReformatVolume::SetFloatingVolume

(

const UniformVolume::SmartConstPtr &

floatingVolume )

[inherited]

Set the floating (transformed) volume for reformatting.

Definition at line 85 of file cmtkReformatVolume.cxx.

Referenced by cmtk::ImagePairNonrigidRegistration::GetReformattedFloatingImage(), cmtk::ImagePairAffineRegistration::GetReformattedFloatingImage(), cmtk::ElasticRegistration::GetReformattedFloatingImage(), cmtk::AffineRegistration::GetReformattedFloatingImage(), cmtk::GroupwiseRegistrationFunctionalBase::GetReformattedImage(), cmtk::AtlasSegmentation::ReformatLabels(), and cmtk::GroupwiseRegistrationOutput::WriteAverageImage().

void cmtk::ImagePairSimilarityJointHistogram::SetFloatingVolume

(

const UniformVolume::SmartConstPtr &

fltVolume )

[virtual, inherited]

Set floating volume.

In addition to setting the floating volume via the base class, this function also performs pre-scaling and parameter selection using Self::PrescaleData(). Afterwards the joint histogram size is re-allocated.

Reimplemented from cmtk::ImagePairSimilarityMeasure.

Definition at line 58 of file cmtkImagePairSimilarityJointHistogram.cxx.

void cmtk::ImagePairSimilarityMeasure::SetFloatingVolume

(

const UniformVolume::SmartConstPtr &

fltVolume )

[virtual, inherited]

Set floating volume.

When the floating volume is set, a new interpolator object is also created.

Reimplemented in cmtk::ImagePairSimilarityJointHistogram.

Definition at line 64 of file cmtkImagePairSimilarityMeasure.cxx.

References cmtk::DATACLASS_GREY, cmtk::DATACLASS_LABEL, cmtk::DATACLASS_UNKNOWN, cmtk::Interpolators::DEFAULT, cmtk::Interpolators::LINEAR, and cmtk::Interpolators::NEAREST_NEIGHBOR.

virtual void cmtk::VoxelMatchingElasticFunctional::SetForceOutside	(	const bool	flag = true,
		const Types::DataItem	value = 0
	)		[pure virtual, inherited]

Set flag and value for forcing pixels outside the floating image.

Implemented in cmtk::VoxelMatchingElasticFunctional_Template< VM >.

Referenced by cmtk::ElasticRegistration::MakeFunctional().

template<class VM>

virtual void cmtk::VoxelMatchingElasticFunctional_Template< VM >::SetForceOutside	(	const bool	flag = true,
		const Types::DataItem	value = 0
	)		[inline, virtual, inherited]

Set flag and value for forcing values outside the floating image.

Implements cmtk::VoxelMatchingElasticFunctional.

Definition at line 384 of file cmtkVoxelMatchingElasticFunctional.h.

template<class W>

void cmtk::VoxelMatchingElasticFunctional_WarpTemplate< W >::SetInverseConsistencyWeight

(

const double

inverseConsistencyWeight )

[inline, inherited]

Set inverse consistency weight.

Definition at line 238 of file cmtkVoxelMatchingElasticFunctional.h.

template<class W>

void cmtk::VoxelMatchingElasticFunctional_WarpTemplate< W >::SetInverseTransformation

(

typename W::SmartPtr &

inverseTransformation )

[inline, inherited]

Set inverse transformation.

Definition at line 232 of file cmtkVoxelMatchingElasticFunctional.h.

void cmtk::FunctionalAffine2D::SetNumberOfBins	(	const size_t	minBins,
		const size_t	maxBins = 0
	)		[inherited]

Set minimum and maximum number of bins for histogram-based similarity.

Definition at line 140 of file cmtkFunctionalAffine2D.cxx.

template<class TXform >

void cmtk::GroupwiseRegistrationFunctionalXformTemplateBase< TXform >::SetNumberOfHistogramBins

(

const size_t

numberOfHistogramBins )

[virtual, inherited]

Set number of histogram bins.

Reimplemented in cmtk::CongealingFunctional< TXform >, and cmtk::CongealingFunctional< SplineWarpXform >.

Definition at line 68 of file cmtkGroupwiseRegistrationFunctionalXformTemplateBase.cxx.

template<class TXform >

void cmtk::CongealingFunctional< TXform >::SetNumberOfHistogramBins

(

const size_t

numberOfHistogramBins )

[virtual, inherited]

Set number of histogram bins.

Reimplemented from cmtk::GroupwiseRegistrationFunctionalXformTemplateBase< TXform >.

Definition at line 64 of file cmtkCongealingFunctional.cxx.

Referenced by cmtk::CongealingFunctional< TXform >::CongealingFunctional().

void cmtk::GroupwiseRegistrationFunctionalBase::SetParameter	(	const size_t	xform,
		const size_t	param,
		const Types::Coordinate	value
	)		[virtual, inherited]

Set single parameter value with separate xform and parameter index.

Definition at line 335 of file cmtkGroupwiseRegistrationFunctionalBase.cxx.

void cmtk::GroupwiseRegistrationFunctionalBase::SetParameter	(	const size_t	param,
		const Types::Coordinate	value
	)		[virtual, inherited]

Set single parameter value.

Definition at line 328 of file cmtkGroupwiseRegistrationFunctionalBase.cxx.

void cmtk::FunctionalAffine2D::SetParamVector

(

CoordinateVector &

v )

[virtual, inherited]

Set parameter vector without evaluating the functional.

Definition at line 191 of file cmtkFunctionalAffine2D.cxx.

void cmtk::GroupwiseRegistrationFunctionalBase::SetParamVector

(

CoordinateVector &

v )

[virtual, inherited]

Set parameter vector.

Definition at line 306 of file cmtkGroupwiseRegistrationFunctionalBase.cxx.

References cmtk::Vector< T >::Elements.

void cmtk::GroupwiseRegistrationFunctionalBase::SetParamVector	(	CoordinateVector &	v,
		const size_t	xformIdx
	)		[virtual, inherited]

Set parameter vector for a given transformation.

Definition at line 319 of file cmtkGroupwiseRegistrationFunctionalBase.cxx.

References cmtk::Vector< T >::Elements.

void cmtk::VolumeInjectionReconstruction::SetReferenceImage

(

UniformVolume::SmartPtr &

referenceImage )

[inherited]

Set optional separate reference image for motion parameter estimation.

Definition at line 451 of file cmtkVolumeInjectionReconstruction.cxx.

void cmtk::ImagePairSimilarityJointHistogram::SetReferenceVolume

(

const UniformVolume::SmartConstPtr &

refVolume )

[virtual, inherited]

Set reference volume.

In addition to setting the reference volume via the base class, this function also performs pre-scaling and parameter selection using Self::PrescaleData(). Afterwards the joint histogram size is re-allocated.

Reimplemented from cmtk::ImagePairSimilarityMeasure.

Definition at line 51 of file cmtkImagePairSimilarityJointHistogram.cxx.

void cmtk::ReformatVolume::SetReferenceVolume

(

const UniformVolume::SmartConstPtr &

referenceVolume )

[inherited]

Set the reference volume for reformatting.

Definition at line 78 of file cmtkReformatVolume.cxx.

Referenced by cmtk::ImagePairNonrigidRegistration::GetReformattedFloatingImage(), cmtk::ImagePairAffineRegistration::GetReformattedFloatingImage(), cmtk::ElasticRegistration::GetReformattedFloatingImage(), cmtk::AffineRegistration::GetReformattedFloatingImage(), cmtk::GroupwiseRegistrationFunctionalBase::GetReformattedImage(), cmtk::AtlasSegmentation::ReformatLabels(), and cmtk::GroupwiseRegistrationOutput::WriteAverageImage().

void cmtk::ImagePairSimilarityMeasure::SetReferenceVolume

(

const UniformVolume::SmartConstPtr &

refVolume )

[virtual, inherited]

Set reference volume.

Reimplemented in cmtk::ImagePairSimilarityJointHistogram.

Definition at line 57 of file cmtkImagePairSimilarityMeasure.cxx.

void cmtk::GroupwiseRegistrationFunctionalBase::SetTargetImages

(

std::vector< UniformVolume::SmartPtr > &

tImages )

[virtual, inherited]

Set target images.

Parameters:

tImages

Vector of all images to be registered.

Definition at line 232 of file cmtkGroupwiseRegistrationFunctionalBase.cxx.

void cmtk::SplineWarpCongealingFunctional::SetTemplateGrid	(	UniformVolume::SmartPtr &	templateGrid,
		const int	downsample = 1,
		const bool	useTemplateData = false
	)		[virtual, inherited]

Call inherited function and allocate local storage.

Reimplemented from cmtk::CongealingFunctional< SplineWarpXform >.

Definition at line 53 of file cmtkSplineWarpCongealingFunctional.cxx.

void cmtk::GroupwiseRegistrationFunctionalBase::SetTemplateGrid	(	UniformVolume::SmartPtr &	templateGrid,
		const int	downsample = 1,
		const bool	useTemplateData = false
	)		[virtual, inherited]

Set template grid.

Parameters:

templateGrid	The template grid that defines size and resolution for the implicit registration template.
downsample	Downsampling factor
useTemplateData	Flag to use template data, not just grid

Reimplemented in cmtk::CongealingFunctional< TXform >, cmtk::GroupwiseRegistrationFunctionalXformTemplate< SplineWarpXform >, cmtk::GroupwiseRegistrationRMIFunctional< TXform >, cmtk::SplineWarpCongealingFunctional, cmtk::CongealingFunctional< SplineWarpXform >, and cmtk::GroupwiseRegistrationRMIFunctional< SplineWarpXform >.

Definition at line 141 of file cmtkGroupwiseRegistrationFunctionalBase.cxx.

References cmtk::META_FS_PATH, cmtk::META_IMAGE_ORIENTATION, cmtk::META_IMAGE_ORIENTATION_ORIGINAL, cmtk::META_SPACE, and cmtk::META_SPACE_ORIGINAL.

template<class TXform >

void cmtk::GroupwiseRegistrationRMIFunctional< TXform >::SetTemplateGrid	(	UniformVolume::SmartPtr &	templateGrid,
		const int	downsample = 1,
		const bool	useTemplateData = false
	)		[virtual, inherited]

Set template grid.

Parameters:

templateGrid	The template grid that defines size and resolution for the implicit registration template.
downsample	Downsampling factor
useTemplateData	Flag to use template pixel data, not just grid, in registration

Reimplemented from cmtk::GroupwiseRegistrationFunctionalBase.

Definition at line 64 of file cmtkGroupwiseRegistrationRMIFunctional.cxx.

template<class TXform >

void cmtk::CongealingFunctional< TXform >::SetTemplateGrid	(	UniformVolume::SmartPtr &	templateGrid,
		const int	downsample = 1,
		const bool	useTemplateData = false
	)		[virtual, inherited]

Set template grid.

Parameters:

templateGrid	The template grid that defines size and resolution for the implicit registration template.
downsample	Grid downsampling factor
useTemplateData	Flag to use template pixel data, not just grid, in registration

Reimplemented from cmtk::GroupwiseRegistrationFunctionalBase.

Reimplemented in cmtk::SplineWarpCongealingFunctional.

Definition at line 111 of file cmtkCongealingFunctional.cxx.

void cmtk::VolumeInjectionReconstruction::SetupHistogramKernels

(

const TypedArray *

originalData )

[private, inherited]

Setup kernels and histograms for image entropy estimation.

Definition at line 131 of file cmtkVolumeInjectionReconstruction.cxx.

References cmtk::TypedArray::GetEntropy(), cmtk::TypedArrayNoiseEstimatorNaiveGaussian::GetNoiseLevelSigma(), cmtk::TypedArray::GetRange(), and M_PI.

template<class VM , class W >

void cmtk::ImagePairSymmetricNonrigidRegistrationFunctionalTemplate< VM, W >::SetWarpXform	(	SplineWarpXform::SmartPtr &	warpFwd,
		SplineWarpXform::SmartPtr &	warpBwd
	)		[virtual, inherited]

Set warp for forward and backward functional.

Implements cmtk::ImagePairSymmetricNonrigidRegistrationFunctional.

Definition at line 56 of file cmtkImagePairSymmetricNonrigidRegistrationFunctional.cxx.

virtual void cmtk::VoxelMatchingElasticFunctional::SetWarpXform

(

SplineWarpXform::SmartPtr &

warp )

[pure virtual, inherited]

Set Warp transformation.

This virtual function will be overridden by the derived classes that add the actual warp transformation as a template parameters. It serves as a common access point to update the warp transformation after construction of the functional.

Implemented in cmtk::ParallelElasticFunctional< VM >, and cmtk::VoxelMatchingElasticFunctional_WarpTemplate< SplineWarpXform >.

void cmtk::ImagePairNonrigidRegistrationFunctional::SetWarpXform

(

SplineWarpXform::SmartPtr &

warp )

[pure virtual, inherited]

Set Warp transformation.

This virtual function will be overridden by the derived classes that add the actual warp transformation as a template parameters. It serves as a common access point to update the warp transformation after construction of the functional.

Implemented in cmtk::ImagePairNonrigidRegistrationFunctionalTemplate< VM >.

Definition at line 143 of file cmtkImagePairNonrigidRegistrationFunctional.cxx.

void cmtk::ReformatVolume::SetWarpXform

(

const WarpXform::SmartPtr &

warpXform )

[inherited]

Set the local deformation to be applied to the reference grid.

Definition at line 97 of file cmtkReformatVolume.cxx.

References cmtk::ReformatVolume::m_WarpXform.

Referenced by cmtk::ImagePairNonrigidRegistration::GetReformattedFloatingImage(), cmtk::ElasticRegistration::GetReformattedFloatingImage(), cmtk::GroupwiseRegistrationFunctionalBase::GetReformattedImage(), cmtk::AtlasSegmentation::ReformatLabels(), and cmtk::GroupwiseRegistrationOutput::WriteAverageImage().

template<class VM >

void cmtk::SymmetricElasticFunctional_Template< VM >::SetWarpXform	(	SplineWarpXform::SmartPtr &	warpFwd,
		SplineWarpXform::SmartPtr &	warpBwd
	)		[virtual, inherited]

Set warp for forward and backward functional.

Implements cmtk::SymmetricElasticFunctional.

Definition at line 55 of file cmtkSymmetricElasticFunctional.cxx.

template<class W>

void cmtk::VoxelMatchingElasticFunctional_WarpTemplate< W >::SetWarpXform

(

typename W::SmartPtr &

warp )

[virtual, inherited]

Set warp transformation.

In the multi-threaded implementation, Warp[0] will be linked directly to the given warp, while for all other threads a copy of the original object is created by a call to WarpXform::Clone().

Reimplemented in cmtk::ParallelElasticFunctional< VM >.

Definition at line 144 of file cmtkVoxelMatchingElasticFunctional.cxx.

References cmtk::Memory::DeleteArray().

template<class TMetricFunctional >

cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::SplineWarpMultiChannelRegistrationFunctional

(

)

[inherited]

Default constructor.

Definition at line 52 of file cmtkSplineWarpMultiChannelRegistrationFunctional.txx.

template<class TMetricFunctional >

template<class TAffineMetricFunctional >

cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::SplineWarpMultiChannelRegistrationFunctional

(

AffineMultiChannelRegistrationFunctional< TAffineMetricFunctional > &

affineFunctional )

[inherited]

Constructor from affine multi-channel functional.

Definition at line 64 of file cmtkSplineWarpMultiChannelRegistrationFunctional.txx.

References cmtk::TemplateMultiChannelRegistrationFunctional< AffineXform, TMultiChannelMetricFunctional >::GetTransformation().

cmtk::SymmetryPlaneFunctional::SymmetryPlaneFunctional

(

UniformVolume::SmartPtr &

volume )

[inherited]

Constructor.

Definition at line 45 of file cmtkSymmetryPlaneFunctional.cxx.

cmtk::SymmetryPlaneFunctional::SymmetryPlaneFunctional	(	UniformVolume::SmartPtr &	volume,
		const Types::DataItemRange &	valueRange
	)		[inherited]

Constructor with value range limits.

Definition at line 53 of file cmtkSymmetryPlaneFunctional.cxx.

void cmtk::SplineWarpCongealingFunctional::UpdateActiveControlPoints

(

)

[private, virtual, inherited]

Update deactivated control points.

Implements cmtk::GroupwiseRegistrationFunctionalXformTemplate< SplineWarpXform >.

Definition at line 93 of file cmtkSplineWarpCongealingFunctional.cxx.

References cmtk::FixedVector< NDIM, T >::begin(), and cmtk::StdErr.

void cmtk::SplineWarpGroupwiseRegistrationRMIFunctional::UpdateActiveControlPoints

(

)

[private, virtual, inherited]

Update deactivated control points.

Implements cmtk::GroupwiseRegistrationFunctionalXformTemplate< SplineWarpXform >.

Definition at line 153 of file cmtkSplineWarpGroupwiseRegistrationRMIFunctional.cxx.

References cmtk::FixedVector< NDIM, T >::begin(), and cmtk::StdErr.

void cmtk::SplineWarpGroupwiseRegistrationRMIFunctional::UpdateControlPointSchedule

(

)

[private, virtual, inherited]

Update control point schedule for gradient approximation.

Definition at line 124 of file cmtkSplineWarpGroupwiseRegistrationRMIFunctional.cxx.

References cmtk::WarpXform::GetNumberOfControlPoints(), and cmtk::WarpXform::m_Dims.

void cmtk::SplineWarpGroupwiseRegistrationRMIFunctional::UpdateInformationByControlPoint

(

)

[private, virtual, inherited]

Update local information by control point.

Definition at line 55 of file cmtkSplineWarpGroupwiseRegistrationRMIFunctional.cxx.

void cmtk::GroupwiseRegistrationFunctionalBase::UpdateProbabilisticSamples

(

)

[protected, virtual, inherited]

Update probablistic samples.

This function generates a new list of random pixel indices for sampling the images. It is called every m_ProbabilisticSampleUpdatesAfter calls to Evaluate().

Definition at line 404 of file cmtkGroupwiseRegistrationFunctionalBase.cxx.

void cmtk::SplineWarpCongealingFunctional::UpdateStandardDeviationByPixel

(

)

[private, virtual, inherited]

Update standard deviation by pixel.

Reimplemented from cmtk::CongealingFunctional< SplineWarpXform >.

Definition at line 84 of file cmtkSplineWarpCongealingFunctional.cxx.

template<class TXform >

void cmtk::CongealingFunctional< TXform >::UpdateStandardDeviationByPixel

(

)

[protected, virtual, inherited]

Update standard deviation by pixel.

Reimplemented in cmtk::SplineWarpCongealingFunctional.

Definition at line 328 of file cmtkCongealingFunctional.cxx.

References cmtk::ThreadPool::GetGlobalThreadPool(), and cmtk::ThreadPool::Run().

template<class TXform >

void cmtk::CongealingFunctional< TXform >::UpdateStandardDeviationByPixelThreadFunc	(	void *const	args,
		const size_t	taskIdx,
		const size_t	taskCnt,
		const	size_t,
		const	size_t
	)		[static, private, inherited]

Thread function to update standard dedviations by pixel.

Definition at line 372 of file cmtkCongealingFunctional.cxx.

References cmtk::ThreadParameters< T >::thisObject.

template<class TMetricFunctional >

void cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::UpdateTransformationData

(

)

[private, virtual, inherited]

Update all transformation-related data after init, refine, or image change.

Definition at line 111 of file cmtkSplineWarpMultiChannelRegistrationFunctional.txx.

template<class TMetricFunctional >

void cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::UpdateTransformationFixedControlPoints

(

)

[private, virtual, inherited]

Update fixed and active control points in transformation.

Definition at line 144 of file cmtkSplineWarpMultiChannelRegistrationFunctional.txx.

References cmtk::Region< NDIM, T >::From(), cmtk::TypedArray::Get(), cmtk::TypedArray::GetData(), cmtk::Histogram< T >::GetEntropy(), cmtk::Histogram< T >::Increment(), cmtk::Console::printf(), cmtk::HistogramBase::SetRange(), cmtk::StdErr, cmtk::Region< NDIM, T >::To(), and cmtk::HistogramBase::ValueToBin().

template<class VM >

void cmtk::VoxelMatchingElasticFunctional_Template< VM >::UpdateWarpFixedParameters

(

)

[inherited]

Update set of active and passive parameters.

This function computes local entropies in the neighborhood of all control points of the Warp transformation. Those control points for which both reference and floating image have less than half the maximum entropy in this neighborhood as compared to the rest of the image are set passive. The passive parameters are not considered for gradient computation and therefore save significant computation time.

We cannot use the precomputed table of VOIs here because in "fast" mode, these VOIs are smaller than we want them here.

Definition at line 175 of file cmtkVoxelMatchingElasticFunctional.cxx.

References cmtk::DATACLASS_LABEL, cmtk::Region< NDIM, T >::From(), and cmtk::Region< NDIM, T >::To().

template<class W>

virtual size_t cmtk::VoxelMatchingElasticFunctional_WarpTemplate< W >::VariableParamVectorDim

(

)

const [inline, virtual, inherited]

Return the number of variable parameters of the transformation.

Reimplemented from cmtk::Functional.

Definition at line 304 of file cmtkVoxelMatchingElasticFunctional.h.

void cmtk::MultiChannelRegistrationFunctionalBase::VerifyImageSize	(	const UniformVolume *	imgA,
		const UniformVolume *	imgB
	)		[private, inherited]

Verify size and geometry of newly added image channels against already added channels.

Definition at line 103 of file cmtkMultiChannelRegistrationFunctionalBase.cxx.

References cmtk::DataGrid::GetDims(), and cmtk::Volume::Size.

void cmtk::VolumeInjectionReconstruction::VolumeInjectionAnisotropic	(	const Types::Coordinate	kernelSigmaFactor,
		const Types::Coordinate	kernelRadiusFactor
	)		[inherited]

Create initial approximation using anisotropic volume injection.

Parameters:

kernelSigmaFactor	Gaussian kernel sigma (standard deviation) factor (multiple of per-dimension pass image spacing)
kernelRadiusFactor	Gaussian kernel cut-off radius factor (multiple of per-dimension pass image spacing)

Definition at line 217 of file cmtkVolumeInjectionReconstruction.cxx.

References cmtk::Xform::Apply(), cmtk::AXIS_X, cmtk::AXIS_Y, cmtk::AXIS_Z, cmtk::DataGrid::GetDataAt(), cmtk::DataGrid::GetDims(), cmtk::UniformVolume::GetPlaneCoord(), cmtk::UniformVolume::GetVoxelIndexNoBounds(), and cmtk::FixedVector< NDIM, T >::RootSumOfSquares().

void cmtk::VolumeInjectionReconstruction::VolumeInjectionIsotropic	(	const Types::Coordinate	kernelSigma,
		const Types::Coordinate	kernelRadius
	)		[inherited]

Create initial approximation using isotropic volume injection.

Parameters:

kernelSigma	Gaussian kernel sigma (standard deviation) parameter
kernelRadius	Gaussian kernel cut-off radius.

Definition at line 318 of file cmtkVolumeInjectionReconstruction.cxx.

References cmtk::AffineXform::ApplyInPlace(), cmtk::AXIS_X, cmtk::AXIS_Y, cmtk::AXIS_Z, cmtk::DataGrid::GetDataAt(), cmtk::UniformVolume::GetGridLocation(), cmtk::DataGrid::GetIndexFromOffset(), cmtk::DataGrid::GetNumberOfPixels(), and NULL.

cmtk::VolumeInjectionReconstruction::VolumeInjectionReconstruction	(	const UniformVolume *	originalImage,
		const int	numberOfPasses,
		const int	interleaveAxis
	)		[inherited]

Constructor from single interleaved image.

Take original image. Set interleaved image count and stacking axis. Construct separate 3D image stacks for interleaved passes. Allocate corrected image.

Parameters:

originalImage	Smart pointer to the original image with motion artifacts.
numberOfPasses	The number of interleaved passes, i.e., the number of pass images that comprise the final image.
interleaveAxis	Between-slice axis of the interleaved acquisition.

Definition at line 50 of file cmtkVolumeInjectionReconstruction.cxx.

References cmtk::UniformVolume::CloneGrid(), cmtk::UniformVolume::GetInterleavedSubVolume(), and cmtk::TYPE_FLOAT.

cmtk::VolumeInjectionReconstruction::VolumeInjectionReconstruction	(	const UniformVolume *	reconstructionGrid,
		std::vector< UniformVolume::SmartPtr > &	images
	)		[inherited]

Constructor for general volume reconstruction from multiple acquired images.

Definition at line 83 of file cmtkVolumeInjectionReconstruction.cxx.

References cmtk::UniformVolume::CloneGrid(), cmtk::TypedArray::GetData(), and cmtk::TYPE_FLOAT.

cmtk::VoxelMatchingCrossCorrelation::VoxelMatchingCrossCorrelation	(	const UniformVolume *	refVolume,
		const UniformVolume *	fltVolume
	)		[inherited]

Constructor.

For reference and floating volume, InitDataset is called.

Parameters:

refVolume	The reference (fixed) volume.
fltVolume	The floating (transformed) volume.

Definition at line 43 of file cmtkVoxelMatchingCrossCorrelation.cxx.

cmtk::VoxelMatchingElasticFunctional::VoxelMatchingElasticFunctional	(	UniformVolume::SmartPtr &	reference,
		UniformVolume::SmartPtr &	floating
	)		[protected, inherited]

Constructor.

Definition at line 58 of file cmtkVoxelMatchingElasticFunctional.cxx.

References NULL.

template<class VM>

cmtk::VoxelMatchingElasticFunctional_Template< VM >::VoxelMatchingElasticFunctional_Template	(	UniformVolume::SmartPtr &	reference,
		UniformVolume::SmartPtr &	floating
	)		[inline, inherited]

Constructor.

Init pointers to volume and transformation objects and initialize internal data structures.

Parameters:

reference	The reference (i.e. static) volume.
floating	The floating (i.e. transformed) volume.

Definition at line 357 of file cmtkVoxelMatchingElasticFunctional.h.

References NULL.

template<class W>

cmtk::VoxelMatchingElasticFunctional_WarpTemplate< W >::VoxelMatchingElasticFunctional_WarpTemplate	(	UniformVolume::SmartPtr &	reference,
		UniformVolume::SmartPtr &	floating
	)		[inline, protected, inherited]

Constructor.

Definition at line 324 of file cmtkVoxelMatchingElasticFunctional.h.

cmtk::VoxelMatchingMeanSquaredDifference::VoxelMatchingMeanSquaredDifference	(	const UniformVolume *	refVolume,
		const UniformVolume *	fltVolume
	)		[inherited]

Constructor.

For reference and model volume, InitDataset is called.

Parameters:

refVolume	The reference (fixed) volume.
fltVolume	The floating (moving) volume.

Definition at line 43 of file cmtkVoxelMatchingMeanSquaredDifference.cxx.

template<class T , ScalarDataType DT, Interpolators::InterpolationEnum I>

cmtk::VoxelMatchingMetric< T, DT, I >::VoxelMatchingMetric	(	const UniformVolume *	refVolume,
		const UniformVolume *	fltVolume,
		const bool	initData = true
	)		[inherited]

Constructor.

For reference and model volume, InitDataset is called.

Parameters:

refVolume	The reference (fixed) volume.
fltVolume	The model (transformed) volume.
initData	If this flag is set (default), then the internal representation of the pixel data for both volumes is also created. Derived classes may want to prevent this if they define their own specific initialization (e.g., igsVoxelMatchingJointHistogram).

Definition at line 46 of file cmtkVoxelMatchingMetric.cxx.

cmtk::VoxelRegistration::VoxelRegistration

(

)

[inherited]

Default constructor.

Definition at line 54 of file cmtkVoxelRegistration.cxx.

References cmtk::VoxelRegistration::CoarsestResolution, NULL, cmtk::VoxelRegistration::OptimizerStepFactor, and cmtk::VoxelRegistration::UseMaxNorm.

void cmtk::ImagePairNonrigidRegistrationFunctional::WeightedDerivative	(	double &	lower,
		double &	upper,
		SplineWarpXform &	warp,
		const int	param,
		const Types::Coordinate	step
	)		const [protected, inherited]

Return weighted combination of similarity and grid energy derivatives.

Definition at line 97 of file cmtkImagePairNonrigidRegistrationFunctional.cxx.

References cmtk::WarpXform::GetDerivativeInverseConsistencyError(), cmtk::WarpXform::GetDerivativeLandmarksMSD(), cmtk::SplineWarpXform::GetGridEnergyDerivative(), and cmtk::SplineWarpXform::GetJacobianConstraintDerivative().

template<class W>

void cmtk::VoxelMatchingElasticFunctional_WarpTemplate< W >::WeightedDerivative	(	double &	lower,
		double &	upper,
		W &	warp,
		const int	param,
		const Types::Coordinate	step
	)		const [protected, inherited]

Return weighted combination of similarity and grid energy derivatives.

Definition at line 82 of file cmtkVoxelMatchingElasticFunctional.cxx.

template<class W>

Self::ReturnType cmtk::VoxelMatchingElasticFunctional_WarpTemplate< W >::WeightedTotal	(	const typename Self::ReturnType	metric,
		const W *	warp
	)		const [inline, protected, inherited]

Return weighted combination of voxel similarity and grid energy.

Definition at line 246 of file cmtkVoxelMatchingElasticFunctional.h.

bool cmtk::GroupwiseRegistrationFunctionalBase::Wiggle

(

)

[protected, virtual, inherited]

Update probabilistic sample table..

Reimplemented from cmtk::Functional.

Reimplemented in cmtk::CongealingFunctional< TXform >, cmtk::GroupwiseRegistrationFunctionalXformTemplate< SplineWarpXform >, cmtk::GroupwiseRegistrationRMIFunctional< TXform >, cmtk::CongealingFunctional< SplineWarpXform >, and cmtk::GroupwiseRegistrationRMIFunctional< SplineWarpXform >.

Definition at line 506 of file cmtkGroupwiseRegistrationFunctionalBase.cxx.

References cmtk::META_FS_PATH.

template<class TXform >

bool cmtk::CongealingFunctional< TXform >::Wiggle

(

)

[protected, virtual, inherited]

Update probabilistic sample table..

Reimplemented from cmtk::GroupwiseRegistrationFunctionalBase.

Definition at line 313 of file cmtkCongealingFunctional.cxx.

template<class TXform >

bool cmtk::GroupwiseRegistrationRMIFunctional< TXform >::Wiggle

(

)

[protected, virtual, inherited]

Update probabilistic sample table..

Reimplemented from cmtk::GroupwiseRegistrationFunctionalBase.

Definition at line 375 of file cmtkGroupwiseRegistrationRMIFunctional.cxx.

void cmtk::ImageSymmetryPlaneCommandLineBase::WriteAligned

(

UniformVolume::SmartConstPtr &

originalVolume )

const [private, inherited]

Write image aligned w.r.t. the symmetry plane.

Definition at line 420 of file cmtkImageSymmetryPlaneCommandLineBase.cxx.

References cmtk::TypedArray::Create(), cmtk::ReformatVolume::CreateInterpolator(), cmtk::TypedArray::GetDataSize(), cmtk::TypedArray::GetRange(), cmtk::TypedArray::GetType(), cmtk::Types::Range< T >::m_UpperBound, and cmtk::VolumeIO::Write().

bool cmtk::GroupwiseRegistrationOutput::WriteAverageImage	(	const char *	path,
		const cmtk::Interpolators::InterpolationEnum	interp = cmtk::Interpolators::LINEAR,
		const bool	useTemplateData = false
	)		[inherited]

Reformat and write average image.

Parameters:

interp	Selection of interpolation method (via igsReformatVolume).
useTemplateData	If true, template image data is included in averaging.

Definition at line 139 of file cmtkGroupwiseRegistrationOutput.cxx.

References cmtk::Memory::DeleteArray(), cmtk::TypedArray::Get(), cmtk::TypedArray::GetData(), cmtk::META_FS_PATH, cmtk::ReformatVolume::PlainReformat(), cmtk::ReformatVolume::SetAffineXform(), cmtk::ReformatVolume::SetFloatingVolume(), cmtk::ReformatVolume::SetInterpolation(), cmtk::ReformatVolume::SetReferenceVolume(), cmtk::ReformatVolume::SetWarpXform(), cmtk::StdErr, cmtk::TYPE_FLOAT, and cmtk::TYPE_USHORT.

void cmtk::ImageSymmetryPlaneCommandLineBase::WriteDifference

(

UniformVolume::SmartConstPtr &

originalVolume )

const [private, inherited]

Write difference image between original and mirrored image.

Definition at line 316 of file cmtkImageSymmetryPlaneCommandLineBase.cxx.

References cmtk::TypedArray::Create(), cmtk::ReformatVolume::CreateInterpolator(), cmtk::GetSignedDataType(), and cmtk::VolumeIO::Write().

bool cmtk::GroupwiseRegistrationOutput::WriteGroupwiseArchive

(

const char *

path )

const [inherited]

Write template specifications and transformations to a single file.

Definition at line 52 of file cmtkGroupwiseRegistrationOutput.cxx.

References cmtk::TypedStream::Close(), cmtk::TypedStream::IsValid(), and cmtk::ClassStream::Open().

void cmtk::ImageSymmetryPlaneCommandLineBase::WriteMarkPlane

(

UniformVolume::SmartConstPtr &

originalVolume )

const [private, inherited]

Write original image with marked symmetry plane.

Definition at line 392 of file cmtkImageSymmetryPlaneCommandLineBase.cxx.

References cmtk::VolumeIO::Write().

void cmtk::ImageSymmetryPlaneCommandLineBase::WriteMirror

(

UniformVolume::SmartConstPtr &

originalVolume )

const [private, inherited]

Write mirrored image.

Definition at line 356 of file cmtkImageSymmetryPlaneCommandLineBase.cxx.

References cmtk::TypedArray::Create(), cmtk::ReformatVolume::CreateInterpolator(), and cmtk::VolumeIO::Write().

bool cmtk::GroupwiseRegistrationOutput::WriteXformsSeparateArchives	(	const char *	path,
		const char *	templatePath
	)		[inherited]

Write each transformations to a different typedstream archive.

Definition at line 83 of file cmtkGroupwiseRegistrationOutput.cxx.

References cmtk::StudyList::AddStudy(), cmtk::StudyList::AddXform(), cmtk::MetaInformationObject::m_MetaInformation, and cmtk::META_FS_PATH.

cmtk::AffineRegistration::~AffineRegistration

(

)

[virtual, inherited]

Destructor.

Definition at line 69 of file cmtkAffineRegistration.cxx.

template<class TXform >

cmtk::CongealingFunctional< TXform >::~CongealingFunctional

(

)

[virtual, inherited]

Destructor.

Definition at line 53 of file cmtkCongealingFunctional.cxx.

References cmtk::Memory::DeleteArray().

cmtk::ElasticRegistrationCommandLine::~ElasticRegistrationCommandLine

(

)

[inherited]

Destructor.

Definition at line 353 of file cmtkElasticRegistrationCommandLine.cxx.

cmtk::GroupwiseRegistrationFunctionalBase::~GroupwiseRegistrationFunctionalBase

(

)

[virtual, inherited]

Destructor.

Definition at line 91 of file cmtkGroupwiseRegistrationFunctionalBase.cxx.

References cmtk::Memory::DeleteArray().

template<class TXform >

cmtk::GroupwiseRegistrationFunctionalXformTemplateBase< TXform >::~GroupwiseRegistrationFunctionalXformTemplateBase

(

)

[virtual, inherited]

Destructor.

Definition at line 61 of file cmtkGroupwiseRegistrationFunctionalXformTemplateBase.cxx.

template<class TXform >

cmtk::GroupwiseRegistrationRMIFunctional< TXform >::~GroupwiseRegistrationRMIFunctional

(

)

[virtual, inherited]

Destructor.

Definition at line 56 of file cmtkGroupwiseRegistrationRMIFunctional.cxx.

cmtk::ImagePairAffineRegistration::~ImagePairAffineRegistration

(

)

[virtual, inherited]

Destructor.

Definition at line 63 of file cmtkImagePairAffineRegistration.cxx.

cmtk::ImagePairNonrigidRegistrationCommandLine::~ImagePairNonrigidRegistrationCommandLine

(

)

[inherited]

Destructor.

Definition at line 316 of file cmtkImagePairNonrigidRegistrationCommandLine.cxx.

cmtk::ImagePairNonrigidRegistrationFunctional::~ImagePairNonrigidRegistrationFunctional

(

)

[virtual, inherited]

Virtual destructor.

Definition at line 87 of file cmtkImagePairNonrigidRegistrationFunctional.cxx.

References cmtk::Memory::DeleteArray().

cmtk::ProtocolCallback::~ProtocolCallback

(

)

[virtual, inherited]

Destructor.

Closes protocol stream.

Definition at line 60 of file cmtkProtocolCallback.cxx.

cmtk::RegistrationCallback::~RegistrationCallback

(

)

[virtual, inherited]

Virtual destructor.

Definition at line 60 of file cmtkRegistrationCallback.cxx.

cmtk::VoxelMatchingElasticFunctional::~VoxelMatchingElasticFunctional

(

)

[virtual, inherited]

Destructor.

Definition at line 74 of file cmtkVoxelMatchingElasticFunctional.cxx.

References cmtk::Memory::DeleteArray().

template<class VM>

virtual cmtk::VoxelMatchingElasticFunctional_Template< VM >::~VoxelMatchingElasticFunctional_Template

(

)

[inline, virtual, inherited]

Virtual destructor.

Definition at line 376 of file cmtkVoxelMatchingElasticFunctional.h.

References cmtk::Memory::DeleteArray().

template<class W>

virtual cmtk::VoxelMatchingElasticFunctional_WarpTemplate< W >::~VoxelMatchingElasticFunctional_WarpTemplate

(

)

[inline, protected, virtual, inherited]

Dummy virtual destructor.

Definition at line 330 of file cmtkVoxelMatchingElasticFunctional.h.

cmtk::VoxelRegistration::~VoxelRegistration

(

)

[virtual, inherited]

Destructor.

Definition at line 79 of file cmtkVoxelRegistration.cxx.

---

Variable Documentation

JointHistogram<unsigned int>::SmartPtr cmtk::VoxelMatchingElasticFunctional::ConsistencyHistogram [protected, inherited]

Histogram used for consistency computation.

Definition at line 154 of file cmtkVoxelMatchingElasticFunctional.h.

size_t cmtk::VoxelMatchingElasticFunctional::Dim [protected, inherited]

Dimension of warp parameter vector.

Definition at line 157 of file cmtkVoxelMatchingElasticFunctional.h.

template<class VM>

DataGrid::IndexType::ValueType cmtk::VoxelMatchingElasticFunctional_Template< VM >::DimsX [protected, inherited]

Shortcut variables for x, y, z dimension of the reference image.

Definition at line 589 of file cmtkVoxelMatchingElasticFunctional.h.

template<class VM>

DataGrid::IndexType::ValueType cmtk::VoxelMatchingElasticFunctional_Template< VM >::DimsY [protected, inherited]

Definition at line 589 of file cmtkVoxelMatchingElasticFunctional.h.

template<class VM>

DataGrid::IndexType::ValueType cmtk::VoxelMatchingElasticFunctional_Template< VM >::DimsZ [protected, inherited]

Definition at line 589 of file cmtkVoxelMatchingElasticFunctional.h.

template<class VM>

DataGrid::IndexType::ValueType cmtk::VoxelMatchingElasticFunctional_Template< VM >::FltDimsX [protected, inherited]

Shorcut variables for x and y dimensions of the floating image.

Definition at line 592 of file cmtkVoxelMatchingElasticFunctional.h.

template<class VM>

DataGrid::IndexType::ValueType cmtk::VoxelMatchingElasticFunctional_Template< VM >::FltDimsY [protected, inherited]

Definition at line 592 of file cmtkVoxelMatchingElasticFunctional.h.

template<class VM>

SmartPointer<VM> cmtk::VoxelMatchingElasticFunctional_Template< VM >::IncrementalMetric [protected, inherited]

Metric object for incremental computation.

Before computing the incremental metric after change of one parameter, the global metric is copied to this object. It is then used for in-place application of all necessary changes, leaving the original metric intact.

See also:

EvaluateIncremental

Definition at line 586 of file cmtkVoxelMatchingElasticFunctional.h.

bool cmtk::InterruptSignalReceived [static]

Flag that is set upon SIGINT signal.

Definition at line 48 of file cmtkRegistrationCallback.cxx.

Referenced by cmtkRegistrationCallbackDispatchSIGINT().

template<class W>

double cmtk::VoxelMatchingElasticFunctional_WarpTemplate< W >::InverseConsistencyWeight [protected, inherited]

Weight for inverse consistency constraint.

Definition at line 228 of file cmtkVoxelMatchingElasticFunctional.h.

template<class W>

W::SmartPtr cmtk::VoxelMatchingElasticFunctional_WarpTemplate< W >::InverseTransformation [protected, inherited]

Optional inverse transformation for inverse-consistent deformation.

Definition at line 225 of file cmtkVoxelMatchingElasticFunctional.h.

Types::Coordinate cmtk::ImageSymmetryPlaneCommandLineBase::m_Accuracy [private, inherited]

Optimization "accuracy" (really, precision)

Definition at line 104 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Referenced by cmtk::ImageSymmetryPlaneCommandLineBase::ImageSymmetryPlaneCommandLineBase().

const char* cmtk::ImageSymmetryPlaneCommandLineBase::m_AlignedOutFile [private, inherited]

Optional output path for aligned file.

Definition at line 131 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Referenced by cmtk::ImageSymmetryPlaneCommandLineBase::ImageSymmetryPlaneCommandLineBase().

CommandLine cmtk::ImageSymmetryPlaneCommandLineBase::m_CommandLine [private, inherited]

Definition at line 193 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Referenced by cmtk::ImageSymmetryPlaneCommandLineBase::ImageSymmetryPlaneCommandLineBase().

const char* cmtk::ImageSymmetryPlaneCommandLineBase::m_DifferenceOutFile [private, inherited]

Optional output path for file with subtraction between input and mirrored input.

Definition at line 140 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Referenced by cmtk::ImageSymmetryPlaneCommandLineBase::ImageSymmetryPlaneCommandLineBase().

bool cmtk::ImageSymmetryPlaneCommandLineBase::m_DisableOptimization [private, inherited]

Flag to disable optimization.

Definition at line 113 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Referenced by cmtk::ImageSymmetryPlaneCommandLineBase::ImageSymmetryPlaneCommandLineBase().

bool cmtk::ImageSymmetryPlaneCommandLineBase::m_FixOffset [private, inherited]

Flag to fix symmetry plane offset parameter (i.e., do not optimize "Rho")

Definition at line 125 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Referenced by cmtk::ImageSymmetryPlaneCommandLineBase::ImageSymmetryPlaneCommandLineBase().

template<class VM>

bool cmtk::VoxelMatchingElasticFunctional_Template< VM >::m_ForceOutsideFlag [protected, inherited]

Flag for forcing pixel values outside the floating image.

Definition at line 575 of file cmtkVoxelMatchingElasticFunctional.h.

template<class VM>

VM::Exchange cmtk::VoxelMatchingElasticFunctional_Template< VM >::m_ForceOutsideValueRescaled [protected, inherited]

Rescaled byte value for forcing pixel values outside the floating image.

Definition at line 578 of file cmtkVoxelMatchingElasticFunctional.h.

const char* cmtk::ImageSymmetryPlaneCommandLineBase::m_InFileName [private, inherited]

Input image file path.

Definition at line 164 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Referenced by cmtk::ImageSymmetryPlaneCommandLineBase::ImageSymmetryPlaneCommandLineBase().

InitialPlaneEnum cmtk::ImageSymmetryPlaneCommandLineBase::m_InitialPlane [private, inherited]

Initial plane orientation: default to sagittal for human images.

Definition at line 178 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Referenced by cmtk::ImageSymmetryPlaneCommandLineBase::ImageSymmetryPlaneCommandLineBase().

Interpolators::InterpolationEnum cmtk::ImageSymmetryPlaneCommandLineBase::m_Interpolation [private, inherited]

Interpolation method for reformatted image generation.

Definition at line 107 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Referenced by cmtk::ImageSymmetryPlaneCommandLineBase::ImageSymmetryPlaneCommandLineBase().

int cmtk::ImageSymmetryPlaneCommandLineBase::m_Levels [private, inherited]

Number of multi-resolution levels.

Definition at line 110 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Referenced by cmtk::ImageSymmetryPlaneCommandLineBase::ImageSymmetryPlaneCommandLineBase().

const char* cmtk::ImageSymmetryPlaneCommandLineBase::m_MarkedOutFile [private, inherited]

Optional output path for file with marked symmetry plane.

Definition at line 137 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Referenced by cmtk::ImageSymmetryPlaneCommandLineBase::ImageSymmetryPlaneCommandLineBase().

bool cmtk::ImageSymmetryPlaneCommandLineBase::m_MarkPlaneAligned [private, inherited]

Flag for marking the symmetry plane in the aligned file.

Definition at line 134 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Referenced by cmtk::ImageSymmetryPlaneCommandLineBase::ImageSymmetryPlaneCommandLineBase().

Types::DataItem cmtk::ImageSymmetryPlaneCommandLineBase::m_MarkPlaneValue [private, inherited]

Data value used for marking the symmetry plane in output images.

Definition at line 146 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Referenced by cmtk::ImageSymmetryPlaneCommandLineBase::ImageSymmetryPlaneCommandLineBase().

float cmtk::ImageSymmetryPlaneCommandLineBase::m_MaxValue [private, inherited]

Minimum data value (lower threshold).

Definition at line 95 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Referenced by cmtk::ImageSymmetryPlaneCommandLineBase::ImageSymmetryPlaneCommandLineBase().

bool cmtk::ImageSymmetryPlaneCommandLineBase::m_MaxValueSet [private, inherited]

Flag for valid (user-set) maximum data value.

Definition at line 98 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Referenced by cmtk::ImageSymmetryPlaneCommandLineBase::ImageSymmetryPlaneCommandLineBase().

float cmtk::ImageSymmetryPlaneCommandLineBase::m_MinValue [private, inherited]

Minimum data value (lower threshold).

Definition at line 89 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Referenced by cmtk::ImageSymmetryPlaneCommandLineBase::ImageSymmetryPlaneCommandLineBase().

bool cmtk::ImageSymmetryPlaneCommandLineBase::m_MinValueSet [private, inherited]

Flag for valid (user-set) minimum data value.

Definition at line 92 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Referenced by cmtk::ImageSymmetryPlaneCommandLineBase::ImageSymmetryPlaneCommandLineBase().

const char* cmtk::ImageSymmetryPlaneCommandLineBase::m_MirrorOutFile [private, inherited]

Optional output path for mirrored file.

Definition at line 128 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Referenced by cmtk::ImageSymmetryPlaneCommandLineBase::ImageSymmetryPlaneCommandLineBase().

Types::DataItem cmtk::ImageSymmetryPlaneCommandLineBase::m_PadOutValue [private, inherited]

User-provided padding value.

Definition at line 152 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Referenced by cmtk::ImageSymmetryPlaneCommandLineBase::ImageSymmetryPlaneCommandLineBase().

bool cmtk::ImageSymmetryPlaneCommandLineBase::m_PadOutValueSet [private, inherited]

Flag for user-provided padding value.

Definition at line 149 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Referenced by cmtk::ImageSymmetryPlaneCommandLineBase::ImageSymmetryPlaneCommandLineBase().

Units::Degrees cmtk::ImageSymmetryPlaneCommandLineBase::m_Phi [private, inherited]

Symmetry plane "Phi" angle parameter.

Definition at line 122 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Types::Coordinate cmtk::ImageSymmetryPlaneCommandLineBase::m_Rho [private, inherited]

Symmetry plane "Rho" parameter (offset).

Definition at line 116 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Types::Coordinate cmtk::ImageSymmetryPlaneCommandLineBase::m_Sampling [private, inherited]

Image sampling (highest resampled resolution).

Definition at line 101 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Referenced by cmtk::ImageSymmetryPlaneCommandLineBase::ImageSymmetryPlaneCommandLineBase().

const char* cmtk::ImageSymmetryPlaneCommandLineBase::m_SymmetryOutFileName [private, inherited]

Optional output path for symmetry plane.

Definition at line 155 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Referenced by cmtk::ImageSymmetryPlaneCommandLineBase::ImageSymmetryPlaneCommandLineBase().

const char* cmtk::ImageSymmetryPlaneCommandLineBase::m_SymmetryParameters [private, inherited]

Optional output path for symmetry plane parameters.

Definition at line 158 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Referenced by cmtk::ImageSymmetryPlaneCommandLineBase::ImageSymmetryPlaneCommandLineBase().

const char* cmtk::ImageSymmetryPlaneCommandLineBase::m_SymmetryParametersFile [private, inherited]

Optional input path for previously computed symmetry plane parameters.

Definition at line 161 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Referenced by cmtk::ImageSymmetryPlaneCommandLineBase::ImageSymmetryPlaneCommandLineBase().

ParametricPlane cmtk::ImageSymmetryPlaneCommandLineBase::m_SymmetryPlane [private, inherited]

The symmetry plane object.

Definition at line 83 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Units::Degrees cmtk::ImageSymmetryPlaneCommandLineBase::m_Theta [private, inherited]

Symmetry plane "Theta" angle parameter.

Definition at line 119 of file cmtkImageSymmetryPlaneCommandLineBase.h.

bool cmtk::ImageSymmetryPlaneCommandLineBase::m_Verbose [private, inherited]

Verbosity flag.

Definition at line 86 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Referenced by cmtk::ImageSymmetryPlaneCommandLineBase::ImageSymmetryPlaneCommandLineBase().

const char* cmtk::ImageSymmetryPlaneCommandLineBase::m_WriteXformPath [private, inherited]

Optional output path for the alignment transformation.

Definition at line 143 of file cmtkImageSymmetryPlaneCommandLineBase.h.

Referenced by cmtk::ImageSymmetryPlaneCommandLineBase::ImageSymmetryPlaneCommandLineBase().

Vector3D cmtk::VoxelMatchingElasticFunctional::ReferenceFrom [protected, inherited]

Coordinate of the beginning of the reference colume crop area.

Definition at line 175 of file cmtkVoxelMatchingElasticFunctional.h.

Vector3D cmtk::VoxelMatchingElasticFunctional::ReferenceTo [protected, inherited]

Coordinate of the end of the reference colume crop area.

Definition at line 178 of file cmtkVoxelMatchingElasticFunctional.h.

ImagePairNonrigidRegistrationCommandLine * cmtk::ImagePairNonrigidRegistrationCommandLine::StaticThis = NULL [static, inherited]

Static pointer to this object.

Definition at line 151 of file cmtkImagePairNonrigidRegistrationCommandLine.h.

Referenced by cmtkImagePairNonrigidRegistrationCommandLineDispatchSIGUSR1().

ElasticRegistrationCommandLine * cmtk::ElasticRegistrationCommandLine::StaticThis = NULL [static, inherited]

Static pointer to this object.

Definition at line 164 of file cmtkElasticRegistrationCommandLine.h.

Referenced by cmtkElasticRegistrationCommandLineDispatchSIGUSR1().

std::vector<Types::Coordinate> cmtk::VoxelMatchingElasticFunctional::StepScaleVector [protected, inherited]

Parameter scaling vector.

This array holds the scaling factors for all warp parameters as returned by the transformation class. These factors can be used to equalized all parameter modifications during gradient computation etc.

Definition at line 164 of file cmtkVoxelMatchingElasticFunctional.h.

Vector3D* cmtk::VoxelMatchingElasticFunctional::VectorCache [protected, inherited]

Storage for simultaneously retrieving multiple deformed vectors.

Definition at line 181 of file cmtkVoxelMatchingElasticFunctional.h.

DataGrid::RegionType* cmtk::VoxelMatchingElasticFunctional::VolumeOfInfluence [protected, inherited]

Volume of influence table.

This array holds the precomputed volumes of influence for all transformation parameters. Six successive numbers per parameter define the voxel range with respect to the reference colume grid that is affected by the respective parameter.

Definition at line 172 of file cmtkVoxelMatchingElasticFunctional.h.

template<class W>

W::SmartPtr cmtk::VoxelMatchingElasticFunctional_WarpTemplate< W >::Warp [inherited]

Pointer to the local warp transformation.

Definition at line 221 of file cmtkVoxelMatchingElasticFunctional.h.

template<class VM>

VM::Exchange* cmtk::VoxelMatchingElasticFunctional_Template< VM >::WarpedVolume [protected, inherited]

Ground transformed volume.

Definition at line 572 of file cmtkVoxelMatchingElasticFunctional.h.

bool cmtk::VoxelMatchingElasticFunctional::WarpNeedsFixUpdate [protected, inherited]

Warp's fixed parameters need to be updated.

This flag is set when the warp transformation is set or modified. It signals that the active and passive parameters of the transformation will have to be updated before the next gradient computation.

Definition at line 151 of file cmtkVoxelMatchingElasticFunctional.h.