Utility class for reformatting volume data. More...

#include <cmtkReformatVolume.h>

Collaboration diagram for cmtk::ReformatVolume:

Classes
class	GetTransformedReferenceTP
class	Jacobian
	Function class for reformating of a Jacobian map. More...
class	Plain
	Function class for plain reformating. More...
Public Types
enum	AveragingMode { MODE_MEAN, MODE_MEDIAN, MODE_ROBUST90 }
	Constants for transformation field mode. More...
enum	Mode { REFORMAT_PLAIN, REFORMAT_JACOBIAN }
	Constants for extended reformatting mode. More...
typedef ReformatVolume	Self
	This class.
typedef SmartPointer< Self >	SmartPtr
	Smart pointer to this class.
Public Member Functions
	cmtkGetSetMacroDefault (float, LowerThresholdReference, FLT_MIN)
	Threshold for the reference image.
	cmtkGetSetMacroDefault (float, LowerThresholdFloating, FLT_MIN)
	Threshold for the floating image.
	cmtkGetSetMacroDefault (float, UpperThresholdReference, FLT_MAX)
	Threshold for the reference image.
	cmtkGetSetMacroDefault (float, UpperThresholdFloating, FLT_MAX)
	Threshold for the floating image.
	cmtkGetSetMacroDefault (bool, UsePaddingValue, true)
	Flag whether the PADDING value is defined by client.
	cmtkGetSetMacro (Types::DataItem, PaddingValue)
	PADDING value as defined by client.
	ReformatVolume ()
	Default constructor.
void	SetInterpolation (const cmtk::Interpolators::InterpolationEnum interpolation)
	Set interpolation mode.
UniformVolumeInterpolatorBase::SmartPtr	CreateInterpolator (const UniformVolume::SmartConstPtr &volume)
	Create interpolator object for given volume according to interpolation mode set in this object.
void	SetUserDataType (const ScalarDataType dataType)
	Set user-defined data type.
void	SetReferenceVolume (const UniformVolume::SmartConstPtr &referenceVolume)
	Set the reference volume for reformatting.
void	SetFloatingVolume (const UniformVolume::SmartConstPtr &floatingVolume)
	Set the floating (transformed) volume for reformatting.
void	SetAffineXform (const AffineXform::SmartPtr &affineXform)
	Set affine transformation to be applied to the floating volume.
void	SetWarpXform (const WarpXform::SmartPtr &warpXform)
	Set the local deformation to be applied to the reference grid.
const UniformVolume::SmartPtr	PlainReformat ()
	Plain reformatting.
TypedArray::SmartPtr	PlainReformat (const int plane, TypedArray::SmartPtr &target=TypedArray::SmartPtr::Null, const size_t targetOffset=0)
	Plain reformatting of a single plane.
UniformVolume *	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.
UniformVolume *	GetTransformedReference (Types::Coordinate *const volumeOffset=NULL)
	Apply forward warp transformation to reference volume.
UniformVolume *	GetTransformedReferenceJacobianAvg (const std::vector< SplineWarpXform::SmartPtr > xformList, Types::Coordinate const volumeOffset=NULL, const bool includeReferenceData=true)
	Average Jacobians into deformed reference coordinate system.
Static Public Member Functions
static UniformVolumeInterpolatorBase::SmartPtr	CreateInterpolator (const cmtk::Interpolators::InterpolationEnum interpolation, const UniformVolume::SmartConstPtr &volume)
	Create interpolator object for given volume according to interpolation mode set in this object.
template<class TInterpolator , class Fct >
static TypedArray::SmartPtr	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	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.
Private Member Functions
const UniformVolume::SmartPtr	MakeTargetVolume () const
	Make target volume matching (reoriented) reference volume.
UniformVolume *	CreateTransformedReference (Types::Coordinate const bbFrom, Types::Coordinate const delta, Types::Coordinate *const volumeOffset=NULL)
	Create uniform volume with correct dimensions for reformatted reference.
Static Private Member Functions
static CMTK_THREAD_RETURN_TYPE	GetTransformedReferenceGrey (void *const arg)
	Apply forward warp transformation to grey-level reference volume.
static CMTK_THREAD_RETURN_TYPE	GetTransformedReferenceGreyAvg (void *const arg)
	Apply forward warp transformation to average grey-level reference volume.
static CMTK_THREAD_RETURN_TYPE	GetTransformedReferenceLabel (void *const arg)
	Apply forward warp transformation to label reference volume.
static CMTK_THREAD_RETURN_TYPE	GetTransformedReferenceJacobianAvgThread (void *const arg)
	Thread function: average Jacobians into deformed reference system.
Private Attributes
cmtk::Interpolators::InterpolationEnum	Interpolation
	Interpolation mode.
ScalarDataType	m_UserDataType
	User-selected data type for reformatted data.
UniformVolume::SmartConstPtr	ReferenceVolume
	Pointer to the reference volume.
UniformVolume::SmartConstPtr	FloatingVolume
	Pointer to the floating volume.
AffineXform::SmartConstPtr	m_AffineXform
	Pointer to the affine transformation of the floating volume.
WarpXform::SmartConstPtr	m_WarpXform
	Pointer to the local deformation of the reference grid.

Detailed Description

Utility class for reformatting volume data.

This class takes two volume data sets, and affine and an (optional) local deformation. It provides member functions to reformat from one of the images a slice plane corresponding exactly to one of the original planes from the respective other images. The class provides optional checkerboard filling of areas with no valid original image data present.

Definition at line 76 of file cmtkReformatVolume.h.