Base class for groupwise registration functionals. More...

#include <cmtkGroupwiseRegistrationFunctionalBase.h>

Inheritance diagram for cmtk::GroupwiseRegistrationFunctionalBase:

Collaboration diagram for cmtk::GroupwiseRegistrationFunctionalBase:

Classes
class	BadXform
	Exception for "bad transformation". More...
Public Types
typedef Functional	Superclass
	Type of parent class.
typedef GroupwiseRegistrationFunctionalBase	Self
	Type of this class.
typedef SmartPointer< Self >	SmartPtr
	Smart pointer.
Public Member Functions
	GroupwiseRegistrationFunctionalBase ()
	Constructor.
virtual	~GroupwiseRegistrationFunctionalBase ()
	Destructor.
virtual void	SetFreeAndRereadImages (const bool flag=true)
	Set flag for freeing and rereading images.
virtual void	SetRepeatIntensityHistogramMatching (const bool flag=true)
	Set flag for repeated histogram-based intensity matching.
virtual void	CreateTemplateGridFromTargets (const std::vector< UniformVolume::SmartPtr > &targets, const int downsample=0)
	Create template grid based on target images.
virtual void	CreateTemplateGrid (const DataGrid::IndexType &dims, const UniformVolume::CoordinateVectorType &deltas)
	Create template grid based on geometry.
virtual void	SetTemplateGrid (UniformVolume::SmartPtr &templateGrid, const int downsample=1, const bool useTemplateData=false)
	Set template grid.
virtual UniformVolume::SmartPtr &	GetTemplateGrid ()
	Retrieve the template grid.
virtual const UniformVolume *	GetTemplateGrid () const
	Retrieve the template grid.
virtual void	SetTargetImages (std::vector< UniformVolume::SmartPtr > &tImages)
	Set target images.
virtual void	GetOriginalTargetImages (std::vector< UniformVolume::SmartPtr > &tImages)
	Get the original target images.
virtual std::vector < UniformVolume::SmartPtr > &	GetOriginalTargetImages ()
	Get the original target images.
virtual size_t	GetNumberOfTargetImages () const
	Get number of target images.
virtual UniformVolume::SmartPtr	GetOriginalTargetImage (const size_t imageIdx)
	Get a smart pointer to one original target image.
virtual const UniformVolume *	GetOriginalTargetImage (const size_t imageIdx) const
	Get a constant pointer to one original target image.
virtual void	SetGaussianSmoothImagesSigma (const Types::Coordinate gaussianSmoothImagesSigma)
	Set Gaussian smoothing kernel width for target images.
virtual void	SetUserBackgroundValue (const byte value=0)
	Set user-defined image background value to be substituted outside the field of view.
virtual void	UnsetUserBackgroundValue ()
	Unset user-defined image background value.
virtual void	SetForceZeroSum (const bool forceZeroSum=true)
	Set flag for zero-sum updates.
virtual void	SetForceZeroSumFirstN (const size_t forceZeroSumFirstN)
	Set count for restricted zero-sum updates.
virtual void	SetActiveImagesFromTo (const size_t from, const size_t to)
	Set range of currently active images.
virtual void	SetActiveXformsFromTo (const size_t from, const size_t to)
	Set range of currently active transformations.
virtual void	SetProbabilisticSampleDensity (const float density)
	Set probabilistic sampling density.
virtual void	SetProbabilisticSampleUpdatesAfter (const int iterations)
	Set number of iterations after which probabilistic samples are updated.
void	SetXforms (const std::vector< Xform::SmartPtr > &xformVector)
	Set transformations.
virtual const Xform *	GetGenericXformByIndex (const size_t idx) const
	Get coordinate transformation for one image in the group.
virtual Xform::SmartPtr	GetGenericXformByIndex (const size_t idx)
	Get coordinate transformation for one image in the group.
virtual const Xform *	GetGenericActiveXformByIndex (const size_t idx) const
	Get coordinate transformation for one active image in the group.
virtual Xform::SmartPtr	GetGenericActiveXformByIndex (const size_t idx)
	Get coordinate transformation for one active image in the group.
virtual Types::Coordinate	GetParamStep (const size_t idx, const Types::Coordinate mmStep=1) const
	Get parameter stepping in milimeters.
virtual size_t	ParamVectorDim () const
	Return the functional's parameter vector dimension.
virtual size_t	VariableParamVectorDim () const
	Return the number of variable parameters of the transformation.
virtual void	GetParamVector (CoordinateVector &v)
	Get parameter vector.
virtual void	SetParamVector (CoordinateVector &v)
	Set parameter vector.
virtual void	SetParamVector (CoordinateVector &v, const size_t xformIdx)
	Set parameter vector for a given transformation.
virtual void	SetParameter (const size_t param, const Types::Coordinate value)
	Set single parameter value.
virtual void	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	EvaluateAt (CoordinateVector &v)
	Evaluate functional with given parameter vector.
virtual Self::ReturnType	EvaluateWithGradient (CoordinateVector &v, CoordinateVector &g, const Types::Coordinate step=1)
	Compute functional value and gradient.
virtual void	AllocateStorage ()
	Allocate storage for reformatted images etc.
void	DebugWriteImages ()
	Write all images for debug purposes.
Protected Member Functions
virtual void	ForceZeroSumGradient (CoordinateVector &g) const
	Enforce gradient to be zero-sum over all images.
virtual void	UpdateProbabilisticSamples ()
	Update probablistic samples.
virtual void	InterpolateAllImages ()
	Interpolate all moving images.
virtual void	InterpolateImage (const size_t idx, byte *const destination)
	Interpolate given moving image to template.
virtual bool	Wiggle ()
	Update probabilistic sample table..
virtual UniformVolume::SmartPtr	PrepareSingleImage (UniformVolume::SmartPtr &image)
	Prepare data for one image.
virtual void	PrepareTargetImages ()
	Smooth and pre-scale target images.
virtual const UniformVolume::SmartPtr	GetReformattedImage (const UniformVolume::SmartPtr &targetGrid, const size_t idx) const
	Reformat one image to a given target grid.
Protected Attributes
size_t	m_NumberOfThreads
	Number of threads in thread pool (for allocation of temporary thread memory).
size_t	m_NumberOfTasks
	Number of tasks for thread pool (for allocation of task arguments and results).
bool	m_FreeAndRereadImages
	Flag for freeing and re-reading original images if using smoothed data.
bool	m_ForceZeroSum
	Flag for enforcing zero-sum parameter changes.
size_t	m_ForceZeroSumFirstN
	Restrict zero-sum computation to first N images.
size_t	m_ActiveImagesFrom
	Currently active images from index.
size_t	m_ActiveImagesTo
	Currently active images to index (plus 1).
size_t	m_ActiveXformsFrom
	Currently active transformations from index.
size_t	m_ActiveXformsTo
	Currently active transformations to index (plus 1).
size_t	m_TemplateNumberOfPixels
	Number of pixels in template.
size_t	m_TemplateNumberOfSamples
	Number of samples drawn from the pixels in template.
UniformVolume::SmartPtr	m_TemplateGrid
	Template grid (not pixel data).
bool	m_UseTemplateData
	Flag for use of template pixel data in registration.
std::vector< byte >	m_TemplateData
	Prepared (smoothed, scaled etc.) data of the template image if used in registration.
std::vector < UniformVolume::SmartPtr >	m_ImageVector
	Vector of image volumes with pre-scaled pixel values.
std::vector < UniformVolume::SmartPtr >	m_OriginalImageVector
	Vector of original image volumes.
std::vector< Xform::SmartPtr >	m_XformVector
	Vector of transformations.
float	m_ProbabilisticSampleDensity
	Probabilistic sample count.
std::vector< size_t >	m_ProbabilisticSamples
	Pixel indices of probabilistic samples.
int	m_ProbabilisticSampleUpdatesAfter
	Number of iterations (calls to Evaluate()) after which probabilistic samples are updated.
int	m_ProbabilisticSampleUpdatesSince
	Current number of iterations since last update of probabilistic samples.
std::vector< byte * >	m_Data
	Vector of reformatted and rescaled image data.
std::vector< byte >	m_TempData
	Temporary data allocated at correct size of template grid.
Types::Coordinate	m_GaussianSmoothImagesSigma
	Kernel width in [mm] for Gaussian smoothing of target images.
byte	m_UserBackgroundValue
	User-defined value to fill regions outside FOV.
bool	m_UserBackgroundFlag
	Flag for user-defined background value.
size_t	m_ParametersPerXform
	Number of parameters per transformation..
bool	m_RepeatIntensityHistogramMatching
	Repeat histogram-based intensity matching after each stage.
Static Protected Attributes
static const byte	m_PaddingValue = 255
	Value used to mark regions outside the FOV.
Private Member Functions
void	CopyTemplateData ()
	Copy template data from TypedArray to byte vector.
Friends
class	GroupwiseRegistrationFunctionalAffineInitializer
	Initializer class shall be our friend.

Detailed Description

Base class for groupwise registration functionals.

This class provides the lowest-level components of groupwise image registration, such as image IO, preprocessing, generic access to transformation and image vectors, and parameters common to all algorithms such as zero-sum optimization.

Definition at line 63 of file cmtkGroupwiseRegistrationFunctionalBase.h.

Member Typedef Documentation

typedef GroupwiseRegistrationFunctionalBase cmtk::GroupwiseRegistrationFunctionalBase::Self

Type of this class.

Reimplemented from cmtk::Functional.

Definition at line 72 of file cmtkGroupwiseRegistrationFunctionalBase.h.

typedef SmartPointer<Self> cmtk::GroupwiseRegistrationFunctionalBase::SmartPtr

Smart pointer.

Reimplemented from cmtk::Functional.

Definition at line 75 of file cmtkGroupwiseRegistrationFunctionalBase.h.

typedef Functional cmtk::GroupwiseRegistrationFunctionalBase::Superclass

Type of parent class.

Definition at line 69 of file cmtkGroupwiseRegistrationFunctionalBase.h.

Member Function Documentation

virtual const Xform* cmtk::GroupwiseRegistrationFunctionalBase::GetGenericActiveXformByIndex ( const size_t idx ) const [inline, virtual]

Get coordinate transformation for one active image in the group.

Parameters:

idx	Index of the volume/transformation.

Returns:: Transformation for the selected volume.

Definition at line 282 of file cmtkGroupwiseRegistrationFunctionalBase.h.

virtual Xform::SmartPtr cmtk::GroupwiseRegistrationFunctionalBase::GetGenericActiveXformByIndex ( const size_t idx ) [inline, virtual]

Get coordinate transformation for one active image in the group.

Parameters:

idx	Index of the volume/transformation.

Returns:: Transformation for the selected volume.

Definition at line 291 of file cmtkGroupwiseRegistrationFunctionalBase.h.

virtual const Xform* cmtk::GroupwiseRegistrationFunctionalBase::GetGenericXformByIndex ( const size_t idx ) const [inline, virtual]

Get coordinate transformation for one image in the group.

Parameters:

idx	Index of the volume/transformation.

Returns:: Transformation for the selected volume.

Definition at line 264 of file cmtkGroupwiseRegistrationFunctionalBase.h.

virtual Xform::SmartPtr cmtk::GroupwiseRegistrationFunctionalBase::GetGenericXformByIndex ( const size_t idx ) [inline, virtual]

Get coordinate transformation for one image in the group.

Parameters:

idx	Index of the volume/transformation.

Returns:: Transformation for the selected volume.

Definition at line 273 of file cmtkGroupwiseRegistrationFunctionalBase.h.

virtual size_t cmtk::GroupwiseRegistrationFunctionalBase::GetNumberOfTargetImages ( ) const [inline, virtual]

Get number of target images.

Definition at line 161 of file cmtkGroupwiseRegistrationFunctionalBase.h.

virtual UniformVolume::SmartPtr cmtk::GroupwiseRegistrationFunctionalBase::GetOriginalTargetImage ( const size_t imageIdx ) [inline, virtual]

Get a smart pointer to one original target image.

Definition at line 168 of file cmtkGroupwiseRegistrationFunctionalBase.h.

virtual const UniformVolume* cmtk::GroupwiseRegistrationFunctionalBase::GetOriginalTargetImage ( const size_t imageIdx ) const [inline, virtual]

Get a constant pointer to one original target image.

Definition at line 175 of file cmtkGroupwiseRegistrationFunctionalBase.h.

virtual void cmtk::GroupwiseRegistrationFunctionalBase::GetOriginalTargetImages ( std::vector< UniformVolume::SmartPtr > & tImages ) [inline, virtual]

Get the original target images.

Definition at line 147 of file cmtkGroupwiseRegistrationFunctionalBase.h.

virtual std::vector<UniformVolume::SmartPtr>& cmtk::GroupwiseRegistrationFunctionalBase::GetOriginalTargetImages ( ) [inline, virtual]

Get the original target images.

Definition at line 154 of file cmtkGroupwiseRegistrationFunctionalBase.h.

virtual Types::Coordinate cmtk::GroupwiseRegistrationFunctionalBase::GetParamStep	(	const size_t	idx,
		const Types::Coordinate	mmStep = `1`
	)		const `[inline, virtual]`

Get parameter stepping in milimeters.

Parameters:

idx	Parameter index.
mmStep	Desired step length. This is typically used as a scalar factor for the default (1mm) step size.

Returns:: Step of given parameter that corresponds to 1 mm effective motion.

Reimplemented from cmtk::Functional.

Definition at line 301 of file cmtkGroupwiseRegistrationFunctionalBase.h.

virtual UniformVolume::SmartPtr& cmtk::GroupwiseRegistrationFunctionalBase::GetTemplateGrid ( ) [inline, virtual]

Retrieve the template grid.

Definition at line 128 of file cmtkGroupwiseRegistrationFunctionalBase.h.

virtual const UniformVolume* cmtk::GroupwiseRegistrationFunctionalBase::GetTemplateGrid ( ) const [inline, virtual]

Retrieve the template grid.

Definition at line 135 of file cmtkGroupwiseRegistrationFunctionalBase.h.

virtual void cmtk::GroupwiseRegistrationFunctionalBase::InterpolateImage	(	const size_t	idx,
		byte *const	destination
	)		`[inline, protected, virtual]`

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 in cmtk::GroupwiseRegistrationFunctionalXformTemplate< TXform >, cmtk::GroupwiseRegistrationFunctionalXformTemplate< AffineXform >, and cmtk::GroupwiseRegistrationFunctionalXformTemplate< SplineWarpXform >.

Definition at line 471 of file cmtkGroupwiseRegistrationFunctionalBase.h.

virtual size_t cmtk::GroupwiseRegistrationFunctionalBase::ParamVectorDim ( ) const [inline, virtual]

Return the functional's parameter vector dimension.

We assume that all transformations have the same number of parameters. This is true for affine transformations.

Implements cmtk::Functional.

Definition at line 318 of file cmtkGroupwiseRegistrationFunctionalBase.h.

virtual void cmtk::GroupwiseRegistrationFunctionalBase::SetActiveImagesFromTo	(	const size_t	from,
		const size_t	to
	)		`[inline, virtual]`

Set range of currently active images.

The "to" parameter is the index of the last active image plus one, so it can be used directly as the upper bound in a "for" loop.

Definition at line 218 of file cmtkGroupwiseRegistrationFunctionalBase.h.

virtual void cmtk::GroupwiseRegistrationFunctionalBase::SetActiveXformsFromTo	(	const size_t	from,
		const size_t	to
	)		`[inline, virtual]`

Set range of currently active transformations.

The "to" parameter is the index of the last active transformation plus one, so it can be used directly as the upper bound in a "for" loop.

Reimplemented in cmtk::GroupwiseRegistrationFunctionalXformTemplate< SplineWarpXform >.

Definition at line 228 of file cmtkGroupwiseRegistrationFunctionalBase.h.

virtual void cmtk::GroupwiseRegistrationFunctionalBase::SetForceZeroSum ( const bool forceZeroSum = true ) [inline, virtual]

Set flag for zero-sum updates.

Definition at line 202 of file cmtkGroupwiseRegistrationFunctionalBase.h.

virtual void cmtk::GroupwiseRegistrationFunctionalBase::SetForceZeroSumFirstN ( const size_t forceZeroSumFirstN ) [inline, virtual]

Set count for restricted zero-sum updates.

Definition at line 208 of file cmtkGroupwiseRegistrationFunctionalBase.h.

virtual void cmtk::GroupwiseRegistrationFunctionalBase::SetFreeAndRereadImages ( const bool flag = true ) [inline, virtual]

Set flag for freeing and rereading images.

If registration uses smoothed images, the original data can be freed after smoothing and reread from the file system if needed again. This saves roughly 1/2 of memory allocation.

Definition at line 91 of file cmtkGroupwiseRegistrationFunctionalBase.h.

virtual void cmtk::GroupwiseRegistrationFunctionalBase::SetGaussianSmoothImagesSigma ( const Types::Coordinate gaussianSmoothImagesSigma ) [inline, virtual]

Set Gaussian smoothing kernel width for target images.

Non-positive values turn off smoothing.

Definition at line 183 of file cmtkGroupwiseRegistrationFunctionalBase.h.

virtual void cmtk::GroupwiseRegistrationFunctionalBase::SetProbabilisticSampleDensity ( const float density ) [inline, virtual]

Set probabilistic sampling density.

Definition at line 236 of file cmtkGroupwiseRegistrationFunctionalBase.h.

virtual void cmtk::GroupwiseRegistrationFunctionalBase::SetProbabilisticSampleUpdatesAfter ( const int iterations ) [inline, virtual]

Set number of iterations after which probabilistic samples are updated.

Definition at line 243 of file cmtkGroupwiseRegistrationFunctionalBase.h.

virtual void cmtk::GroupwiseRegistrationFunctionalBase::SetRepeatIntensityHistogramMatching ( const bool flag = true ) [inline, virtual]

Set flag for repeated histogram-based intensity matching.

Definition at line 97 of file cmtkGroupwiseRegistrationFunctionalBase.h.

virtual void cmtk::GroupwiseRegistrationFunctionalBase::SetUserBackgroundValue ( const byte value = 0 ) [inline, virtual]

Set user-defined image background value to be substituted outside the field of view.

Definition at line 189 of file cmtkGroupwiseRegistrationFunctionalBase.h.

void cmtk::GroupwiseRegistrationFunctionalBase::SetXforms ( const std::vector< Xform::SmartPtr > & xformVector ) [inline]

Set transformations.

Definition at line 251 of file cmtkGroupwiseRegistrationFunctionalBase.h.

virtual void cmtk::GroupwiseRegistrationFunctionalBase::UnsetUserBackgroundValue ( ) [inline, virtual]

Unset user-defined image background value.

Definition at line 196 of file cmtkGroupwiseRegistrationFunctionalBase.h.

virtual size_t cmtk::GroupwiseRegistrationFunctionalBase::VariableParamVectorDim ( ) const [inline, virtual]

Return the number of variable parameters of the transformation.

Returns:: This function returns the same value as ParamVectorDim(). Non-varying parameters (e.g., rotation centers) are handled via parameter step values.

Reimplemented from cmtk::Functional.

Definition at line 328 of file cmtkGroupwiseRegistrationFunctionalBase.h.