mirtk::RegisteredImage Class Reference

#include <RegisteredImage.h>

Inheritance diagram for mirtk::RegisteredImage:

Collaboration diagram for mirtk::RegisteredImage:

Public Types
enum	Channel
	Enumeration of registered image channel indices.
typedef GenericImage< double >	DisplacementImageType
	Type of cached displacement fields.
typedef GenericImage< VoxelType >	InputGradientType
	Type of untransformed gradient image.
typedef GenericImage< VoxelType >	InputHessianType
	Type of untransformed Hessian image.
typedef GenericImage< VoxelType >	InputImageType
	Type of untransformed input image.
Public Types inherited from mirtk::GenericImage< double >
typedef voxel_info< ScalarType >::RealType	RealScalarType
	Floating point type corresponding to scalar type of voxel type.
typedef voxel_info< VoxelType >::RealType	RealType
typedef voxel_info< VoxelType >::ScalarType	ScalarType
	Scalar type corresponding to voxel type.
typedef double	VoxelType
	Voxel type.
Public Types inherited from mirtk::BaseImage
enum	OrientationCode { ,   L2R = 1, R2L = 2, P2A = 3, A2P = 4,   I2S = 5, S2I = 6 }
	Orientation codes (same as defined in nifti1_io.h, e.g., NIFTI_L2R) More...
typedef double	VoxelType

Public Member Functions
enum InterpolationMode	GetInterpolationMode () const
void	Initialize (const ImageAttributes &, int=0)
	mirtkComponentMacro (DisplacementImageType, FixedDisplacement)
	Pre-computed fixed displacements.
	mirtkComponentMacro (DisplacementImageType, Displacement)
	Pre-computed displacements.
	mirtkPublicAggregateMacro (InputImageType, InputImage)
	Untransformed input image.
	mirtkPublicAggregateMacro (const class Transformation, Transformation)
	Current transformation estimate.
	mirtkPublicAggregateMacro (WorldCoordsImage, WorldCoordinates)
	Pre-computed image to world coordinates.
	mirtkPublicAggregateMacro (DisplacementImageType, ExternalDisplacement)
	Externally pre-computed displacements to use.
	mirtkPublicAttributeMacro (enum InterpolationMode, InterpolationMode)
	Interpolation mode.
	mirtkPublicAttributeMacro (enum ExtrapolationMode, ExtrapolationMode)
	Extrapolation mode.
	mirtkPublicAttributeMacro (bool, CacheWorldCoordinates)
	Whether to use pre-computed world coordinates.
	mirtkPublicAttributeMacro (bool, CacheFixedDisplacement)
	Whether to use pre-computed fixed displacements.
	mirtkPublicAttributeMacro (bool, CacheDisplacement)
	Whether to use pre-computed displacements.
	mirtkPublicAttributeMacro (bool, SelfUpdate)
	Whether self-update is enabled.
	mirtkPublicAttributeMacro (double, MinIntensity)
	Minimum foreground intensity of warped image or NaN.
	mirtkPublicAttributeMacro (double, MaxIntensity)
	Maximum foreground intensity of warped image or NaN.
	mirtkPublicAttributeMacro (double, GradientSigma)
	mirtkPublicAttributeMacro (double, HessianSigma)
	mirtkPublicAttributeMacro (bool, PrecomputeDerivatives)
	mirtkPublicAttributeMacro (int, MaxGradientPercentile)
	mirtkPublicAttributeMacro (double, MaxGradientMagnitude)
	When positive and not inf, linearly rescale gradient vectors to this maximum magnitude.
	mirtkPublicComponentMacro (InputGradientType, InputGradient)
	Untransformed input gradient image.
	mirtkPublicComponentMacro (InputHessianType, InputHessian)
	Untransformed input Hessian image.
	mirtkPublicComponentMacro (WorldCoordsImage, ImageToWorld)
	Pre-computed image to world coordinates.
	mirtkReadOnlyAttributeMacro (double, MinInputIntensity)
	Minimum foreground intensity of input image.
	mirtkReadOnlyAttributeMacro (double, MaxInputIntensity)
	Maximum foreground intensity of input image.
int	NumberOfChannels () const
	Number of registered channels.
int	NumberOfVoxels () const
	Number of voxels per registered channel.
int	Offset (int) const
	Offset of channel c with respect to the start of the image data.
RegisteredImage &	operator= (const RegisteredImage &)
	Assignment operator.
void	Recompute (const blocked_range3d< int > &region)
void	Recompute ()
	RegisteredImage ()
	Constructor.
	RegisteredImage (const RegisteredImage &)
	Copy constructor.
void	Update (const blocked_range3d< int > &region, bool intensity=true, bool gradient=false, bool hessian=false, bool force=false)
void	Update (const blocked_range3d< int > &region, const DisplacementImageType *disp, bool intensity=true, bool gradient=false, bool hessian=false)
void	Update (bool intensity=true, bool gradient=false, bool hessian=false, bool force=false)
	~RegisteredImage ()
	Destructor.
Public Member Functions inherited from mirtk::GenericImage< double >
void	Clear ()
	Clear an image.
virtual BaseImage *	Copy () const
	Create copy of this image.
void	CopyFrom (const VoxelType *)
	Copy image data from 1D array.
void	CopyFrom (const BaseImage &)
	Copy image data from other image of same size.
void	CopyFrom (const GenericImage &)
	Copy image data from other image of same size.
bool	CropPad (int margin=0)
	Crop/pad image background.
VoxelType *	Data (int=0)
	Get raw pointer to contiguous image data.
VoxelType *	Data (int, int, int=0, int=0)
	Get raw pointer to contiguous image data.
const VoxelType *	Data (int=0) const
	Get raw pointer to contiguous image data.
const VoxelType *	Data (int, int, int=0, int=0) const
	Get raw pointer to contiguous image data.
virtual void	FlipXT (bool modify_origin=false)
	Flip x and t axis, always also swaps voxel size.
virtual void	FlipXY (bool modify_origin=false)
	Flip x and y axis, always also swaps voxel size.
virtual void	FlipXZ (bool modify_origin=false)
	Flip x and z axis, always also swaps voxel size.
virtual void	FlipYT (bool modify_origin=false)
	Flip y and t axis, always also swaps voxel size.
virtual void	FlipYZ (bool modify_origin=false)
	Flip y and z axis, always also swaps voxel size.
virtual void	FlipZT (bool modify_origin=false)
	Flip z and t axis, always also swaps voxel size.
	GenericImage ()
	Default constructor.
	GenericImage (const char *)
	Constructor from image file.
	GenericImage (int, int, int=1, int=1, VoxelType *data=NULL)
	Constructor for given image size.
	GenericImage (int, int, int, int, int, VoxelType *data=NULL)
	Constructor for given image size.
	GenericImage (const ImageAttributes &, VoxelType *data=NULL)
	Constructor for given image attributes.
	GenericImage (const ImageAttributes &, int, VoxelType *data=NULL)
	Constructor for given image attributes.
	GenericImage (const BaseImage &)
	Copy constructor for image.
	GenericImage (const GenericImage &)
	Copy constructor for image.
	GenericImage (const GenericImage< TVoxel2 > &)
	Copy constructor for image of different type.
VoxelType	Get (int) const
	Function for pixel get access.
VoxelType	Get (int, int, int=0, int=0) const
	Function for pixel get access.
virtual double	GetAsDouble (int) const
	Function for pixel get access as double.
virtual double	GetAsDouble (int, int, int=0, int=0) const
	Function for pixel get access as double.
virtual void	GetAsVector (Vector &, int) const
	Function for pixel get access as double.
virtual void	GetAsVector (Vector &, int, int, int=0, int=0) const
	Function for pixel get access as double.
virtual Vector	GetAsVector (int) const
	Function for pixel get access as double.
virtual Vector	GetAsVector (int, int, int=0, int=0) const
	Function for pixel get access as double.
RealType	GetAverage (int=1) const
virtual void *	GetDataPointer (int=0)
	Get raw pointer to contiguous image data.
virtual const void *	GetDataPointer (int=0) const
	Get raw pointer to contiguous image data.
virtual void *	GetDataPointer (int, int, int=0, int=0)
	Get raw pointer to contiguous image data.
virtual const void *	GetDataPointer (int, int, int=0, int=0) const
	Get raw pointer to contiguous image data.
virtual int	GetDataType () const
	Get enumeration value corresponding to voxel type.
virtual double	GetDataTypeMax () const
	Maximum value a pixel can hold without overflowing.
virtual double	GetDataTypeMin () const
	Minimum value a pixel can hold without overflowing.
virtual int	GetDataTypeSize () const
	Get size of each voxel in bytes.
GenericImage	GetFrame (int, int=-1) const
	Get time instance (i.e., frame) or channel of image.
void	GetFrame (GenericImage &, int, int=-1) const
	Get time instance (i.e., frame) or channel of image.
virtual void	GetFrame (BaseImage *&, int, int=-1) const
	Get time instance (i.e., frame) or channel of image.
void	GetMaxPosition (Point &, int=1, int=0) const
	Get Max Intensity position around the point.
void	GetMinMax (VoxelType &, VoxelType &) const
	Minimum and maximum pixel values get accessor.
void	GetMinMax (VoxelType &, VoxelType &, VoxelType) const
	Minimum and maximum pixel values get accessor with padding.
void	GetMinMax (VoxelType *, VoxelType *) const
void	GetMinMax (VoxelType *, VoxelType *, VoxelType) const
void	GetMinMaxPad (VoxelType *, VoxelType *, VoxelType) const
VoxelType *	GetPointerToVoxels (int=0, int=0, int=0, int=0)
const VoxelType *	GetPointerToVoxels (int=0, int=0, int=0, int=0) const
GenericImage	GetRegion (int, int) const
	Get image consisting of specified 2D slice.
void	GetRegion (GenericImage &, int, int) const
	Get image consisting of specified 2D slice.
virtual void	GetRegion (BaseImage *&, int, int) const
	Get image consisting of specified 2D slice.
GenericImage	GetRegion (int, int, int, int, int, int) const
	Get image consisting of specified 3D subregion.
void	GetRegion (GenericImage &, int, int, int, int, int, int) const
	Get image consisting of specified 3D subregion.
virtual void	GetRegion (BaseImage *&, int, int, int, int, int, int) const
	Get image consisting of specified 3D subregion.
GenericImage	GetRegion (int, int, int, int, int, int, int, int) const
	Get image consisting of specified 4D subregion.
void	GetRegion (GenericImage &, int, int, int, int, int, int, int, int) const
	Get image consisting of specified 4D subregion.
virtual void	GetRegion (BaseImage *&, int, int, int, int, int, int, int, int) const
	Get image consisting of specified 4D subregion.
RealType	GetSD (int=1) const
	Standard Deviation of the pixels.
void	GravityCenter (Point &, int=1, int=0) const
	Get Gravity center position of a given window.
virtual void	Initialize ()
	Initialize a previously allocated image.
virtual void	Initialize (const ImageAttributes &, int, VoxelType *data)
	Initialize an image.
void	Initialize (const ImageAttributes &, int)
	Initialize an image.
void	Initialize (const ImageAttributes &, VoxelType *data=NULL)
	Initialize an image.
void	Initialize (int, int, int, int, int, VoxelType *data=NULL)
	Initialize an image.
void	Initialize (int, int, int=1, int=1, VoxelType *data=NULL)
	Initialize an image.
RealType	Mean (bool fg=true) const
int	N () const
	Number of vector components per voxel.
	operator bool () const
	Cast to bool, checks if this image has been initialized and ready for use.
BinaryImage	operator!= (VoxelType) const
	Get binary mask for voxels which are not equal the scalar.
VoxelType &	operator() (int)
	Function for pixel access from via operators.
const VoxelType &	operator() (int) const
	Function for pixel access from via operators.
VoxelType &	operator() (int, int, int=0, int=0)
	Function for pixel access from via operators.
const VoxelType &	operator() (int, int, int=0, int=0) const
	Function for pixel access from via operators.
GenericImage	operator* (const GenericImage &) const
	Multiply images voxel-wise.
GenericImage	operator* (double) const
	Multiply image by scalar.
GenericImage &	operator*= (const GenericImage &)
	Multipy voxels.
GenericImage &	operator*= (double)
	Multiply by scalar.
GenericImage	operator+ (const GenericImage &) const
	Add images.
GenericImage	operator+ (double) const
	Add scalar to image.
GenericImage &	operator+= (const GenericImage &)
	Add image.
GenericImage &	operator+= (double)
	Add scalar.
GenericImage	operator- (const GenericImage &) const
	Subtract images.
GenericImage	operator- (double) const
	Subtract scalar from image.
GenericImage &	operator-= (const GenericImage &)
	Subtract image.
GenericImage &	operator-= (double)
	Subtract scalar.
GenericImage	operator/ (const GenericImage &) const
	Divide images voxel-wise.
GenericImage	operator/ (double) const
	Divide image by scalar.
GenericImage &	operator/= (const GenericImage &)
	Divide voxels.
GenericImage &	operator/= (double)
	Divide by scalar.
GenericImage	operator< (VoxelType) const
	Clamp image given lower threshold.
GenericImage &	operator<= (VoxelType)
	Clamp image given lower threshold.
GenericImage &	operator= (VoxelType)
	Assign constant value to each voxel.
GenericImage< VoxelType > &	operator= (const BaseImage &)
	Assignment operator with implicit cast to double and then VoxelType.
GenericImage< VoxelType > &	operator= (const GenericImage &)
	Assignment operator.
GenericImage< VoxelType > &	operator= (const GenericImage< TVoxel2 > &)
	Assignment operator with implicit cast.
bool	operator== (const GenericImage< TVoxel2 > &) const
GenericImage	operator> (VoxelType) const
	Clamp image given upper threshold.
GenericImage &	operator>= (VoxelType)
	Clamp image given upper threshold.
void	Put (int, VoxelType)
	Function for pixel put access.
void	Put (int, int, VoxelType)
	Function for pixel put access.
void	Put (int, int, int, VoxelType)
	Function for pixel put access.
void	Put (int, int, int, int, VoxelType)
	Function for pixel put access.
virtual void	PutAsDouble (int, double)
	Function for pixel put access.
virtual void	PutAsDouble (int, int, double)
	Function for pixel put access.
virtual void	PutAsDouble (int, int, int, double)
	Function for pixel put access.
virtual void	PutAsDouble (int, int, int, int, double)
	Function for pixel put access.
virtual void	PutAsVector (int, const Vector &)
	Function for pixel put access.
virtual void	PutAsVector (int, int, const Vector &)
	Function for pixel put access.
virtual void	PutAsVector (int, int, int, const Vector &)
	Function for pixel put access.
virtual void	PutAsVector (int, int, int, int, const Vector &)
	Function for pixel put access.
virtual void	PutBackgroundValueAsDouble (double, bool)
	Put background value.
void	PutMinMax (VoxelType, VoxelType)
	Linearly rescale intensities.
virtual void	Read (const char *)
	Read image from file.
virtual void	ReflectT (bool modify_axes=false)
	Reflect image along t.
virtual void	ReflectX (bool modify_axes=false)
	Reflect image along x.
virtual void	ReflectY (bool modify_axes=false)
	Reflect image along y.
virtual void	ReflectZ (bool modify_axes=false)
	Reflect image along z.
virtual void	SwapXT (bool modify_axes=true)
	Swap x and t axis.
virtual void	SwapXY (bool modify_axes=true)
	Swap x and y axis.
virtual void	SwapXZ (bool modify_axes=true)
	Swap x and z axis.
virtual void	SwapYT (bool modify_axes=true)
	Swap y and t axis.
virtual void	SwapYZ (bool modify_axes=true)
	Swap y and z axis.
virtual void	SwapZT (bool modify_axes=true)
	Swap z and t axis.
virtual void	Write (const char *) const
	Write image to file.
	~GenericImage ()
	Destructor.
Public Member Functions inherited from mirtk::BaseImage
const ImageAttributes &	Attributes () const
	Gets the image attributes.
void	BoundingBox (int &, int &, int &, int &) const
	Get 2D bounding box of image foreground.
void	BoundingBox (int &, int &, int &, int &, int &, int &) const
	Get 3D bounding box of image foreground.
void	BoundingBox (int &, int &, int &, int &, int &, int &, int &, int &) const
	Get 3D+t bounding box of image foreground.
int	CenterOfForeground (Point &center) const
int	CenterOfForeground (Point &center, double padding) const
void	ClearBackgroundValue ()
	Clear background value.
void	ClearMask (bool=false)
	Clear mask upon n-th call after n preceeding InitializeMask calls.
ImageAttributes	ForegroundDomain (int i1, int j1, int k1, int i2, int j2, int k2, bool orthogonal=true) const
ImageAttributes	ForegroundDomain (bool orthogonal=true) const
ImageAttributes	ForegroundDomain (double padding, bool orthogonal=true) const
VoxelType	Get (int) const
	Get pixel value at voxel with given index.
VoxelType	Get (int, int, int=0, int=0) const
	Get pixel value at voxel with given lattice coordinates.
const Matrix &	GetAffineMatrix () const
double	GetBackgroundValueAsDouble () const
	Get background value.
const ImageAttributes &	GetImageAttributes () const
const Matrix &	GetImageToWorldMatrix () const
	Return transformation matrix for image to world coordinates.
BinaryImage *	GetMask (bool=false)
	Get foreground mask (optionally, take over ownership)
const BinaryImage *	GetMask () const
	Get foreground mask.
virtual void	GetMinMaxAsDouble (double &, double &) const
	Minimum and maximum pixel values get accessor.
void	GetMinMaxAsDouble (double *, double *) const
	Minimum and maximum pixel values get accessor.
int	GetNumberOfVoxels () const
void	GetOrientation (double *, double *, double *=NULL) const
	Get image x- and y-axis and z-axis.
Point	GetOrigin () const
	Image origin get access.
void	GetOrigin (double &, double &, double &) const
	Image origin get access.
void	GetOrigin (double &, double &, double &, double &) const
	Image origin get access.
void	GetPixelSize (double &, double &) const
	Voxel dimensions get access.
void	GetPixelSize (double &, double &, double &) const
	Voxel dimensions get access.
void	GetPixelSize (double &, double &, double &, double &) const
	Voxel dimensions get access.
void	GetPixelSize (double *, double *, double *) const
	Voxel dimensions get access.
void	GetPixelSize (double *, double *, double *, double *) const
	Voxel dimensions get access.
void *	GetScalarPointer (int=0, int=0, int=0, int=0)
const void *	GetScalarPointer (int=0, int=0, int=0, int=0) const
int	GetScalarType () const
double	GetScalarTypeMax () const
double	GetScalarTypeMin () const
int	GetScalarTypeSize () const
int	GetT () const
	Returns the number of voxels in the t-direction.
double	GetTOrigin () const
	Get temporal origin.
double	GetTSize () const
	Returns the size of a voxel in the t-direction.
const Matrix &	GetWorldToImageMatrix () const
	Return transformation matrix for world to image coordinates.
int	GetX () const
	Returns the number of voxels in the x-direction.
double	GetXSize () const
	Returns the size of a voxel in the x-direction.
int	GetY () const
	Returns the number of voxels in the y-direction.
double	GetYSize () const
	Returns the size of a voxel in the y-direction.
int	GetZ () const
	Returns the number of voxels in the z-direction.
double	GetZSize () const
	Returns the size of a voxel in the z-direction.
bool	HasBackground () const
	Whether any voxel is within background.
bool	HasBackgroundValue () const
	Whether a background value has been set.
bool	HasMask () const
bool	HasSpatialAttributesOf (const BaseImage *) const
	Checks if this image shares the same spatial attributes with another image.
double	ImageToTime (double) const
	Image to time coordinate conversion.
void	ImageToWorld (double &, double &) const
	Image to world coordinate conversion with two doubles.
void	ImageToWorld (double &, double &, double &) const
	Image to world coordinate conversion with three doubles.
void	ImageToWorld (Point &) const
	Image to world coordinate conversion with a given point.
void	ImageToWorld (Vector3 &) const
	Convert vector w.r.t. image axes to vector w.r.t. world axes.
void	ImageToWorld (WorldCoordsImage &i2w, bool _3D=true) const
void	ImageToWorld (double *i2w, bool _3D=true) const
void	ImageToWorld (PointSet &) const
	Adds world coordinates of each voxel to given point set.
void	IndexToVoxel (int, int &, int &) const
	Function to convert index to pixel coordinates.
void	IndexToVoxel (int, int &, int &, int &) const
	Function to convert index to pixel coordinates.
void	IndexToVoxel (int, int &, int &, int &, int &) const
	Function to convert index to pixel coordinates.
void	IndexToWorld (int, double &, double &) const
	Get world coordinates (in mm) of pixl.
void	IndexToWorld (int, double &, double &, double &) const
	Get world coordinates (in mm) of pixel.
void	IndexToWorld (int, Point &) const
	Get world coordinates (in mm) of pixel.
Point	IndexToWorld (int) const
	Get world coordinates (in mm) of pixel.
void	InitializeMask (int t=-1, bool=false)
	Initialize mask if not done yet or none is set.
bool	IsBackground (int) const
	Whether voxel is within background without index-out-of-bounds check.
bool	IsBackground (int, int, int=0, int=0) const
	Whether voxel is within background without index-out-of-bounds check.
bool	IsBoundary (int) const
	Whether voxel index is at boundary of finite image domain.
bool	IsBoundary (int, int) const
	Whether voxel indices are at boundary of finite 2D image domain.
bool	IsBoundary (int, int, int) const
	Whether voxel indices are at boundary of finite 3D image domain.
bool	IsBoundary (int, int, int, int) const
	Whether voxel indices are at boundary of finite 4D image domain.
bool	IsBoundingBoxInsideForeground (int, int, int, int) const
	Whether all voxels within a 2D bounding region are inside foreground region.
bool	IsBoundingBoxInsideForeground (int, int, int, int, int, int) const
	Whether all voxels within a 3D bounding region are inside foreground region.
bool	IsBoundingBoxInsideForeground (int, int, int, int, int, int, int, int) const
	Whether all voxels within a 4D bounding region are inside foreground region.
bool	IsEmpty () const
	Whether image is uninitialized.
bool	IsForeground (int) const
	Whether voxel is within foreground without index-out-of-bounds check.
bool	IsForeground (int, int, int=0, int=0) const
	Whether voxel is within foreground without index-out-of-bounds check.
bool	IsInFOV (double, double, double)
	Returns true if point is within the field of view of image.
bool	IsInside (int) const
	Whether voxel index is within finite image domain.
bool	IsInside (int, int) const
	Whether voxel indices are within finite 2D image domain.
bool	IsInside (int, int, int) const
	Whether voxel indices are within finite 3D image domain.
bool	IsInside (int, int, int, int) const
	Whether voxel indices are within finite 4D image domain.
bool	IsInsideForeground (int) const
	Whether voxel is index is within finite image domain and part of foreground region.
bool	IsInsideForeground (int, int, int=0, int=0) const
	Whether voxel indices are within finite image domain and part of foreground region.
bool	IsNextToBackground (int) const
	Whether at least one neighboring voxel is outside the finite foreground region.
bool	IsNextToBackground (int, int, int=0, int=0) const
	Whether at least one neighboring voxel is outside the finite foreground region.
bool	IsNextToForeground (int) const
	Whether at least one neighboring voxel is inside the finite foreground region.
bool	IsNextToForeground (int, int, int=0, int=0) const
	Whether at least one neighboring voxel is inside the finite foreground region.
bool	IsOutside (int) const
	Whether voxel is index is outside finite image domain.
bool	IsOutside (int, int) const
	Whether voxel indices are outside finite 4D image domain.
bool	IsOutside (int, int, int) const
	Whether voxel indices are outside finite 4D image domain.
bool	IsOutside (int, int, int, int) const
	Whether voxel indices are outside finite 4D image domain.
bool	IsOutsideForeground (int) const
	Whether voxel is index is outside finite image domain or part of background region.
bool	IsOutsideForeground (int, int, int=0, int=0) const
	Whether voxel indices are outside finite image domain or part of background region.
int	NumberOfSpatialVoxels () const
	Returns the total number of spatial voxels.
int	NumberOfVoxels () const
	Returns the total number of voxels.
BaseImage &	operator= (const BaseImage &)
	Assignment operator.
void	Orientation (OrientationCode &, OrientationCode &, OrientationCode &) const
	Get orientation of axis relative to patient.
bool	OwnsMask () const
virtual void	Print (Indent=0) const
	Print image information.
void	PutAffineMatrix (const Matrix &, bool=false)
void	PutBackgroundValueAsDouble (double)
	Put background value.
void	PutMask (BinaryImage *, bool=false)
	Set foreground mask.
virtual void	PutMinMaxAsDouble (double, double)
	Minimum and maximum pixel values put accessor.
void	PutOrientation (double *, double *, double *=NULL)
	Put image x- and y-axis and z-axis.
void	PutOrigin (const Point &)
	Image origin put access.
void	PutOrigin (double, double, double)
	Image origin put access.
void	PutOrigin (double, double, double, double)
	Image origin put access.
void	PutPixelSize (double, double, double)
	Voxel dimensions put access.
void	PutPixelSize (double, double, double, double)
	Voxel dimensions put access.
void	PutTOrigin (double)
	Put temporal origin.
void	PutTSize (double)
	Set temporal voxel size, i.e., to zero for vector field and non-zero for temporal sequence.
void	ResetAffineMatrix ()
void	ResetBackgroundValueAsDouble (double)
int	T () const
	Returns the number of voxels in the t-direction.
double	TimeToImage (double) const
	Time to image coordinate conversion.
double	TSize () const
	Returns the size of a voxel in the t-direction.
int	VoxelToIndex (int, int, int=0, int=0) const
	Function to convert pixel to index.
void	WorldToImage (double &, double &) const
	World to image coordinate conversion with two doubles.
void	WorldToImage (double &, double &, double &) const
	World to image coordinate conversion with three doubles.
void	WorldToImage (Point &) const
	World to image coordinate conversion with a given point.
void	WorldToImage (Vector3 &) const
	Convert vector w.r.t. world axes to vector w.r.t. image axes.
int	X () const
	Returns the number of voxels in the x-direction.
double	XSize () const
	Returns the size of a voxel in the x-direction.
int	Y () const
	Returns the number of voxels in the y-direction.
double	YSize () const
	Returns the size of a voxel in the y-direction.
int	Z () const
	Returns the number of voxels in the z-direction.
double	ZSize () const
	Returns the size of a voxel in the z-direction.
virtual	~BaseImage ()
	Destructor.
Public Member Functions inherited from mirtk::Object
virtual const char *	NameOfClass () const =0
	Get name of class, which this object is an instance of.
virtual ParameterList	Parameter () const
	Get parameter name/value pairs.
bool	Parameter (const ParameterList &)
	Set parameters from name/value pairs.
virtual bool	Set (const char *name, const char *value)
virtual	~Object ()
	Destructor.

Protected Member Functions
void	ComputeInputGradient (double sigma)
void	ComputeInputHessian (double sigma)
Protected Member Functions inherited from mirtk::GenericImage< double >
void	AllocateImage (VoxelType *=NULL)
	Allocate image memory.
Protected Member Functions inherited from mirtk::BaseImage
	BaseImage ()
	Default constructor.
	BaseImage (const ImageAttributes &, int=-1)
	Constructor.
	BaseImage (const BaseImage &)
	Copy constructor.
void	PutAttributes (const ImageAttributes &)
	Puts attributes of image.
void	UpdateMatrix ()
	Update coordinate transformation.
Protected Member Functions inherited from mirtk::Object
template<typename... Args>
void	Throw (ErrorType err, const char *func, Args... args) const

Protected Attributes
int	_NumberOfActiveLevels
	Number of active levels.
int	_NumberOfPassiveLevels
	Number of passive levels (fixed transformation)
int	_Offset [13]
	Offsets of the different registered image channels.
Protected Attributes inherited from mirtk::GenericImage< double >
VoxelType *	_data
	Pointer to image data.
bool	_dataOwner
	Whether image data memory itself is owned by this instance.
VoxelType ****	_matrix
Protected Attributes inherited from mirtk::BaseImage
ImageAttributes	_attr
	Image attributes.
double	_bg
	Background value - may also be NaN for floating point images.
bool	_bgSet
	Whether a background value was set.
BinaryImage *	_mask
	Foreground mask.
int	_maskOwner
Matrix	_matI2W
	Transformation matrix from image coordinates to (transformed) world coordinates.
Matrix	_matW2I
	Transformation matrix from (transformed) world coordinates to image coordinates.
int	_NumberOfVoxels
	Total number of voxels.

Additional Inherited Members
Static Public Member Functions inherited from mirtk::BaseImage
static BaseImage *	New (const char *)
	Read file and construct image.
static BaseImage *	New (const BaseImage *)
	Construct image copy of same type.
static BaseImage *	New (int)
	Construct image with given voxel type.
Static Public Member Functions inherited from mirtk::Object
static const char *	NameOfType ()
	Get name of this class type.
Static Protected Member Functions inherited from mirtk::Object
template<typename... Args>
static void	ThrowStatic (ErrorType err, const char *cls, const char *func, Args... args)

Detailed Description

Registered image such as fixed target image or transformed source image

An instance of this (multi-channel) image class stores the intensities of a registered image after alignment using the current transformation estimate. If no (changing) transformation is set, the image is considered to be fixed and is thus only updated once during the initialization. If a transformation is set, however, upon every update of the input transformation, the new moving image intensities are computed by applying the current transformation and interpolating the input image intensities. For the computation of the similarity measure gradient, the warped image derivatives are stored along with the intensities in the consecutive image channels of the registered image instance (i.e., t dimension). In case of a gradient field similarity measure, these derivatives include not only the 1st order, but also 2nd order derivatives needed for the similarity measure gradient computation. An image similarity specifies which channels are required for its evaluation by calling the Initialize function with a suitable number of channels (i.e., 1, 4, or 10) and request their udpate using the appropriate parameters of the Update function.

The assignment of the transformed intensities and derivatives to the fourth dimension (i.e. channels) of the registered image is as follows:

• t=0: Transformed intensity
• t=1: Transformed 1st order derivative w.r.t x
• t=2: Transformed 1st order derivative w.r.t y
• t=3: Transformed 1st order derivative w.r.t z
• t=4: Transformed 2nd order derivative w.r.t xx
• t=5: Transformed 2nd order derivative w.r.t xy
• t=6: Transformed 2nd order derivative w.r.t xz
• t=7: Transformed 2nd order derivative w.r.t yy
• t=8: Transformed 2nd order derivative w.r.t yz
• t=9: Transformed 2nd order derivative w.r.t zz

Definition at line 70 of file RegisteredImage.h.

Member Function Documentation

ComputeInputGradient()

void mirtk::RegisteredImage::ComputeInputGradient ( double  sigma )

protected

(Pre-)compute gradient of input image

Parameters

[in]

sigma

Standard deviation of Gaussian smoothing filter in voxels.

ComputeInputHessian()

void mirtk::RegisteredImage::ComputeInputHessian ( double  sigma )

protected

(Pre-)compute Hessian of input image

Parameters

[in]

sigma

Standard deviation of Gaussian smoothing filter in voxels.

GetInterpolationMode()

enum InterpolationMode mirtk::RegisteredImage::GetInterpolationMode

(

)

const

Get interpolation mode

When _InterpolationMode is Interpolation_Default, this function returns the respective default interpolation mode with or without padding.

Initialize()

void mirtk::RegisteredImage::Initialize ( const ImageAttributes &  , int  = 0  )

virtual

Initialize image

This function is called by the image similarity to set the attributes of the registered image, i.e., the attributes of the discrete image domain on which similarity is to be evaluated. It initializes the image to zero. The Update function must be called to initialize the output image intensities and derivatives before similarity can be evaluated.

Implements mirtk::BaseImage.

mirtkPublicAttributeMacro() [1/4]

mirtk::RegisteredImage::mirtkPublicAttributeMacro	(	double	,
		GradientSigma
	)

Standard deviation of Gaussian smoothing kernel applied before 1st order derivative computations in voxel units

mirtkPublicAttributeMacro() [2/4]

mirtk::RegisteredImage::mirtkPublicAttributeMacro	(	double	,
		HessianSigma
	)

Standard deviation of Gaussian smoothing kernel applied before 2nd order derivative computations in voxel units

mirtkPublicAttributeMacro() [3/4]

mirtk::RegisteredImage::mirtkPublicAttributeMacro	(	bool	,
		PrecomputeDerivatives
	)

Whether to precompute image derivatives true: Compute derivatives of input image and transform these false: Use derivative of interpolation kernel to evaluate image derivative

mirtkPublicAttributeMacro() [4/4]

mirtk::RegisteredImage::mirtkPublicAttributeMacro	(	int	,
		MaxGradientPercentile
	)

Maximum gradient magnitude as percentile of all gradient magnitudes

Note

Used only when _PrecomputeDerivatives is enabled.

Recompute() [1/2]

void mirtk::RegisteredImage::Recompute

(

const blocked_range3d< int > &

region

)

Force update of all output channels

This convenience function always recomputes all output channels within the specified image region. To do so, it calls the Update function with force set to true. It is commonly used after Initialize in an application where the input image and transformation are not being modified or when the SelfUpdate of the image has been disabled to explicitly recompute the image content after the input was modified.

Recompute() [2/2]

void mirtk::RegisteredImage::Recompute

(

)

Force update of all output channels

This convenience function always recomputes all output channels. To do so, it calls the Update function with force set to true. It is commonly used after Initialize in an application where the input image and transformation are not being modified or when the SelfUpdate of the image has been disabled to explicitly recompute the image content after the input was modified.

Update() [1/3]

void mirtk::RegisteredImage::Update	(	const blocked_range3d< int > &	region,
		bool	intensity = true,
		bool	gradient = false,
		bool	hessian = false,
		bool	force = false
	)

Update image intensity and transformed derivatives

This function updates the requested output image channels only within the specified image region. If the image is not transformed or only warped by a fixed transformation, this function does nothing. Set force to true to initialize this image even if it does not change over the course of the registration or use the corresponding Recompute function.

Parameters

[in]	region	Image region to update.
[in]	intensity	Request update of scalar intensities.
[in]	gradient	Request update of 1st order derivatives.
[in]	hessian	Request update of 2nd order derivatives.
[in]	force	Force update in any case.

Update() [2/3]

void mirtk::RegisteredImage::Update	(	const blocked_range3d< int > &	region,
		const DisplacementImageType *	disp,
		bool	intensity = true,
		bool	gradient = false,
		bool	hessian = false
	)

Update image intensity and transformed derivatives using custom displacements

Parameters

[in]	region	Image region to update.
[in]	disp	Custom displacement field to use.
[in]	intensity	Request update of scalar intensities.
[in]	gradient	Request update of 1st order derivatives.
[in]	hessian	Request update of 2nd order derivatives.

Update() [3/3]

void mirtk::RegisteredImage::Update	(	bool	intensity = true,
		bool	gradient = false,
		bool	hessian = false,
		bool	force = false
	)

Update image intensity and transformed derivatives

This function only updates the specified image channels if the self-update of this image is enabled and only if a (changing) transformation is set. If the image is not transformed or only warped by a fixed transformation, this function does nothing. Use force=true to initialize this image even if does not change over the course of the registration.

Parameters

[in]	intensity	Request update of scalar intensities.
[in]	gradient	Request update of 1st order derivatives.
[in]	hessian	Request update of 2nd order derivatives.
[in]	force	Force update in any case.

---

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

• RegisteredImage.h