FFD vector field deformation transform. More...

#include <aims/registration/ffd.h>

Inheritance diagram for aims::FfdTransformation:

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Collaboration diagram for aims::FfdTransformation:

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Public Member Functions
	FfdTransformation (int dimX=0, int dimY=1, int dimZ=1, float sizeX=1., float sizeY=1., float sizeZ=1.)

template<typename T>
	FfdTransformation (int dimX, int dimY, int dimZ, const carto::rc_ptr< carto::Volume< T > > &test_volume)

template<typename T>
	FfdTransformation (int dimX, int dimY, int dimZ, const carto::Volume< T > &test_volume)

	FfdTransformation (const FfdTransformation &other)

	FfdTransformation (const carto::rc_ptr< carto::Volume< Point3df > > &other)

FfdTransformation &	operator= (const FfdTransformation &other)

	operator const carto::VolumeRef< Point3df > & () const

	operator carto::VolumeRef< Point3df > & ()

	operator const carto::rc_ptr< carto::Volume< Point3df > > & () const

	operator carto::rc_ptr< carto::Volume< Point3df > > & ()

carto::rc_ptr< carto::Volume< Point3df > > &	ctrlDeformations ()

bool	isIdentity () const CARTO_OVERRIDE
	Always false, because testing for identity is expensive.

bool	isDirect () const override

Point3df	getCtrlKnot (int nx, int ny, int nz) const

void	updateCtrlKnot (int nx, int ny, int nz, const Point3df &newCtrlKnot)

void	updateAllCtrlKnot (const carto::rc_ptr< carto::Volume< Point3df > > &newCtrlKnotGrid)

void	updateAllCtrlKnotFromDeformation (const carto::rc_ptr< carto::Volume< Point3df > > &newDeformationGrid)

void	increaseResolution (const Point3d &addKnots)

Point3dd	deformation (const Point3dd &p_mm) const

Point3dd	ffdCoord (const Point3dd &p_mm) const

int	dimX () const

int	dimY () const

int	dimZ () const

int	getSizeX () const

int	getSizeY () const

int	getSizeZ () const

std::vector< int >	getSize () const

float	sizeX () const

float	sizeY () const

float	sizeZ () const

std::vector< float >	getVoxelSize () const

bool	isFlat (int i) const

bool	isXFlat () const

bool	isYFlat () const

bool	isZFlat () const

virtual void	updateDimensions ()

void	printControlPointsGrid () const

void	writeDebugCtrlKnots (const std::string &filename) const

void	writeDebugDeformations (const std::string &filename, int dimX, int dimY, int dimZ, float sizeX, float sizeY, float sizeZ) const

void	write (const std::string &filename) const

carto::rc_ptr< soma::Transformation3d >	operator* (const soma::Transformation3d &other) const

virtual carto::rc_ptr< soma::Transformation3d >	operator* (const carto::rc_ptr< soma::Transformation3d > &other) const

void	buildFromOther (const soma::Transformation3d &other)

virtual carto::rc_ptr< soma::Transformation3d >	composed (const carto::rc_ptr< soma::Transformation3d > &other) const =0

virtual carto::rc_ptr< soma::Transformation3d >	leftComposed (const carto::rc_ptr< soma::Transformation3d > &other) const =0

Public Member Functions inherited from soma::Transformation3d
virtual	~Transformation3d ()

Point3dd	transform (double x, double y, double z) const

Point3dd	transform (const Point3dd &pos) const

Point3df	transform (const Point3df &dir) const

Point3df	transform (float x, float y, float z) const

Point3d	transform (const Point3d &p) const

Point3di	transform (const Point3di &p) const

Point3di	transform (int x, int y, int z) const

virtual std::vector< double >	transform (const std::vector< double > &pos) const

virtual std::vector< float >	transform (const std::vector< float > &pos) const

virtual std::vector< int >	transform (const std::vector< int > &pos) const

virtual std::vector< double >	transformVector (const std::vector< double > &pos) const

virtual std::vector< float >	transformVector (const std::vector< float > &pos) const

virtual std::vector< int >	transformVector (const std::vector< int > &pos) const

Public Member Functions inherited from soma::Transformation
virtual	~Transformation ()

virtual Transformation &	operator= (const Transformation &other)

carto::Object	header ()

const carto::Object	header () const

void	setHeader (carto::Object ph)

virtual bool	invertible () const

virtual std::unique_ptr< Transformation >	getInverse () const

Public Member Functions inherited from carto::RCObject
	RCObject ()

	RCObject (const RCObject &)

RCObject &	operator= (const RCObject &)

virtual	~RCObject ()

Protected Member Functions
Point3dd	splineVoxToMm (const Point3dd &p) const

Point3dd	mmToSplineVox (const Point3dd &p) const

void	updateGridResolution (const carto::rc_ptr< carto::Volume< Point3df > > &newGrid)

virtual Point3dd	_deformation (const Point3dd &p_mm) const =0

Protected Member Functions inherited from soma::Transformation3d
	Transformation3d ()

virtual Point3dd	transformDouble (double x, double y, double z) const=0

virtual Point3dd	transformPoint3dd (const Point3dd &pos) const

virtual Point3df	transformPoint3df (const Point3df &dir) const

virtual Point3d	transformPoint3d (const Point3d &p) const

virtual Point3di	transformPoint3di (const Point3di &p) const

virtual Point3df	transformFloat (float x, float y, float z) const

virtual Point3di	transformInt (int x, int y, int z) const

Protected Member Functions inherited from soma::Transformation
	Transformation ()

Protected Attributes
carto::VolumeRef< Point3df >	_ctrlPointDelta

int	_dimx

int	_dimy

int	_dimz

float	_vsx

float	_vsy

float	_vsz

bool	_flatx

bool	_flaty

bool	_flatz

Protected Attributes inherited from soma::Transformation
carto::Object	_header

Additional Inherited Members
Public Types inherited from carto::RCObject
typedef int	RefCounterType

Static Public Member Functions inherited from soma::Transformation
static std::vector< T >	vadd (const std::vector< T > &v1, const std::vector< T > &v2)

static std::vector< T >	vsub (const std::vector< T > &v1, const std::vector< T > &v2)

static std::vector< T >	vadd (const std::vector< T > &v1, const T &v2)

static std::vector< T >	vsub (const std::vector< T > &v1, const T &v2)

static std::vector< T >	vadd (const T &v1, const std::vector< T > &v2)

static std::vector< T >	vsub (const T &v1, const std::vector< T > &v2)

Detailed Description

FFD vector field deformation transform.

Free Form Deformation is the registration technique used to build the vector fields. This class is dedicated to the application of the vector field deformation to transform coordinates.

Vector fields are stored in volumes VolumeRef<Point3df>.

Definition at line 37 of file ffd.h.

Constructor & Destructor Documentation

◆ FfdTransformation() [1/5]

aims::FfdTransformation::FfdTransformation	(	int	dimX = 0,
		int	dimY = 1,
		int	dimZ = 1,
		float	sizeX = 1.,
		float	sizeY = 1.,
		float	sizeZ = 1. )

References dimX(), dimY(), dimZ(), sizeX(), sizeY(), and sizeZ().

Referenced by FfdTransformation(), operator=(), aims::SplineFfd::SplineFfd(), aims::SplineFfd::SplineFfd(), and aims::TrilinearFfd::TrilinearFfd().

◆ FfdTransformation() [2/5]

template<typename T>

aims::FfdTransformation::FfdTransformation	(	int	dimX,
		int	dimY,
		int	dimZ,
		const carto::rc_ptr< carto::Volume< T > > &	test_volume )

inline

Definition at line 156 of file ffd.h.

References _ctrlPointDelta, _dimx, _dimy, _dimz, _flatx, _flaty, _flatz, dimX(), dimY(), dimZ(), and updateDimensions().

◆ FfdTransformation() [3/5]

template<typename T>

aims::FfdTransformation::FfdTransformation	(	int	dimX,
		int	dimY,
		int	dimZ,
		const carto::Volume< T > &	test_volume )

inline

Definition at line 174 of file ffd.h.

References _ctrlPointDelta, _dimx, _dimy, _dimz, _flatx, _flaty, _flatz, dimX(), dimY(), dimZ(), carto::VolumeProxy< typename T >::getSizeX(), carto::VolumeProxy< typename T >::getSizeY(), carto::VolumeProxy< typename T >::getSizeZ(), carto::VolumeProxy< typename T >::getVoxelSize(), and updateDimensions().

◆ FfdTransformation() [4/5]

aims::FfdTransformation::FfdTransformation ( const FfdTransformation & other )

References FfdTransformation().

◆ FfdTransformation() [5/5]

aims::FfdTransformation::FfdTransformation ( const carto::rc_ptr< carto::Volume< Point3df > > & other )

Member Function Documentation

◆ _deformation()

virtual Point3dd aims::FfdTransformation::_deformation ( const Point3dd & p_mm ) const

protectedpure virtual

◆ buildFromOther()

void aims::FfdTransformation::buildFromOther ( const soma::Transformation3d & other )

◆ composed()

virtual carto::rc_ptr< soma::Transformation3d > aims::FfdTransformation::composed ( const carto::rc_ptr< soma::Transformation3d > & other ) const

pure virtual

Implemented in aims::SplineFfd, and aims::TrilinearFfd.

◆ ctrlDeformations()

carto::rc_ptr< carto::Volume< Point3df > > & aims::FfdTransformation::ctrlDeformations ( )

inline

Definition at line 61 of file ffd.h.

References _ctrlPointDelta.

◆ deformation()

Point3dd aims::FfdTransformation::deformation ( const Point3dd & p_mm ) const

◆ dimX()

int aims::FfdTransformation::dimX ( ) const

inline

Definition at line 88 of file ffd.h.

References _dimx.

Referenced by FfdTransformation(), FfdTransformation(), FfdTransformation(), aims::SplineFfd::SplineFfd(), aims::SplineFfd::SplineFfd(), aims::SplineFfd::SplineFfd(), aims::TrilinearFfd::TrilinearFfd(), aims::TrilinearFfd::TrilinearFfd(), and writeDebugDeformations().

◆ dimY()

int aims::FfdTransformation::dimY ( ) const

inline

Definition at line 89 of file ffd.h.

References _dimy.

Referenced by FfdTransformation(), FfdTransformation(), FfdTransformation(), aims::SplineFfd::SplineFfd(), aims::SplineFfd::SplineFfd(), aims::SplineFfd::SplineFfd(), aims::TrilinearFfd::TrilinearFfd(), aims::TrilinearFfd::TrilinearFfd(), and writeDebugDeformations().

◆ dimZ()

int aims::FfdTransformation::dimZ ( ) const

inline

Definition at line 90 of file ffd.h.

References _dimz.

Referenced by FfdTransformation(), FfdTransformation(), FfdTransformation(), aims::SplineFfd::SplineFfd(), aims::SplineFfd::SplineFfd(), aims::SplineFfd::SplineFfd(), aims::TrilinearFfd::TrilinearFfd(), aims::TrilinearFfd::TrilinearFfd(), and writeDebugDeformations().

◆ ffdCoord()

Point3dd aims::FfdTransformation::ffdCoord ( const Point3dd & p_mm ) const

inline

Definition at line 84 of file ffd.h.

References mmToSplineVox().

◆ getCtrlKnot()

Point3df aims::FfdTransformation::getCtrlKnot	(	int	nx,
		int	ny,
		int	nz ) const

◆ getSize()

std::vector< int > aims::FfdTransformation::getSize ( ) const

inline

Definition at line 94 of file ffd.h.

References _dimx, _dimy, and _dimz.

◆ getSizeX()

int aims::FfdTransformation::getSizeX ( ) const

inline

Definition at line 91 of file ffd.h.

References _dimx.

◆ getSizeY()

int aims::FfdTransformation::getSizeY ( ) const

inline

Definition at line 92 of file ffd.h.

References _dimy.

◆ getSizeZ()

int aims::FfdTransformation::getSizeZ ( ) const

inline

Definition at line 93 of file ffd.h.

References _dimz.

◆ getVoxelSize()

std::vector< float > aims::FfdTransformation::getVoxelSize ( ) const

inline

Definition at line 100 of file ffd.h.

References _vsx, _vsy, and _vsz.

◆ increaseResolution()

void aims::FfdTransformation::increaseResolution ( const Point3d & addKnots )

◆ isDirect()

bool aims::FfdTransformation::isDirect ( ) const

overridevirtual

Implements soma::Transformation.

◆ isFlat()

bool aims::FfdTransformation::isFlat ( int i ) const

inline

Definition at line 103 of file ffd.h.

References _flatx, _flaty, and _flatz.

◆ isIdentity()

bool aims::FfdTransformation::isIdentity ( ) const

inlinevirtual

Always false, because testing for identity is expensive.

Reimplemented from soma::Transformation.

Definition at line 65 of file ffd.h.

◆ isXFlat()

bool aims::FfdTransformation::isXFlat ( ) const

inline

Definition at line 113 of file ffd.h.

References _flatx.

◆ isYFlat()

bool aims::FfdTransformation::isYFlat ( ) const

inline

Definition at line 114 of file ffd.h.

References _flaty.

◆ isZFlat()

bool aims::FfdTransformation::isZFlat ( ) const

inline

Definition at line 115 of file ffd.h.

References _flatz.

◆ leftComposed()

virtual carto::rc_ptr< soma::Transformation3d > aims::FfdTransformation::leftComposed ( const carto::rc_ptr< soma::Transformation3d > & other ) const

pure virtual

Implemented in aims::SplineFfd, and aims::TrilinearFfd.

◆ mmToSplineVox()

Point3dd aims::FfdTransformation::mmToSplineVox ( const Point3dd & p ) const

inlineprotected

Definition at line 199 of file ffd.h.

References sizeX(), sizeY(), and sizeZ().

Referenced by ffdCoord().

◆ operator carto::rc_ptr< carto::Volume< Point3df > > &()

aims::FfdTransformation::operator carto::rc_ptr< carto::Volume< Point3df > > & ( )

inline

Definition at line 59 of file ffd.h.

References _ctrlPointDelta.

◆ operator carto::VolumeRef< Point3df > &()

aims::FfdTransformation::operator carto::VolumeRef< Point3df > & ( )

inline

Definition at line 55 of file ffd.h.

References _ctrlPointDelta.

◆ operator const carto::rc_ptr< carto::Volume< Point3df > > &()

aims::FfdTransformation::operator const carto::rc_ptr< carto::Volume< Point3df > > & ( ) const

inline

Definition at line 57 of file ffd.h.

References _ctrlPointDelta.

◆ operator const carto::VolumeRef< Point3df > &()

aims::FfdTransformation::operator const carto::VolumeRef< Point3df > & ( ) const

inline

Definition at line 53 of file ffd.h.

References _ctrlPointDelta.

◆ operator*() [1/2]

virtual carto::rc_ptr< soma::Transformation3d > aims::FfdTransformation::operator* ( const carto::rc_ptr< soma::Transformation3d > & other ) const

virtual

◆ operator*() [2/2]

carto::rc_ptr< soma::Transformation3d > aims::FfdTransformation::operator* ( const soma::Transformation3d & other ) const

◆ operator=()

FfdTransformation & aims::FfdTransformation::operator= ( const FfdTransformation & other )

References FfdTransformation().

◆ printControlPointsGrid()

void aims::FfdTransformation::printControlPointsGrid ( ) const

◆ sizeX()

float aims::FfdTransformation::sizeX ( ) const

inline

Definition at line 97 of file ffd.h.

References _vsx.

Referenced by FfdTransformation(), mmToSplineVox(), aims::SplineFfd::SplineFfd(), splineVoxToMm(), aims::TrilinearFfd::TrilinearFfd(), and writeDebugDeformations().

◆ sizeY()

float aims::FfdTransformation::sizeY ( ) const

inline

Definition at line 98 of file ffd.h.

References _vsy.

Referenced by FfdTransformation(), mmToSplineVox(), aims::SplineFfd::SplineFfd(), splineVoxToMm(), aims::TrilinearFfd::TrilinearFfd(), and writeDebugDeformations().

◆ sizeZ()

float aims::FfdTransformation::sizeZ ( ) const

inline

Definition at line 99 of file ffd.h.

References _vsz.

Referenced by FfdTransformation(), mmToSplineVox(), aims::SplineFfd::SplineFfd(), splineVoxToMm(), aims::TrilinearFfd::TrilinearFfd(), and writeDebugDeformations().

◆ splineVoxToMm()

Point3dd aims::FfdTransformation::splineVoxToMm ( const Point3dd & p ) const

inlineprotected

Definition at line 191 of file ffd.h.

References sizeX(), sizeY(), and sizeZ().

◆ updateAllCtrlKnot()

void aims::FfdTransformation::updateAllCtrlKnot ( const carto::rc_ptr< carto::Volume< Point3df > > & newCtrlKnotGrid )

◆ updateAllCtrlKnotFromDeformation()

void aims::FfdTransformation::updateAllCtrlKnotFromDeformation ( const carto::rc_ptr< carto::Volume< Point3df > > & newDeformationGrid )

◆ updateCtrlKnot()

void aims::FfdTransformation::updateCtrlKnot	(	int	nx,
		int	ny,
		int	nz,
		const Point3df &	newCtrlKnot )

◆ updateDimensions()

virtual void aims::FfdTransformation::updateDimensions ( )

virtual

Reimplemented in aims::SplineFfd.

Referenced by FfdTransformation(), and FfdTransformation().

◆ updateGridResolution()

void aims::FfdTransformation::updateGridResolution ( const carto::rc_ptr< carto::Volume< Point3df > > & newGrid )

protected

◆ write()

void aims::FfdTransformation::write ( const std::string & filename ) const

◆ writeDebugCtrlKnots()

void aims::FfdTransformation::writeDebugCtrlKnots ( const std::string & filename ) const

◆ writeDebugDeformations()

void aims::FfdTransformation::writeDebugDeformations	(	const std::string &	filename,
		int	dimX,
		int	dimY,
		int	dimZ,
		float	sizeX,
		float	sizeY,
		float	sizeZ ) const

References dimX(), dimY(), dimZ(), sizeX(), sizeY(), and sizeZ().

Member Data Documentation

◆ _ctrlPointDelta

carto::VolumeRef<Point3df> aims::FfdTransformation::_ctrlPointDelta

protected

Definition at line 148 of file ffd.h.

Referenced by ctrlDeformations(), FfdTransformation(), FfdTransformation(), operator carto::rc_ptr< carto::Volume< Point3df > > &(), operator carto::VolumeRef< Point3df > &(), operator const carto::rc_ptr< carto::Volume< Point3df > > &(), and operator const carto::VolumeRef< Point3df > &().

◆ _dimx

int aims::FfdTransformation::_dimx

protected

Definition at line 149 of file ffd.h.

Referenced by dimX(), FfdTransformation(), FfdTransformation(), getSize(), and getSizeX().

◆ _dimy

int aims::FfdTransformation::_dimy

protected

Definition at line 149 of file ffd.h.

Referenced by dimY(), FfdTransformation(), FfdTransformation(), getSize(), and getSizeY().

◆ _dimz

int aims::FfdTransformation::_dimz

protected

Definition at line 149 of file ffd.h.

Referenced by dimZ(), FfdTransformation(), FfdTransformation(), getSize(), and getSizeZ().

◆ _flatx

bool aims::FfdTransformation::_flatx

protected

Definition at line 151 of file ffd.h.

Referenced by FfdTransformation(), FfdTransformation(), isFlat(), and isXFlat().

◆ _flaty

bool aims::FfdTransformation::_flaty

protected

Definition at line 151 of file ffd.h.

Referenced by FfdTransformation(), FfdTransformation(), isFlat(), and isYFlat().

◆ _flatz

bool aims::FfdTransformation::_flatz

protected

Definition at line 151 of file ffd.h.

Referenced by FfdTransformation(), FfdTransformation(), isFlat(), and isZFlat().

◆ _vsx

float aims::FfdTransformation::_vsx

protected

Definition at line 150 of file ffd.h.

Referenced by getVoxelSize(), and sizeX().

◆ _vsy

float aims::FfdTransformation::_vsy

protected

Definition at line 150 of file ffd.h.

Referenced by getVoxelSize(), and sizeY().

◆ _vsz

float aims::FfdTransformation::_vsz

protected

Definition at line 150 of file ffd.h.

Referenced by getVoxelSize(), and sizeZ().

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

aims/registration/ffd.h

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ FfdTransformation() [1/5]

◆ FfdTransformation() [2/5]

◆ FfdTransformation() [3/5]

◆ FfdTransformation() [4/5]

◆ FfdTransformation() [5/5]

Member Function Documentation

◆ _deformation()

◆ buildFromOther()

◆ composed()

◆ ctrlDeformations()

◆ deformation()

◆ dimX()

◆ dimY()

◆ dimZ()

◆ ffdCoord()

◆ getCtrlKnot()

◆ getSize()

◆ getSizeX()

◆ getSizeY()

◆ getSizeZ()

◆ getVoxelSize()

◆ increaseResolution()

◆ isDirect()

◆ isFlat()

◆ isIdentity()

◆ isXFlat()

◆ isYFlat()

◆ isZFlat()

◆ leftComposed()

◆ mmToSplineVox()

◆ operator carto::rc_ptr< carto::Volume< Point3df > > &()

◆ operator carto::VolumeRef< Point3df > &()

◆ operator const carto::rc_ptr< carto::Volume< Point3df > > &()

◆ operator const carto::VolumeRef< Point3df > &()

◆ operator*() [1/2]

◆ operator*() [2/2]

◆ operator=()

◆ printControlPointsGrid()

◆ sizeX()

◆ sizeY()

◆ sizeZ()

◆ splineVoxToMm()

◆ updateAllCtrlKnot()

◆ updateAllCtrlKnotFromDeformation()

◆ updateCtrlKnot()

◆ updateDimensions()

◆ updateGridResolution()

◆ write()

◆ writeDebugCtrlKnots()

◆ writeDebugDeformations()

Member Data Documentation

◆ _ctrlPointDelta

◆ _dimx

◆ _dimy

◆ _dimz

◆ _flatx

◆ _flaty

◆ _flatz

◆ _vsx

◆ _vsy

◆ _vsz