#include <geometry.h>

Inheritance diagram for Geometry:

[legend]

Public Member Functions
	Geometry (const STD_string &label="unnamedGeometry")

	Geometry (const Geometry &ia)

Geometry &	operator= (const Geometry &ia)

Geometry &	set_Mode (geometryMode mode)

geometryMode	get_Mode () const

Geometry &	set_FOV (direction dir, double fov)

double	get_FOV (direction dir) const

Geometry &	set_offset (direction dir, double offset)

double	get_offset (direction dir) const

Geometry &	set_nSlices (unsigned int nslices)

unsigned int	get_nSlices () const

Geometry &	set_sliceThickness (double thick)

Geometry &	set_sliceDistance (double dist)

double	get_sliceDistance () const

dvector	get_readVector () const

dvector	get_phaseVector () const

dvector	get_sliceVector () const

dvector	get_sliceOffsetVector () const

double	get_sliceThickness () const

darray	get_cornerPoints (const Geometry &background, unsigned int backgrslice) const

Geometry &	set_orientation (sliceOrientation orientation)

sliceOrientation	get_orientation () const

void	get_orientation (double &heightAng, double &azimutAng, double &inplaneAng, bool &revSlice) const

Geometry &	set_orientation (double heightAng, double azimutAng, double inplaneAng, bool revSlice=false)

Geometry &	set_orientation_and_offset (const dvector &readvec, const dvector &phasevec, const dvector &slicevec, const dvector &centervec)

dvector	get_center () const

RotMatrix	get_gradrotmatrix (bool transpose=false) const

dvector	transform (const dvector &rpsvec, bool inverse=false) const

Geometry &	transpose_inplane (bool reverse_read=false, bool reverse_phase=false)

Geometry &	reset ()

Geometry &	update ()

Public Member Functions inherited from LDRblock
	LDRblock (const STD_string &title="Parameter List")

	LDRblock (const LDRblock &block)

	~LDRblock ()

LDRblock &	operator= (const LDRblock &block)

LDRblock &	merge (LDRblock &block, bool onlyUserPars=true)

LDRblock &	unmerge (LDRblock &block)

STD_string	printval (const STD_string &parameterName, bool append_unit=false) const

bool	parseval (const STD_string &parameterName, const STD_string &value)

int	parseblock (const STD_string &source, const LDRserBase &serializer=LDRserJDX())

unsigned int	numof_pars () const

LDRbase *	get_parameter (const STD_string &ldrlabel)

bool	parameter_exists (const STD_string &ldrlabel) const

LDRblock &	set_prefix (const STD_string &prefix)

LDRblock &	set_embedded (bool embedded)

bool	is_embedded () const

LDRbase &	operator[] (unsigned int i)

const LDRbase &	operator[] (unsigned int i) const

LDRbase &	get_parameter_by_id (int id)

LDRblock &	create_copy (const LDRblock &src)

LDRblock &	append_copy (const LDRbase &src)

LDRblock &	copy_ldr_vals (const LDRblock &src)

bool	operator== (const LDRblock &rhs) const

bool	operator< (const LDRblock &rhs) const

bool	compare (const LDRblock &rhs, const STD_list< STD_string > *exclude=0, double accuracy=0.0) const

STD_string	print (const LDRserBase &serializer=LDRserJDX()) const

LDRbase &	set_parmode (parameterMode parameter_mode)

LDRbase &	set_filemode (fileMode file_mode)

STD_string	get_parx_code (parxCodeType type) const

STD_ostream &	print2stream (STD_ostream &os, const LDRserBase &serializer) const

bool	parsevalstring (const STD_string &, const LDRserBase *ser=0)

bool	parse (STD_string &parstring, const LDRserBase &serializer)

STD_string	printvalstring (const LDRserBase *ser=0) const

LDRbase *	create_copy () const

STD_string	get_typeInfo (bool parx_equivtype=false) const

int	load (const STD_string &filename, const LDRserBase &serializer=LDRserJDX())

int	write (const STD_string &filename, const LDRserBase &serializer=LDRserJDX()) const

Public Member Functions inherited from LDRbase
virtual double	get_minval () const

virtual double	get_maxval () const

bool	has_minmax () const

const STD_string &	get_description () const

LDRbase &	set_description (const STD_string &descr)

virtual svector	get_alternatives () const

const STD_string &	get_unit () const

LDRbase &	set_unit (const STD_string &un)

virtual parameterMode	get_parmode () const

virtual fileMode	get_filemode () const

virtual GuiProps	get_gui_props () const

virtual LDRbase &	set_gui_props (const GuiProps &)

JcampDxProps	get_jdx_props () const

LDRbase &	set_jdx_props (const JcampDxProps &jp)

Public Member Functions inherited from Labeled
	Labeled (const STD_string &label="unnamed")

Labeled &	set_label (const STD_string &label)

const STD_string &	get_label () const

Labeled &	operator= (const Labeled &l)

Public Member Functions inherited from List< I, P, R >
	List ()

	~List ()

List &	operator= (const List &l)

List &	clear ()

List &	append (R item)

List &	remove (R item)

unsigned int	size () const

iter	get_begin ()

iter	get_end ()

constiter	get_const_begin () const

constiter	get_const_end () const

Static Public Member Functions
static sliceOrientation	get_slice_orientation (const dvector &svec)

Additional Inherited Members
Public Types inherited from List< I, P, R >
typedef STD_list< P >::iterator	iter

typedef STD_list< P >::const_iterator	constiter

Protected Member Functions inherited from LDRblock
LDRblock &	append_member (LDRbase &ldr, const STD_string ldrlabel="")

Detailed Description

Geometry Settings.

Depending on the selected geometryMode, this class describes a pack of parallel and congruent slices, or a 3D volume, .i.e. a voxel.

The patients x,y,z coordinate system used for the gradients is as follows: If standing in front of the magnet with the feet of the patient pointing towards you, the axes are oriented

x: from right to left (in the final image left/right will then have the correct polarity)
y: from bottom to top (floor to ceiling)
z: pointing away from you to the patients head

The three orientation angles 'heightAngle', 'azimutAngle', and 'inplaneAngle' (in degree) describe the orientation of the slicepack/voxel relative to the x/y/z-coordinate system of the gradients. If all these angles are zero, the read/phase/slice-system of the slicepack/voxel is the same as the x/y/z-system of the gradients. Otherwise, the system is rotated by the following angles (in the given order):

azimutAngle: Anti-clockwise rotation around y-axis.
heightAngle: Angle between slice vector (which is perp. to the slice) and x-z-plane
inplaneAngle: Clockwise rotation around slice vector.

Definition at line 179 of file geometry.h.

Constructor & Destructor Documentation

◆ Geometry() [1/2]

Geometry::Geometry ( const STD_string & label = "unnamedGeometry" )

Constructs a Geometry with the given label

◆ Geometry() [2/2]

Geometry::Geometry ( const Geometry & ia )

Copy constructor

Member Function Documentation

◆ get_center()

dvector Geometry::get_center ( ) const

Returns a vector pointing to the center of the slicepack/voxel.

◆ get_cornerPoints()

darray Geometry::get_cornerPoints	(	const Geometry &	background,
		unsigned int	backgrslice
	)		const

Returns a 5-dimensional array that contains the corner points of the slices/voxels where indexing is as follows: (unsigned int slice,sliceBoundary boundary1,sliceBoundary boundary2,sliceBoundary boundary3, axis direction) with

slice: The slice for the point
boundary1: The boundary in the read direction
boundary2: The boundary in the phase direction
boundary3: The boundary in the slice direction, the size is 1 in slicepack mode
direction: The x,y,z index

The points are transformed to slice 'backgrslice' the coordinate system of 'background'.

◆ get_FOV()

double Geometry::get_FOV ( direction dir ) const

Returns the Field Of View in the specified direction

◆ get_gradrotmatrix()

RotMatrix Geometry::get_gradrotmatrix ( bool transpose = false ) const

Returns the rotation matrix to convert the gradient strengths in the sequence coordinate system (read,phase,slice) to the laboratory system (x,y,z). If 'transpose' is set to true, the transposed matrix is returned.

◆ get_Mode()

geometryMode Geometry::get_Mode ( ) const

inline

Returns the geometry selection mode

Definition at line 206 of file geometry.h.

◆ get_nSlices()

unsigned int Geometry::get_nSlices ( ) const

inline

Returns the number of slices of the current slice pack

Definition at line 237 of file geometry.h.

◆ get_offset()

double Geometry::get_offset ( direction dir ) const

Returns the spatial offset in the specified direction

◆ get_orientation() [1/2]

sliceOrientation Geometry::get_orientation ( ) const

inline

Returns the principal anatomical slice orientation

Definition at line 309 of file geometry.h.

◆ get_orientation() [2/2]

void Geometry::get_orientation	(	double &	heightAng,
		double &	azimutAng,
		double &	inplaneAng,
		bool &	revSlice
	)		const

Returns the orientation of the slice, i.e. the three orientation angles 'heightAng', 'azimutAng' and 'inplaneAng'. 'revSlice' returns whether the slice direction (handness) is reversed.

◆ get_phaseVector()

dvector Geometry::get_phaseVector ( ) const

Returns the normalised vector for the phase direction in the laboratory system of reference

◆ get_readVector()

dvector Geometry::get_readVector ( ) const

Returns the normalised vector for the read direction in the laboratory system of reference

◆ get_slice_orientation()

static sliceOrientation Geometry::get_slice_orientation ( const dvector & svec )

static

Returns the principal anatomical slice orientation of slice normal 'svec'.

◆ get_sliceDistance()

double Geometry::get_sliceDistance ( ) const

inline

Returns the slice interslice distance

Definition at line 252 of file geometry.h.

◆ get_sliceOffsetVector()

dvector Geometry::get_sliceOffsetVector ( ) const

Returns the vector of spatial offsets in slice direction for the different slices of the slicepack.

◆ get_sliceThickness()

double Geometry::get_sliceThickness ( ) const

inline

Returns the slice thickness for the slices

Definition at line 277 of file geometry.h.

◆ get_sliceVector()

dvector Geometry::get_sliceVector ( ) const

Returns the normalised vector for the slice direction in the laboratory system of reference

◆ operator=()

Geometry& Geometry::operator= ( const Geometry & ia )

Assignment operator

◆ reset()

Geometry& Geometry::reset ( )

Resets the slicepacks geometry to its inintial state

◆ set_FOV()

Geometry& Geometry::set_FOV	(	direction	dir,
		double	fov
	)

Sets the Field Of View in the specified direction

◆ set_Mode()

Geometry& Geometry::set_Mode ( geometryMode mode )

Sets the geometry selection mode

◆ set_nSlices()

Geometry& Geometry::set_nSlices ( unsigned int nslices )

Sets the number of slices of the current slice pack

◆ set_offset()

Geometry& Geometry::set_offset	(	direction	dir,
		double	offset
	)

Sets the spatial offset in the specified direction

◆ set_orientation() [1/2]

Geometry& Geometry::set_orientation	(	double	heightAng,
		double	azimutAng,
		double	inplaneAng,
		bool	revSlice = `false`
	)

Specifies the orientation of the slice pack by giving the three orientation angles 'heightAng', 'azimutAng' and 'inplaneAng'. Optionally, the slice direction can be reversed by setting 'revSlice' to true.

◆ set_orientation() [2/2]

Geometry& Geometry::set_orientation ( sliceOrientation orientation )

Set the angle parameters to match the specified anatomical slice orientation

◆ set_orientation_and_offset()

Geometry& Geometry::set_orientation_and_offset	(	const dvector &	readvec,
		const dvector &	phasevec,
		const dvector &	slicevec,
		const dvector &	centervec
	)

Specifies the orientation of the slicepack/voxel by giving the three vectors 'readvec', 'phasevec', and 'slicevec' which point in read, phase, and slice direction. The vector 'offset' must contain the spatial offset of the center of the slicepack/voxel.

◆ set_sliceDistance()

Geometry& Geometry::set_sliceDistance ( double dist )

Sets the slice interslice distance

◆ set_sliceThickness()

Geometry& Geometry::set_sliceThickness ( double thick )

Sets the slice thickness of the current slice pack

◆ transform()

dvector Geometry::transform	(	const dvector &	rpsvec,
		bool	inverse = `false`
	)		const

Coordinate transformation from sequence coordinate system (read,phase,slice) of slice 'slice' to laboratory system (x,y,z), or vice versa if 'inverse' is set to 'true'.

◆ transpose_inplane()

Geometry& Geometry::transpose_inplane	(	bool	reverse_read = `false`,
		bool	reverse_phase = `false`
	)

Transpose geometry in-plane, 'reverse_read' and 'reverse_phase' can be used to reverse read/phase direction before transposing.

◆ update()

Geometry& Geometry::update ( )

Updates internal relations of the geometry parameters

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

geometry.h

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Geometry() [1/2]

◆ Geometry() [2/2]

Member Function Documentation

◆ get_center()

◆ get_cornerPoints()

◆ get_FOV()

◆ get_gradrotmatrix()

◆ get_Mode()

◆ get_nSlices()

◆ get_offset()

◆ get_orientation() [1/2]

◆ get_orientation() [2/2]

◆ get_phaseVector()

◆ get_readVector()

◆ get_slice_orientation()

◆ get_sliceDistance()

◆ get_sliceOffsetVector()

◆ get_sliceThickness()

◆ get_sliceVector()

◆ operator=()

◆ reset()

◆ set_FOV()

◆ set_Mode()

◆ set_nSlices()

◆ set_offset()

◆ set_orientation() [1/2]

◆ set_orientation() [2/2]

◆ set_orientation_and_offset()

◆ set_sliceDistance()

◆ set_sliceThickness()

◆ transform()

◆ transpose_inplane()

◆ update()