MAGSI-based Magnetization Simulator. More...

#include <seqsim.h>

Inheritance diagram for SeqSimMagsi:

[legend]

Public Member Functions
	SeqSimMagsi (const STD_string &label="unnamedSeqSimMagsi")

	SeqSimMagsi (const SeqSimMagsi &ssm)

	~SeqSimMagsi ()

SeqSimMagsi &	operator= (const SeqSimMagsi &ssm)

unsigned int	get_total_size () const

SeqSimMagsi &	reset_magnetization ()

SeqSimMagsi &	set_initial_vector (float Mx, float My, float Mz)

const farray &	get_Mx () const

const farray &	get_My () const

const farray &	get_Mz () const

const farray &	get_Mamp () const

const farray &	get_Mpha () const

SeqSimMagsi &	update ()

SeqSimMagsi &	set_online_simulation (bool onlineflag)

SeqSimMagsi &	set_intravoxel_simulation (bool ivflag)

SeqSimMagsi &	set_numof_threads (unsigned int n)

SeqSimMagsi &	set_spat_rotmatrix (const RotMatrix &rotmatrix)

bool	do_simulation ()

void	prepare_simulation (const Sample &sample, CoilSensitivity transmit_coil=0, CoilSensitivity receive_coil=0, ProgressMeter *progmeter=0)

cvector	simulate (const SeqSimInterval &simvals, double gamma)

void	finalize_simulation ()

bool	kernel (const SeqSimInterval &simvals, cvector &signal, int &, unsigned int begin, unsigned int end)

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

Public Member Functions inherited from ThreadedLoop< SeqSimInterval, cvector, int >
	ThreadedLoop ()

bool	init (unsigned int numof_threads, unsigned int loopsize)

void	destroy ()

bool	execute (const SeqSimInterval &in, STD_vector< cvector > &outvec)

Public Member Functions inherited from SeqClass
SeqClass &	set_temporary ()

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="")

Protected Member Functions inherited from SeqClass
void	marshall_error () const

virtual void	clear_container ()

virtual bool	prep ()

Static Protected Member Functions inherited from SeqClass
static void	clear_temporary ()

static void	clear_containers ()

Detailed Description

MAGSI-based Magnetization Simulator.

This is a simulator to calculate the time evolution of a magnetization grid in 4 dimension (frequency and three spatial dimensions). This simulation of the Bloch-Torrey equations is performed by means of the MAGSI algorith (c.f. Journal of Magnetic Resonance 180:29-38, 2006). Simulation usually involves the following steps:

Initialize the simulator by prepare_simulation() using a virtual sample.
Iterative simulation by simulate() using a structure with piece-wise constant fields.
Finish simulation by calling finalize_simulation().

Definition at line 113 of file seqsim.h.

Constructor & Destructor Documentation

◆ SeqSimMagsi() [1/2]

SeqSimMagsi::SeqSimMagsi ( const STD_string & label = "unnamedSeqSimMagsi" )

Constructs a simulator labeled 'object_label'.

◆ SeqSimMagsi() [2/2]

SeqSimMagsi::SeqSimMagsi ( const SeqSimMagsi & ssm )

Copy constructor

◆ ~SeqSimMagsi()

SeqSimMagsi::~SeqSimMagsi ( )

Destructor

Member Function Documentation

◆ do_simulation()

bool SeqSimMagsi::do_simulation ( )

Returns whether simulation should be performed, i.e. whether the 'online' flag is true or 'update' was activated.

◆ finalize_simulation()

void SeqSimMagsi::finalize_simulation ( )

virtual

Call this function after a simulation (i.e. after successive calls to simulate() )

Implements SeqSimAbstract.

◆ get_Mamp()

const farray& SeqSimMagsi::get_Mamp ( ) const

inline

Returns the amplitude of the transverse magnetisation

Definition at line 170 of file seqsim.h.

◆ get_Mpha()

const farray& SeqSimMagsi::get_Mpha ( ) const

inline

Returns the phase of the transverse magnetisation

Definition at line 175 of file seqsim.h.

◆ get_Mx()

const farray& SeqSimMagsi::get_Mx ( ) const

inline

Returns the real part of the transverse magnetisation

Definition at line 155 of file seqsim.h.

◆ get_My()

const farray& SeqSimMagsi::get_My ( ) const

inline

Returns the imaginary part of the transverse magnetisation

Definition at line 160 of file seqsim.h.

◆ get_Mz()

const farray& SeqSimMagsi::get_Mz ( ) const

inline

Returns the longitudinal magnetisation

Definition at line 165 of file seqsim.h.

◆ get_total_size()

unsigned int SeqSimMagsi::get_total_size ( ) const

inline

Returns the overall size of the array

Definition at line 140 of file seqsim.h.

◆ kernel()

bool SeqSimMagsi::kernel	(	const SeqSimInterval &	in,
		cvector &	out,
		int &	local,
		unsigned int	begin,
		unsigned int	end
	)

virtual

Overload this function to do the work of one thread using input 'in', generating output 'out' with thread-local storage 'local' for the the loop inidices (begin <= i < end).

Implements ThreadedLoop< SeqSimInterval, cvector, int >.

◆ operator=()

SeqSimMagsi& SeqSimMagsi::operator= ( const SeqSimMagsi & ssm )

Assignment operator

◆ prepare_simulation()

void SeqSimMagsi::prepare_simulation	(	const Sample &	sample,
		CoilSensitivity *	transmit_coil = `0`,
		CoilSensitivity *	receive_coil = `0`,
		ProgressMeter *	progmeter = `0`
	)

virtual

Prepare a simulation (i.e. before successive calls to simulate() ) with the parameters:

sample: The virtual sample
transmit_coil: Transmitter coil, 0 for none
receive_coil: Receiver coil, 0 for none
progmeter: Status indicator to trace progress, 0 for none

Implements SeqSimAbstract.

◆ reset_magnetization()

SeqSimMagsi& SeqSimMagsi::reset_magnetization ( )

Set each magnetization to initial state 'initial_vector', which is (0,0,1) by default

◆ set_initial_vector()

SeqSimMagsi& SeqSimMagsi::set_initial_vector	(	float	Mx,
		float	My,
		float	Mz
	)

Set the vector for the initial magnetization

◆ set_intravoxel_simulation()

SeqSimMagsi& SeqSimMagsi::set_intravoxel_simulation ( bool ivflag )

inline

Specifies whether intra-voxel magnetzation gradients are considered during simulation

Definition at line 192 of file seqsim.h.

◆ set_numof_threads()

SeqSimMagsi& SeqSimMagsi::set_numof_threads ( unsigned int n )

inline

Specifies the number of threads used during simulation

Definition at line 197 of file seqsim.h.

◆ set_online_simulation()

SeqSimMagsi& SeqSimMagsi::set_online_simulation ( bool onlineflag )

inline

Specifies whether simulation should be performed everytime update() is called

Definition at line 186 of file seqsim.h.

◆ set_spat_rotmatrix()

SeqSimMagsi& SeqSimMagsi::set_spat_rotmatrix ( const RotMatrix & rotmatrix )

Specifies a rotation matrix for the spatial domain, i.e. the magnetization array will be rotated in space using the specified rotation matrix.

◆ simulate()

cvector SeqSimMagsi::simulate	(	const SeqSimInterval &	simvals,
		double	gamma
	)

virtual

Simulation with

simvals: The magnetic fields during a time interval
gamma: Gyromagnetic ration of the nucleus observed Return value: Signal in each receiver channel

Implements SeqSimAbstract.

◆ update()

SeqSimMagsi& SeqSimMagsi::update ( )

Updates all parameter relations

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

seqsim.h

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SeqSimMagsi() [1/2]

◆ SeqSimMagsi() [2/2]

◆ ~SeqSimMagsi()

Member Function Documentation

◆ do_simulation()

◆ finalize_simulation()

◆ get_Mamp()

◆ get_Mpha()

◆ get_Mx()

◆ get_My()

◆ get_Mz()

◆ get_total_size()

◆ kernel()

◆ operator=()

◆ prepare_simulation()

◆ reset_magnetization()

◆ set_initial_vector()

◆ set_intravoxel_simulation()

◆ set_numof_threads()

◆ set_online_simulation()

◆ set_spat_rotmatrix()

◆ simulate()

◆ update()