Base class for methods (sequences) More...

#include <seqmeth.h>

Inheritance diagram for SeqMethod:

[legend]

Public Member Functions
	SeqMethod (const STD_string &method_label)

virtual	~SeqMethod ()

bool	clear ()

bool	init ()

bool	build ()

bool	prepare ()

bool	update_timings ()

bool	prep_acquisition () const

const char *	get_description () const

int	process (int argc, char *argv[])

int	load_protocol (const STD_string &filename)

int	write_protocol (const STD_string &filename) const

LDRblock &	get_methodPars ()

int	load_sequencePars (const STD_string &filename)

int	write_sequencePars (const STD_string &filename) const

bool	set_sequenceParameter (const STD_string &parameter_label, const STD_string &value)

SeqMethod &	set_commonPars (const SeqPars &pars)

SeqPars &	get_commonPars ()

SeqMethod &	set_geometry (const Geometry &geo)

Geometry &	get_geometry ()

int	load_geometry (const STD_string &filename)

int	write_geometry (const STD_string &filename) const

Study &	get_studyInfo ()

int	write_systemInfo (const STD_string &filename) const

int	load_systemInfo (const STD_string &filename)

SeqMethod &	init_systemInfo (double basicfreq, double maxgrad, double slewrate)

int	write_recoInfo (const STD_string &filename) const

int	write_meas_contex (const STD_string &prefix) const

double	get_totalDuration () const

STD_string	get_main_nucleus () const

unsigned int	get_numof_acquisitions () const

STD_list< const SeqPulsar * >	get_active_pulsar_pulses () const

unsigned int	event (eventContext &context) const

Public Member Functions inherited from SeqObjList
	SeqObjList (const STD_string &object_label="unnamedSeqObjList")

	SeqObjList (const SeqObjList &so)

SeqObjList &	operator= (const SeqObjList &so)

SeqObjList &	operator= (const SeqObjLoop &sl)

SeqObjList &	operator= (const SeqDecoupling &sd)

SeqObjList &	operator= (const SeqObjBase &soa)

SeqObjList &	operator= (SeqGradObjInterface &sgoa)

SeqObjList &	operator= (SeqGradChan &sgc)

SeqObjList &	operator= (SeqGradChanList &sgcl)

SeqObjList &	operator+= (const SeqObjBase &soa)

SeqObjList &	operator+= (SeqGradObjInterface &sgoa)

SeqObjList &	operator+= (SeqGradChan &sgc)

SeqObjList &	operator+= (SeqGradChanList &sgcl)

SeqObjList &	set_gradrotmatrixvector (const SeqRotMatrixVector &matrixVec)

STD_string	get_program (programContext &context) const

double	get_duration () const

STD_string	get_properties () const

void	query (queryContext &context) const

RecoValList	get_recovallist (unsigned int reptimes, LDRkSpaceCoords &coords) const

SeqValList	get_freqvallist (freqlistAction action) const

SeqValList	get_delayvallist () const

double	get_rf_energy () const

Public Member Functions inherited from SeqTreeObj
bool	contains (const SeqTreeObj *sto) const

void	tree (SeqTreeCallbackAbstract *display) const

Public Member Functions inherited from SeqClass
SeqClass &	set_temporary ()

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< SeqObjBase, const SeqObjBase *, const SeqObjBase & >
	List ()

	~List ()

List &	operator= (const List &l)

List &	clear ()

List &	append (const SeqObjBase & item)

List &	remove (const SeqObjBase & item)

unsigned int	size () const

iter	get_begin ()

iter	get_end ()

constiter	get_const_begin () const

constiter	get_const_end () const

Protected Member Functions
virtual void	method_pars_init ()=0

virtual void	method_seq_init ()=0

virtual void	method_rels ()=0

virtual void	method_pars_set ()=0

SeqMethod &	append_parameter (LDRbase &ldr, const STD_string &label, parameterMode parmode=edit)

SeqMethod &	set_sequence (const SeqObjBase &s)

SeqMethod &	set_description (const char *descr)

virtual unsigned int	numof_testcases () const

unsigned int	get_current_testcase () const

Protected Member Functions inherited from SeqObjList
void	clear_container ()

bool	prep ()

	SeqObjList (const STD_string &object_label="unnamedSeqObjList")

	SeqObjList (const SeqObjList &so)

SeqObjList &	operator= (const SeqObjList &so)

SeqObjList &	operator= (const SeqObjLoop &sl)

SeqObjList &	operator= (const SeqDecoupling &sd)

SeqObjList &	operator= (const SeqObjBase &soa)

SeqObjList &	operator= (SeqGradObjInterface &sgoa)

SeqObjList &	operator= (SeqGradChan &sgc)

SeqObjList &	operator= (SeqGradChanList &sgcl)

SeqObjList &	operator+= (const SeqObjBase &soa)

SeqObjList &	operator+= (SeqGradObjInterface &sgoa)

SeqObjList &	operator+= (SeqGradChan &sgc)

SeqObjList &	operator+= (SeqGradChanList &sgcl)

SeqObjList &	set_gradrotmatrixvector (const SeqRotMatrixVector &matrixVec)

STD_string	get_program (programContext &context) const

double	get_duration () const

STD_string	get_properties () const

void	query (queryContext &context) const

RecoValList	get_recovallist (unsigned int reptimes, LDRkSpaceCoords &coords) const

SeqValList	get_freqvallist (freqlistAction action) const

SeqValList	get_delayvallist () const

double	get_rf_energy () const

bool	contains (const SeqTreeObj *sto) const

void	tree (SeqTreeCallbackAbstract *display) const

Protected Member Functions inherited from SeqClass
void	marshall_error () const

SeqClass &	set_temporary ()

Protected 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)

Protected Member Functions inherited from List< SeqObjBase, const SeqObjBase *, const SeqObjBase & >
	List ()

	~List ()

List &	operator= (const List &l)

List &	clear ()

List &	append (const SeqObjBase & item)

List &	remove (const SeqObjBase & item)

unsigned int	size () const

iter	get_begin ()

iter	get_end ()

constiter	get_const_begin () const

constiter	get_const_end () const

Protected Attributes
SeqPars *	commonPars

Friends
class	SeqMethodProxy

class	SeqCmdLine

Additional Inherited Members
Public Types inherited from List< SeqObjBase, const SeqObjBase *, const SeqObjBase & >
typedef STD_list< const SeqObjBase * >::iterator	iter

typedef STD_list< const SeqObjBase * >::const_iterator	constiter

Protected Types inherited from List< SeqObjBase, const SeqObjBase *, const SeqObjBase & >
typedef STD_list< const SeqObjBase * >::iterator	iter

typedef STD_list< const SeqObjBase * >::const_iterator	constiter

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

static void	clear_containers ()

Detailed Description

Base class for methods (sequences)

The base class for all NMR sequences. To create a new sequence, write a new class which is derived from SeqMethod and overload the following virtual functions with the specified functionality:

void method_pars_init(): Initialize sequence parameters (set default values, append to the list of registered parameters of the method)
void method_seq_init(): Create the internal layout of the sequence, i.e. the sequence tree
void method_rels(): Calculate timings of the sequence
void method_pars_set(): Finalize the sequence

To get an idea what has to be done in each function, please take a look at the example sequences.

Definition at line 155 of file seqmeth.h.

Constructor & Destructor Documentation

◆ SeqMethod()

SeqMethod::SeqMethod ( const STD_string & method_label )

Constructs a method with the given label.

◆ ~SeqMethod()

virtual SeqMethod::~SeqMethod ( )

virtual

Destructor

Member Function Documentation

◆ append_parameter()

SeqMethod& SeqMethod::append_parameter	(	LDRbase &	ldr,
		const STD_string &	label,
		parameterMode	parmode = `edit`
	)

protected

Append a user defined parameter to the list of parameters that describe the method

◆ build()

bool SeqMethod::build ( )

inline

Performs state transition to 'built'

Definition at line 185 of file seqmeth.h.

◆ clear()

bool SeqMethod::clear ( )

inline

Performs state transition to 'empty'

Definition at line 175 of file seqmeth.h.

◆ event()

unsigned int SeqMethod::event ( eventContext & context ) const

virtual

Queries the sequence tree for events, returns the number of events executed

Reimplemented from SeqObjList.

◆ get_active_pulsar_pulses()

STD_list<const SeqPulsar*> SeqMethod::get_active_pulsar_pulses ( ) const

Returns a list of Pulsar pulses which are currently active.

◆ get_commonPars()

SeqPars& SeqMethod::get_commonPars ( )

inline

Returns the current set of common sequence parameters

Definition at line 259 of file seqmeth.h.

◆ get_current_testcase()

unsigned int SeqMethod::get_current_testcase ( ) const

inlineprotected

Returns the index of the current test case, used in method_pars_init to assign different parameter settings for each test case.

Definition at line 394 of file seqmeth.h.

◆ get_description()

const char* SeqMethod::get_description ( ) const

inline

Returns the description of the method

Definition at line 211 of file seqmeth.h.

◆ get_geometry()

Geometry& SeqMethod::get_geometry ( )

inline

Returns the current geometry

Definition at line 269 of file seqmeth.h.

◆ get_main_nucleus()

STD_string SeqMethod::get_main_nucleus ( ) const

inline

Returns the current main nucleus of the sequence, i.e. the nucleus for which both, excitation and acquisition, will be performed

Definition at line 319 of file seqmeth.h.

◆ get_methodPars()

LDRblock& SeqMethod::get_methodPars ( )

inline

Returns the method-specific parameters

Definition at line 233 of file seqmeth.h.

◆ get_numof_acquisitions()

unsigned int SeqMethod::get_numof_acquisitions ( ) const

Returns the total number of acquisition windows in the sequence.

◆ get_studyInfo()

Study& SeqMethod::get_studyInfo ( )

inline

Returns reference to the current study info

Definition at line 284 of file seqmeth.h.

◆ get_totalDuration()

double SeqMethod::get_totalDuration ( ) const

Returns the scan duration for this method

◆ init()

bool SeqMethod::init ( )

inline

Performs state transition to 'initialised'

Definition at line 180 of file seqmeth.h.

◆ init_systemInfo()

SeqMethod& SeqMethod::init_systemInfo	(	double	basicfreq,
		double	maxgrad,
		double	slewrate
	)

Initialises the method with the given system-specific stuff

◆ load_geometry()

int SeqMethod::load_geometry ( const STD_string & filename )

inline

Loads the current geometry from disk

Definition at line 274 of file seqmeth.h.

◆ load_protocol()

int SeqMethod::load_protocol ( const STD_string & filename )

Loads the sequence protocol (systemInfo, geometryInfo, sequencePars) from file 'filename'

◆ load_sequencePars()

int SeqMethod::load_sequencePars ( const STD_string & filename )

Loads the sequence parameters (commonPars & methodPars) from file

◆ load_systemInfo()

int SeqMethod::load_systemInfo ( const STD_string & filename )

Loads the systemInfo from disk

◆ method_pars_init()

virtual void SeqMethod::method_pars_init ( )

protectedpure virtual

This function must be implemented by the method programmer. It should contain all code that initialies parameters of the method.

◆ method_pars_set()

virtual void SeqMethod::method_pars_set ( )

protectedpure virtual

This function must be implemented by the method programmer. It should contain all code that is called only once before the sequence is started, e.g. the setup of the reconsruction.

◆ method_rels()

virtual void SeqMethod::method_rels ( )

protectedpure virtual

This function must be implemented by the method programmer. It should contain all code that changes the aspects of the sequence objects without changing their serialisation, .e.g. timing calculations should be coded in this function.

◆ method_seq_init()

virtual void SeqMethod::method_seq_init ( )

protectedpure virtual

This function must be implemented by the method programmer. It should contain all code that initialises the sequence objects and their arrangement.

◆ numof_testcases()

virtual unsigned int SeqMethod::numof_testcases ( ) const

inlineprotectedvirtual

This function can be implemented by the method programmer to indicate how many different use cases are there to be tested during sequence test.

Definition at line 388 of file seqmeth.h.

◆ prep_acquisition()

bool SeqMethod::prep_acquisition ( ) const

Prepares the acquisition parameters, i.e. recoInfo structure and performs platform specific preparation (generating pulse program, etc.). This function will be called by the current frontend (ODIN GUI, odin2idea, ...) prior to the measurement.

◆ prepare()

bool SeqMethod::prepare ( )

inline

Performs state transition to 'prepared'

Definition at line 190 of file seqmeth.h.

◆ process()

int SeqMethod::process	(	int	argc,
		char *	argv[]
	)

This function is used in the ODINMAIN function to hand over control to the SeqMethod object.

◆ set_commonPars()

SeqMethod& SeqMethod::set_commonPars ( const SeqPars & pars )

Sets the current set of common sequence parameters

◆ set_description()

SeqMethod& SeqMethod::set_description ( const char * descr )

inlineprotected

Specifies the description of the method

Definition at line 381 of file seqmeth.h.

◆ set_geometry()

SeqMethod& SeqMethod::set_geometry ( const Geometry & geo )

inline

Sets the current geometry to 'geo'

Definition at line 264 of file seqmeth.h.

◆ set_sequence()

SeqMethod& SeqMethod::set_sequence ( const SeqObjBase & s )

protected

This function is used to specify the sequence of this method that will be played out

◆ set_sequenceParameter()

bool SeqMethod::set_sequenceParameter	(	const STD_string &	parameter_label,
		const STD_string &	value
	)

Sets the value of the sequence parameter 'parameter_label' to 'value'. Returns true if successful.

◆ update_timings()

bool SeqMethod::update_timings ( )

Updates the timing of the sequence (TR, TE) without changing its structure. If the sequence is not yet in the 'built' state, this state will be obtained first.

◆ write_geometry()

int SeqMethod::write_geometry ( const STD_string & filename ) const

inline

Writes the current geometry to disk

Definition at line 279 of file seqmeth.h.

◆ write_meas_contex()

int SeqMethod::write_meas_contex ( const STD_string & prefix ) const

Writes all files which describe the measurement, uses the given filename-prefix

◆ write_protocol()

int SeqMethod::write_protocol ( const STD_string & filename ) const

inline

Writes the sequence protocol (systemInfo, geometryInfo, sequencePars) to file 'filename'

Definition at line 227 of file seqmeth.h.

◆ write_recoInfo()

int SeqMethod::write_recoInfo ( const STD_string & filename ) const

Writes the recoInfo to disk

◆ write_sequencePars()

int SeqMethod::write_sequencePars ( const STD_string & filename ) const

Writes the sequence parameters (commonPars & methodPars) to file

◆ write_systemInfo()

int SeqMethod::write_systemInfo ( const STD_string & filename ) const

inline

Writes the systemInfo to disk

Definition at line 289 of file seqmeth.h.

Member Data Documentation

◆ commonPars

SeqPars* SeqMethod::commonPars

protected

Pointer to the current set of common sequence parameters

Definition at line 400 of file seqmeth.h.

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

seqmeth.h

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SeqMethod()

◆ ~SeqMethod()

Member Function Documentation

◆ append_parameter()

◆ build()

◆ clear()

◆ event()

◆ get_active_pulsar_pulses()

◆ get_commonPars()

◆ get_current_testcase()

◆ get_description()

◆ get_geometry()

◆ get_main_nucleus()

◆ get_methodPars()

◆ get_numof_acquisitions()

◆ get_studyInfo()

◆ get_totalDuration()

◆ init()

◆ init_systemInfo()

◆ load_geometry()

◆ load_protocol()

◆ load_sequencePars()

◆ load_systemInfo()

◆ method_pars_init()

◆ method_pars_set()

◆ method_rels()

◆ method_seq_init()

◆ numof_testcases()

◆ prep_acquisition()

◆ prepare()

◆ process()

◆ set_commonPars()

◆ set_description()

◆ set_geometry()

◆ set_sequence()

◆ set_sequenceParameter()

◆ update_timings()

◆ write_geometry()

◆ write_meas_contex()

◆ write_protocol()

◆ write_recoInfo()

◆ write_sequencePars()

◆ write_systemInfo()

Member Data Documentation

◆ commonPars