/usr/include/odinseq/seqmeth.h is in libodin-dev 1.8.5-2ubuntu1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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seqmeth.h - description
-------------------
begin : Thu Aug 9 2001
copyright : (C) 2001 by Thies H. Jochimsen
email : jochimse@cns.mpg.de
***************************************************************************/
/***************************************************************************
* *
* This program is free software; you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation; either version 2 of the License, or *
* (at your option) any later version. *
* *
***************************************************************************/
#ifndef SEQMETH_H
#define SEQMETH_H
#include <tjutils/tjstate.h>
#include <tjutils/tjhandler.h>
#include <odinpara/protocol.h>
#include <odinseq/seqlist.h>
#include <odinseq/seqplatform.h>
//////////////////////////////////////////////////////////////////////
// forward declarations
class SeqMethod;
class SeqPulsar;
//////////////////////////////////////////////////////////////////////
/**
* @ingroup odinseq_internals
* Proxy class to deal with different ODIN methods at once
*/
class SeqMethodProxy : public StaticHandler<SeqMethodProxy> {
public:
SeqMethodProxy() {
Log<Seq> odinlog("SeqMethodProxy","SeqMethodProxy()");
}
static void set_current_method(unsigned int index);
static SeqMethod* get_current_method();
static unsigned int get_numof_methods();
static unsigned int delete_methods();
static const char* get_method_label();
static const char* get_status_string();
// pointer-like syntax to access current method
SeqMethod* operator -> () {return get_current_method();}
SeqMethod& operator [] (unsigned int index);
static bool load_method_so(const STD_string& so_filename);
// functions to initialize/delete static members by the StaticHandler template class
static void init_static();
static void destroy_static();
protected:
// called by derivedmethod classes to register themselves
static void register_method(SeqMethod* meth);
private:
// struct to store references to all registered methods
struct MethodList : public STD_list<SeqMethod*>, public Labeled {};
static SingletonHandler<MethodList,false> registered_methods;
// struct to store references to the current method
struct MethodPtr : public Labeled {
SeqMethod* ptr;
};
static SingletonHandler<MethodPtr,false> current_method;
static SeqMethod* empty_method;
};
//////////////////////////////////////////////////////////////////////
/*
State diagram for SeqMethod, i.e. for all NMR sequences:
Possible transitions between states are indicated by
the corresponding member functions that perform the transition.
empty <--------\
|
| | clear()
| init() |
| |
V |
|
initialised ---|
|
| |
| build() |
| |
V |
|
built ---------|
|
| |
| prepare() |
| |
V |
|
prepared ------'
*/
/**
* @ingroup odinseq
*
* \brief 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.
*/
class SeqMethod : protected SeqMethodProxy, public SeqObjList, public virtual JDXeditCaller, public StateMachine<SeqMethod> {
public:
/**
* Constructs a method with the given label.
*/
SeqMethod(const STD_string& method_label);
/**
* Destructor
*/
virtual ~SeqMethod();
// public interface to obtain the different states:
/**
* Performs state transition to 'empty'
*/
bool clear() {return empty.obtain_state();}
/**
* Performs state transition to 'initialised'
*/
bool init() {return initialised.obtain_state();}
/**
* Performs state transition to 'built'
*/
bool build() {return built.obtain_state();}
/**
* Performs state transition to 'prepared'
*/
bool prepare() {return prepared.obtain_state();}
/**
* 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.
*/
bool update_timings();
/**
* 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.
*/
bool prep_acquisition() const;
/**
* Returns the description of the method
*/
const char* get_description() const {return description.c_str();}
/**
* This function is used in the ODINMAIN function to hand over control to the SeqMethod object.
*/
int process(int argc, char *argv[]);
/**
* Loads the sequence protocol (systemInfo, geometryInfo, sequencePars) from file 'filename'
*/
int load_protocol(const STD_string& filename);
/**
* Writes the sequence protocol (systemInfo, geometryInfo, sequencePars) to file 'filename'
*/
int write_protocol(const STD_string& filename) const {create_protcache(); return protcache->write(filename);}
/**
* Returns the method-specific parameters
*/
JcampDxBlock& get_methodPars() {return *methodPars;}
/**
* Loads the sequence parameters (commonPars & methodPars) from file
*/
int load_sequencePars(const STD_string& filename);
/**
* Writes the sequence parameters (commonPars & methodPars) to file
*/
int write_sequencePars(const STD_string& filename) const;
/**
* Sets the value of the sequence parameter 'parameter_label' to 'value'.
* Returns true if successful.
*/
bool set_sequenceParameter(const STD_string& parameter_label, const STD_string& value);
/**
* Sets the current set of common sequence parameters
*/
SeqMethod& set_commonPars(const SeqPars& pars);
/**
* Returns the current set of common sequence parameters
*/
SeqPars& get_commonPars() {return (*commonPars);}
/**
* Sets the current geometry to 'geo'
*/
SeqMethod& set_geometry(const Geometry& geo) {geometryInfo->operator = (geo); return *this;}
/**
* Returns the current geometry
*/
Geometry& get_geometry() {return *(geometryInfo.unlocked_ptr());}
/**
* Loads the current geometry from disk
*/
int load_geometry(const STD_string& filename) {return geometryInfo->load(filename);}
/**
* Writes the current geometry to disk
*/
int write_geometry(const STD_string& filename) const {return geometryInfo->write(filename);}
/**
* Returns reference to the current study info
*/
Study& get_studyInfo() {return *(studyInfo.unlocked_ptr());}
/**
* Writes the systemInfo to disk
*/
int write_systemInfo(const STD_string& filename) const {return systemInfo->write(filename);}
/**
* Loads the systemInfo from disk
*/
int load_systemInfo(const STD_string& filename);
/**
* Initialises the method with the given system-specific stuff
*/
SeqMethod& init_systemInfo(double basicfreq,double maxgrad,double slewrate);
/**
* Writes the recoInfo to disk
*/
int write_recoInfo(const STD_string& filename) const;
/**
* Writes all files which describe the measurement, uses the given filename-prefix
*/
int write_meas_contex(const STD_string& prefix) const;
/**
* Returns the scan duration for this method
*/
double get_totalDuration() const;
/**
* Returns the current main nucleus of the sequence, i.e. the nucleus for which both, excitation and acquisition, will be performed
*/
STD_string get_main_nucleus() const {return systemInfo->get_main_nucleus();}
/**
* Returns the total number of acquisition windows in the sequence.
*/
unsigned int get_numof_acquisitions() const;
/**
* Returns a list of Pulsar pulses which are currently
* active.
*/
STD_list<const SeqPulsar*> get_active_pulsar_pulses() const;
// overloaded virtual functions from SeqTreeObj
unsigned int event(eventContext& context) const;
// leave this public for idea_emulation
void set_current_testcase(unsigned int index) {if(index<numof_testcases()) current_testcase=index;}
protected:
/**
* This function must be implemented by the method programmer. It should contain all
* code that initialies parameters of the method.
*/
virtual void method_pars_init() = 0;
/**
* This function must be implemented by the method programmer. It should contain all
* code that initialises the sequence objects and their arrangement.
*/
virtual void method_seq_init() = 0;
/**
* 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.
*/
virtual void method_rels() = 0;
/**
* 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.
*/
virtual void method_pars_set() = 0;
/**
* Append a user defined parameter to the list of parameters that describe the method
*/
SeqMethod& append_parameter(JcampDxClass& ldr,const STD_string& label,parameterMode parmode=edit);
/**
* This function is used to specify the sequence of this method that will be played out
*/
SeqMethod& set_sequence(const SeqObjBase& s);
/**
* Specifies the description of the method
*/
SeqMethod& set_description(const char* descr) {description=descr;return *this;}
/**
* This function can be implemented by the method programmer to indicate
* how many different use cases are there to be tested during sequence test.
*/
virtual unsigned int numof_testcases() const {return 1;}
/**
* Returns the index of the current test case, used in method_pars_init to
* assign different parameter settings for each test case.
*/
unsigned int get_current_testcase() const {return current_testcase;}
/**
* Pointer to the current set of common sequence parameters
*/
SeqPars* commonPars;
private:
friend class SeqMethodProxy;
friend class SeqCmdLine;
void set_parblock_labels();
bool calc_timings();
// overloaded virtual function from JDXeditCaller
void parameter_relations(JDXeditWidget* editwidget);
// interface for quick access to current platform
mutable SeqPlatformProxy platform;
// block to hold method-specific parameters
JcampDxBlock* methodPars;
STD_string description;
unsigned int current_testcase;
// cache handle to method plug-in so that it can be removed later
void *dl_handle;
void create_protcache() const;
mutable Protocol* protcache; // used for returning reference to protocol, local static object does not work on VxWorks
// states and their transition functions:
State<SeqMethod> empty;
bool reset();
State<SeqMethod> initialised;
bool empty2initialised();
State<SeqMethod> built;
bool initialised2built();
State<SeqMethod> prepared;
bool built2prepared();
};
//////////////////////////////////////////////////////////////////////
// Macro to include in every sequence file to create an entry point
// Double-stage macros to stringize METHOD_LABEL, see http://c-faq.com/ansi/stringize.html
#define ODINMETHOD_STRINGIZE_MACRO(x) #x
#define ODINMETHOD_STRINGIZE(x) ODINMETHOD_STRINGIZE_MACRO(x)
#ifdef NO_CMDLINE
#define ODINMETHOD_ENTRY_POINT \
int ODINMAIN(int argc, char *argv[]) {\
return (new METHOD_CLASS(ODINMETHOD_STRINGIZE(METHOD_LABEL)))->process(argc,argv); \
}
#else
#define ODINMETHOD_ENTRY_POINT \
int ODINMAIN(int argc, char *argv[]) {\
if(LogBase::set_log_levels(argc,argv,false)) return 0; \
return (new METHOD_CLASS(ODINMETHOD_STRINGIZE(METHOD_LABEL)))->process(argc,argv); \
}
#endif
#endif
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