/usr/include/odinseq/seqacq.h is in libodin-dev 1.8.5-2ubuntu1.
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seqacq.h - description
-------------------
begin : Wed Aug 8 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 SEQACQ_H
#define SEQACQ_H
#include <tjutils/tjhandler.h>
#include <odinseq/seqobj.h>
#include <odinseq/seqfreq.h>
#include <odinseq/seqvec.h>
#include <odinseq/seqdriver.h>
class SeqGradChanParallel; // forward declaration
////////////////////////////////////////////////////////////////
/**
* @ingroup odinseq_internals
* This is the abstract base class for all objects that have the
* property of acquiring a signal
*/
class SeqAcqInterface : public virtual SeqFreqChanInterface {
public:
/**
* Returns the duration of the acquisition window without padding delays.
*/
virtual double get_acquisition_duration() const {if(marshall) return marshall->get_acquisition_duration(); else marshall_error(); return 0.0;}
/**
* Returns the the duration from the the beginnig of the acquisition
* object to the middle of the acquisition window.
*/
virtual double get_acquisition_center() const {if(marshall) return marshall->get_acquisition_center(); else marshall_error(); return 0.0;}
/**
* Returns the the duration from the the beginnig of the acquisition
* object to the beginnig of the acquisition window (the point
* of time where data starts to be acquired).
*/
virtual double get_acquisition_start() const {if(marshall) return marshall->get_acquisition_start(); else marshall_error(); return 0.0;}
/**
* Returns the total number of sampling points, without oversampling
*/
virtual unsigned int get_npts() const {if(marshall) return marshall->get_npts(); else marshall_error(); return 0;}
/**
* Sets the sweepwidth 'sw' without oversampling and oversampling factor 'os_factor' for this acquisition object, os_factor=1 means no oversampling.
*/
virtual SeqAcqInterface& set_sweepwidth(double sw, float os_factor) {if(marshall) marshall->set_sweepwidth(sw,os_factor); else marshall_error(); return *this;}
/**
* Returns the sweepwidth factor
*/
virtual double get_sweepwidth() const {if(marshall) return marshall->get_sweepwidth(); else marshall_error(); return 0.0;}
/**
* Returns the oversampling factor
*/
virtual float get_oversampling() const {if(marshall) return marshall->get_oversampling(); else marshall_error(); return 0.0;}
/**
* Specifies a regridding matrix for this ADC (for automatic reconstruction)
*/
virtual SeqAcqInterface& set_readout_shape(const fvector& shape, unsigned int dstsize) {if(marshall) marshall->set_readout_shape(shape, dstsize); else marshall_error(); return *this;}
/**
* Specifies a vector 'vec' which indexes the data dimension 'dim'.
* The current index for each acquisition is retrieved from the vector.
* This is relevant for automatic reconstruction.
* An additional vector 'valvec' of double values can be given,
* which is attached to this dimension, e.g. different TEs in the echo
* dimension.
*/
virtual SeqAcqInterface& set_reco_vector(recoDim dim, const SeqVector& vec, const dvector& valvec=dvector()) {if(marshall) marshall->set_reco_vector(dim, vec, valvec); else marshall_error(); return *this;}
/**
* Sets the default value 'index' for the reco index in dimension 'dim'.
* This is relevant for automatic reconstruction.
*/
virtual SeqAcqInterface& set_default_reco_index(recoDim dim, unsigned int index) {if(marshall) marshall->set_default_reco_index(dim, index); else marshall_error(); return *this;}
/**
* Sets the template mode of this acquisition object.
* This is also relevant for automatic reconstruction.
*/
virtual SeqAcqInterface& set_template_type(templateType type) {if(marshall) marshall->set_template_type(type); return set_default_reco_index(templtype,type);}
/**
* Specifies whether the data points should be reversed, only relevant
* for automatic reconstruction
*/
virtual SeqAcqInterface& set_reflect_flag(bool flag) {if(marshall) marshall->set_reflect_flag(flag); else marshall_error(); return *this;}
protected:
SeqAcqInterface() : marshall(0) {}
virtual ~SeqAcqInterface() {}
void set_marshall(SeqAcqInterface* mymarshall) {marshall=mymarshall;} // to be used in constructor code
private:
friend class SeqAcqDeph;
// to be used by SeqAcqDeph to retrieve pre-dephasing gradients from acquisition object.
// Overload this function if your acq needs pre-dephasers, return them by appending them to 'dephobj'.
// Returns any possible vector object as the return value.
virtual const SeqVector* get_dephgrad(SeqGradChanParallel& dephobj, bool rephase) const {if(marshall) return marshall->get_dephgrad(dephobj,rephase); return 0;}
SeqAcqInterface* marshall; // for marshalling member functions to a sub-object
};
/////////////////////////////////////////////////////////////////////////
/**
* @ingroup odinseq_internals
* The base class for platform specific drivers of acquisition windows
*/
class SeqAcqDriver : public SeqDriverBase {
public:
SeqAcqDriver() {}
virtual ~SeqAcqDriver() {}
/**
* Returns possible sweepwidth closest to 'desired_sweep_widht'
*/
virtual double adjust_sweepwidth(double desired_sweep_widht) const = 0;
/**
* Prepare driver, let driver adjust reco coordinate 'recoindex'
*/
virtual bool prep_driver(kSpaceCoord& recoindex, double sweepwidth, unsigned int nAcqPoints, double acqcenter, int freqchannel) = 0;
/**
* Delay prior to actual acquisition
*/
virtual double get_predelay() const = 0;
/**
* Delay following actual acquisition depending on 'sweepwidth'
*/
virtual double get_postdelay(double sweepwidth) const = 0;
virtual void event(eventContext& context, double start) const = 0;
virtual STD_string get_program(programContext& context, unsigned int phaselistindex) const = 0;
virtual STD_string get_instr_label() const = 0;
virtual unsigned int get_numof_channels() const = 0;
virtual SeqAcqDriver* clone_driver() const = 0;
};
/////////////////////////////////////////////////////////////////////////
/**
* @addtogroup odinseq
* @{
*/
/**
* \brief Acquisition
*
* This class represents an acquisition window
*/
class SeqAcq : public virtual SeqAcqInterface, public SeqObjBase, public SeqFreqChan {
public:
/**
* Constructs an acquisition window labeled 'object_label' with the following properties:
* - nAcqPoints: The number of sampling points that will be acquired during the acquisition
* - sweepwidth: The sampling frequency without oversampling
* - os_factor: The oversampling factor, os_factor=1 means no oversampling
* - nucleus: The nucleus for which the acquisition should be performed. The default
* is to acquire on the protons resonance freuency.
* - phaselist: This is an array of phases at which the acquired signal will be
* demodulated. The actual phase for each acquisition is determined
* by cycling through this array of phases which are represented
* in degree.
* - freqlist: This is an array of frequency offsets at which the acquired signal
* will be demodulated.
*/
SeqAcq(const STD_string& object_label, unsigned int nAcqPoints, double sweepwidth,
float os_factor=1.0, const STD_string& nucleus="",
const dvector& phaselist=0,const dvector& freqlist=0);
/**
* Constructs an acquisition window which is a copy of 'sa'
*/
SeqAcq(const SeqAcq& sa);
/**
* Constructs an empty acquisition window with the given label.
*/
SeqAcq(const STD_string& object_label="unnamedSeqAcq");
/**
* Destructor
*/
~SeqAcq();
/**
* Sets the number of sampling points that will be acquired during the acquisition
*/
SeqAcq& set_npts(unsigned int nAcqPoints);
/**
* Returns the sweep width
*/
double get_sweep_width() const {return sweep_width;}
/**
* This assignment operator will make this object become an exact copy of 'sa'.
*/
SeqAcq& operator = (const SeqAcq& sa);
/**
* Specifies a an explicit k-space Trajectory for this ADC (for automatic reconstruction)
*/
void set_kspace_traj(const farray& kspaceTraj);
/**
* Specifies a complex vector which is is used to weight each point in this ADC (for automatic reconstruction)
*/
void set_weight_vec(const cvector& weightVec);
/**
* Sets the relative point in time (between 0 and 1) when k-space center is passed, the default is 0.5.
* Will be used in get_acquisition_center().
*/
SeqAcq& set_rel_center(double relative_kspace_center) {rel_center=relative_kspace_center; return *this;}
/**
* Returns the k-space index of this ADCs
*/
const kSpaceCoord& get_kcoord() const;
// overwriting virtual functions of SeqAcqInterface
double get_acquisition_duration() const {return secureDivision(npts,sweep_width);}
double get_acquisition_center() const;
double get_acquisition_start() const {return acqdriver->get_predelay();}
unsigned int get_npts() const {return npts;}
SeqAcqInterface& set_sweepwidth(double sw, float os_factor);
double get_sweepwidth() const {return sweep_width;}
float get_oversampling() const {return oversampl;}
SeqAcqInterface& set_readout_shape(const fvector& shape, unsigned int dstsize);
SeqAcqInterface& set_reco_vector(recoDim dim, const SeqVector& vec, const dvector& valvec=dvector());
SeqAcqInterface& set_default_reco_index(recoDim dim, unsigned int index);
SeqAcqInterface& set_reflect_flag(bool flag) {reflect_flag=flag; return *this;}
// overwriting virtual functions of SeqTreeObj
STD_string get_program(programContext& context) const;
double get_duration() const;
SeqValList get_freqvallist(freqlistAction action) const;
void query(queryContext& context) const {SeqTreeObj::query(context); context.numof_acqs=1;}
RecoValList get_recovallist(unsigned int reptimes, JDXkSpaceCoords& coords) const;
unsigned int event(eventContext& context) const;
STD_string get_properties() const;
private:
friend class SeqMethod;
friend class SeqEpiDriverParavision;
friend class SeqEpiDriverEpic;
void common_init();
// overwriting virtual functions of SeqFreqChan
double get_freqchan_duration() const {return get_acquisition_duration();}
STD_string get_driver_instr_label() const {return acqdriver->get_instr_label();}
// overwriting virtual functions of SeqClass
bool prep();
mutable kSpaceCoord kcoord;
mutable SeqDriverInterface<SeqAcqDriver> acqdriver;
double sweep_width;
unsigned int npts;
float oversampl;
double rel_center;
bool reflect_flag;
int readoutIndex;
int trajIndex;
int weightIndex;
// safe pointers to vectors to create indices for the ADC
// pointer to pointer is used here to avoid delete[] bug in GCC2.9
Handler<const SeqVector*>** dimvec;
int default_recoindex[n_recoIndexDims];
};
/** @}
*/
#endif
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