/usr/include/odinseq/seqgradecho.h is in libodin-dev 1.8.8-2ubuntu1.
This file is owned by root:root, with mode 0o644.
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seqgradecho.h - description
-------------------
begin : Mon Feb 17 2003
copyright : (C) 2000-2014 by Thies H. Jochimsen
email : thies@jochimsen.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 SEQGRADECHO_H
#define SEQGRADECHO_H
#include <odinseq/seqgradpulse.h>
#include <odinseq/seqgradphase.h>
#include <odinseq/seqacqread.h>
#include <odinseq/seqacqdeph.h>
#include <odinseq/seqpulsar.h>
#include <odinseq/seqsimvec.h>
/**
* @addtogroup odinseq
* @{
*/
/**
* \brief Gradient echo module
*
* A gradient echo module (excitation pulse + phase encoding + frequency encoding).
* This is a convenience class which groups a number of low-level sequence
* objects together. All objects necessary to produce a gradient echo are part
* of this class, except the excitation pulse. The latter is passed per reference
* (no copy is created within the module, it uses a safe pointer to the pulse).
*
*/
class SeqGradEcho : public SeqObjList, public virtual SeqGradInterface, public virtual SeqAcqInterface {
// virtual functions of SeqFreqChanInterface are marhshalled to acqread
public:
/**
* Constructs a 2D (i.e. multi-slice) gradient echo module labeled 'object_label' with the following properties:
* - exc: The excitation pulse
* - sweepwidth: The sampling frequency
* - readnpts: Matrix size in frequency-encoding direction
* - FOVread: The FOV in frequency-encoding direction
* - phasenpts: Matrix size in phase-encoding direction
* - FOVphase: The FOV in phase-encoding direction
* - scheme: The phase encoding scheme
* - reorder: The reordering scheme
* - nsegments: The number of segments for segmented reordering
* - reduction: Reduction factor for parallel imaging (sparsely sampled k-space)
* - acl_bands: Number of autocalibration bands (bunch of adjacent lines between actual k-space lines) for GRAPPA
* - balanced: Whether rephasers (+ exc dephaser) should be added after acquisition, suitable for SSFP sequences
* - partial_fourier_phase: The amount of partial Fourier undersampling in phase encoding direction (0=no undersampling, 1=half fourier)
* - partial_fourier_read: The amount of partial Fourier undersampling in readout direction (0=no undersampling, 1=half fourier)
* - partial_fourier_read_at_end: If set to 'true', partial Fourier will omit data at the end of the readout
* - os_factor: The oversampling factor, os_factor=1 means no oversampling
* - nucleus: The nucleus to observe
*/
SeqGradEcho(const STD_string& object_label, SeqPulsar& exc,
double sweepwidth, unsigned int readnpts, float FOVread,
unsigned int phasenpts, float FOVphase, encodingScheme scheme=linearEncoding,
reorderScheme reorder=noReorder, unsigned int nsegments=1, unsigned int reduction=1, unsigned int acl_bands=DEFAULT_ACL_BANDS,
bool balanced=false, float partial_fourier_phase=0.0, float partial_fourier_read=0.0, bool partial_fourier_read_at_end=false,
float os_factor=1.0, const STD_string& nucleus="");
/**
* Constructs a gradient echo module labeled 'object_label' for 3D imaging with the following properties:
* - readnpts: Matrix size in frequency-encoding direction
* - FOVread: The FOV in frequency-encoding direction
* - phasenpts: Matrix size in phase-encoding direction
* - FOVphase: The FOV in phase-encoding direction
* - slicenpts: Matrix size in the 2nd phase-encoding (slice) direction
* - FOVslice: The FOV in the 2nd phase-encoding (slice) direction
* - exc: The excitation pulse
* - sweepwidth: The sampling frequency
* - reduction: Reduction factor for parallel imaging (sparsely sampled k-space), the factor applies to both phase-encoding directions
* - acl_bands: Number of autocalibration bands (bunch of adjacent lines between actual k-space lines) for GRAPPA
* - balanced: Whether rephasers (+ exc dephaser) should be added after acquisition, suitable for SSFP sequences
* - partial_fourier_phase: The amount of partial Fourier undersampling in phase encoding direction (0=no undersampling, 1=half fourier)
* - partial_fourier_read: The amount of partial Fourier undersampling in readout direction (0=no undersampling, 1=half fourier)
* - partial_fourier_read_at_end: If set to 'true', partial Fourier will omit data at the end of the readout
* - os_factor: The oversampling factor, os_factor=1 means no oversampling
* - nucleus: The nucleus to observe
*/
SeqGradEcho(const STD_string& object_label,
unsigned int readnpts, float FOVread, unsigned int phasenpts, float FOVphase, unsigned int slicenpts, float FOVslice,
SeqPulsar& exc, double sweepwidth,
unsigned int reduction=1, unsigned int acl_bands=DEFAULT_ACL_BANDS,
bool balanced=false, float partial_fourier_phase=0.0, float partial_fourier_read=0.0, bool partial_fourier_read_at_end=false,
float os_factor=1.0, const STD_string& nucleus="");
/**
* Constructs an empty SeqGradEcho
*/
SeqGradEcho(const STD_string& object_label="unnamedSeqGradEcho");
/**
* Constructs a copy of 'sge'
*/
SeqGradEcho(const SeqGradEcho& sge);
/**
* Assignment operator that makes this object become a copy of 'sge'
*/
SeqGradEcho& operator = (const SeqGradEcho& sge);
/**
* Returns the phase encoding vector as a sequence object (for loop insertion)
*/
SeqVector& get_pe_vector();
/**
* Sets the reordering scheme and the number of segments for phase encoding
*/
SeqGradEcho& set_pe_reorder_scheme(reorderScheme scheme,unsigned int nsegments);
/**
* Returns the phase encoding reordering vector (for loop insertion)
*/
const SeqVector& get_pe_reorder_vector() const;
/**
* Returns the 2nd phase encoding vector as a sequence object (for loop insertion)
*/
SeqVector& get_pe3d_vector();
/**
* Returns the excitation pulse as a sequence object (for loop insertion)
*/
const SeqVector& get_exc_vector() const {return *pulsptr.get_handled();}
/**
* Sets the reordering scheme for the frequency list of the excitation pulse
*/
SeqGradEcho& set_freq_reorder_scheme(reorderScheme scheme,unsigned int nsegments=1) {(*pulsptr.get_handled()).set_reorder_scheme(scheme,nsegments); return *this;}
/**
* Returns the reorder vector for the frequency list of the excitation pulse (for loop insertion)
*/
const SeqVector& get_freq_reorder_vector() const {return (*pulsptr.get_handled()).get_reorder_vector();}
/**
* Returns the echo time (from the middle of excitation pulse to the middle of the acquisition window)
*/
double get_echo_time() const;
/**
* Places an additional sequence object between excitation and readout
*/
SeqGradEcho& set_midpart(const SeqObjBase& soa);
// implementing virtual functions of SeqGradInterface
SeqGradInterface& set_strength(float gradstrength) {return *this;} // nothing useful
float get_strength() const {return 0.0;} // nothing useful
SeqGradInterface& invert_strength();
double get_gradduration() const {return get_duration();}
SeqGradInterface& set_gradrotmatrix(const RotMatrix& matrix);
fvector get_gradintegral() const;
// marshalling virtual functions of SeqAcqInterface to acqread, except:
double get_acquisition_center() const {return get_preacq()+acqread.get_acquisition_center();}
double get_acquisition_start() const {return get_preacq()+acqread.get_acquisition_start();}
SeqAcqInterface& set_template_type(templateType type);
private:
double get_preacq() const;
void common_init(const STD_string& objlabel);
void build_seq();
// hide these functions from the user
SeqAcqInterface& set_pe_vector(const SeqVector& pevec) {return *this;}
Handler<SeqPulsNdim*> pulsptr;
SeqPulsarReph pls_reph;
SeqGradVector phase;
SeqGradVector phase3d;
SeqGradVector phase_rew;
SeqGradVector phase3d_rew;
SeqSimultanVector phasesim;
SeqSimultanVector phasesim3d;
SeqSimultanVector phasereordsim;
SeqAcqRead acqread;
SeqGradConst readdeph;
SeqParallel postexcpart;
SeqParallel postacqpart;
SeqObjList midpart;
geometryMode mode;
bool balanced_grads;
};
/** @}
*/
#endif
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