/usr/include/odinseq/seqdiffweight.h is in libodin-dev 1.8.8-2ubuntu1.
This file is owned by root:root, with mode 0o644.
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seqdiffweight.h - description
-------------------
begin : Wed Feb 12 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 SEQDIFFWEIGHT_H
#define SEQDIFFWEIGHT_H
#include <odinseq/seqparallel.h>
#include <odinseq/seqlist.h>
#include <odinseq/seqgrad.h>
#include <odinseq/seqgradpulse.h>
#include <odinseq/seqgradconst.h>
#include <odinseq/seqsimvec.h>
/**
* @addtogroup odinseq
* @{
*/
/**
*
* \brief Diffusion Weighting
*
* A bipolar gradient pulse for diffusion weighting
*
* The b-value and the properties of the gradient pulses are connected through the equation
*
* b = gamma^2 * delta^2 ( Delta - delta/3 ) G^2
*
* - b: b-value
* - gamma: gyromagnetic ratio
* - delta: gradient pulse duration
* - Delta: gradient pulse separation, the duration of midpart (sequence part which is enclosed by the two gradient) is considered here
* - G: gradient strength
*
* The order in which the series of b-values is played out can be cyclically
* reordered by using the vector which is returned by the get_reorder_vector()
* function: At each iteration of this vector, the b-values are exchanged cyclically.
*/
class SeqDiffWeight : public SeqObjList, public SeqSimultanVector, public virtual SeqGradInterface {
public:
/**
* Constructs a bipolar gradient pulse labeled 'object_label' with the following properties:
* - bvals: The b-values for diffusion weighting, a postive value means that the first
* gradient pulse will have positive polarity and the second gradient pulse a negative polarity.
* These polarities are swapped in case of a negative b-value.
* - maxgradstrength: The maximum gradient strength to use for the maximum b-value
* - midpart: The sequence part which will be enclosed by the two gradient pulses.
* - chan: The gradient channel for the gradient pulses.
* - stejskalTanner: If set to 'true', both gradients will have the same polarity
* - nucleus: The nucleus for which the gradient pulses will be calculated
*/
SeqDiffWeight(const STD_string& object_label, const fvector& bvals, float maxgradstrength,
const SeqObjBase& midpart, direction chan, bool stejskalTanner=false, const STD_string& nucleus = "" );
/**
* Constructs a bipolar gradient pulse labeled 'object_label' with the following properties:
* - ndir: Number of uniformly ditributed directions
* - bvals: The b-values for diffusion weighting, a postive value means that the first
* gradient pulse will have positive polarity and the second gradient pulse a negative polarity.
* These polarities are swapped in case of a negative b-value.
* - maxgradstrength: The maximum gradient strength to use for the maximum b-value
* - midpart: The sequence part which will be enclosed by the two gradient pulses.
* - baseline_rep: Repetition rate of the baseline (b=0) scan. Not repeated if zero.
* - stejskalTanner: If set to 'true', both gradients will have the same polarity
* - nucleus: The nucleus for which the gradient pulses will be calculated
*/
SeqDiffWeight(const STD_string& object_label, unsigned int ndir, const fvector& bvals, float maxgradstrength,
const SeqObjBase& midpart, unsigned int baseline_rep=0, bool stejskalTanner=false, const STD_string& nucleus = "" );
/**
* Default constructor
*/
SeqDiffWeight(const STD_string& object_label = "unnamedSeqDiffWeight" );
/**
* Copy constructor
*/
SeqDiffWeight(const SeqDiffWeight& sgdw) {SeqDiffWeight::operator = (sgdw);}
/**
* Assignment operator
*/
SeqDiffWeight& operator = (const SeqDiffWeight& sgdw);
/**
* Returns the first gradient lobe
*/
const SeqGradInterface& get_grad1() const {return par1;}
/**
* Returns the second gradient lobe
*/
const SeqGradInterface& get_grad2() const {return par2;}
/**
* Returns the duration of the first gradient lobe
*/
double get_grad1_duration() const {return par1.get_duration();}
/**
* Returns the duration of the second gradient lobe
*/
double get_grad2_duration() const {return par2.get_duration();}
/**
* Returns the duration of the part in the middle between the two gradient lobes
*/
double get_midpart_duration() const {return middle_part.get_duration();}
/**
* Returns the b-vectors used in subsequent order.
*/
const darray& get_b_vectors() const {return b_vectors_cache;}
// overloading virtual function from SeqGradInterface
SeqGradInterface& set_strength(float gradstrength);
SeqGradInterface& invert_strength();
float get_strength() const;
fvector get_gradintegral() const;
double get_gradduration() const;
SeqGradInterface& set_gradrotmatrix(const RotMatrix& matrix);
// final overrider of virtual functions from SeqClass
void clear_container() {SeqObjList::clear(); SeqSimultanVector::clear();}
// implemented virtual functions from SeqVector
bool is_qualvector() const {return false;}
private:
void build_seq();
SeqGradVectorPulse pfg1[n_directions];
SeqGradVectorPulse pfg2[n_directions];
SeqParallel par1;
SeqParallel par2;
SeqObjList middle_part;
darray b_vectors_cache;
};
//////////////////////////////////////////////////////////////////////////////////////////
/**
*
* \brief Flow-Compensated Diffusion Weighting
*
* A flow-compensated gradient train for diffusion weighting
*
*/
class SeqDiffWeightFlowComp : public SeqGradChanList, public SeqSimultanVector {
public:
/**
* Constructs a flow-compensated gradient train labeled 'object_label' with the following properties:
* - bvals: The b-values for diffusion weighting, a postive value means that the first
* gradient pulse will have positive polarity and the second gradient pulse a negative polarity.
* These polarities are swapped in case of a negative b-value
* - maxgradstrength: The maximum gradient strength to use for the maximum b-value
* - chan: The gradient channel for the gradient pulses
* - stimdelay: Extra delay between gradient sub-pulses to avoid stimulation
* - nucleus: The nucleus for which the gradient pulses will be calculated
*/
SeqDiffWeightFlowComp(const STD_string& object_label, const fvector& bvals, float maxgradstrength,
direction chan, double stimdelay=1.0, const STD_string& nucleus = "" );
/**
* Default constructor
*/
SeqDiffWeightFlowComp(const STD_string& object_label = "unnamedSeqDiffWeightFlowComp" );
/**
* Copy constructor
*/
SeqDiffWeightFlowComp(const SeqDiffWeightFlowComp& sgdwfc) {SeqDiffWeightFlowComp::operator = (sgdwfc);}
/**
* Assignment operator
*/
SeqDiffWeightFlowComp& operator = (const SeqDiffWeightFlowComp& sgdwfc);
// final overrider of virtual functions from SeqClass
void clear_container() {SeqGradChanList::clear(); SeqSimultanVector::clear();}
// implemented virtual functions from SeqVector
bool is_qualvector() const {return false;}
private:
void build_seq();
SeqGradVectorPulse pfg1;
SeqGradVectorPulse pfg2;
SeqGradVectorPulse pfg3;
SeqGradDelay delay;
};
/** @}
*/
#endif
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