example_mrisd_spin_echo.m

%% Init

close all
clear
clc

% motsly for time axis scaling
pulse_dur = 1;
grad_dur = 2;
TE = 10; % this places ADC middle (and RF middle if needed)
TR = 15;


%% Create the diagram object
% "channel" types are {'RF', 'G_SS', 'G_PE', 'G_RO', 'ADC'}. Each channe is one curve container.
%
% Gradients are seperated into "logical" axis : slice selective, phase encoding, readout

% Create diagram object
% This object will contain all the information
% All rf, gradient, adc objects are also objects, contained in a diagram
DIAGRAM = mrisd.diagram('spin_echo');


%% Create each graphic element and set their paramters except position in time

% Create RF excitation
RF_090            = DIAGRAM.add_rf_pulse('RF_090');
RF_090.flip_angle = 90;
RF_090.magnitude  = 0.5; % half the magnitude(1) because there will be a 180° pulse

% Create RF refocusing
RF_180 = DIAGRAM.add_rf_pulse('RF_180');
RF_180.flip_angle = 180;

% Create ADC
ADC = DIAGRAM.add_adc('ADC');

% Create SliceSelective Gradient "setter"
G_SS090set = DIAGRAM.add_gradient_slice_selection('G_SS090set');

% Create SliceSelective Gradient "rewinder"
G_SS090rew           = DIAGRAM.add_gradient_slice_selection('G_SS090rew');
G_SS090rew.magnitude = -1;

% Create PhaseEncoding Gradient "setter"
G_PEset = DIAGRAM.add_gradient_phase_encoding('G_PEset');
G_PEset.n_lines = 5;

% Create SliceRefocussing Gradient "setter"
G_SS180set = DIAGRAM.add_gradient_slice_selection('G_SS180set');

% Create ReadOut gradient "prephase"
G_ROpre           = DIAGRAM.add_gradient_readout('G_ROpre');
G_ROpre.magnitude = -1;

% Create ReadOut gradient for ADC
G_ROadc      = DIAGRAM.add_gradient_readout('G_ROadc');

ECHO           = DIAGRAM.add_echo('ECHO');
ECHO.asymmetry = 0.50; % default = 0.5 (middle), range from 0 to 1

annot_halfTE = DIAGRAM.add_annotation('TE/2');
annot_TE     = DIAGRAM.add_annotation('TE'  );

nextRF            = DIAGRAM.add_rf_pulse('nextRF');
nextRF.flip_angle = RF_090.flip_angle;
nextRF.magnitude  = RF_090.magnitude;

nextGSS      = DIAGRAM.add_gradient_slice_selection('nextGSS');

annot_TR     = DIAGRAM.add_annotation('TR');


%% Timings
%
% Each element (rf_pulse, gradient, adc) have 4 timing values :
% - onset
% - middle (default : duration/2)
% - offset
% - duration (default : offset-onset)
%
% And gradients have also :
% - dur_ramp_up
% - dur_flattop
% - dur_ramp_down  (duration = dur_ramp_up + dur_flattop + dur_ramp_down)
%

% Place the main objects, used to define TE, TE/2, ...

RF_090.set_as_initial_element(pulse_dur); % set duration(use input argument), .onset = 0, ...

RF_180.duration = pulse_dur;
RF_180.set_middle_using_TRTE(RF_090.middle + TE/2); % this sets .middle, then the rest (onset/offset/duration)

ADC.duration = grad_dur;
ADC.set_middle_using_TRTE(RF_090.middle + TE);
ECHO.set_using_ADC(ADC);

% Now place gradients

G_SS090set.set_flattop_on_rf(RF_090); % will set all timings

G_SS090rew.set_moment(G_SS090set.get_rewind_moment()); % will set all .dur*, but no .onset or .offset
G_SS090rew.set_onset_at_elem_offset(G_SS090set);

G_PEset.set_total_duration(grad_dur);
G_PEset.set_onset_at_elem_offset(G_SS090rew);

G_SS180set.set_flattop_on_rf(RF_180);

G_ROadc.set_flattop_on_adc(ADC);
G_ROpre.set_moment(G_ROadc.get_prephase_moment());
G_ROpre.set_offset_at_elem_onset(G_ROadc);

annot_halfTE.set_onset_and_duration(RF_090.middle, TE/2);
annot_TE.    set_onset_and_duration(RF_090.middle, TE  );

% for TR visualization :

nextRF.duration = RF_090.duration;
nextRF.set_middle_using_TRTE(RF_090.middle + TR);

nextGSS.set_flattop_on_rf(nextRF);

annot_TR.set_onset_and_duration(RF_090.middle, TR);


%% Now we draw
% Many checks will be performed in the .draw(), asserions should help filling missing informations.

DIAGRAM.Draw();

% save the fig :
% DIAGRAM.save_fig('spin_echo.png')
% DIAGRAM.save_fig('spin_echo.svg')