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Copy pathgenerate_movie_for_inept.m
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generate_movie_for_inept.m
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clear all
every_pt=500;
%every_pt=2500;% this is to speed up generation
for center_antiphase_arrow=[0 1]
for loop_j=0
for mainlooop=0:6
if mainlooop==0
text_title='Pulse Evolution PI(y) inv(J) Evolution (no chemical shift evolution)';
file_name=['Spin_echo_for_INEPT_PIy_NO_chem_shift_evol.avi'];
end
if mainlooop==1
text_title='Pulse Evolution PI(x) inv(J) Evolution (no chemical shift evolution)';
file_name=['Spin_echo_for_INEPT_PIx_NO_chem_shift_evol.avi'];
end
if mainlooop==2
text_title='Pulse Evolution PI(y) inv(J) Evolution ';
file_name=['Spin_echo_for_INEPT_PIy_chem_shift_evol.avi'];
end
if mainlooop==3
text_title='Pulse Evolution PI(x) inv(J) Evolution ';
file_name=['Spin_echo_for_INEPT_PIx_chem_shift_evol.avi'];
end
if mainlooop==4
text_title='Pulse Evolution PI(y) inv(J) Evolution (imperfect tau value)';
file_name=['Spin_echo_for_INEPT_PIy_chem_shift_evol_imperfect_tau.avi'];
end
if mainlooop==5
text_title='Pulse Evolution PI(x) inv(J) Evolution (imperfect tau value)';
file_name=['Spin_echo_for_INEPT_PIx_chem_shift_evol_imperfect_tau.avi'];
end
if every_pt==2500
file_name=['delete_quick_' file_name];
end
if center_antiphase_arrow
file_name=['Centered_antiphase_arrow_' file_name];
end
writerObj = VideoWriter([file_name]);
% for mainlooop=-3
clear stor_tr
clear stor_tr_crude
clear stor_t_crude
clear stor_t
main_ratio=90;
figure(1)
[v1 v2]=view([-30 25]);
v1=-30;
v2=25;
v1=-60;
v2=25;
view([v1 v2]);
% Z = peaks;
% surf(Z)
% axis tight manual
% ax = gca;
% ax.NextPlot = 'replaceChildren';
% writerObj = VideoWriter(['mov_' num2str(mainlooop) '.mp4']);
writerObj.Quality = 75;%75 is default
open(writerObj);
axis tight
set(gca,'nextplot','replacechildren');
set(gcf,'Renderer','zbuffer');
list_of_values= 0.00:1:main_ratio+1;
loops = 360;
loops = 1;
count_sto=1;
F(size(list_of_values,2)+1) = struct('cdata',[],'colormap',[]);
counter_frames=1;
pul_dur=10e-6;
angle_pulse=90/180*pi;%90 deg
ampli_hz=(angle_pulse/pul_dur)/(2*pi);
disp(['pulse amplitude : ' num2str(ampli_hz) ' Hz'])
loop_offset=0+000*1000;
start_pt=[0 -1 0];
evol_time=0.1;
pulse_time=0.04;
tmax=evol_time+pulse_time;
center=10.123421;
center=0;
if mainlooop>1
center=0.33;
end
J=0.2*2*pi;%pefect refocus...
J=1;%pefect refocus...
if mainlooop>=4
J=1.1;
end
larmo=[center ]+[-J/2 J/2];
starting_vector=[ 0 -1 0];
pos_mag=(starting_vector'*ones(1,size(larmo,2)))';%starts on x...
t_step=0.05;
firstr1=0;
tau=10;%(defaul no second pulse
% if mod(round(t*20),6)==0
R2=0;
R1=0;
before_180=1;
for t = 0:0.000001:tmax
% for t = 0:0.000001:0.05
% X = sin(loopj*pi/10)*Z;
%surf(X,Z)
% larmo=[10.123122 ];
increment_tilt=pi/100000;
inc=0;
angle_rot=0;
if (t>evol_time/2) && (t<(evol_time/2+pulse_time))
angle_rot=pi*(t-evol_time/2)/((pulse_time));
% apply pi pulse
if (mainlooop ==1) || (mainlooop ==3) || (mainlooop ==5)
% pos_mag(:,1)=-pos_mag(:,1);before_180=0;
rfy=5/(pulse_time/0.02);
rfx=0.0000000;
else
% pos_mag(:,2)=-pos_mag(:,2);before_180=0;
rfx=5/(pulse_time/0.02);
rfy=0.0000000;
end
allow_evol=0;
else
rfx=0.0000000;
rfy=0.0000000;
allow_evol=1;
end
% tilt_angle=atan((ampli_hz/loop_offset));
% if tilt_angle<0, tilt_angle=tilt_angle+pi;end
for loop=1:size(larmo,2)
v=[rfx rfy allow_evol*larmo(1,loop) ];
di=cross(v,pos_mag(loop,:));
pos_mag(loop,:)=pos_mag(loop,:)+di*increment_tilt;
end
% di=di/norm(pos_mag);
% pos_mag(1,1)=pos_mag(1,1)*exp(-R2*increment_tilt);
% pos_mag(1,2)=pos_mag(1,2)*exp(-R2*increment_tilt);
if R1~=0
if firstr1==0
valref=pos_mag(1,3);diff=1-valref;
firstr1=1;
end
diff=diff*((exp(-R1*increment_tilt)));
pos_mag(1,3)=1-diff;
end
rf=rfx+rfy;
nu_eff=sqrt(loop_offset*loop_offset+ampli_hz*ampli_hz);
%
% how_much_further=2;
% if size(factor,2)==1
% plot3(how_much_further*[0 sin(tilt_angle)],[0 0],how_much_further*[0 cos(tilt_angle)],'k--')
% text(how_much_further*[sin(tilt_angle)],[ 0],how_much_further*[ cos(tilt_angle)],'Beff')
%
% end
% %%%%%%%%%%%%%%%%%
%
%
% figure('Units','inches', 'PaperPositionMode','auto', 'Position',[0 0 4 4]);
% end
if before_180
if (t>evol_time/2)
before_180=0;
J=-J;
larmo=[center ]+[-J/2 J/2];
end
end
% end
%work on figure
if mod(round(t*1e6),every_pt)==0
where_low=-3;
disp(['time: ' num2str(t) '/' max(num2str(tmax)) ' ' num2str(rf)] )
cur_f=figure(1);clf;hold on
% black arrow
how_much_higher=-2.2;
for loop=1:size(larmo,2)
fig_gen_spheres(pos_mag(loop,:),[v1 v2],'k',0)
fig_gen_spheres(pos_mag(loop,:),[v1 v2],'k',how_much_higher)
end
%midd arro
% view
% [v1 v2]=view([50 30]);
cen_vect=pos_mag(1,:)*0.5+0.5*pos_mag(2,:);
color_inphase='g';
color_antiphase='r';
mi_dist=0.2;
if sum(sum((cen_vect).*(cen_vect)))>(mi_dist/2)*(mi_dist/2)
fig_gen_spheres(cen_vect,[v1 v2],color_inphase)
else
plot3( [0 cen_vect(:,1)],[0 cen_vect(:,2)],[ 0 cen_vect(:,3)],color_inphase,'LineWidth',2)
end
%in first sphere
if sum(sum(((pos_mag(1,:)-cen_vect).*(pos_mag(1,:)-cen_vect))))>(mi_dist/2)*(mi_dist/2)
%at end...
% fig_gen_spheres([ pos_mag(1,:);cen_vect],[v1 v2],color_antiphase)
% fig_gen_spheres([ pos_mag(2,:);cen_vect],[v1 v2],color_antiphase)
%centered
fig_gen_spheres([ pos_mag(1,:);cen_vect]-cen_vect*center_antiphase_arrow,[v1 v2],color_antiphase)
fig_gen_spheres([ pos_mag(2,:);cen_vect]-cen_vect*center_antiphase_arrow,[v1 v2],color_antiphase)
else
plot3( pos_mag(:,1),pos_mag(:,2),pos_mag(:,3),color_antiphase,'LineWidth',2)
end
% %in second sphere
% if sum(sum(((pos_mag(1,:)-cen_vect).*(pos_mag(1,:)-cen_vect))))>(mi_dist/2)*(mi_dist/2)
% %at end...
% % fig_gen_spheres([ pos_mag(1,:);cen_vect],[v1 v2],color_antiphase)
% % fig_gen_spheres([ pos_mag(2,:);cen_vect],[v1 v2],color_antiphase)
% %centered
% fig_gen_spheres([ pos_mag(1,:);cen_vect]-cen_vect*center_antiphase_arrow,[v1 v2],color_antiphase)
% fig_gen_spheres([ pos_mag(2,:);cen_vect]-cen_vect*center_antiphase_arrow,[v1 v2],color_antiphase)
% else
% plot3( pos_mag(:,1),pos_mag(:,2),pos_mag(:,3),color_antiphase,'LineWidth',2)
% end
%on second sphere
pos_mag_other=pos_mag;
pos_mag_other(:,3)=sqrt(power(pos_mag_other(:,1)-cen_vect(1,1),2)+power(pos_mag_other(:,2)-cen_vect(1,2),2)+power(pos_mag_other(:,3)-cen_vect(1,3),2));
if (mainlooop ==1) || (mainlooop ==3) || (mainlooop ==5)
pos_mag_other(:,2)=0*pos_mag_other(:,3);
pos_mag_other(:,1)=sin(angle_rot)*pos_mag_other(:,3);
else
pos_mag_other(:,1)=0*pos_mag_other(:,3);
pos_mag_other(:,2)=sin(angle_rot)*pos_mag_other(:,3);
end
pos_mag_other(:,3)=pos_mag_other(:,3)*cos(angle_rot);
if sum(sum(((pos_mag(1,:)-cen_vect).*(pos_mag(1,:)-cen_vect))))>(mi_dist/2)*(mi_dist/2)
%at end...
% fig_gen_spheres([ pos_mag(1,:);cen_vect],[v1 v2],color_antiphase)
% fig_gen_spheres([ pos_mag(2,:);cen_vect],[v1 v2],color_antiphase)
%centered
fig_gen_spheres([ pos_mag_other(1,:);[0 0 0]]+[0 0 how_much_higher],[v1 v2],color_antiphase)
fig_gen_spheres([ -pos_mag_other(1,:);[0 0 0]]+[0 0 how_much_higher],[v1 v2],color_antiphase)
else
plot3( pos_mag_other(:,1),pos_mag_other(:,2),pos_mag_other(:,3)+[ how_much_higher],color_antiphase,'LineWidth',2)
end
% store last point for full trajectory plot
stor_tr_crude(count_sto,:)=pos_mag(1,:);
stor_t_crude(count_sto,:)=t;
count_sto=count_sto+1;
% interpolation of
[stor_tr, stor_t]=interp_to_smooth(stor_tr_crude,stor_t_crude);
% plot3(stor_tr(:,1),stor_tr(:,2),stor_tr(:,3),'k-','linewidth',1.25)
% plot3( [0.5 0.5],[-1 1],[where_low where_low],'k-')
% plot3(-[0.5 0.5],[-1 1],[where_low where_low],'k-')
% plot3(-[0.0 0.0],[-1 1],[where_low where_low],'k:')
% plot3(+[1 1],[-1 1],[where_low where_low],'k:')
% plot3([-1 1],[-1 -1],[where_low where_low],'k-')
% plot3(-[1 1],[-1 1],[where_low where_low]+0.5,'k-')
% plot3(-[1 1],[-1 1],[where_low where_low]+1,'k:')
% plot3(-[1 1],[-1 1],[where_low where_low]+0,'k:')
% plot3(-[1 1],[-1 -1],[0 1 ]+where_low,'k-')
%
rf_arrow=1.0;
if rfx>0
plot3( [-rf_arrow rf_arrow],[0 0],[ 0 0],'c','LineWidth',2)
text( [- rf_arrow]*1.1,[0 ],[ 0],'Inversion pulse')
plot3( [-rf_arrow rf_arrow],[0 0],[ 0 0]+how_much_higher,'c','LineWidth',2)
text( [- rf_arrow]*1.1,[0 ],[ 0]+how_much_higher,'Inversion pulse')
end
if rfy>0
plot3( [0 0],[-rf_arrow rf_arrow],[ 0 0],'c','LineWidth',2)
text([0 ], [ -rf_arrow]*1.1,[ 0],'Inversion pulse')
plot3( [0 0],[-rf_arrow rf_arrow],[ 0 0]+how_much_higher,'c','LineWidth',2)
text([0 ], [ -rf_arrow]*1.1,[ 0]+how_much_higher,'Inversion pulse')
end
% list_t=2*(t/tmax)*(1:size(stor_tr,1))/size(stor_tr,1)-1;
list_t=2*(t/tmax)*(stor_t)/max(abs(stor_t))-1;
% plot3( 0.5+0.5*stor_tr(:,1),list_t,stor_tr(:,3)*0+where_low,'g-','linewidth',1.25)
% plot3(-0.5+0.5*stor_tr(:,2),list_t,stor_tr(:,3)*0+where_low,'b-','linewidth',1.25)
% plot3(stor_tr(:,3)*0-1,list_t,0.5+0.5*stor_tr(:,3)+where_low,'r-','linewidth',1.25)
% phase_a=cos(anglet/360*2*pi)+j*sin(anglet/360*2*pi);%as complex number
% phase_a=phase_a/(abs(phase_a));
% [dist_in_hz erro_in_deg]=shap_fn3d(loopj-1,mainlooop,main_ratio);
% [dist_in_hz erro_in_deg]=shap_fn3d(loopj-1,mainlooop,main_ratio);
axis([ -1 1 -1 1 where_low-0.3 1])
%plot3(store_traj(:,1),store_traj(:,2),store_traj(:,3),'k-','linewidth',1.5)
%plot3(store_traj(:,1),store_traj(:,2),0*store_traj(:,3),'k-','linewidth',1)
axis off
set(gcf,'color','w');
text(0,0,1.3,text_title,'HorizontalAlignment','center')
draw_unit_circle([0;0;0])
draw_unit_circle([0;0;how_much_higher])
drawnow;
tmp_frame = getframe;
if counter_frames==1
si=size(tmp_frame.cdata);
else
tmp_frame.cdata=tmp_frame.cdata(1:si(1,1),1:si(1,2),1:si(1,3));
end
F(counter_frames)=tmp_frame;
writeVideo(writerObj,F(counter_frames));
counter_frames=counter_frames+1;
end
end
close(writerObj);
%movie(F,2)
% figure(111)
% clf
% plot(store_dis_in_hz(:,1),store_erro_in_deg(:,1),'b-');
% hold on
% plot(store_dis_in_hz(:,2),store_erro_in_deg(:,2),'r-');
% print('-depsc','-tiff','-r600',[ 'Phase_error_nearby_small_signals' num2str(main_ratio) '.eps']);%here
end
end
end