Shahriar_system

%% field propagation
t_1=t_1*1e6; % time now measured in uS
figure(1)
subplot(1,2,1); imagesc(z_1, t_1, I1_out_1); colorbar
xlabel('z')
ylabel('t (uS)')
zlabel('I_1')
title('I_1')
subplot(1,2,2); imagesc(z_1, t_1, If_out_1); colorbar
xlabel('z')
ylabel('t (uS)')
zlabel('I_f')
title('I_f')




%% fields before and after the cell
% remove high frequency component from probe
I1_out_after=I1_out_1(:,end);
[b, a]=butter(3, 0.01);
I1_out_after_filtered=filtfilt(b,a,I1_out_after);
ampl=max(I1_out_1(:,1));

[m,max_pos_before]=max(I1_out_1(:,1) ); [m,max_pos_after]=max(I1_out_after_filtered );
delay_time=t_1(max_pos_after)-t_1(max_pos_before);
printf('delay time  = %f uS\n',delay_time);

figure(2)
subplot(1,2,1);
plot( ...
	t_1,I1_out_1(:,1)/ampl,'-;before normalized;'  ...
%	,t_1,I1_out_1(:,end)/ampl, '-;after normalized;' ...
	,t_1,I1_out_after_filtered/ampl, '-;after smoothed;' ...
	,t_1,I1_out_after_filtered/max(I1_out_after_filtered), '-;after smoothed and normalized ;' ...
	)
xlabel('t (uS)')
ylabel('I_1')
title('I_1 propagation')
subplot(1,2,2);
plot( ...
	t_1,If_out_1(:,1),'-;before;',  ...
	t_1,If_out_1(:,end), '-;after;' ...
	)
xlabel('t (uS)')
ylabel('I_f')
title('I_f propagation')

return;

%% all density matrix elements in one plot
% diagonal populations, 
% upper triangle real part of coherences, 
% lower diagonal imaginary part of coherences
figure(3)
subplot(3,3,1); imagesc (z_2, t_2, r11_out_2);  caxis([0,1]); colorbar
xlabel('z')
ylabel('t')
zlabel('rho_{11}')
title('rho_{11}')
subplot(3,3,5); imagesc (z_2, t_2, r22_out_2);  caxis([0,1]); colorbar
xlabel('z')
ylabel('t')
zlabel('rho_{22}')
title('rho_{22}')
subplot(3,3,9); imagesc (z_2, t_2, r33_out_2);  caxis([0,1]); colorbar
xlabel('z')
ylabel('t')
zlabel('rho_{33}')
title('rho_{33}')
% real parts of coherences
subplot(3,3,2); imagesc(z_2, t_2, r12_re_out_2); colorbar
xlabel('z')
ylabel('t')
zlabel('Real(rho_{12})')
title('Real(rho_{12})')
subplot(3,3,3); imagesc(z_2, t_2, r13_re_out_2); colorbar
xlabel('z')
ylabel('t')
zlabel('Real(rho_{13})')
title('Real(rho_{13})')
subplot(3,3,6); imagesc(z_2, t_2, r23_re_out_2); colorbar
xlabel('z')
ylabel('t')
zlabel('Real(rho_{23})')
title('Real(rho_{23})')
% imaginary parts of coherences
subplot(3,3,4); imagesc(z_2, t_2, r12_im_out_2); colorbar
xlabel('z')
ylabel('t')
zlabel('Imag(rho_{12})')
title('Imag(rho_{12})')
subplot(3,3,7); imagesc(z_2, t_2, r13_im_out_2); colorbar
xlabel('z')
ylabel('t')
zlabel('Imag(rho_{13})')
title('Imag(rho_{13})')
subplot(3,3,8); imagesc(z_2, t_2, r23_im_out_2); colorbar
xlabel('z')
ylabel('t')
zlabel('Imag(rho_{23})')
title('Imag(rho_{23})')