1 files changed, 99 insertions, 0 deletions
diff --git a/xmds2/realistic_Rb/pp_I2.m b/xmds2/realistic_Rb/pp_I2.m
new file mode 100644
index 0000000..47b5f48
--- /dev/null
+++ b/xmds2/realistic_Rb/pp_I2.m
@@ -0,0 +1,99 @@
+% suppress output of plots on display
+set (0, "defaultfigurevisible", "off") 
+
+realistic_Rb
+
+%% field I2  propagation
+z_1=z_1*100; % z in cm
+t_1=t_1*1e6; % time now measured in uS
+figure(1)
+%set(gca,'fontsize',20); 
+imagesc(z_1, t_1, I2_out_1); colorbar
+tmin=-0.4;
+tmax= 0.4;
+ylim([tmin,tmax],'manual');	
+xlabel('z (cm)')
+ylabel('t (uS)')
+zlabel('I_2')
+title('I_2')
+print('-color','-depsc2', '-tight', '-S200,120', 'fields_propagation_I2.eps')
+
+desired_x_size=200;
+desired_y_size=200;
+xskip=ceil(length(z_1)/desired_x_size);
+yskip=ceil(length(t_1)/desired_y_size);
+map2dat('I2.dat',z_1,t_1, I2_out_1, xskip, yskip);
+
+
+%% field I4  propagation
+figure(2)
+
+imagesc(z_1, t_1, I4_out_1); colorbar
+tmin=-0.4;
+tmax= 0.4;
+ylim([tmin,tmax],'manual');	
+xlabel('z (cm)')
+ylabel('t (uS)')
+zlabel('I_4')
+title('I_4')
+print('-color','-depsc2', '-tight', '-S200,120', 'fields_propagation_I4.eps')
+map2dat('I4.dat',z_1,t_1, I4_out_1, xskip, yskip);
+
+
+
+
+
+%% fields before and after the cell
+figure(3)
+%set(gca,'fontsize',30); 
+plot( ...
+	t_1,I2_out_1(:,1),'.-;I_2 before;', "linewidth", 4  ...
+	,t_1,I2_out_1(:,end), '-;I_2 after;', "linewidth", 4 ...
+	,t_1,I4_out_1(:,end), '-;I_4 after;', "linewidth", 4 ...
+	)
+xlabel('t (uS)')
+ylabel('I (1/s)^2')
+title('Fields before and after cell')
+legend('location', 'northeast');
+
+[b, a]=butter(3, 0.05);
+I2_out_after=I2_out_1(:,end);
+I2_out_after_filtered=filtfilt(b,a,I2_out_after);
+settling_time=0.01; %uS
+t_good_indx=t_1> min(t_1 + settling_time);
+[m,max_pos_before]=max(I2_out_1(t_good_indx,1) ); [m,max_pos_after]=max(I2_out_after_filtered(t_good_indx));
+delay_time=t_1(max_pos_after)-t_1(max_pos_before);
+printf('Second field delay time  = %f uS\n',delay_time);
+
+%set(gca,'fontsize',40); 
+%set (gcf,'paperposition',[0.5 0 2.5,1.5]); % IMPORTANT to shrink eps size for readable fonts
+%print('-color','-depsc2', '-tight','-S200,120', 'fields_before_after_cell.eps')
+print('-color','-depsc2', 'fields_before_after_cell.eps')
+
+figure(4)
+I2_max_in=max(I2_out_1(t_good_indx,1));
+I2_max_out=max(I2_out_1(t_good_indx,end));
+I4_max_out=max(I4_out_1(t_good_indx,end));
+I2_in_norm=(I2_out_1(:,1))/I2_max_in;
+I2_out_norm=(I2_out_1(:,end))/I2_max_out;
+I4_out_norm=(I4_out_1(:,end))/I4_max_out;
+tmin=-.05;
+tmax=.05;
+indx=(t_1>=tmin & t_1<=tmax);  % soom in in time to this region
+plot( ...
+	t_1(indx),I2_in_norm(indx),'.-;I_2 before;', "linewidth", 4,  ...
+	t_1(indx),I2_out_norm(indx), '-;I_2 after;', "linewidth", 4 ...
+	,t_1(indx),I4_out_norm(indx), '-;I_4 after;', "linewidth", 4 ...
+	)
+legend('location', 'southeast');
+xlim([tmin,tmax],'manual');	
+ylim([0.5,1],'manual');	
+xlabel('t (uS)')
+ylabel('I normalized')
+title('Fields before and after cell normalized')
+%set (gcf,'paperposition',[0.5 0 2.5,1.5]); % IMPORTANT to shrink eps size for readable fonts
+%print('-color','-depsc2', '-tight','-S200,120', 'fields_before_after_cell_normalized.eps')
+print('-color','-depsc2',  'fields_before_after_cell_normalized.eps')
+
+fid_stamp=fopen ("pp_I2.stamp", "a+");
+fclose (fid_stamp);