Making plots prettier for intro figure.

ternary_frap.m

@@ -45,20 +45,24 @@ x_seed = fminsearch(f_min, x_seed, opt);
 [cost, v_fit, r_n, v_fit_end] = to_minimize(s, ts, x_seed, 'simple_drop', s(:, end));
 %% Plot for 
 figure; hold on;
-plot(s(1:10:400, :)', 'Color', [0.12156   0.4666666   0.7058823], 'LineWidth', 1.5);
-plot(v_fit(1:10:400, :)', '--', 'Color', [1.   0.49803   0.0549], 'LineWidth', 1.5);
+s_all = T.sol(1:end, 1:400)./max(max(T.sol(1:end, 1:30)))/1.022;
+plot(T.x(1:340), s_all(1:10:200, 1:340), 'Color', [135/255  204/255 250/255], 'LineWidth', 2.5);
+plot(T.x(1:30), v_fit(1:10:200, :)', '.', 'Color', [0.8314    0.2275    0.0902], 'MarkerSize', 10);
 make_graph_pretty('$x [\mu m]$', 'intensity [a.u.]', '');
-% print([T.pa, 'Timecourse_model_only'],'-depsc')
+print([T.pa, 'Timecourse_model_only'],'-depsc')
 %% Plot boundary condition (read out)
 figure; hold on;
-plot(ts, s(:, end))
+plot(ts(1:200), s(1:200, end))
 make_graph_pretty('t [s]', 'intensity [a.u.]', '');
 print([T.pa, 'Timecourse_BC'],'-depsc')
+%% Fit boundary condition with exponential
+f = fit(ts(1:200), s(1:200, end), 'B+C-B*exp(-x/tau)-C*exp(-x/tau2)');
+plot(f)
 %% Plot flux at boundary (x close to 1) Only works close to boundary!
-T = Ternary_model(2, 'FRAP', [], linspace(0.0, 400, 2000));
-T.e_g0 = 0.001;
-T.b = 0.001;
-T.solve_tern_frap();
+% T = Ternary_model(2, 'FRAP', [], linspace(0.0, 400, 2000));
+% T.e_g0 = 0.001;
+% T.b = 0.001;
+% T.solve_tern_frap();
 [~, ind_in] = min(abs(T.x+T.a+0.02)); % Find x position of boundary close to 0.9
 % Calculate local diffusion coefficient
 g0 = Ternary_model.gamma0((T.x(ind_in)+T.x(ind_in+1))/2, T.a, T.b, T.e_g0, T.o_g0);
@@ -74,5 +78,5 @@ Diffs_out = D_out*diff(T.sol')/(T.x(ind_out+1)-T.x(ind_out));
 figure; hold on;
 plot(Diffs_in(ind_in, :))
 plot(Diffs_out(ind_out, :));
-make_graph_pretty('time', 'ratio outside/inside', 'unbleached component');
+make_graph_pretty('time', '$\vec{j}$', 'boundary flux inside/outside of drop');
 axis([0, 200, 0, 0.035])
\ No newline at end of file