Minor modifications, new script to extract beam waist

Estimations/EstimatesForAccordionLattice.m

@@ -36,6 +36,7 @@ LatticeSpacing = Wavelength ./ (2.*sin((theta*pi/180)/2));
 
 figure(1);
 set(gcf,'Position',[100 100 950 750])
+set(gca,'FontSize',16,'Box','On','Linewidth',2);
 plot(theta, LatticeSpacing * 1E6, LineWidth=2.0)
 xlim([0 19]);
 ylim([0.5 21]);
@@ -67,6 +68,7 @@ nu_z         = Omega_z ./ (2*pi);
 
 figure(2);
 set(gcf,'Position',[100 100 950 750])
+set(gca,'FontSize',16,'Box','On','Linewidth',2);
 plot(LatticeSpacings * 1E6, nu_z * 1E-3, LineWidth=2.0)
 xlim([0.5 21]);
 xlabel('Lattice spacing (µm)', FontSize=16)
@@ -97,6 +99,7 @@ units            = ' E_r';
 
 figure(3);
 set(gcf,'Position',[100 100 950 750])
+set(gca,'FontSize',16,'Box','On','Linewidth',2);
 plot(Powers, TrapDepthsToPlot, LineWidth=2.0)
 xlim([0.0 5.25]);
 xlabel('Powers (W)', FontSize=16)
@@ -111,6 +114,7 @@ RecoilEnergy   = PlanckConstant^2 ./ (8 .* Dy164Mass .* LatticeSpacing.^2);
 
 figure(4);
 set(gcf,'Position',[100 100 950 750])
+set(gca,'FontSize',16,'Box','On','Linewidth',2);
 semilogy(LatticeSpacing * 1E6, RecoilEnergy/PlanckConstant, LineWidth=2.0)
 xlim([0.5 21]);
 xlabel('Lattice spacing (µm)', FontSize=16)
@@ -124,6 +128,7 @@ ExpansionTime             = linspace(1E-3, 20.0E-3, 100);
 
 figure(5);
 set(gcf,'Position',[100 100 950 750])
+set(gca,'FontSize',16,'Box','On','Linewidth',2);
 labels = [];
 
 for ls = [2E-6:2E-6:5E-6 6E-6:6E-6:20E-6]
@@ -155,6 +160,7 @@ TrapDepthsInUnitsOfRecoilEnergy = TrapDepthsInHz ./ TwoPhotonRecoilEnergyInHz;
 
 figure(6);
 set(gcf,'Position',[100 100 950 750])
+set(gca,'FontSize',16,'Box','On','Linewidth',2);
 plot(TrapDepthsInUnitsOfRecoilEnergy, RabiOscillationFrequency .* 1E-3, LineWidth=2.0)
 xlim([0 4]);
 xlabel('Trap depths (E_r)', FontSize=16)
@@ -182,6 +188,7 @@ PopulationInFirstOrders         = C .* (sin(0.5 .* PulseDurations .* (RabiOscill
 
 figure(7);
 set(gcf,'Position',[100 100 950 750])
+set(gca,'FontSize',16,'Box','On','Linewidth',2);
 plot(PulseDurations .* 1E6, PopulationInFirstOrders, LineWidth=2.0, DisplayName=['\bf Power = ' num2str(Power) ' W / Trap depth = ' num2str(round(TrapDepthsInUnitsOfRecoilEnergy, 1)) ' E_r'])
 xlabel('Pulse duration (µs)', FontSize=16)
 ylabel('Fraction of atoms in first order', FontSize=16)

Estimations/EstimatesForStaticLattice.m

@@ -66,6 +66,7 @@ end
 figure(1)
 clf
 set(gcf,'Position',[50 50 950 750])
+set(gca,'FontSize',16,'Box','On','Linewidth',2);
 imagesc(Power_values, waist_values * 1e6, R_z_matrix);  % Specify x and y data for axes
 hold on
 [contour_matrix, contour_handle] = contour(Power_values, waist_values * 1e6, R_z_matrix, 'LineColor', 'white', 'LineWidth', 1.5);
@@ -81,6 +82,7 @@ title(['\bf Thomas-Fermi Radius @ Lattice Spacing = ' num2str(LatticeConstant *
 figure(2)
 clf
 set(gcf,'Position',[50 50 950 750])
+set(gca,'FontSize',16,'Box','On','Linewidth',2);
 imagesc(Power_values, waist_values * 1e6, omega_eff_matrix);  % Specify x and y data for axes
 hold on
 [contour_matrix, contour_handle] = contour(Power_values, waist_values * 1e6, omega_eff_matrix, 'LineColor', 'white', 'LineWidth', 1.5);

Estimations/ExtractParametersFromCavityModeProfile.m

@@ -15,15 +15,16 @@ CavitySignal = CavitySignal - yoffset;
 Time         = Time - xoffset;
 
 % Plot the data
-figure;
+figure(1);
+clf; 
+set(gcf,'Position',[50 50 950 750])
+set(gca,'FontSize',16,'Box','On','Linewidth',2); 
 scatter(Time, CavitySignal, 10, 'b', 'filled', 'MarkerFaceAlpha', 0.5);
-grid on;
-
-% Format the plot
 xlabel('\bf Time (s)', 'FontSize', 16);
 ylabel('\bf Voltage (V)', 'FontSize', 16);
 title('\bf Cavity Signal', 'FontSize', 16);
 set(gca, 'FontSize', 12);
+grid on;
 
 %% Fit cavity signal
 

Estimations/ExtractWaist.m

@@ -0,0 +1,79 @@
+z                 = sort((26:-1:1))*1e-3;
+d                 = sort([246, 240, 235, 230, 226, 222, 218, 215, 213, 210, 206, 204, 201, 199, 197, 195, 194, 193, 192, 191, 190, 191, 190, 189, 189, 189])*1e-6;
+Wavelength        = 532e-9;
+TrimIndex         = 7;
+Seed              = [100e-6 -5e-2];
+
+[w0, dw0, z0, dz0]  = extractWaist(z, d, Wavelength, Seed, TrimIndex);
+
+%% 
+
+z                 = z0;
+f                 = 500e-3;
+Mr                = abs(f/(z-f));
+r                 = zr/(z-f);
+M                 = Mr/sqrt(1+r^2);
+zp_to_f           = M^2*(z-f)*10^6; % distance of waist to focal point in um
+w0p               = M*w0*1e3;       % waist after objective in um
+
+%%
+
+z                 = z0+dz0;
+f                 = 50e-3;
+Mr                = abs(f/(z-f));
+r                 = zr/(z-f);
+M                 = Mr/sqrt(1+r^2);
+zp_to_fmax        = M^2*(z-f)*10^6; % distance of waist ot focal point in um
+w0pmax            = M*w0*1e3;       % waist after objective in um
+  
+z                 = z0-dz0;
+f                 = 50e-3;
+Mr                = abs(f/(z-f));
+r                 = zr/(z-f);
+M                 = Mr/sqrt(1+r^2);
+zp_to_fmin        = M^2*(z-f)*10^6; % distance of waist ot focal point in um
+w0pmin            = M*w0*1e3; % waist after objective in um
+
+function [w0, dw0, z0, dz0]  = extractWaist(z, d, lb, seed, trim_idx)
+    
+    w                 = d/2;
+    
+    fitmodel_waist    = @(w0,z0,x)w0*sqrt(1+(x-z0).^2/(pi.*w0.^2/lb).^2);
+    fitmodel_waist_far= @(w0,z0,x)(x-z0)*lb/pi./w0;
+    
+    lower_bounds      = [0, -inf]; % Setting lower bound for w0 as 0 to prevent negative waist sizes
+    upper_bounds      = [inf, inf];
+    z_trimmed         = z(end-trim_idx:end);
+    w_trimmed         = w(end-trim_idx:end);
+    fitwaistfar       = fit(z_trimmed', w_trimmed', fitmodel_waist_far, 'StartPoint', seed, 'Lower', lower_bounds, 'Upper', upper_bounds); % fit first as if waist far away
+    
+    seed              = [fitwaistfar.w0 fitwaistfar.z0];
+    fitwaist          = fit(z', w', fitmodel_waist, 'StartPoint', seed, 'Lower', lower_bounds, 'Upper', upper_bounds);
+    
+    ci                = confint(fitwaist,1-exp(-1)); %63% uncertainty confidence interval
+    ws                = ci(:,1)*1e3; % in mm
+    w0                = mean(ws);
+    dw0               = diff(ws)/2;
+    z0s               = ci(:,2)*1e3; % in mm
+    z0                = mean(z0s);
+    dz0               = diff(z0s)/2;
+    
+    % Plot
+    zplot             = linspace(-0.03, 0.03, 1001);
+    waistplot         = feval(fitwaist,zplot);
+    waistplotfar      = feval(fitwaistfar, zplot);
+     
+    figure(1); 
+    clf; 
+    set(gcf,'Position',[100 100 950 750])
+    set(gca,'FontSize',16,'Box','On','Linewidth',2); 
+    hold all
+    plot(z*1e3, w*1e6, 'ok', 'Linewidth',2, 'DisplayName', 'Measured Data')
+    plot(zplot*1e3, waistplot*1e6,'r-','Linewidth',2, 'DisplayName', 'Fit at near distances')
+    plot(zplot*1e3, waistplotfar*1e6,'b--','Linewidth',2,  'DisplayName', 'Fit at far distances') 
+    ylim([min(w)*1e6, max(w)*1e6])
+    grid on
+    xlabel('Distance (mm)');
+    ylabel('Beam Radius (mum)')
+    legend('Location', 'NorthWest')
+end

Estimations/GaussianABCDCalculator.m

@@ -285,7 +285,7 @@ function plotResult(func, var, rang)
     % Create a figure
     figure;
     set(gcf, 'Position', [100 100 950 750]);
-
+    set(gca,'FontSize',16,'Box','On','Linewidth',2);
     % Plot the function and its negative
     plot(rang, y_vals, 'b'); hold on;
     plot(rang, y_neg_vals, 'b');

Estimations/ModellingImagingAberrations.m

@@ -86,6 +86,7 @@ function plotZernike(n, m, NumberOfGridPoints)
     figure(1)
     clf
     set(gcf,'Position',[50 50 950 750])
+    set(gca,'FontSize',16,'Box','On','Linewidth',2);
     surf(X, Y, Z, 'EdgeColor', 'none');
     colormap jet;
     colorbar;
@@ -131,6 +132,7 @@ function plotImage(xvals, yvals, image, titlestring)
     figure
     clf
     set(gcf,'Position',[50 50 950 750])
+    set(gca,'FontSize',16,'Box','On','Linewidth',2);
     imagesc(xvals, yvals, image);
     colorbar;
     colormap jet;