Path of laser beam over a scanned area showing blanking

scanBeamPathDiagram

function scanBeamPathDiagram
    % Generate a figure showing a scanned beam with scan and image field
    %
    % The path of a resonant-scanned focused beam over a sample. The beam moves
    % sinusoidally along the fast axis whilst being scanned up/down with a galvo.
    % The area over which the beam moves is known as the “scan field”. On the left and
    % right edges the beam slows and turns around. In these areas the potential for
    % photodamage is greatest, as the beam is travelling more slowly over the sample.
    % Thus the beam is “blanked” or disabled during these epochs. In a resonant scanning
    % microscope the beam is blanked about 30% of the time. The image field (red lines
    % and gray region) is the area over which the beam is on and capable of exciting
    % fluorescence. The dotted lines indicate the blanked turn-around regions.
    %
    %


    nCycles = 20; % number of scan beam cycles to plot

    % Generate the scan waveform
    x = sin(0.5*pi : 0.01 : (nCycles*2*pi + 0.5*pi));
    y = 1:length(x);

    fillFraction = 0.7;

    clf
    set(gcf,'Color','w')
    plot(x,y,':k')
    hold on
    axis tight square
    set(gca,'XTick',[],'YTick',[])

    f = find(x<-fillFraction | x>fillFraction);
    x(f)=nan;
    y(f)=nan;
    plot(x,y,'-r')

    % Patch showing the image field (i.e. the sub-region within the scan field that is
    % being imaged).
    yl = ylim;
    Y = [yl,fliplr(yl)];
    X = [-fillFraction,-fillFraction,fillFraction,fillFraction];
    p = patch(X,Y,0, ...
        'FaceColor',[1,1,1]*0.5, ...
        'FaceAlpha',0.25, ...
        'EdgeColor', 'none');

    sideColor = [1,1,1]*0.5;
    plot([-fillFraction,-fillFraction],yl,'-','color',sideColor)
    plot([fillFraction,fillFraction],yl,'-','color',sideColor)