read_file_loop_new.m

% For real-time alignment of MLA, used in coupled with the Miniscope DAQ software.
% Updated 01-16-2024.
clear

%%
indir = 'E:\Data\2024_01_19\15_50_10\MiniLFMv2';
PeakDist = 18;   % MLA lenslet pitch (40um / 2.2um = 18px)
px_pitch = 2.2;         % [um]
im_size = [1944,2592];  % image/sensor size[px]

% initialize output variable
peak_pos_x = [PeakDist:PeakDist:im_size(2)];
peak_pos_y = [PeakDist:PeakDist:im_size(1)]';

peakdata.pos(:,1) = repmat(peak_pos_y,length(peak_pos_x),1);
peakdata.pos(:,2) = repelem(peak_pos_x,length(peak_pos_y));
peakdata.XWidth = ones(size(peakdata.pos,1),1);

%%
s = scatter(peakdata.pos(:,2), peakdata.pos(:,1), 5, peakdata.XWidth * px_pitch, 'filled'); % initialize figure
set(gcf,'position',[100,250,im_size(2)/3,im_size(1)/3]);
xlim([0,im_size(2)]);
ylim([0,im_size(1)]);
colorbar;
clim([0,8]);
box on;

while true
    % Find the latest image
    filelist = dir([indir filesep '*.avi']);
    idx = find([filelist.datenum] == max([filelist.datenum]),1,'last');
    latestfile = fullfile(indir, filelist(idx).name);
    im_file = fullfile(indir, 'current_frame.tiff');
    
    % Read the last frame and convert to Tiff
    disp(['Convert and open: ' latestfile]);
    system(['C:\vazirilab\ffmpeg\bin\ffmpeg -hide_banner -loglevel error -y -i ' latestfile ' ' im_file]); % Use ffmpeg to convert avi to tiff file.
    frame = imread(im_file);    
    
    try
        peakdata = FastPeakFind_new(frame); % Find peaks and calculate peak widths
        
        % 2-px wide 2200-px long horizontal line to determine the alignment with maximum peak number.
        [Lroi_y,Lroi_x] = find(peakdata.idx(im_size(1)/2-PeakDist:im_size(1)/2+PeakDist, 100:100+2*PeakDist));
        LP_y = Lroi_y(2)+im_size(1)/2-PeakDist-1; % convert to original image coordinate
        LP_x = Lroi_x(2)+100-1;
        aline = sum(peakdata.idx(LP_y:LP_y+1, LP_x:LP_x+2200));       
        %plot([LP_x,LP_x+2200], [LP_y,LP_y],'r-', 'Marker','*','MarkerSize',12,'LineWidth',2);
        
        % Update image in real time
        set(s,'XData',peakdata.pos(:,2),'YData',peakdata.pos(:,1),'CData',peakdata.XWidth * px_pitch);       
        drawnow
        title({[filelist(idx).name ', perfect alignment has 121 peaks, currently ' sprintf('%d',sum(aline))],...
            ['Peak value : ' sprintf('Avg = %0.2f',mean(peakdata.int)), ...
            sprintf(' STD = %0.2f',std(single(peakdata.int)))], ['Peak width : ' ...
            sprintf('Avg = %0.2f',mean(peakdata.XWidth*px_pitch)), ...
            sprintf(' STD = %0.2f',std(peakdata.XWidth*px_pitch)) '[um]']});       
    
    catch ME
        disp(ME);
        title({[filelist(idx).name ', an error occurs in findpeaks']});
    end
end