% Convert 'traces' matrix into input file for QuB
% Upon running this program, select the desired *_traces.dat file(s) generated
% by Generate_time_traces_TIF_SiMREPS.m
% Output will be named *_traces.txt; these files can be loaded into QuB for HMM
% analysis
close all; clear all;
[traces_file, traces_path, fi] = uigetfile('*traces.dat','MultiSelect','on');

cd(traces_path);

if iscell(traces_file) == 0
    traces_file_mat = traces_file;
    clear traces_file;
    traces_file{1} = traces_file_mat;
    clear traces_file_mat;
end

for tracesnum = 1:size(traces_file,2)
    
    traces_filename = strcat(traces_path,traces_file{tracesnum});
    
    save_file = strcat(traces_filename(1:length(traces_filename)-4),'.txt');
    
    fid = fopen(save_file, 'At');
    
    traces = load(traces_filename,'-mat');
    traces = traces.traces;
    
    ntraces = size(traces,1);
    nframes = size(traces,2);
    
    qubmat = zeros(0,2);
    
    traces = round(traces);
    
    for m = 1:ntraces
        if mod(m,10)==0
            disp(num2str(m));
        end
        trace = traces(m,:);
        %     trace = trace - min(trace);
        %     trace = trace./max(trace);
       
        for n = 1:nframes
            fprintf(fid,'%d\t %6.4f\n', n, trace(n));
        end
        fprintf(fid,'\n');
    end
    
    fclose(fid);
    
end

disp('Done writing traces to file.');