% This is the initial file to begin
% calls functions and functions within teh function to perform FRET Efficiency measuremnts 
% Before using this code, make sure to edit the code to change the variable names accordingly, so that Matlab read the files without throwing an error. 
% unmixed images were used - variable names for us to read are - Turquoise, Venus, and DRAQ5


prompt={'How many folder to reslice'}; %enter how many folders to analyze
name='number';
numlines=1;
def={'imagename','31','76'};
answer=inputdlg(prompt,name,numlines);

num=str2double(answer);
% loops for the number of folders you specified and read the directory inofrmation of each selected folder
for i=1:num
    if i == 1
    dir=uigetdir;
    else
       dirp1=uigetdir;
       dir=[dir,'@$',dirp1]; 
    end
end

dir_array=strsplit(dir,'@$');

[alg,scale,threshold,iterations,steps,reduc,frequencyX,frequencyY,frequencyZ]=fret_rescaling_reslicing_colormap_ui;
% further FRET calculations are performed on one folder (data set) after the other 
for j=1:num
    parent_directory=cell2mat(dir_array(j));
    frrcf(parent_directory,alg,scale,threshold,iterations,steps,reduc,frequencyX,frequencyY,frequencyZ);
end