auto_mask_directory.m

function [] = auto_mask_directory()
run('Aro_parameters.m');

dye = dyesUsed{1};
if ~exist([ImageDir filesep dye], 'dir')
    disp('[ERROR] The images have not been trimmed/placed in the proper folders! Please trim first.');
    return;
end
current_files = dir([ImageDir filesep dye filesep '*.tif']);
tif_files = {current_files.name};
disp(tif_files);

if isempty(tif_files)
    disp('[ERROR] There appear to be no images in the directory for this dye! Please check your image files.');
    return;
end

ParSegmentationMaskDir = [SegmentationMaskDir];
ParImageDir = [ImageDir];
PardyesUsed = dyesUsed;
ParBadMaskList = [BadMaskList];


parfor i = 1:numel(tif_files)
   name = tif_files{i};
   SegmentationMaskDir = ParSegmentationMaskDir;
   ImageDir = ParImageDir;
   dyesUsed = PardyesUsed;
   BadMaskList = ParBadMaskList;
   dye = '';
   for d = 1:length(dyesUsed)
       k = strfind(name, dyesUsed{d});
       if ~isempty(k)
           dye = dyesUsed{d};
           d = length(dyesUsed);
       end
   end
   dye_name_length = length(dye);
   mask_name = strcat('Mask_', name(dye_name_length+1:length(name)-4));
   isbad = auto_mask([ImageDir filesep dye filesep name], [SegmentationMaskDir filesep mask_name]);
   for b = 1:numel(isbad)
       if isbad(b)
           fileID = fopen(BadMaskList, 'a');
           fprintf(fileID, [mask_name '_' num2str(b) '.tif\n']);
           fclose(fileID);
           disp(['[WARNING] Possible bad mask produced at ' mask_name]);
       end
   end
end
clear;
return;