cleanSuperSegger

 cleanSuperSegger : used to clean up the flag files created during
 superSegger.

 INPUT : 
   dirname_xy : xy directory 
   startEnd : superSegger step to start on adn step to end on.
   skip : number of frames to skip.

 Copyright (C) 2016 Wiggins Lab
 Written by Paul Wiggins & Stella Stylianidou.
 University of Washington, 2016
 This file is part of SuperSegger.

0001 function cleanSuperSegger (dirname_xy, startEnd, skip)
0002 % cleanSuperSegger : used to clean up the flag files created during
0003 % superSegger.
0004 %
0005 % INPUT :
0006 %   dirname_xy : xy directory
0007 %   startEnd : superSegger step to start on adn step to end on.
0008 %   skip : number of frames to skip.
0009 %
0010 % Copyright (C) 2016 Wiggins Lab
0011 % Written by Paul Wiggins & Stella Stylianidou.
0012 % University of Washington, 2016
0013 % This file is part of SuperSegger.
0014 
0015 % SuperSegger is free software: you can redistribute it and/or modify
0016 % it under the terms of the GNU General Public License as published by
0017 % the Free Software Foundation, either version 3 of the License, or
0018 % (at your option) any later version.
0019 %
0020 % SuperSegger is distributed in the hope that it will be useful,
0021 % but WITHOUT ANY WARRANTY; without even the implied warranty of
0022 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
0023 % GNU General Public License for more details.
0024 %
0025 % You should have received a copy of the GNU General Public License
0026 % along with SuperSegger.  If not, see <http://www.gnu.org/licenses/>.
0027 
0028 
0029 dirname_xy = fixDir(dirname_xy);
0030 dirname_full  = [dirname_xy,'seg_full',filesep];
0031 dirname_seg = [dirname_xy,'seg',filesep];
0032 dirname_cell = [dirname_xy,'cell',filesep];
0033 %warning('off','MATLAB:DELETE:Permission')
0034 
0035 if startEnd(1) <= 2 && startEnd(2) >=2     
0036     stamp_name = [dirname_seg,'.doSegFull'];
0037     if exist(stamp_name,'file')
0038         delete(stamp_name)
0039     end
0040     delete([dirname_seg,'*seg.mat*']);
0041 end
0042 
0043 
0044 if startEnd(1) <= 3 && startEnd(2) >=3     
0045     stamp_name = [dirname_seg,'.trackOptiStripSmall-Step1.mat'];
0046     delete(stamp_name);
0047 end
0048 
0049 if startEnd(1) <= 4 && startEnd(2) >=4     
0050     stamp_name = [dirname_seg,'.trackOptiLinkCell-Step2.mat'];
0051     delete([dirname_seg,'*err.mat']);
0052     delete(stamp_name);
0053     if skip>1
0054         stamp_name =  [dirname_seg,'.trackOptiSkipMerge-Step2merge.mat'];
0055         delete(stamp_name);
0056         stamp_name = [dirname_seg,'.trackOptiLinkCell-Step2merge.mat'];
0057         delete(stamp_name);
0058     end
0059 end
0060 
0061 
0062 if startEnd(1) <= 5 && startEnd(2) >=5    
0063     stamp_name = [dirname_seg,'.trackOptiCellMarker-Step3.mat'];
0064     delete(stamp_name);
0065 end
0066 
0067 if startEnd(1) <= 6 && startEnd(2) >=6    
0068     stamp_name = [dirname_seg,'.trackOptiFluor-Step4.mat'];
0069     delete(stamp_name);
0070 end
0071 
0072 
0073 if startEnd(1) <= 7 && startEnd(2) >=7    
0074     stamp_name = [dirname_seg,'.trackOptiMakeCell-Step5.mat'];
0075     delete(stamp_name);
0076 end
0077 
0078 
0079 if startEnd(1) <= 8 && startEnd(2) >=8    
0080     stamp_name = [dirname_seg,'.trackOptiFindFoci-Step6.mat'];
0081     delete(stamp_name);
0082 end
0083 
0084 
0085 if startEnd(1) <= 9 && startEnd(2) >=9    
0086     stamp_name = [dirname_seg,'.trackOptiClist-Step7.mat'];
0087     delete(stamp_name);
0088     delete ([dirname_xy,'clist.mat']); % clist
0089 end
0090 
0091 
0092 if startEnd(1) <= 10 && startEnd(2) >=10    
0093     stamp_name = [dirname_seg,'.trackOptiCellFiles-Step8.mat'];
0094     delete(stamp_name);
0095     delete ([dirname_cell,'*.mat']); % cell files
0096 end
0097 
0098 
0099 
0100 
0101 end