source: trunk/src/series/ima_levels_batch.m @ 977

Last change on this file since 977 was 977, checked in by g7moreau, 4 years ago
  • Update Copyright 2008-2017 notice
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1%'ima_levels': rescale the image intensity to reduce strong luminosity peaks
2%------------------------------------------------------------------------
3% function GUI_input=ima_levels(num_i1,num_i2,num_j1,num_j2,Series)
4%
5%OUTPUT
6% GUI_input=list of options in the GUI series.fig needed for the function
7%
8%INPUT:
9%num_i1: series of first indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ)
10%num_i2:  series of second indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ)
11%num_j1:  series of first indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ )
12%num_j2:  series of second indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ)
13%Series: Matlab structure containing information set by the series interface% relabel_i_j: relabel an image series with two indices, according to the time matrix given by ImaDoc
14%----------------------------------------------------------------------
15
16%=======================================================================
17% Copyright 2008-2017, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
18%   http://www.legi.grenoble-inp.fr
19%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
20%
21%     This file is part of the toolbox UVMAT.
22%
23%     UVMAT is free software; you can redistribute it and/or modify
24%     it under the terms of the GNU General Public License as published
25%     by the Free Software Foundation; either version 2 of the license,
26%     or (at your option) any later version.
27%
28%     UVMAT is distributed in the hope that it will be useful,
29%     but WITHOUT ANY WARRANTY; without even the implied warranty of
30%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
31%     GNU General Public License (see LICENSE.txt) for more details.
32%=======================================================================
33
34function GUI_input=ima_levels_batch(num_i1,num_i2,num_j1,num_j2,Series)
35%requests for the visibility of input windows in the GUI series  (activated directly by the selection in the menu ACTION)
36if ~exist('num_i1','var')
37    GUI_input={};
38    return %exit the function
39end
40
41%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%enable waitbar
42hseries=guidata(Series.hseries);%handles of the GUI series
43WaitbarPos=get(hseries.waitbar_frame,'Position');
44%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
45
46basename=fullfile(Series.RootPath,Series.RootFile) ;
47
48%create dir of the new images
49[dir_images,namebase]=fileparts(basename);
50[path,subdir_ima]=fileparts(dir_images);
51dircur=pwd;
52cd(path);
53mkdir([subdir_ima '_levels']);
54  [xx,msg2] = fileattrib([subdir_ima '_levels'],'+w','g'); %yield writing access (+w) to user group (g)
55if ~strcmp(msg2,'')
56    msgbox_uvmat('ERROR',['pb of permission for ' subdir_ima ': ' msg2])%error message for directory creation
57    cd(dircur)
58    return
59end
60cd(dircur);
61basename_new=fullfile(path,[subdir_ima '_levels'],namebase);
62
63% read imadoc
64%[XmlData,warntext]=imadoc2struct([basename '.xml']);
65% nbfield1=size(XmlData.Time,1);
66% nbfield2=size(XmlData.Time,2);
67
68msgbox_uvmat('CONFIRMATION','apply image rescaling function levels.m ');
69
70%copy the xml file
71if exist([basename '.xml'],'file')
72    copyfile([basename '.xml'],[basename_new '.xml']);% copy the .civ file
73end
74
75%main loop
76batch_file_list={};
77nbfield=size(num_i1,2);
78nbfield2=size(num_i1,1);
79for ifile=1:nbfield
80    update_waitbar(hseries.waitbar,WaitbarPos,ifile/nbfield)
81    stopstate=get(hseries.RUN,'BusyAction');
82    if isequal(stopstate,'queue') % enable STOP command
83        for jfile=1:nbfield2
84            OutputFile=name_generator(basename_new,num_i1(jfile,ifile),num_j1(jfile,ifile),'',Series.NomType);
85            filename=name_generator(basename,num_i1(jfile,ifile),num_j1(jfile,ifile),Series.FileExt,Series.NomType);
86            filename_new=name_generator(basename_new,num_i1(jfile,ifile),num_j1(jfile,ifile),'.png',Series.NomType);
87            path_series=[fileparts(which('civ')) '/series'];
88           
89            filename_bat=[OutputFile '.bat'];
90            [fid,message]=fopen(filename_bat,'w');
91            if isequal(fid,-1)
92                msgbox_uvmat('ERROR', ['creation of .bat file: ' message])
93                return
94            end
95            fprintf(fid,['/opt/matlab/R2011a/bin/matlab -nodisplay -nosplash -r "cd(''' path_series ''');'...
96                'A=imread(' filename ');C=levels(A);imwrite(C,' filename_new ');exit"']);
97            fclose(fid);
98            if isunix
99                system(['chmod +x ' filename_bat]);
100            end
101            batch_file_list{length(batch_file_list)+1}=filename_bat;
102        end
103    end
104end
105
106
107ncores=1;
108walltime_onejob=10;%seconds
109filename_joblist=fullfile(path,[subdir_ima '_levels'],'job_list.txt')
110fid=fopen(filename_joblist,'w+')
111for p=1:length(batch_file_list)
112    fprintf(fid,[batch_file_list{p} '\n']);
113end
114fclose(fid);
115oar_command=['oarsub -n ima_levels '...
116    '-l /core=' num2str(ncores) ','...
117    'walltime=' datestr(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,13) ' '...
118    '-E ' regexprep(filename_joblist,'\.txt\>','.errors') ' '...
119    '-O ' regexprep(filename_joblist,'\.txt\>','.log') ' '...
120    '"oar-parexec -f ' filename_joblist ' -l ' filename_joblist '.log"'];
121filename_oarcommand=fullfile(path,[subdir_ima '_levels'],'oar_command');
122fid=fopen(filename_oarcommand,'w');
123fprintf(fid,[oar_command '\n']);
124fclose(fid);
125display(oar_command);
126eval(['! . ' filename_oarcommand])
127
128
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