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