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| 2 | %%% extract a series of image folders from RDvision |
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| 3 | % to run on the cluster, edit the file extract.sh in the folder TOP_view or SCANSIDE, |
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| 4 | % Then oarsub -l "walltime=20:00:00" /fsnet/project/coriolis/2018/18ADDUCE/TOP_View/extract.sh |
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| 5 | function batch_extract_rdvision(RootDir,FirstFolder) |
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| 6 | %%%%%%%%%%%%%% CHOOSE THE ROOT FOLDER %%%%%%%%%% |
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| 7 | %RootDir='TOP_View' |
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| 8 | %RootDir='SCANSIDE';% |
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| 9 | %%%%%%%%%%%%%%%%%%%%%%% |
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| 10 | RootFolder=fullfile('/fsnet/project/coriolis/2018/18ADDUCE',RootDir); |
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| 11 | ParamFile=fullfile(RootFolder,'extract_param.xml'); |
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| 12 | %XmlFile='/fsnet/project/coriolis/2018/18ADDUCE/TOP_View/im.xml'; |
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| 13 | Param=xml2struct(ParamFile); |
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| 14 | switch RootDir |
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| 15 | case 'TOP_View' |
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| 16 | XmlFile=''; |
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| 17 | Param.OutputRootFile='Falcon'; |
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| 18 | case 'SCANSIDE' |
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| 19 | XmlFile='im.xml'; |
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| 20 | Param.OutputRootFile='im'; |
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| 21 | end |
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| 22 | ListStruct=dir(RootFolder); % get structure of the Root directory |
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| 23 | ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray |
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| 24 | ListNames=ListCells(1,:);%list of file names |
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| 25 | index_dir=find(strcmp('isdir',fieldnames(ListStruct)));%detect folders |
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| 26 | check_dir=cell2mat(ListCells(index_dir,:));% =1 for directories, =0 for files |
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| 27 | ListDir=ListNames(check_dir); |
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| 28 | FirstFolder |
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| 29 | first=find(strcmp(FirstFolder,ListDir)) |
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| 30 | NbFolders=1%5; %totql number of folders to process |
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| 31 | % first=9;% #3 is the first folder in the list (#1='.', #2='..') |
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| 32 | % disp('first folder') |
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| 33 | % dd(first).name |
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| 34 | % last=15;%19; |
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| 35 | % disp('last folder') |
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| 36 | % dd(last).name |
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| 37 | |
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| 38 | for ilist=first:first+NbFolders-1 |
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| 39 | Param.InputTable{1}=fullfile(RootFolder,ListDir{ilist});%folder exp |
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| 40 | ddd=dir(Param.InputTable{1}); |
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| 41 | Param.InputTable{2}=ddd(3).name; |
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| 42 | DataFolder=fullfile(Param.InputTable{1},Param.InputTable{2}); |
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| 43 | ExtractFolder=fullfile(Param.InputTable{1},[Param.InputTable{2} '.extract']); |
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| 44 | mkdir(ExtractFolder) |
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| 45 | if ~isempty(XmlFile) |
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| 46 | copyfile(fullfile(RootFolder,XmlFile),fullfile(DataFolder,[Param.OutputRootFile '.xml'])); |
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| 47 | end |
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| 48 | seqname=fullfile(DataFolder,[Param.InputTable{3} Param.InputTable{5}]); |
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| 49 | [A,FileInfo,timestamps,errormsg]=read_rdvision(seqname,[]); |
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| 50 | Param.IndexRange.last_i=str2num(FileInfo.numberoffiles); |
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| 51 | Param.OutputSubDir=Param.InputTable{2}; |
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| 52 | Param.ActionInput.LogPath= DataFolder; |
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| 53 | extract_rdvision(Param)% apply the function used in series |
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| 54 | end |
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| 55 | %%%%% COMMAND CLUSTER |
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| 56 | %oarsub -l "walltime=10:00:00" /fsnet/project/coriolis/2018/18ADDUCE/SCANSIDE/extract.sh -E /fsnet/project/coriolis/2018/18ADDUCE/SCANSIDE/error -O /fsnet/project/coriolis/2018/18ADDUCE/SCANSIDE/stdout |
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