[1123] | 1 | |
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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 | %%%%%%%%%%%%%% CHOOSE THE ROOT FOLDER %%%%%%%%%% |
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| 6 | |
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[1159] | 7 | RootDir='1_DATA' |
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[1123] | 8 | %RootFolder=fullfile('/fsnet/project/coriolis/2018/18JEVERB',RootDir); |
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[1159] | 9 | %RootFolder=fullfile('/fsnet/project/edt/2021/21CORIOFARM',RootDir) |
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| 10 | RootFolder=fullfile('/fsnet/project/coriolis/2024/24PLUME',RootDir) |
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[1123] | 11 | %ParamFile=fullfile(RootFolder,'extract_param.xml'); |
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| 12 | %Param=xml2struct(ParamFile); |
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| 13 | |
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| 14 | ListStruct=dir(RootFolder); % get structure of the Root directory |
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| 15 | index_dir=find(strcmp('isdir',fieldnames(ListStruct)));%detect folder info in structure ListStruct |
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| 16 | ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray |
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| 17 | check_dir=cell2mat(ListCells(index_dir,:));% =1 for directories, =0 for files |
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| 18 | ListCells=ListCells(:,check_dir); |
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| 19 | ListCells(:,1:2)=[]; |
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| 20 | ListNames=ListCells(1,:); |
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| 21 | List2extract={}; |
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| 22 | List2delete={}; |
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| 23 | List2check={}; |
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| 24 | |
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| 25 | %% loop on experiments |
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| 26 | for ilist=1:numel(ListNames)%loop on experiments |
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| 27 | ListNames{ilist} |
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| 28 | SubFolder=fullfile(RootFolder,ListNames{ilist}); |
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| 29 | ListStructSub=dir(SubFolder); % get structure of the Root directory |
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| 30 | index_dir=find(strcmp('isdir',fieldnames(ListStructSub)));%detect folder info in structure ListStruct |
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| 31 | ListCellsSub=struct2cell(ListStructSub);% transform dir struct to a cell arrray |
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| 32 | check_dir=cell2mat(ListCellsSub(index_dir,:));% =1 for directories, =0 for files |
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| 33 | ListCellsSub=ListCellsSub(:,check_dir); |
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| 34 | ListCellsSub(:,1:2)=[]; |
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| 35 | ListNamesSub=ListCellsSub(1,:); |
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| 36 | ind_rdvision=[]; |
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| 37 | for isub=1:numel(ListNamesSub)% loop on data folders of the current experiment |
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| 38 | ListStructSubSub=dir(fullfile(RootFolder,ListNames{ilist},ListNamesSub{isub})); % get structure of the Root directory |
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| 39 | index_dir=find(strcmp('isdir',fieldnames(ListStructSubSub)));%detect folder info in structure ListStruct |
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| 40 | ListCellsSubSub=struct2cell(ListStructSubSub);% transform dir struct to a cell arrray |
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| 41 | check_dir=cell2mat(ListCellsSubSub(index_dir,:));% =1 for directories, =0 for files |
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| 42 | ListCellsSubSub=ListCellsSubSub(:,check_dir); |
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| 43 | ListCellsSubSub(:,1:2)=[]; |
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| 44 | ListNamesSubSub=ListCellsSubSub(1,:); |
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| 45 | ind_rdvision=[]; |
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| 46 | for isubsub=1:numel(ListNamesSubSub) |
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[1159] | 47 | if ~isempty(regexp(ListNamesSubSub{isubsub},'^2024-')) |
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[1123] | 48 | ind_rdvision=[ind_rdvision isubsub];%detect rdvision folders |
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| 49 | end |
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| 50 | end |
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| 51 | |
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| 52 | %% extract the rdvision image series if it was not done |
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| 53 | if numel(ind_rdvision)==1% |
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| 54 | DataFolder=fullfile(RootFolder,ListNames{ilist},ListNamesSub{isub},ListNamesSubSub{ind_rdvision}); |
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| 55 | if isempty(regexp(DataFolder,'.extract$'))% if the detected folder is not .extract |
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| 56 | % ExtractFolder=fullfile(Param.InputTable{1},[Param.InputTable{2} '.extract']); |
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| 57 | % mkdir(ExtractFolder) |
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| 58 | % % if ~isempty(XmlFile) |
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| 59 | % % copyfile(fullfile(RootFolder,XmlFile),fullfile(DataFolder,[Param.OutputRootFile '.xml'])); |
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| 60 | % % end |
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| 61 | % seqname=fullfile(DataFolder,[Param.InputTable{3} Param.InputTable{5}]); |
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| 62 | % [A,FileInfo,timestamps,errormsg]=read_rdvision(seqname,[]); |
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| 63 | % Param.IndexRange.last_i=str2num(FileInfo.numberoffiles); |
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| 64 | % Param.OutputSubDir=Param.InputTable{2}; |
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| 65 | % Param.ActionInput.LogPath= DataFolder; |
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| 66 | % extract_rdvision(Param)% apply the function used in series |
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| 67 | % [ListNames{ilist} ' extracted'] |
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| 68 | List2extract=[List2extract;DataFolder]; |
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| 69 | end |
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| 70 | end |
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| 71 | |
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| 72 | %% delete the rdvision source if the extraction has been done |
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| 73 | Checkdelete=0; |
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| 74 | ExtractFolder=fullfile(RootFolder,ListNames{ilist},ListNamesSub{isub}); |
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| 75 | status=''; |
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| 76 | if numel(ind_rdvision)==2 |
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| 77 | for irdvision=1:2 |
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| 78 | CheckExtract(irdvision)=isempty(regexp(fullfile(RootFolder,ListNames{ilist},ListNamesSub{isub},ListNamesSubSub{irdvision}), '.extract$')); |
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| 79 | end |
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| 80 | status='extract missing'; |
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| 81 | if numel(find(CheckExtract))==1 |
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| 82 | ExtractFolder=fullfile(RootFolder,ListNames{ilist},ListNamesSub{isub},ListNamesSubSub{find(CheckExtract)}); |
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| 83 | PngFolder=fullfile(RootFolder,ListNames{ilist},ListNamesSub{isub},'im'); |
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| 84 | status='image folder not created'; |
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| 85 | if exist(ExtractFolder,'dir') && exist(PngFolder,'dir') |
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| 86 | filename_seq=fullfile(ExtractFolder,'im.seq'); |
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[1159] | 87 | try |
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[1123] | 88 | s=ini2struct(filename_seq); |
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| 89 | FileInfo=s.sequenceSettings; |
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| 90 | if isfield(s.sequenceSettings,'numberoffiles') |
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| 91 | NumberOfFrames=str2double(s.sequenceSettings.numberoffiles); |
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| 92 | else |
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| 93 | status='bad seq file'; |
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| 94 | end |
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[1159] | 95 | catch ME |
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| 96 | disp(['error in ' filename_seq]) |
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| 97 | end |
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[1123] | 98 | DirPng=dir(PngFolder); |
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| 99 | if numel(DirPng)==NumberOfFrames+2 |
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| 100 | Checkdelete=1; |
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| 101 | else |
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| 102 | status=['extraction not finished,' num2str(numel(DirPng)-2) ' images extracted']; |
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| 103 | end |
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| 104 | end |
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| 105 | end |
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| 106 | % |
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| 107 | % |
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| 108 | % Param.InputTable{1}=fullfile(RootFolder,ListDir{ilist});%folder exp |
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| 109 | % ddd=dir(Param.InputTable{1}); |
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| 110 | % Param.InputTable{2}=ddd(3).name; |
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| 111 | % DataFolder=fullfile(Param.InputTable{1},Param.InputTable{2}); |
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| 112 | % ExtractFolder=fullfile(Param.InputTable{1},[Param.InputTable{2} '.extract']); |
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| 113 | % mkdir(ExtractFolder) |
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| 114 | % if ~isempty(XmlFile) |
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| 115 | % copyfile(fullfile(RootFolder,XmlFile),fullfile(DataFolder,[Param.OutputRootFile '.xml'])); |
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| 116 | % end |
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| 117 | % seqname=fullfile(DataFolder,[Param.InputTable{3} Param.InputTable{5}]); |
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| 118 | % [A,FileInfo,timestamps,errormsg]=read_rdvision(seqname,[]); |
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| 119 | % Param.IndexRange.last_i=str2num(FileInfo.numberoffiles); |
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| 120 | % Param.OutputSubDir=Param.InputTable{2}; |
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| 121 | % Param.ActionInput.LogPath= DataFolder; |
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| 122 | % extract_rdvision(Param)% apply the function used in series |
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| 123 | end |
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| 124 | if Checkdelete |
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| 125 | List2delete=[List2delete;ExtractFolder]; |
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| 126 | %rmdir(ExtractFolder,'s') |
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| 127 | elseif ~isempty(status) |
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| 128 | List2check=[List2check;[ExtractFolder ' ' status]]; |
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| 129 | end |
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| 130 | end |
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| 131 | end |
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| 132 | List2extract |
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| 133 | List2check |
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| 134 | List2delete |
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| 135 | if ~isempty(List2delete) |
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| 136 | Answer = questdlg('delete listed folders(Y/N)'); |
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| 137 | if strcmp(Answer,'Yes') |
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| 138 | for ifolder=1:numel(List2delete) |
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| 139 | rmdir(List2delete{ifolder},'s') |
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| 140 | end |
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| 141 | end |
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| 142 | end |
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