Changeset 1053

Timestamp:

Jul 17, 2018, 11:37:31 AM (6 years ago)

Author:

sommeria

Message:

bed_scan added

Location:

trunk/src

Files:

• batch_extract_rdvision.m (modified) (3 diffs)
• series/bed_scan.m (added)

trunk/src/batch_extract_rdvision.m

@@ -3 +3 @@
 % to run on the cluster, edit the file extract.sh in the folder TOP_view or SCANSIDE, 
 % Then oarsub -l "walltime=20:00:00" /fsnet/project/coriolis/2018/18ADDUCE/TOP_View/extract.sh
-function batch_extract_rdvision(RootDir,FirstFolder)
-%%%%%%%%%%%%%%  CHOOSE THE ROOT FOLDER %%%%%%%%%%
-%RootDir='TOP_View'
-%RootDir='SCANSIDE';%
-%%%%%%%%%%%%%%%%%%%%%%%
+function batch_extract_rdvision(RootDir)
+
 RootFolder=fullfile('/fsnet/project/coriolis/2018/18ADDUCE',RootDir);
 ParamFile=fullfile(RootFolder,'extract_param.xml');
-%XmlFile='/fsnet/project/coriolis/2018/18ADDUCE/TOP_View/im.xml';
+XmlFile=fullfile(RootFolder,'im.xml');
 Param=xml2struct(ParamFile);
 switch RootDir
@@ -26 +23 @@
 check_dir=cell2mat(ListCells(index_dir,:));% =1 for directories, =0 for files
 ListDir=ListNames(check_dir);
-FirstFolder
-first=find(strcmp(FirstFolder,ListDir))
-NbFolders=1%5; %totql number of folders to process
+ind_bad=[find(strcmp('.',ListDir)) find(strcmp('..',ListDir))];
+ListDir(ind_bad)=[];
+
+%NbFolders=1%5; %totql number of folders to process
 % first=9;% #3 is the first folder in the list (#1='.', #2='..')
 % disp('first folder')
@@ -36 +34 @@
 % dd(last).name
 
-for ilist=first:first+NbFolders-1
-    Param.InputTable{1}=fullfile(RootFolder,ListDir{ilist});%folder exp
-    ddd=dir(Param.InputTable{1});
-    Param.InputTable{2}=ddd(3).name;
-    DataFolder=fullfile(Param.InputTable{1},Param.InputTable{2});
-    ExtractFolder=fullfile(Param.InputTable{1},[Param.InputTable{2} '.extract']);
-    mkdir(ExtractFolder)
-    if ~isempty(XmlFile)
-    copyfile(fullfile(RootFolder,XmlFile),fullfile(DataFolder,[Param.OutputRootFile '.xml']));
+%for ilist=first:first+NbFolders-1
+for ilist=1:numel(ListDir)
+    disp([ListDir{ilist} ' opened'])
+    ddd=dir(fullfile(RootFolder,ListDir{ilist}));
+    dddCells=struct2cell(ddd);% transform dir struct to a cell arrray
+    dddNames=dddCells(1,:);%list of file names
+    checkdone=false;
+    checkrdvision=0;
+    for iname=1:numel(dddNames)
+        checkdone=~isempty(regexp(dddNames{iname},'.extract$'));
+        if checkdone
+            disp('already extracted')
+            break
+        end
+        checkrdvision=checkrdvision+isequal(regexp(dddNames{iname},'^2018-'),1)
     end
-    seqname=fullfile(DataFolder,[Param.InputTable{3} Param.InputTable{5}]);
-    [A,FileInfo,timestamps,errormsg]=read_rdvision(seqname,[]);
-    Param.IndexRange.last_i=str2num(FileInfo.numberoffiles);   
-    Param.OutputSubDir=Param.InputTable{2};
-    Param.ActionInput.LogPath= DataFolder;
-    extract_rdvision(Param)% apply the function used in series
+    if ~checkdone
+        if checkrdvision==0
+            disp('no rdvision folder')
+        elseif checkrdvision>1
+            disp('multiple rdvision folders, no extraction')
+        else
+            Param.InputTable{1}=fullfile(RootFolder,ListDir{ilist});%folder exp
+            Param.InputTable{2}=ddd(3).name;
+            DataFolder=fullfile(Param.InputTable{1},Param.InputTable{2});
+            ExtractFolder=fullfile(Param.InputTable{1},[Param.InputTable{2} '.extract']);
+            mkdir(ExtractFolder)
+            if ~isempty(XmlFile)
+                copyfile(XmlFile,fullfile(DataFolder,[Param.OutputRootFile '.xml']));
+            end
+            seqname=fullfile(DataFolder,[Param.InputTable{3} Param.InputTable{5}]);
+            [A,FileInfo,timestamps,errormsg]=read_rdvision(seqname,[]);
+            Param.IndexRange.last_i=str2num(FileInfo.numberoffiles);
+            Param.OutputSubDir=Param.InputTable{2};
+            Param.ActionInput.LogPath= DataFolder;
+            extract_rdvision(Param)% apply the function used in series
+            disp([ListDir{ilist} ' extracted'])
+        end
+    end
 end
+'PROGRAM END'
 %%%%% COMMAND CLUSTER
 %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