Index: /trunk/src/browse_data.m =================================================================== --- /trunk/src/browse_data.m (revision 933) +++ /trunk/src/browse_data.m (revision 934) @@ -87,5 +87,5 @@ %% initialize the GUI -if ~(exist('DataSeries','var') && exist(DataSeries,'dir')) +if ~(exist('DataSeries','var') && ischar(DataSeries) && exist(DataSeries,'dir')) DataSeries=pwd;% current dir is the starting data series by default end @@ -273,5 +273,6 @@ ListFiles=ListCells(1,:);%list of dir and file names cell_remove=regexp(ListFiles,'^(-|\.|\+/\.)');% detect strings beginning by '-' ,'.' or '+/.'(dir beginning by . ) - check_keep=cellfun('isempty', cell_remove); + cell_remove_tild=regexp(ListFiles,'~$');% detect tild the end of file nqme (do not list) + check_keep=cellfun('isempty', cell_remove) & cellfun('isempty', cell_remove_tild); check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files for ilist=1:numel(ListFiles) @@ -282,4 +283,5 @@ else %update the list of dataSeries [tild,msg]=fileattrib(mirror); + msg.Name=regexprep(msg.Name,'^/.','/');%remove the dot in /. at the beginning of the name if ~strcmp(msg.Name,mirror)% if it is a link ListFiles{ilist}=['~' ListFiles{ilist}];%mark link by '@' in the list Index: /trunk/src/series.m =================================================================== --- /trunk/src/series.m (revision 933) +++ /trunk/src/series.m (revision 934) @@ -469,5 +469,5 @@ RootPathCell=InputTable(:,1); SubDirCell=InputTable(:,2); -oldfile=fullfile(RootPathCell{1},SubDirCell{1}); +oldfile=fullfile(InputTable{1,1},InputTable{1,2}); if isempty(oldfile) % use a file name stored in prefdir @@ -481,18 +481,65 @@ end end -%% launch the browser -fileinput=uigetfile_uvmat('pick an input file in the series',oldfile); -hh=dir(fileinput); -if numel(hh)>1 - msgbox_uvmat('ERROR','invalid input, probably a broken link'); -else - if ~isempty(fileinput) - display_file_name(handles,fileinput,'one') - end -end -append='one'; -set(handles.MenuOpenCampaign,'ForegroundColor',[1 1 0]) -drawnow -browse_campaign(handles,append); + +OutPut=browse_data(oldfile,'on','on');% open the GUI browse_data to get select a campaign dir, experiment and device +NbLines=numel(OutPut.Experiment)*numel(OutPut.DataSeries); +icount=0; +for iexp=1:numel(OutPut.Experiment) + for idevice=1:numel(OutPut.DataSeries) + icount=icount+1; + InputTable{icount,1}=fullfile(OutPut.Campaign,OutPut.Experiment{iexp}); + InputTable{icount,2}=OutPut.DataSeries{idevice}; + if isempty(InputTable{icount,3}) + if icount>1 + InputTable{icount,3}=InputTable{icount-1,3}; + else + InputTable{icount,3}=''; + end + end + if isempty(InputTable{icount,4}) + if icount>1 + InputTable{icount,4}=InputTable{icount-1,4}; + else + InputTable{icount,4}=''; + end + end + if isempty(InputTable{icount,5}) + if icount>1 + InputTable{icount,5}=InputTable{icount-1,5}; + else + InputTable{icount,5}=''; + end + end + end +end +if size(InputTable,1)>icount + InputTable(icount+1:size(InputTable,1),:)=[]; +end +set(handles.InputTable,'Data',InputTable) +REFRESH_Callback(hObject, eventdata, handles) +% DataSeries=fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.DataSeries{1}); +% fileinput=uigetfile_uvmat('pick an input file',DataSeries); +% hh=dir(fileinput); +% if numel(hh)>1 +% msgbox_uvmat('ERROR','invalid input, probably a broken link'); +% return +% end +% +% +% +% %% launch the browser +% fileinput=uigetfile_uvmat('pick an input file in the series',oldfile); +% hh=dir(fileinput); +% if numel(hh)>1 +% msgbox_uvmat('ERROR','invalid input, probably a broken link'); +% else +% if ~isempty(fileinput) +% display_file_name(handles,fileinput,'one') +% end +% end +% append='one'; +% set(handles.MenuOpenCampaign,'ForegroundColor',[1 1 0]) +% drawnow +% browse_campaign(handles,append); %------------------------------------------------------------------------ @@ -1486,5 +1533,4 @@ errormsg='';%default error message xmlfile=fullfile(path_series,'PARAM.xml'); -%test_batch=0;%default: ,no batch mode available if ~exist(xmlfile,'file') [success,message]=copyfile(fullfile(path_series,'PARAM.xml.default'),xmlfile); @@ -1505,5 +1551,6 @@ end ActionFullName=fullfile(get(handles.ActionPath,'String'),ActionName); -%% If a compiled version has been selected (ext .sh) check weather it needs to be recompiled + +%% If a compiled version has been selected (ext .sh) check wether it needs to be recompiled if strcmp(ActionExt,'.sh') TransformPath=''; @@ -1515,9 +1562,8 @@ [mcrmajor, mcrminor] = mcrversion; MCRROOT = ['MCRROOT',int2str(mcrmajor),int2str(mcrminor)]; - %hver=ver('MATLAB'); - %MCRROOT=['MCRROOT' regexprep(hver.Version,'\.','')];%suppress the dot in version number RunTime = getenv(MCRROOT); ActionNameVersion=[ActionName '_' MCRROOT]; ActionFullName=fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']); + % compile the .m file if the .sh file does not exist yet if ~exist(ActionFullName,'file') answer=msgbox_uvmat('INPUT_Y-N','compiled version has not been created: compile now?'); @@ -1552,4 +1598,5 @@ end end + set(handles.ActionExt,'BackgroundColor',[1 1 1]) set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch @@ -1774,15 +1821,10 @@ if isempty(Param.IndexRange.NbSlice) Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i; - % Param.IndexRange.first_i=ref_i(1+(iprocess-1)*BlockLength); if Param.IndexRange.first_i>last_i NbProcess=iprocess-1;% leave the loop, we are at the end of the calculation break end - %Param.IndexRange.last_i=min(ref_i(iprocess*BlockLength),last_i); - %Param.IndexRange.last_i=min(first_i+(iprocess)*BlockLength*incr_i-1,last_i); Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1); else %multislices (then incr_i is not empty) - % Param.IndexRange.first_i= first_i+incr_i*(iprocess-1); - % Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice; Param.IndexRange.first_i= first_i+iprocess-1; Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice; @@ -1791,17 +1833,4 @@ Param.InputTable{ilist,1}=regexprep(Param.InputTable{ilist,1},'\','/');%correct path name for PCWIN system end - - % if isempty(Param.IndexRange.NbSlice)% process by blocks of i index - % Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i; - % if Param.IndexRange.first_i>last_i - % NbProcess=iprocess-1; - % break% leave the loop, we are at the end of the calculation - % end - % Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1); - % else% process by slices of i index if NbSlice is defined, computation in a single process if NbSlice =1 - % Param.IndexRange.first_i= first_i+iprocess-1; - % Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice; - % end - if isfield(Param,'OutputSubDir') @@ -1819,8 +1848,4 @@ end end - % [success,msg] = fileattrib(filexml{iprocess},'+w','g');% allow writing access for the group of users, recursively in the folder - % if success==0 - % msgbox_uvmat('WARNING',{['unable to set group write access to ' filexml{iprocess} ':']; msg});%error message for directory creation - % end end if strcmp (RunMode,'local') @@ -1840,8 +1865,5 @@ end end -% [success,msg] = fileattrib(DirXml,'+w','g','s');% allow writing access for the group of users, recursively in the folder -% if success==0 -% msgbox_uvmat('WARNING',{['unable to set group write access to ' DirXml ':']; msg});%error message for directory creation -% end + if ~strcmp (RunMode,'local') && ~strcmp(RunMode,'python') %% processing on a different session of the same computer (background) or cluster, create executable files @@ -1879,14 +1901,5 @@ first_i,last_i,first_j,last_j); filelog_global=fullfile(OutputDir,'0_LOG',filelog_global); - - % [success,msg] = fileattrib(DirLog,'+w','g','s');% allow writing access for the group of users, recursively in the folder - % if success==0 - % msgbox_uvmat('WARNING',{['unable to set group write access to ' DirLog ':']; msg});%error message for directory creation - % end - % [success,msg] = fileattrib(fullfile(OutputDir,'0_EXE'),'+w','g','s');% allow writing access for the group of users, recursively in the folder - % if success==0 - % msgbox_uvmat('WARNING',{['unable to set group write access to ' fullfile(OutputDir,'0_EXE') ':']; msg});%error message for directory creation - % end - % + for iprocess=1:NbProcess @@ -1894,9 +1907,4 @@ batch_file_list{iprocess}=fullfile(OutputDir,'0_EXE',regexprep(extxml{iprocess},'.xml$',ExeExt)); - % [fid,message]=fopen(batch_file_list{iprocess},'w');% create the executable file - % if isequal(fid,-1) - % errormsg=['creation of ' batch_file_list{iprocess} ':' message]; - % return - % end % set the log file name @@ -1958,5 +1966,5 @@ 'hostname && date \n '... 'umask 002 \n'... - ActionFullName ' ' RunTime ' ' filexml];%allow writting access to created files for user group + ActionFullName ' ' RunTime ' ' filexml{iprocess}];%allow writting access to created files for user group fprintf(fid,cmd);%fill the executable file with the char string cmd fclose(fid);% close the executable file @@ -1979,8 +1987,4 @@ return end - % [success,msg] = fileattrib(batch_file_list{iprocess},'+w','g');% allow writing access for the group of users, recursively in the folder - % if success==0 - % msgbox_uvmat('WARNING',{['unable to set group write access to ' batch_file_list{iprocess} ':']; msg});%error message for directory creation - % end if strcmp(ActionExt,'.sh') cmd=['#!/bin/bash \n '... @@ -2020,5 +2024,4 @@ filename_joblist=fullfile(DirOAR,'job_list.txt');% name of the file containing the list of executables fid=fopen(filename_joblist,'w');%open it for writting - % [success,msg] = fileattrib(filename_joblist,'+w','g');% allow writing access for the group of users, for iprocess=1:length(batch_file_list) fprintf(fid,[batch_file_list{iprocess} '\n']);% write list of exe files @@ -2053,6 +2056,4 @@ '-l ' filename_joblist '.log"']; - - fprintf(oar_command);% display system command on the Matlab command window [status,result]=system(oar_command)% execute system command and show the result (ID number of the launched job) on the Matlab command window @@ -2063,8 +2064,4 @@ fclose(fid); msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched as ' num2str(NbProcess) ' processes in cluster: press STATUS to see results']) - % [success,msg] = fileattrib(DirOAR,'+w','g','s');% allow writing access for the group of users, recursively in the folder - % if success==0 - % msgbox_uvmat('WARNING',{['unable to set group write access to ' DirOAR ':']; msg});%error message for directory creation - % end case 'cluster_pbs' % for LMFA Kepler machine @@ -2121,4 +2118,5 @@ end end + %------------------------------------------------------------------------ function STOP_Callback(hObject, eventdata, handles) @@ -2128,5 +2126,4 @@ set(handles.RUN,'enable','on') set(handles.RUN, 'Value',0) - %------------------------------------------------------------------------ Index: /trunk/src/uvmat.m =================================================================== --- /trunk/src/uvmat.m (revision 933) +++ /trunk/src/uvmat.m (revision 934) @@ -488,23 +488,10 @@ % ----------------------------------------------------------------------- function MenuBrowseCampaign_Callback(hObject, eventdata, handles) -set(handles.MenuOpenCampaign,'ForegroundColor',[1 1 0]) -drawnow +% set(handles.MenuOpenCampaign,'ForegroundColor',[1 1 0]) +% drawnow [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles); DataSeries=fullfile(RootPath,SubDir); if isempty(DataSeries) %loads the previously stored file name and set it as default in the file_input box DataSeries=get(handles.RootPath,'UserData'); -end -% RootPath=get(handles.RootPath,'String'); -% if isempty(RootPath) -% RootPath=get(handles.RootPath,'UserData');%use Rootpath recored from the personal file at uvmat opening -% end -% CampaignPath=fileparts(fileparts(RootPath)); -% DirFull=uigetfile_uvmat('define this path as the Campaign folder:',CampaignPath,'uigetdir'); -% %DirFull = uigetdir(CampaignPath,'Select a Campaign dir, then press OK'); -% if isempty(DirFull) -% return -% end -if isempty(DataSeries)||~ischar(DataSeries) - DataSeries=pwd; end OutPut=browse_data(DataSeries,'on');% open the GUI browse_data to get select a campaign dir, experiment and device