Changeset 1136

Timestamp:

Apr 24, 2024, 11:35:22 AM (6 months ago)

Author:

augier3pi

Message:

Fix launching fluidimage

Location:

trunk/src

Files:

• call_command_clean.m (added)
• command_launch_python.m (modified) (1 diff)
• series.m (modified) (78 diffs)

trunk/src/command_launch_python.m

@@ -1 @@
-%'command_launch_python': creates the command strings for opening a programme in python with a Linux system('GLNX86','GLNXA64','MACI64')
+%'command_launch_python': creates the command string for launching fluidimage
 %------------------------------------------------------------------------
-% function cmd=command_launch_matlab(filelog,ActionPath,ActionName,inputxml)
+% function cmd=command_launch_python(inputxml)
 %
 %OUTPUT
-% cmd=set of system commands (char string) to write 
-                           
+% cmd=set of system commands (char string) to write
 %
 %INPUT:
-% filelog: name (char string)  of the file to collect the output in the Matlab command window
-% ActionPath:  path to the  programme to launch
-% ActionName: name of the programme to launch
-% inputxml: full name, including path, of the xml input parameter file for the programme ActionName
-% option: ='bacground' or 'cluster' depending on the launching option
+% inputxml: path of the xml input parameter file for the program fluidimage
+% option: = 'background' or 'cluster' depending on the launching option
 
-function cmd=command_launch_python(filelog,ActionPath,ActionName,inputxml)
- cmd = ['LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "l = x.split('':'');...' ...
-     ' l = [s for s in l if ''matlab'' not in s]; print('':''.join(l))") ' ...
-                'python -m ' ActionName ' ' inputxml];
-
-% Matlab case:
- % ThreadOption='';
-% if strcmp(option,'cluster')
-%     ThreadOption='-singleCompThread';
-%     inputxml={inputxml};% single input parameter file
-% end
-% matlab_ver = ver('MATLAB');
-% matlab_version = matlab_ver.Version;
-% cmd=[...
-%     '#!/bin/bash\n'...
-%     'source /etc/profile\n'...
-%     'module purge\n'...
-%     'module load matlab/' matlab_version '\n'...% CHOICE OF THE SAME MATLAB VERSION AS THE CURRENT MATLAB SESSION (not mandatory)
-%     'time_start=$(date +%%s)\n'...
-%     'matlab -nodisplay -nosplash -nojvm ''' ThreadOption ''' -logfile ''' filelog ''' <<END_MATLAB\n'...%launch the new Matlab session  without display
-%     'addpath(''' path_uvmat ''');\n'...
-%     'addpath(''' ActionPath ''');\n'];
-% for iprocess=1:numel(inputxml)
-%     cmd=[cmd '' ActionName  '(''' inputxml{iprocess} ''');\n'];
-% end
-% cmd=[cmd  'exit\n' 'END_MATLAB\n'];
-%     if strcmp(option,'background')
-%     cmd=[cmd ...
-%     'time_end=$(date +%%s)\n'...
-%     'echo "global time = " $(($time_end - $time_start)) >> ''' filelog '''\n'];
-%     end
-% 
-% %% case cluster:
-% % matlab_ver = ver('MATLAB');
-% %                     matlab_version = matlab_ver.Version;
-% %                     cmd=[...
-% %                         '#!/bin/bash\n'...
-% %                         'source /etc/profile\n'...
-% %                         'module purge\n'...
-% %                         'module load matlab/' matlab_version '\n'...% CHOICE OF CURRENT MATLAB VERSION
-% %                         'matlab -nodisplay -nosplash -nojvm -singleCompThread -logfile ''' filelog{iprocess} ''' <<END_MATLAB\n'...% open a new Matlab session without display
-% %                         'addpath(''' path_series ''');\n'...
-% %                         'addpath(''' ActionPath ''');\n'...
-% %                         '' ActionName  '(''' filexml{iprocess} ''');\n'...% launch the Matlab function selected by the GUI 'series'
-% %                         'exit\n'...
-% %                         'END_MATLAB\n'];
-% %                 end
-
-
+function cmd=command_launch_python(inputxml)
+    cmd = ['python -m fluidimage.run_from_xml ' inputxml];
+end

trunk/src/series.m

@@ -1 @@
-%'series': master function associated to the GUI series.m for analysis field series  
+%'series': master function associated to the GUI series.m for analysis field series
 %------------------------------------------------------------------------
 % function varargout = series(varargin)
@@ -35 +35 @@
 %------------------------------------------------------------------------
 %------------------------------------------------------------------------
-%  I - MAIN FUNCTION series 
+%  I - MAIN FUNCTION series
 %------------------------------------------------------------------------
 %------------------------------------------------------------------------
@@ -130 +130 @@
 if ~exist('Param','var')
     Param=[]; % default
-end 
+end
 
 %% Read the parameter file series.xml, or created from series.xml.default if it does not exist
@@ -145 +145 @@
         delete(xmlfile);
         [success,message]=copyfile(fullfile(path_series,'series.xml.default'),xmlfile);
-    end  
+    end
     SeriesData.SeriesParam=xml2struct(xmlfile);
 end
@@ -158 +158 @@
 % % command = ['LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "l = x.split('':''); l = [s for s in l if ''matlab'' not in s]; print('':''.join(l))") ' ...
 % %             'python -c "import fluidimage"'];
-% % [code, ~] = system(command); 
+% % [code, ~] = system(command);
 % % if code==0
     ActionExtList={'.m';'.sh';'.py (in dev.)'}; % default choice of extensions (Matlab fct .m or compiled version .sh
@@ -185 +185 @@
 SeriesData.TransformPath=path_transform_fct;% store the standard path for trqnsform functions (needed for compilation)
 
-%% get the user defined functions stored in the personal file uvmat_perso.mat 
+%% get the user defined functions stored in the personal file uvmat_perso.mat
 dir_perso=prefdir;
 profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
@@ -248 +248 @@
 set(handles.TransformName,'Value',TransformIndex)
 set(handles.TransformPath,'String',TransformPathList{TransformIndex})
-   
+
 %% fields input initialisation
 if isfield(Param,'list_fields')&& isfield(Param,'index_fields') &&~isempty(Param.list_fields) &&~isempty(Param.index_fields)
@@ -269 +269 @@
 set(handles.series,'UserData',SeriesData)% initiate Userdata
 if isfield(Param,'InputFile')
-    
+
     %% fill the list of input file series
     InputTable=[{Param.InputFile.RootPath},{Param.InputFile.SubDir},{Param.InputFile.RootFile},{Param.InputFile.NomType},{Param.InputFile.FileExt}];
@@ -282 +282 @@
     end
     set(handles.InputTable,'Data',InputTable)
-    
-    %% define the default path for the output files 
+
+    %% define the default path for the output files
     [InputPath,Device,DeviceExt]=fileparts(InputTable{1,1});
     [InputPath,Experiment,ExperimentExt]=fileparts(InputPath);
@@ -302 +302 @@
     end
     end
-    
+
     %% determine the selected reference field indices for pair display
-    
+
     [tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(Param.InputFile.FileIndex);
     if isempty(i1)
@@ -333 +333 @@
     %% enable field and veltype menus, in accordance with the current action
     ActionName_Callback([],[], handles)
-    
+
     %% set length of waitbar
     displ_time(handles)
-    
+
 else
     set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
@@ -384 +384 @@
 % automatically sets the global properties when the rootfile name is introduced
 % then activate the view-field actionname if selected
-% it is activated either by clicking on the RootPath window or by the 
-% browser 
+% it is activated either by clicking on the RootPath window or by the
+% browser
 %------------------------------------------------------------------------
 %------------------------------------------------------------------------
 % --- fct activated by the browser under 'Open'
-%------------------------------------------------------------------------  
+%------------------------------------------------------------------------
 function MenuBrowse_Callback(hObject, eventdata, handles)
 %% look for the previously opened file 'oldfile'
@@ -481 +481 @@
 %------------------------------------------------------------------------
 % --- fct activated by the browser under 'Open campaign/Browse...'
-%------------------------------------------------------------------------ 
+%------------------------------------------------------------------------
 function MenuBrowseCampaign_Callback(hObject, eventdata, handles)
 
@@ -539 +539 @@
 % --------------------------------------------------------------------
 % function MenuCampaign_Callback(hObject, eventdata, handles)
-% % -------------------------------------------------------------------- 
-% 
+% % --------------------------------------------------------------------
+%
 % OutPut=browse_data(get(hObject,'Label'),'on','on'); % open the GUI browse_data to get select a campaign dir, experiment and device
 % if ~isfield(OutPut,'Campaign')
@@ -704 +704 @@
 %         'append': add a new line to the input table
 function errormsg=display_file_name(handles,Param,iview)
-  
+
 set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
 drawnow
 errormsg=''; % default
 if ischar(Param)
-    fileinput=Param; 
+    fileinput=Param;
 else% input set when series is opened (called by the GUI uvmat)
     fileinput=Param.FileName;
 end
-    
+
 %% get the input root name, indices, file extension and nomenclature NomType
 if isempty(regexp(fileinput,'^http')) && ~exist(fileinput,'file')
@@ -753 +753 @@
 %% enable other menus and uicontrols
 set(handles.RUN, 'Enable','On')
-set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red 
+set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
 set(handles.InputTable,'BackgroundColor',[1 1 0]) % set RootPath edit box  to yellow
 drawnow
@@ -863 +863 @@
 SeriesData.Ref_j2=j2;
 
-%% define the path for the output files 
+%% define the path for the output files
 [InputPath,Device,DeviceExt]=fileparts(InputTable{1,1});
 [InputPath,Experiment,ExperimentExt]=fileparts(InputPath);
@@ -888 +888 @@
 set(handles.InputTable,'BackgroundColor',[1 1 1])
 
-%% initiate input file series and refresh the current field view:     
+%% initiate input file series and refresh the current field view:
 update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview);
 %% enable field and veltype menus, in accordance with the current action
@@ -909 +909 @@
     MinIndex_j=1; % index j set to 1 by default
     MaxIndex_j=1;
-    MinIndex_i=find(i1_series(1,2,:), 1 )-1; % min ref index i detected in the series (corresponding to the first non-zero value of i1_series, except for zero index) 
-    MaxIndex_i=find(i1_series(1,2,:),1,'last' )-1; % max ref index i detected in the series (corresponding to the last non-zero value of i1_series) 
+    MinIndex_i=find(i1_series(1,2,:), 1 )-1; % min ref index i detected in the series (corresponding to the first non-zero value of i1_series, except for zero index)
+    MaxIndex_i=find(i1_series(1,2,:),1,'last' )-1; % max ref index i detected in the series (corresponding to the last non-zero value of i1_series)
 else
     ref_i=squeeze(max(i1_series(1,:,:),[],2)); % select ref_j index for each ref_i
@@ -1072 +1072 @@
     end
     TimeName='video';
-end 
+end
 
 
@@ -1183 +1183 @@
 %------------------------------------------------------------------------
 function [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series)
-%------------------------------------------------------------------------    
+%------------------------------------------------------------------------
 ModeMenu={''};
 if isempty(j2_series)% no j pair
@@ -1389 +1389 @@
 % --- Executes when selected cell(s) is changed in PairString.
 function PairString_CellSelectionCallback(hObject, eventdata, handles)
-%------------------------------------------------------------------------    
+%------------------------------------------------------------------------
 if numel(eventdata.Indices)>=1
     PairString=get(hObject,'Data');
@@ -1454 +1454 @@
 % RunMode='cluster': calculations dispatched in a cluster, using a managing system, 'oar, 'sge, or 'sgb'.
 % In the latter case, the calculation is split in 'packets' of i index (all j indices are contained in a single packet).
-% This splitting is possible only if the different calculations in the series are independent. Otherwise the action 
+% This splitting is possible only if the different calculations in the series are independent. Otherwise the action
 % function imposes a number of processes NbSlice in input, for instance NbSlice=1 for a time series.
 % If NbSlice is not imposed, the splitting in packets (jobs) is determined
@@ -1460 +1460 @@
 % than MaxJobNumber (these parameters are defined in the file series.xml in
 % accordance with the management strategy for the cluster). The jobs are
-% dispatched in parallel into NbCore processors by the cluster managing system. 
+% dispatched in parallel into NbCore processors by the cluster managing system.
 
 function errormsg=launch_action(handles)
@@ -1517 +1517 @@
 end
 
-%% Get  parameters from series.xml 
+%% Get  parameters from series.xml
 errormsg=''; % default error message
 ActionFullName=fullfile(get(handles.ActionPath,'String'),ActionName);
@@ -1542 +1542 @@
     set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
     set(handles.ActionExt,'BackgroundColor',[1 1 0])
-    [mcrmajor, mcrminor] = mcrversion;   
+    [mcrmajor, mcrminor] = mcrversion;
     MCRROOT = ['MCRROOT',int2str(mcrmajor),int2str(mcrminor)];
     RunTime = getenv('MCRROOT'); % Just variable MCRROOT with no version in it's name
@@ -1564 +1564 @@
             errormsg='Action launch interrupted';
             return
-        end       
+        end
     else
         sh_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']));
@@ -1588 +1588 @@
 end
 
-%% set nbre of cluster cores and processes: 
-% NbCore is the number of computer processors used 
-% NbProcess is the number of independent processes in which the required calculation is split. 
+%% set nbre of cluster cores and processes:
+% NbCore is the number of computer processors used
+% NbProcess is the number of independent processes in which the required calculation is split.
 % switch RunMode
 %     case {'local','background'}
@@ -1705 +1705 @@
         OutputSubDir=unique(ListSubdir(:,iexp));
         Param.OutputSubDir=OutputSubDir{1};
-        if numel(OutputSubDir)>1% case 
+        if numel(OutputSubDir)>1% case
             for iout=2:numel(OutputSubDir)
                 Param.OutputSubDir=[Param.OutputSubDir '-' OutputSubDir{iout}];
-            end               
-        end       
+            end
+        end
     end
     [xx,ExpName]=fileparts(Param.InputTable{1,1});
     Param.IndexRange.first_i=str2num(get(handles.num_first_i,'String'));%reset the firrst_i and last_i for multiple experiments, modified by the splitting into NbProcess
     Param.IndexRange.last_i=str2num(get(handles.num_last_i,'String'));
-    
+
     %% create the output data directory if needed, after checking its existence
     OutputDir='';
@@ -1790 +1790 @@
             end
         end
-        
+
     elseif isfield(Param,'ActionInput')&&isfield(Param.ActionInput,'LogPath')% custom definition of the output dir
         OutputDir=Param.ActionInput.LogPath;
@@ -1806 +1806 @@
         Param.Experiment=ListExpOut{iexp};
         Param.Device=ListDeviceOut{iexp};
-        check_input_file_series(handles)      
+        check_input_file_series(handles)
     end
     DirXml=fullfile(OutputDir,'0_XML');
@@ -1821 +1821 @@
     end
     OutputNomType=nomtype2pair(Param.InputTable{1,4}); % nomenclature for output files
-    
+
     %% get the set of reference input field indices
     first_i=1; % first i index to process
@@ -1949 +1949 @@
         RunMode = 'python';
     end
-    
-    
+
+
     %% direct processing on the current Matlab session or creation of command files
     filexml=cell(1,NbProcess); % initialisation of the names of the files containing the processing parameters
@@ -1977 +1977 @@
             Param.InputTable{ilist,1}=regexprep(Param.InputTable{ilist,1},'\','/'); % correct path name for PCWIN system
         end
-        
+
         if isfield(Param,'OutputSubDir')
             t=struct2xml(Param);
@@ -1997 +1997 @@
                 case '.m'
                     h_fun(Param); % direct launching
-                    
+
                 case '.sh'
                     switch computer
@@ -2009 +2009 @@
         end
     end
-    
+
     if ~strcmp (RunMode,'local') && ~strcmp(RunMode,'python')
         %% processing on a different session of the same computer (background) or cluster, create executable files
@@ -2045 +2045 @@
             end
         end
-        
+
         %create the executable and log file names
         file_exe_global=fullfile_uvmat('','',Param.InputTable{1,3},ExeExt,OutputNomType,...
@@ -2053 +2053 @@
             first_i,last_i,first_j,last_j);
         filelog_global=fullfile(OutputDir,'0_LOG',filelog_global);
-        
+
         for iprocess=1:NbProcess
             batch_file_list{iprocess}=fullfile(OutputDir,'0_EXE',regexprep(extxml{iprocess},'.xml$',ExeExt)); % executable file names
@@ -2059 +2059 @@
         end
     end
-    
+
     %% launch the executable files for background or cluster processing
-    
+
     switch RunMode
-        
+
         case 'background'
             [fid,message]=fopen(file_exe_global,'w');
@@ -2115 +2115 @@
                     msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched in background for ' ExpName ': press STATUS to see results'])
             end
-            
+
         case 'cluster' % option 'oar-parexec' used
             %create subdirectory for oar commands
@@ -2174 +2174 @@
             else
                 errormsg=['error for writting the executable file:' errormsg];
-            end       
+            end
             CPUTimeProcess=CPUTime*BlockLength*nbfield_j; % estimated CPU time for one individual process (in minutes)
             LaunchCmdFcn=SeriesData.SeriesParam.ClusterParam.LaunchCmdFcn;
@@ -2194 +2194 @@
             end
             %     case 'cluster_pbs' % for LMFA Kepler machine:  trqnsferred to fct
-            
+
             %         %create subdirectory for pbs command and log files
             %         DirPBS=fullfile(OutputDir,'0_PBS'); % todo : common name OAR/PBS
@@ -2234 +2234 @@
             %         %system(pbs_command);
             %         msgbox_uvmat('CONFIRMATION',[ActionFullName ' command ready to be launched in cluster'])
-            
+
         case 'cluster_sge' % for PSMN % TODO: use the standard 'cluster' config with an external fct
             % Au PSMN, on ne cr??e pas 1 job avec plusieurs c??urs, mais N jobs de 1 c??urs
             % o?? N < 1000.
             %create subdirectory for pbs command and log files
-            
+
             DirSGE=fullfile(OutputDir,'0_SGE');
             if exist(DirSGE,'dir')% delete the content of the dir 0_LOG to allow new input
@@ -2256 +2256 @@
             disp(['Max number of jobs: ' num2str(NbCore)])
             disp(['Images per job: ' num2str(maxImgsPerJob)])
-            
+
             iprocess = 1;
             imgsInJob = [];
@@ -2294 +2294 @@
             msgbox_uvmat('CONFIRMATION',[num2str(currJobIndex-1) ' jobs launched on queue ' qstat_Queue '.'])
         case 'python'
-            ActionName='fluidimage.run_from_xml';% name of the function to launch
-             command = command_launch_python('','',ActionName,filexml{iprocess});
-            % ['LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "l = x.split('':''); l = [s for s in l if ''matlab'' not in s]; print('':''.join(l))") ' ...
-            %     'python -m fluidimage.run_from_xml ' filexml{iprocess}];
+            command = command_launch_python(filexml{iprocess});
             fprintf(['command:\n' command '\n\n'])
-            errorcheck=system(command, '-echo')
+            [status, result] = call_command_clean(command);
     end
     if exist(OutputDir,'dir')
@@ -2396 +2393 @@
     end
     [tild,ActionName,ActionExt]=fileparts(FileName);
-    
+
     % insert the choice in the menu ActionName
     ActionIndex=find(strcmp(ActionName,ActionList),1); % look for the selected function in the menu Action
@@ -2408 +2405 @@
          ActionPathList=[ActionPathList; PathName];
     end
-    
+
     % record the file extension and extend the path list if it is a new extension
     ActionExtList=get(handles.ActionExt,'String');
@@ -2423 +2420 @@
         ActionIndex=ActionIndex-nbremove;
     end
-    
+
     % record action menu, choice and path
     set(handles.ActionName,'Value',ActionIndex)
@@ -2429 +2426 @@
        set(handles.ActionName,'UserData',ActionPathList);
     set(handles.ActionExt,'Value',ActionExtIndex)
-        
+
     %record the user defined menu additions in personal file profil_perso
     dir_perso=prefdir;
@@ -2608 +2605 @@
                 msgbox_uvmat('WARNING','coordinate names do not exist in the second netcdf input file')
             end
-            
+
             set(handles.FieldName_1,'Visible','on')
             set(handles.FieldName_1,'Value',1)
@@ -2730 +2727 @@
 if isfield(ParamOut,'FieldTransform')
     if ~strcmp(ParamOut.FieldTransform,'off')
-    FieldTransformVisible='on';  
+    FieldTransformVisible='on';
     end
     if iscell(ParamOut.FieldTransform)
@@ -2769 +2766 @@
 end
 
-%% definition of the path for the output files 
+%% definition of the path for the output files
 InputTable=get(handles.InputTable,'Data');
 [OutputPath,Device,DeviceExt]=fileparts(InputTable{1,1});
@@ -2782 +2779 @@
 set(handles.OutputPath,'Visible','on')
 set(handles.OutputPathBrowse,'Visible','on')
-    
-%% definition of the subdirectory containing the output files 
+
+%% definition of the subdirectory containing the output files
 
 if  ~(isfield(SeriesData,'ActionName') && strcmp(ActionName,SeriesData.ActionName))
@@ -2812 +2809 @@
         SubDirOut=InputTable{1,2}; % use the first subdir name (+OutputDirExt) as output  subdirectory
     case 'two'
-        OutputDirVisible='on';   
+        OutputDirVisible='on';
         SubDir=InputTable(1:2,2); % set of subdirectories
         SubDirOut=SubDir{1};
@@ -2892 +2889 @@
     % check the existence of the first file in the series
     first_j=[];last_j=[];MinIndex_j=1;MaxIndex_j=1; % default setting for index j
-    if isfield(Param.IndexRange,'first_j') % if index j is used     
+    if isfield(Param.IndexRange,'first_j') % if index j is used
         first_j=Param.IndexRange.first_j;
         last_j=Param.IndexRange.last_j;
@@ -2902 +2899 @@
     [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
     LineIndex=iview(1);
-    if numel(iview)>1      
+    if numel(iview)>1
         answer=msgbox_uvmat('INPUT_TXT',['select the line of the input table:' num2str(iview)] ,num2str(iview(1)));
         LineIndex=str2num(answer);
@@ -2948 +2945 @@
             YName=GetFieldData.Coordinates.Coord_y;
             TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
-            % get the time info                     
+            % get the time info
             TimeTable=get(handles.TimeTable,'Data');
             switch TimeNameStr
@@ -2956 +2953 @@
                     TimeName=['att:' GetFieldData.Time.TimeName];
                     % update the time table
-                    TimeTable{LineIndex,2}=get_time(Param.IndexRange.MinIndex_i(LineIndex),MinIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Min time     
-                    TimeTable{LineIndex,3}=get_time(Param.IndexRange.first_i,first_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % first time              
-                    TimeTable{LineIndex,4}=get_time(Param.IndexRange.last_i,last_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % last time                     
+                    TimeTable{LineIndex,2}=get_time(Param.IndexRange.MinIndex_i(LineIndex),MinIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Min time
+                    TimeTable{LineIndex,3}=get_time(Param.IndexRange.first_i,first_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % first time
+                    TimeTable{LineIndex,4}=get_time(Param.IndexRange.last_i,last_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % last time
                     TimeTable{LineIndex,5}=get_time(Param.IndexRange.MaxIndex_i(LineIndex),MaxIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Max time
                 case 'variable'
@@ -3094 +3091 @@
         set(handles.FieldName_1,'String',[FieldList; {'add_field...'}]);
     end
-end   
+end
 
 
@@ -3122 +3119 @@
 
 %------------------------------------------------------------------------
-% --- determine the list of index pairstring of processing file 
+% --- determine the list of index pairstring of processing file
 function [num_i1,num_i2,num_j1,num_j2,num_i_out,num_j_out]=find_file_indices(num_i,num_j,ind_shift,NomType,mode)
 %------------------------------------------------------------------------
@@ -3152 +3149 @@
         num_j2_col=num_j+ind_shift(2);
         % adjust the first field number
-        indsel=find((num_j1_col >= 1));   
+        indsel=find((num_j1_col >= 1));
         num_j_out=num_j(indsel);
         num_j1_col=num_j1_col(indsel);
@@ -3158 +3155 @@
         [num_i1,num_j1]=meshgrid(num_i,num_j1_col);
         [num_i2,num_j2]=meshgrid(num_i,num_j2_col);
-    end    
+    end
 end
 
@@ -3248 +3245 @@
     end
 else
-    hset_object=findobj(allchild(0),'Tag','set_object'); 
+    hset_object=findobj(allchild(0),'Tag','set_object');
     if ~isempty(hset_object)
         set(get(hset_object,'Children'),'Enable','off')
-    end 
+    end
 end
 
@@ -3385 +3382 @@
 
 %% browse transform functions with the input menu option more...
-if isequal(TransformName,'more...')% browse transform functions     
+if isequal(TransformName,'more...')% browse transform functions
     FileName=uigetfile_uvmat('Pick a transform function',get(handles.TransformPath,'String'),'.m');
     if isempty(FileName)
@@ -3403 +3400 @@
         TransformPathList=[TransformPathList;{TransformPath}];
     else% the input function already exist, we update its path (possibly new)
-        TransformPathList{TransformIndex}=TransformPath; % 
+        TransformPathList{TransformIndex}=TransformPath; %
         set(handles.TransformName,'Value',TransformIndex)
     end
-   % save the new menu in the personal file 'uvmat_perso.mat' 
+   % save the new menu in the personal file 'uvmat_perso.mat'
    dir_perso=prefdir; % personal Matalb directory
    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
@@ -3413 +3410 @@
            TransformListUser{ilist-nb_builtin_transform}=TransformList{ilist};
            TransformPathListUser{ilist-nb_builtin_transform}=TransformPathList{ilist};
-       end 
+       end
        TransformPathListUser=TransformPathListUser';
        TransformListUser=TransformListUser';
        save (profil_perso,'TransformPathListUser','TransformListUser','-append'); % store the root name for future opening of uvmat
-   end 
+   end
 end
 
@@ -3507 +3504 @@
      set(handles.FieldName,'Value',1:numel(ListField))
      set(handles.FieldName,'Visible','on')
-end       
+end
 if isfield(Param,'ActionInput')%  introduce  parameters specific to an Action fct, for instance PIV parameters
 %     set(handles.ActionInput,'Visible','on')
@@ -3526 +3523 @@
     set(handles.EditObject,'Visible','on')
     set(handles.DeleteObject,'Visible','on')
-else     
+else
     set(handles.ProjObjectName,'String','')
     set(handles.ProjObjectName,'Visible','off')
     set(handles.ViewObject,'Visible','off')
     set(handles.EditObject,'Visible','off')
-    set(handles.DeleteObject,'Visible','off')     
-end     
+    set(handles.DeleteObject,'Visible','off')
+end
 set(handles.REFRESH,'BackgroundColor',[1 0 1]); % paint REFRESH button in magenta to indicate that it should be activated
 
@@ -3590 +3587 @@
     Param=read_GUI(handles.series);
     RootPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device);
-    if ~isfield(Param,'OutputSubDir')   
+    if ~isfield(Param,'OutputSubDir')
         msgbox_uvmat('ERROR','no standard sub-directory definition for output files, use a browser to check the output')
         set(handles.status,'BackgroundColor',[0 1 0])
@@ -3614 +3611 @@
 
 
-%------------------------------------------------------------------------   
+%------------------------------------------------------------------------
 % launched by selecting a file on the list
 %------------------------------------------------------------------------
@@ -3641 +3638 @@
     set(hObject,'UserData',FullSelectName)
     hfig=get(hObject,'parent');
-    htitlebox=findobj(hfig,'tag','titlebox');    
+    htitlebox=findobj(hfig,'tag','titlebox');
     set(htitlebox,'String',FullSelectName)
 elseif exist(FullSelectName,'file')%visualise the vel field if it exists
-    FileInfo=get_file_info(FullSelectName);    
+    FileInfo=get_file_info(FullSelectName);
     if strcmp(FileInfo.FileType,'txt')
         edit(FullSelectName)
@@ -3656 +3653 @@
 
 
-%------------------------------------------------------------------------   
+%------------------------------------------------------------------------
 % launched by refreshing the status figure
 %------------------------------------------------------------------------
@@ -3711 +3708 @@
 %% update the waitbar
 hwaitbar=findobj(hfig,'tag','waitbar');
-if ~isempty(NbOutputFile) 
+if ~isempty(NbOutputFile)
     BarPosition=get(hwaitbar,'Position');
     BarPosition(3)=0.9*numel(datnum)/NbOutputFile;
@@ -3717 +3714 @@
 end
 
-%------------------------------------------------------------------------ 
+%------------------------------------------------------------------------
 % --- Executes on selection change in ActionExt.
-%------------------------------------------------------------------------ 
+%------------------------------------------------------------------------
 function ActionExt_Callback(hObject, eventdata, handles)
 
@@ -3733 +3730 @@
 
 %------------------------------------------------------------------------
-% --- set the visibility of relevant velocity type menus: 
+% --- set the visibility of relevant velocity type menus:
 function menu=set_veltype_display(Civ,FileType)
 %------------------------------------------------------------------------
@@ -3792 +3789 @@
 Bottom=ScreenSize(4)-Height-40; % put fig at top right
 hfig=findobj(allchild(0),'Tag','set_slice');
-if ~isempty(hfig),delete(hfig), end; % delete existing version of the GUI 
+if ~isempty(hfig),delete(hfig), end; % delete existing version of the GUI
 hfig=figure('name','set_pairs','tag','set_pairs','MenuBar','none','NumberTitle','off','Unit','points','Position',[Left,Bottom,Width,Height]);
 BackgroundColor=get(hfig,'Color');
@@ -3825 +3822 @@
 viewcell=viewcell';
 ModeMenu={'bursts';'series(Dj)'};
-ModeValue=1;                                               
-                   %i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo                              
+ModeValue=1;
+                   %i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo
 % first raw of the GUI
 uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.88 0.5 0.1],'BackgroundColor',BackgroundColor,...
@@ -3865 +3862 @@
 Mode_Callback(hObject,eventdata)
 
-%------------------------------------------------------------------------    
+%------------------------------------------------------------------------
 function Mode_Callback(hObject,eventdata)
 %% get input info