Context Navigation

← Previous Changeset
Next Changeset →

Changeset 992

Timestamp:

Feb 2, 2017, 10:37:19 PM (8 years ago)

Author:

g7moreau

Message:

replace ;% by ; %

Location:

trunk/src

Files:

: 2 edited

compile.m (modified) (3 diffs)
series.m (modified) (146 diffs)

Legend:

: Unmodified
: Added
: Removed

trunk/src/compile.m

-                      r977
+                      r992
 function compile (FctName,SubfctPath)
 hh=[];% handles of message display window
+hh=[]; % handles of message display window
 if isempty(which('mcc'))
     msgbox_uvmat('ERROR','no Matlab compiler toolbox mcc installed')
 …
 end
 if ~isempty(SubfctPath)
     SubfctPath=['-I ' SubfctPath];%string indicating the option of including the path SubfctPath
+    SubfctPath=['-I ' SubfctPath]; % string indicating the option of including the path SubfctPath
 end
 [mcrmajor, mcrminor] = mcrversion;
 …
 FctNameVersion=[FctName,'_',MCRROOT];
 %hver=ver('MATLAB');
 %FctNameVersion=[FctName '_MCRROOT' regexprep(hver.Version,'\.','')];%suppress the dot in version number
+%FctNameVersion=[FctName '_MCRROOT' regexprep(hver.Version,'\.','')]; % suppress the dot in version number
 try
     disp(['mcc -m -R -nojvm -R -nodisplay -R -singleCompThread ' SubfctPath ' ' FctName '.m'])
     eval(['mcc -m -R -nojvm -R -nodisplay -R -singleCompThread ' SubfctPath ' ' FctName '.m'])% compile the source file [FctName .m], which produces a binary file FctName and a cmd file [run_' FctName '.sh]
     system(['mv -f ' FctName ' bin/']);%move the binary file FctName to the subdir /bin
     system(['sed -e ''''s#/' FctName '#/bin/' FctName '#'''' run_' FctName '.sh > ' FctNameVersion '.sh']);%modify the cmd file and copy it to [FctName '.sh']
     system(['rm run_' FctName '.sh']);% remove the initial cmd file [run_' FctName '.sh]
+    system(['mv -f ' FctName ' bin/']); % move the binary file FctName to the subdir /bin
+    system(['sed -e ''''s#/' FctName '#/bin/' FctName '#'''' run_' FctName '.sh > ' FctNameVersion '.sh']); % modify the cmd file and copy it to [FctName '.sh']
+    system(['rm run_' FctName '.sh']); % remove the initial cmd file [run_' FctName '.sh]
     system(['chmod +x ' FctNameVersion '.sh']); % set the cmd file to 'executable'
 catch ME

trunk/src/series.m

-                      r991
+                      r992
 % position and  size of the GUI at opening
 set(0,'Unit','points')
 ScreenSize=get(0,'ScreenSize');%size of the current screen, in points (1/72 inch)
 Width=900;% prefered width of the GUI in points (1/72 inch)
 Height=624;% prefered height of the GUI in points (1/72 inch)
+ScreenSize=get(0,'ScreenSize'); % size of the current screen, in points (1/72 inch)
+Width=900; % prefered width of the GUI in points (1/72 inch)
+Height=624; % prefered height of the GUI in points (1/72 inch)
 %adjust to screen size (reduced by a min margin)
 RescaleFactor=min((ScreenSize(3)-80)/Width,(ScreenSize(4)-80)/Height);
 …
 Width=Width*RescaleFactor;
 Height=Height*RescaleFactor;
 LeftX=80*RescaleFactor;%position of the left fig side, in pixels (put to the left side, with some margin)
+LeftX=80*RescaleFactor; % position of the left fig side, in pixels (put to the left side, with some margin)
 LowY=round(ScreenSize(4)/2-Height/2); % put at the middle height on the screen
 set(hObject,'Units','points')
 …
 % check default input data
 if ~exist('Param','var')
     Param=[]; %default
+    Param=[]; % default
 end
 %% list of builtin functions in the mebu ActionName
 ActionList={'check_data_files';'aver_stat';'time_series';'civ_series';'merge_proj'};% WARNING: fits with nb_builtin_ACTION=4 in ActionName_callback
+ActionList={'check_data_files';'aver_stat';'time_series';'civ_series';'merge_proj'}; % WARNING: fits with nb_builtin_ACTION=4 in ActionName_callback
 NbBuiltinAction=numel(ActionList);
 set(handles.Action,'UserData',NbBuiltinAction)
 [path_series,name,ext]=fileparts(which('series'));% path to the GUI series
 path_series_fct=fullfile(path_series,'series');%path of the functions in subdirectroy 'series'
+[path_series,name,ext]=fileparts(which('series')); % path to the GUI series
+path_series_fct=fullfile(path_series,'series'); % path of the functions in subdirectroy 'series'
 [code, message] = system...
     ('LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "p.split('':'') |... [s for s in p if ''matlab'' not in s] | '':''.join(p)") python -c "import fluidimage"');
 if code==0
     ActionExtList={'.m';'.sh';'.py (in dev.)'};% default choice of extensions (Matlab fct .m or compiled version .sh
+    ActionExtList={'.m';'.sh';'.py (in dev.)'}; % default choice of extensions (Matlab fct .m or compiled version .sh
 else
     ActionExtList={'.m';'.sh'};  % python options not installed
 end
 ActionPathList=cell(NbBuiltinAction,1);%initiate the cell matrix of Action fct paths
 ActionPathList(:)={path_series_fct}; %set the default path to series fcts to all list members
 RunModeList={'local';'background'};% default choice of extensions (Matlab fct .m or compiled version .sh)
 [s,w]=system('oarstat');% look for cluster system 'oar'
+ActionPathList=cell(NbBuiltinAction,1); % initiate the cell matrix of Action fct paths
+ActionPathList(:)={path_series_fct}; % set the default path to series fcts to all list members
+RunModeList={'local';'background'}; % default choice of extensions (Matlab fct .m or compiled version .sh)
+[s,w]=system('oarstat'); % look for cluster system 'oar'
 if isequal(s,0)
     RunModeList=[RunModeList;{'cluster_oar'}];
 …
     set(handles.CPUTime_txt,'Visible','on'); % make visible button for access to Monika
 end
 [s,w]=system('qstat -help');% look for cluster system 'sge'
+[s,w]=system('qstat -help'); % look for cluster system 'sge'
 if isequal(s,0)
     if regexp(w,'^pbs')
 …
 %% list of builtin transform functions in the menu TransformName
 TransformList={'';'sub_field';'phys';'phys_polar'};% WARNING: must fit with the corresponding menu in uvmat and nb_builtin_transform=4 in  TransformName_callback
+TransformList={'';'sub_field';'phys';'phys_polar'}; % WARNING: must fit with the corresponding menu in uvmat and nb_builtin_transform=4 in  TransformName_callback
 NbBuiltinTransform=numel(TransformList);
 path_transform_fct=fullfile(path_series,'transform_field');
 TransformPathList=cell(NbBuiltinTransform,1);%initiate the cell matrix of Action fct paths
 TransformPathList(:)={path_transform_fct}; %set the default path to series fcts to all list members
+TransformPathList=cell(NbBuiltinTransform,1); % initiate the cell matrix of Action fct paths
+TransformPathList(:)={path_transform_fct}; % set the default path to series fcts to all list members
 %% get the user defined functions stored in the personal file uvmat_perso.mat
 …
 %% selection of the input Action fct
 ActionCheckExist=true(size(ActionList));%initiate the check of the path to the listed action fct
+ActionCheckExist=true(size(ActionList)); % initiate the check of the path to the listed action fct
 for ilist=NbBuiltinAction+1:numel(ActionList)%check  the validity of the path of the user defined Action fct
     ActionCheckExist(ilist)=exist(fullfile(ActionPathList{ilist},[ActionList{ilist} '.m']),'file');
 end
 ActionPathList=ActionPathList(ActionCheckExist,:);% suppress the menu options which are not valid anymore
+ActionPathList=ActionPathList(ActionCheckExist,:); % suppress the menu options which are not valid anymore
 ActionList=ActionList(ActionCheckExist);
 set(handles.ActionName,'String',[ActionList;{'more...'}])
 …
 %% fields input initialisation
 if isfield(Param,'list_fields')&& isfield(Param,'index_fields') &&~isempty(Param.list_fields) &&~isempty(Param.index_fields)
     set(handles.FieldName,'String',Param.list_fields);% list menu fields
     set(handles.FieldName,'Value',Param.index_fields);% selected string index
+    set(handles.FieldName,'String',Param.list_fields); % list menu fields
+    set(handles.FieldName,'Value',Param.index_fields); % selected string index
 end
 if isfield(Param,'Coordinates')
 …
 end
 % if isfield(Param,'Coord_x_str') && ischar(Param.Coord_x_str)
 %         set(handles.Coord_x,'String',Param.Coord_x_str);% list menu fields
+%         set(handles.Coord_x,'String',Param.Coord_x_str); % list menu fields
 % end
 % if isfield(Param,'Coord_y_str')&& ischar(Param.Coord_y_str)
 %         set(handles.Coord_y,'String',Param.Coord_y_str);% list menu fields
+%         set(handles.Coord_y,'String',Param.Coord_y_str); % list menu fields
 % end
 …
     %% fill the list of file series
     InputTable=[{Param.InputFile.RootPath},{Param.InputFile.SubDir},{Param.InputFile.RootFile},{Param.InputFile.NomType},{Param.InputFile.FileExt}];
     if isempty(find(cellfun('isempty',InputTable)==0));% if there is no input file, do not introduce input info
+    if isempty(find(cellfun('isempty',InputTable)==0)); % if there is no input file, do not introduce input info
         set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
         return
 …
         i2=i1;
     end
     ref_i=floor((i1+i2)/2);% reference image number corresponding to the file
+    ref_i=floor((i1+i2)/2); % reference image number corresponding to the file
     % set(handles.num_ref_i,'String',num2str(ref_i));
     if isempty(j1)
 …
         j2=j1;
     end
     ref_j=floor((j1+j2)/2);% reference image number corresponding to the file
+    ref_j=floor((j1+j2)/2); % reference image number corresponding to the file
     SeriesData.ref_i=ref_i;
     SeriesData.ref_j=ref_j;
 …
         {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
     str_find=strcmp(get(hObject,'Label'),MenuFile);
     MenuFile(str_find)=[];% suppress the input file to the list
+    MenuFile(str_find)=[]; % suppress the input file to the list
     for ifile=1:numel(MenuFile)
         set(handles.(['MenuFile_' num2str(ifile)]),'Label',MenuFile{ifile});
 …
 end
 OutPut=browse_data(oldfile,'on','on');% open the GUI browse_data to get select a campaign dir, experiment and device
+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;
 …
 % --------------------------------------------------------------------
 OutPut=browse_data(get(hObject,'Label'),'on','on');% open the GUI browse_data to get select a campaign dir, experiment and device
+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')
     return
 …
 set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
 set(handles.OutputSubDir,'BackgroundColor',[1 0 1])% set edit box OutputSubDir to magenta color to indicate that refresh may be needed
 xx=double(get(handles.series,'CurrentCharacter')); %get the keyboard character
+xx=double(get(handles.series,'CurrentCharacter')); % get the keyboard character
 if ~isempty(xx)
     switch xx
 …
             iline=str2double(get(handles.InputLine,'String'));
             if isequal(iline,size(InputTable,1))% arrow downward
                 InputTable=[InputTable;InputTable(iline,:)];% create a new line as a copy of the last one
+                InputTable=[InputTable;InputTable(iline,:)]; % create a new line as a copy of the last one
                 set(handles.InputTable,'Data',InputTable);
             end
 …
 end
 if ~isempty(find(empty_line));
     InputTable(empty_line,:)=[];%remove empty lines
+    InputTable(empty_line,:)=[]; % remove empty lines
     set(handles.InputTable,'Data',InputTable)
     ListTable={'MinIndex_i','MaxIndex_i','MinIndex_j','MaxIndex_j','PairString','TimeTable'};
     for ilist=1:numel(ListTable)
         Table=get(handles.(ListTable{ilist}),'Data');
         Table(empty_line,:)=[];%remove empty lines
+        Table(empty_line,:)=[]; % remove empty lines
         set(handles.(ListTable{ilist}),'Data',Table);
     end
 …
 %% update MinIndex_i and MaxIndex_i if the input table content has been reduced in line nbre
 MinIndex_i_table=get(handles.MinIndex_i,'Data');%retrieve the min indices in the table MinIndex
+MinIndex_i_table=get(handles.MinIndex_i,'Data'); % retrieve the min indices in the table MinIndex
 set(handles.MinIndex_i,'Data',MinIndex_i_table(1:nbview,:));
 MinIndex_j_table=get(handles.MinIndex_j,'Data');%retrieve the min indices in the table MinIndex
+MinIndex_j_table=get(handles.MinIndex_j,'Data'); % retrieve the min indices in the table MinIndex
 set(handles.MinIndex_j,'Data',MinIndex_j_table(1:nbview,:));
 MaxIndex_i_table=get(handles.MaxIndex_i,'Data');%retrieve the min indices in the table MinIndex
+MaxIndex_i_table=get(handles.MaxIndex_i,'Data'); % retrieve the min indices in the table MinIndex
 set(handles.MaxIndex_i,'Data',MaxIndex_i_table(1:nbview,:));
 MaxIndex_j_table=get(handles.MaxIndex_j,'Data');%retrieve the min indices in the table MinIndex
+MaxIndex_j_table=get(handles.MaxIndex_j,'Data'); % retrieve the min indices in the table MinIndex
 set(handles.MaxIndex_j,'Data',MaxIndex_j_table(1:nbview,:));
 PairString=get(handles.PairString,'Data');%retrieve the min indices in the table MinIndex
+PairString=get(handles.PairString,'Data'); % retrieve the min indices in the table MinIndex
 set(handles.PairString,'Data',PairString(1:nbview,:));
 TimeTable=get(handles.TimeTable,'Data');%retrieve the min indices in the table MinIndex
+TimeTable=get(handles.TimeTable,'Data'); % retrieve the min indices in the table MinIndex
 set(handles.TimeTable,'Data',TimeTable(1:nbview,:));
 …
 set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
 drawnow
 errormsg='';%default
+errormsg=''; % default
 if ischar(Param)
     fileinput=Param;
 …
 SeriesData=get(handles.series,'UserData');
 if strcmp(iview,'append') % display the input data as a new line in the table
     iview=size(InputTable,1)+1;% the next line in InputTable becomes the current line
+    iview=size(InputTable,1)+1; % the next line in InputTable becomes the current line
 %     InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
 elseif strcmp(iview,'one') % refresh the list of  input  file series
     iview=1; %the first line in InputTable becomes the current line
+    iview=1; % the first line in InputTable becomes the current line
     InputTable={'','','','',''};
 %     InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
 …
     set(handles.MaxIndex_j,'Data',[])
     set(handles.PairString,'Data',{''})
     SeriesData.CheckPair=0;%reset the list of input lines with pairs
+    SeriesData.CheckPair=0; % reset the list of input lines with pairs
     SeriesData.i1_series={};
     SeriesData.i2_series={};
 …
     i2=i1;
 end
 ref_i=floor((i1+i2)/2);% reference image number corresponding to the file
+ref_i=floor((i1+i2)/2); % reference image number corresponding to the file
 % set(handles.num_ref_i,'String',num2str(ref_i));
 if isempty(j1)
 …
     j2=j1;
 end
 ref_j=floor((j1+j2)/2);% reference image number corresponding to the file
+ref_j=floor((j1+j2)/2); % reference image number corresponding to the file
 SeriesData.ref_i=ref_i;
 SeriesData.ref_j=ref_j;
 …
 str_find=strcmp(fileinput,MenuFile);
 if isempty(find(str_find,1))
     MenuFile=[{fileinput};MenuFile];%insert the current file if not already in the list
+    MenuFile=[{fileinput};MenuFile]; % insert the current file if not already in the list
 end
 for ifile=1:min(length(MenuFile),5)
 …
 profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
 if exist(profil_perso,'file')
     save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
+    save (profil_perso,'MenuFile','-append'); % store the file names for future opening of uvmat
 else
     save (profil_perso,'MenuFile','-V6'); %store the file names for future opening of uvmat
+    save (profil_perso,'MenuFile','-V6'); % store the file names for future opening of uvmat
 end
 % save the opened file to initiate future opening
 SeriesData.RefFile{iview}=fileinput;% reference opening file for line iview
+SeriesData.RefFile{iview}=fileinput; % reference opening file for line iview
 SeriesData.Ref_i1=i1;
 SeriesData.Ref_i2=i2;
 …
 %% display the min and max indices for the whole file series
 if size(i1_series,2)==2 && min(min(i1_series(:,1,:)))==0
     MinIndex_j=1;% index j set to 1 by default
+    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
     ref_j=squeeze(max(j1_series(1,:,:),[],3));% select ref_i index for each ref_j
+    ref_i=squeeze(max(i1_series(1,:,:),[],2)); % select ref_j index for each ref_i
+    ref_j=squeeze(max(j1_series(1,:,:),[],3)); % select ref_i index for each ref_j
      MinIndex_i=min(find(ref_i))-1;
      MaxIndex_i=max(find(ref_i))-1;
 …
     MinIndex_j=0;
 end
 MinIndex_i_table=get(handles.MinIndex_i,'Data');%retrieve the min indices in the table MinIndex
 MinIndex_j_table=get(handles.MinIndex_j,'Data');%retrieve the min indices in the table MinIndex
 MaxIndex_i_table=get(handles.MaxIndex_i,'Data');%retrieve the min indices in the table MinIndex
 MaxIndex_j_table=get(handles.MaxIndex_j,'Data');%retrieve the min indices in the table MinIndex
+MinIndex_i_table=get(handles.MinIndex_i,'Data'); % retrieve the min indices in the table MinIndex
+MinIndex_j_table=get(handles.MinIndex_j,'Data'); % retrieve the min indices in the table MinIndex
+MaxIndex_i_table=get(handles.MaxIndex_i,'Data'); % retrieve the min indices in the table MinIndex
+MaxIndex_j_table=get(handles.MaxIndex_j,'Data'); % retrieve the min indices in the table MinIndex
 if ~isempty(MinIndex_i)&&~isempty(MaxIndex_i)
     MinIndex_i_table(iview,1)=MinIndex_i;
 …
 %% adjust the first and last indices for the selected series, only if requested by the bounds
 % i index, compare input to min index i
 first_i=str2num(get(handles.num_first_i,'String'));%retrieve previous first i
 % ref_i=str2num(get(handles.num_ref_i,'String'));%index i given by the input field
+first_i=str2num(get(handles.num_first_i,'String')); % retrieve previous first i
+% ref_i=str2num(get(handles.num_ref_i,'String')); % index i given by the input field
 ref_i=1;
 if isfield(SeriesData,'ref_i')
 …
 end
 if isempty(first_i)
     first_i=ref_i;% first_i updated by the input value
+    first_i=ref_i; % first_i updated by the input value
 elseif first_i < MinIndex_i
     first_i=MinIndex_i; % first_i set to the min i index (restricted by oter input lines)
 elseif first_i >MaxIndex_i
     first_i=MaxIndex_i;% first_i set to the max i index (restricted by oter input lines)
+    first_i=MaxIndex_i; % first_i set to the max i index (restricted by oter input lines)
 end
 % j index,  compare input to min index j
 …
 end
 if isempty(first_j)
     first_j=ref_j;% first_j updated by the input value
+    first_j=ref_j; % first_j updated by the input value
 elseif first_j<MinIndex_j
     first_j=MinIndex_j; % first_j set to the min j index (restricted by oter input lines)
 …
 %% number of slices set by default
 NbSlice=[];%default
+NbSlice=[]; % default
 % read  value set by the first series for the append mode (iwiew >1)
 if iview>1 && strcmp(get(handles.num_NbSlice,'Visible'),'on')
 …
 end
 TimeName='';
 Time=[];%default
+Time=[]; % default
 TimeMin=[];
 TimeFirst=[];
 …
         TimeName='xml';
 %                         if XmlData.Time(1,:)==XmlData.Time(2,:)% case starting with index 1
 %                     sizDti=size(XmlData.Time,1)-1;%size of the time vector explicitly defined in the xml file
+%                     sizDti=size(XmlData.Time,1)-1; % size of the time vector explicitly defined in the xml file
 %                     ind_start=1;
 %                 else
 %                     sizDti=size(XmlData.Time,1);% case starting with index 0
+%                     sizDti=size(XmlData.Time,1); % case starting with index 0
 %                     ind_start=0;
 %                 end
 %         % complement the input if the whole time series is not defined
 %             if size(i1_series,3)>size(XmlData.Time,1)-ind_start %only the first time interval is defined, extrapolate to the whole series
 %                 Dti_total=XmlData.Time(end)-XmlData.Time(1);%total time interval covered by the time vector
 %                 missing_indices=sizDti+1+ind_start:size(i1_series,3)+1;% remaining set of frame indices for which time needs to be found
 %                 repeat_nbre=1+floor((missing_indices-sizDti-ind_start)/(sizDti-1));% number of repetitions of Dti
+%                 Dti_total=XmlData.Time(end)-XmlData.Time(1); % total time interval covered by the time vector
+%                 missing_indices=sizDti+1+ind_start:size(i1_series,3)+1; % remaining set of frame indices for which time needs to be found
+%                 repeat_nbre=1+floor((missing_indices-sizDti-ind_start)/(sizDti-1)); % number of repetitions of Dti
 %                 time_indices=1+mod(missing_indices-sizDti-1,sizDti-1);
 %                 for j=1:size(XmlData.Time,2)
 …
         %                 msgbox_uvmat('WARNING','inconsistent number of slices with the first field series');
         %             end
         %             NbSlice=XmlData.Camera.NbSlice;% Nbre of slices from camera
+        %             NbSlice=XmlData.Camera.NbSlice; % Nbre of slices from camera
         %         end
         if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
 …
 if ~isempty(VideoObject)% case of movies
     imainfo=get(VideoObject);
     if isempty(j1_series); %frame index along i
+    if isempty(j1_series); % frame index along i
         Time=zeros(imainfo.NumberOfFrames+1,2);
         Time(:,2)=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)';
 …
     PairString{iview,1}=Menu{1};
 else
     PairString{iview,1}='';%no pair for #iview
+    PairString{iview,1}=''; % no pair for #iview
 end
 set(handles.PairString,'Data',PairString)
 …
 nbview=numel(SeriesData.i1_series);
 j_max=cell(1,nbview);
 MaxIndex_i=ones(1,nbview);%default
 MinIndex_i=ones(1,nbview);%default
+MaxIndex_i=ones(1,nbview); % default
+MinIndex_i=ones(1,nbview); % default
 for iline=1:nbview
     pair_max=squeeze(max(SeriesData.i1_series{iline},[],1)); %max on pair index
     j_max{iline}=max(pair_max,[],1);%max on j index
+    pair_max=squeeze(max(SeriesData.i1_series{iline},[],1)); % max on pair index
+    j_max{iline}=max(pair_max,[],1); % max on j index
     if ~isempty(j_max{iline})
     MaxIndex_i(iline)=max(find(j_max{iline}))-1;% max ref index i
     MinIndex_i(iline)=min(find(j_max{iline}))-1;% min ref index i
+    MaxIndex_i(iline)=max(find(j_max{iline}))-1; % max ref index i
+    MinIndex_i(iline)=min(find(j_max{iline}))-1; % min ref index i
     end
 end
 …
 npx=floor(Position(3));
 file_indices=MinIndex_i+floor(((0.5:npx-0.5)/npx)*range_index)+1;
 CData=zeros(nbview*range_y,npx);% initiate the image representing the existing files
+CData=zeros(nbview*range_y,npx); % initiate the image representing the existing files
 for iline=1:nbview
     ind_y=1+(iline-1)*range_y:iline*range_y;
 …
     CData(ind_y,:)=ones(size(ind_y'))*LineData;
 end
 CData=cat(3,zeros(size(CData)),CData,zeros(size(CData)));%make color images r=0,g,b=0
+CData=cat(3,zeros(size(CData)),CData,zeros(size(CData))); % make color images r=0,g,b=0
 set(handles.FileStatus,'CData',CData);
 …
     end
 else %existence of j pairs
     pair_max=squeeze(max(i1_series,[],1)); %max on pair index
+    pair_max=squeeze(max(i1_series,[],1)); % max on pair index
     j_max=max(pair_max,[],1);
     MaxIndex_i=find(j_max, 1, 'last' )-1;% max ref index i
     MinIndex_i=find(j_max, 1 )-1;% min ref index i
+    MaxIndex_i=find(j_max, 1, 'last' )-1; % max ref index i
+    MinIndex_i=find(j_max, 1 )-1; % min ref index i
     i_max=max(pair_max,[],2);
     MaxIndex_j=find(i_max, 1, 'last' )-1;% max ref index i
     MinIndex_j=find(i_max, 1 )-1;% min ref index i
+    MaxIndex_j=find(i_max, 1, 'last' )-1; % max ref index i
+    MinIndex_j=find(i_max, 1 )-1; % min ref index i
     if MaxIndex_j==MinIndex_j
         ModeValue=1;
 …
         ModeMenu={'bursts';'series(Dj)'};
         if (MaxIndex_j-MinIndex_j)>10
             ModeValue=2;%set mode to series(Dj) if more than 10 j values
+            ModeValue=2; % set mode to series(Dj) if more than 10 j values
         else
             ModeValue=1;
 …
                 if ~isempty(time)
                     if ref_i<=floor(ipair/2)
                         ref_i=floor(ipair/2)+1;% shift ref_i to get the first pair
+                        ref_i=floor(ipair/2)+1; % shift ref_i to get the first pair
                     end
                     Dt=time(ref_i+ceil(ipair/2),ref_j)-time(ref_i-floor(ipair/2),ref_j);
 …
                 if ~isempty(time)
                     if ref_j<=floor(ipair/2)
                         ref_j=floor(ipair/2)+1;% shift ref_i to get the first pair
+                        ref_j=floor(ipair/2)+1; % shift ref_i to get the first pair
                     end
                     Dt=time(ref_i,ref_j+ceil(ipair/2))-time(ref_i,ref_j-floor(ipair/2));
 …
 function displ_time(handles)
 %------------------------------------------------------------------------
 SeriesData=get(handles.series,'UserData');%
+SeriesData=get(handles.series,'UserData'); %
 if ~isfield(SeriesData,'Time')
     return
 end
 PairString=get(handles.PairString,'Data');
 ref_i_1=str2num(get(handles.num_first_i,'String'));%first reference index
 ref_i_2=str2num(get(handles.num_last_i,'String'));%last reference index
+ref_i_1=str2num(get(handles.num_first_i,'String')); % first reference index
+ref_i_2=str2num(get(handles.num_last_i,'String')); % last reference index
 ref_j_1=[];ref_j_2=[];
 if strcmp(get(handles.num_first_j,'Visible'),'on')
 …
             time_last=(SeriesData.Time{iview}(i1_2+1,j1_2+1)+SeriesData.Time{iview}(i2_2+1,j2_1+1))/2;
         end
         TimeTable{iview,3}=time_first; %TODO: take into account pairs
         TimeTable{iview,4}=time_last; %TODO: take into account pairs
+        TimeTable{iview,3}=time_first; % TODO: take into account pairs
+        TimeTable{iview,4}=time_last; % TODO: take into account pairs
     end
 end
 …
 if isempty(pos_first), pos_first=0; end
 if isempty(pos_last), pos_last=1; end
 Position=get(handles.Waitbar,'Position');% position of the waitbar:= [ x,y, width, height]
+Position=get(handles.Waitbar,'Position'); % position of the waitbar:= [ x,y, width, height]
 Position_status=get(handles.FileStatus,'Position');
 Position(1)=Position_status(1)+Position_status(3)*pos_first;
 Position(3)=max(Position_status(3)*(pos_last-pos_first),0.001);% width must remain positive
+Position(3)=max(Position_status(3)*(pos_last-pos_first),0.001); % width must remain positive
 set(handles.Waitbar,'Position',Position)
 update_waitbar(handles.Waitbar,0)
 …
 %% settings of the button RUN
 set(handles.RUN,'BusyAction','queue');% activation of STOP button will set BusyAction to 'cancel'
+set(handles.RUN,'BusyAction','queue'); % activation of STOP button will set BusyAction to 'cancel'
 set(handles.RUN, 'Enable','Off')% avoid further RUN action until the current one is finished
 set(handles.RUN,'BackgroundColor',[1 1 0])%show activation of RUN by yellow color
 …
 %------------------------------------------------------------------------
 function errormsg=launch_action(handles)
 errormsg='';%default
+errormsg=''; % default
 %% read the data on the GUI series
 Param=read_GUI_series(handles);%displayed parameters
 SeriesData=get(handles.series,'UserData');%hidden parameters
+Param=read_GUI_series(handles); % displayed parameters
+SeriesData=get(handles.series,'UserData'); % hidden parameters
 if isfield(SeriesData,'TransformInput')
     Param.TransformInput=SeriesData.TransformInput;
 …
 %% select the Action mode, 'local', 'background' or 'cluster' (if available)
 RunMode='local';%default (needed for first opening of the GUI series)
+RunMode='local'; % default (needed for first opening of the GUI series)
 if isfield(Param.Action,'RunMode')
     RunMode=Param.Action.RunMode;
     Param.Action=rmfield(Param.Action,'RunMode');%remove from the recorded xml file to avoid interference during ImportConfig
 end
 ActionExt='.m';%default
+    Param.Action=rmfield(Param.Action,'RunMode'); % remove from the recorded xml file to avoid interference during ImportConfig
+end
+ActionExt='.m'; % default
 if isfield(Param.Action,'ActionExt')
     ActionExt=Param.Action.ActionExt;% '.m', '.sh' (compiled)  or '.py' (Python)
     Param.Action=rmfield(Param.Action,'ActionExt');%remove from the recorded xml file to avoid interference during ImportConfig
+    ActionExt=Param.Action.ActionExt; % '.m', '.sh' (compiled)  or '.py' (Python)
+    Param.Action=rmfield(Param.Action,'ActionExt'); % remove from the recorded xml file to avoid interference during ImportConfig
 end
 ActionName=Param.Action.ActionName;
 …
 %% Get  PARAM.xml (not used at this stage)
 errormsg='';%default error message
+errormsg=''; % default error message
 xmlfile=fullfile(path_series,'PARAM.xml');
 if ~exist(xmlfile,'file')
 …
 switch RunMode
     case {'local','background'}
         NbCore=1;% no need to split the calculation
+        NbCore=1; % no need to split the calculation
     case 'cluster_oar'
         %%%%% TEST A REMETTRE%%%%%
  %       if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
 %             NbCore=1;% one core used only (limitation of Matlab licences)
+%             NbCore=1; % one core used only (limitation of Matlab licences)
 %             answer=msgbox_uvmat('INPUT_Y-N','Number of cores =1: select the compiled version .sh for multi-core processing. Proceed with the .m version?');
 %             if ~strcmp(answer,'Yes')
 …
     case {'cluster_pbs', 'cluster_sge', 'cluster_qstat_unknown'}
         if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
             NbCore=1;% one core used only (limitation of Matlab licences)
+            NbCore=1; % one core used only (limitation of Matlab licences)
             answer=msgbox_uvmat('INPUT_Y-N','Number of cores =1: select the compiled version .sh for multi-core processing. Proceed with the .m version?');
             if ~strcmp(answer,'Yes')
 …
             NbCore=str2double(answer{1});
             qstat_Queue=answer{2};
             %extra_oar=answer{2};%TODO : fix this for LMFA cluster. Maybe
+            %extra_oar=answer{2}; % TODO : fix this for LMFA cluster. Maybe
             %extrs_oar and extra_pbs are not the best names
         end
 …
     SubDirOut=[get(handles.OutputSubDir,'String') Param.OutputDirExt];
     SubDirOutNew=SubDirOut;
     detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir');% test if  the dir  already exist
     check_create=1; %need to create the result directory by default
+    detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir'); % test if  the dir  already exist
+    check_create=1; % need to create the result directory by default
     CheckOverwrite=1;
     if isfield(Param,'CheckOverwrite')
 …
             check_create=0;
         else
             r=regexp(SubDirOutNew,'(?<root>.*\D)(?<num1>\d+)$','names');%detect whether name ends by a number
+            r=regexp(SubDirOutNew,'(?<root>.*\D)(?<num1>\d+)$','names'); % detect whether name ends by a number
             if isempty(r)
                 r(1).root=[SubDirOutNew '_'];
                 r(1).num1='0';
             end
             SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)];%increment the index by 1 or put 1
             detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir');% test if  the dir  already exists
+            SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)]; % increment the index by 1 or put 1
+            detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir'); % test if  the dir  already exists
             check_create=1;
         end
     end
     Param.OutputDirExt=regexprep(SubDirOutNew,Param.OutputSubDir,'');
     Param.OutputRootFile=Param.InputTable{1,3};% the first sorted RootFile taken for output
+    Param.OutputRootFile=Param.InputTable{1,3}; % the first sorted RootFile taken for output
     set(handles.OutputDirExt,'String',Param.OutputDirExt)
     OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]);% full name (with path) of output directory
+    OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]); % full name (with path) of output directory
     if check_create    % create output directory if it does not exist
         [tild,msg1]=mkdir(OutputDir);
         if ~strcmp(msg1,'')
             errormsg=['cannot create ' OutputDir ': ' msg1];%error message for directory creation
+            errormsg=['cannot create ' OutputDir ': ' msg1]; % error message for directory creation
             return
         end
 …
     [~,msg1]=mkdir(DirXml);
     if ~strcmp(msg1,'')
         errormsg=['cannot create ' DirXml ': ' msg1];%error message for directory creation
+        errormsg=['cannot create ' DirXml ': ' msg1]; % error message for directory creation
         return
     end
 end
 OutputNomType=nomtype2pair(Param.InputTable{1,4});% nomenclature for output files
+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
 last_i=1;% last i index to process
 incr_i=1;% increment step in i index
 first_j=1;% first j index to process
 last_j=1;% last j index to process
 incr_j=1;% increment step in j index
+first_i=1; % first i index to process
+last_i=1; % last i index to process
+incr_i=1; % increment step in i index
+first_j=1; % first j index to process
+last_j=1; % last j index to process
+incr_j=1; % increment step in j index
 if isfield(Param.IndexRange,'first_i')
     first_i=Param.IndexRange.first_i;
 …
     end
 end
 CPUTime=1;% job time estimated at 1 min per iteration (on index i and j) by default
+CPUTime=1; % job time estimated at 1 min per iteration (on index i and j) by default
 if isfield(Param.Action, 'CPUTime') && ~isempty(Param.Action.CPUTime)
     CPUTime=Param.Action.CPUTime;%Note: CpUTime for one iteration ref_i has to be multiplied by the number of j indices nbfield_j
+    CPUTime=Param.Action.CPUTime; % Note: CpUTime for one iteration ref_i has to be multiplied by the number of j indices nbfield_j
 end
 nbfield_j=numel(ref_j); % number of j indices
 BlockLength=numel(ref_i);% by default, job involves the full set of i field indices
+BlockLength=numel(ref_i); % by default, job involves the full set of i field indices
 NbProcess=1;
 switch RunMode
     case {'cluster_oar','cluster_pbs','cluster_sge','cluster_qstat_unknown'}
         if isempty(Param.IndexRange.NbSlice)% if NbSlice is not defined
             BlockLength= ceil(20/(CPUTime*nbfield_j));% short iterations are grouped such that the minimum time of a process is 20 min.
             BlockLength=max(BlockLength,ceil(numel(ref_i)/500));% possibly increase the BlockLength to have less than 500 jobs
+            BlockLength= ceil(20/(CPUTime*nbfield_j)); % short iterations are grouped such that the minimum time of a process is 20 min.
+            BlockLength=max(BlockLength,ceil(numel(ref_i)/500)); % possibly increase the BlockLength to have less than 500 jobs
             NbProcess=ceil(numel(ref_i)/BlockLength) ; % nbre of processes sent to oar
         else
             NbProcess=Param.IndexRange.NbSlice;% the parameter NbSlice sets the nbre of run processes
             NbCore=min(NbCore,NbProcess);% reduces the number of cores if it exceeds the number of processes
+            NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
+            NbCore=min(NbCore,NbProcess); % reduces the number of cores if it exceeds the number of processes
         end
     otherwise
         if ~isempty(Param.IndexRange.NbSlice)
             NbProcess=Param.IndexRange.NbSlice;% the parameter NbSlice sets the nbre of run processes
+            NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
         end
 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
+filexml=cell(1,NbProcess); % initialisation of the names of the files containing the processing parameters
 extxml=cell(1,NbProcess); % initialisation of the set of labels used for the files documenting each process
 for iprocess=1:NbProcess
 …
         Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;
         if Param.IndexRange.first_i>last_i
             NbProcess=iprocess-1;% leave the loop, we are at the end of the calculation
+            NbProcess=iprocess-1; % leave the loop, we are at the end of the calculation
             break
         end
 …
     end
     for ilist=1:size(Param.InputTable,1)
         Param.InputTable{ilist,1}=regexprep(Param.InputTable{ilist,1},'\','/');%correct path name for PCWIN system
+        Param.InputTable{ilist,1}=regexprep(Param.InputTable{ilist,1},'\','/'); % correct path name for PCWIN system
     end
 …
         filexml{iprocess}=fullfile(OutputDir,'0_XML',extxml{iprocess});
         try
             save(t, filexml{iprocess});% save the xml file containing the processing parameters
+            save(t, filexml{iprocess}); % save the xml file containing the processing parameters
         catch ME
             if ~strcmp (RunMode,'local')
 …
         switch ActionExt
             case '.m'
                 h_fun(Param);% direct launching
+                h_fun(Param); % direct launching
             case '.sh'
                 switch computer
                     case {'PCWIN','PCWIN64'} %Windows system
                         filexml=regexprep(filexml,'\\','\\\\');% add '\' so that '\' are left as characters
                         system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]);% TODO: adapt to DOS system
+                        filexml=regexprep(filexml,'\\','\\\\'); % add '\' so that '\' are left as characters
+                        system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]); % TODO: adapt to DOS system
                     case {'GLNX86','GLNXA64','MACI64'}%Linux  system
                         system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]);
 …
 if ~strcmp (RunMode,'local') && ~strcmp(RunMode,'python')
     %% processing on a different session of the same computer (background) or cluster, create executable files
     batch_file_list=cell(NbProcess,1);% initiate the list of executable files
     DirExe=fullfile(OutputDir,'0_EXE');%directory name for executable files
+    batch_file_list=cell(NbProcess,1); % initiate the list of executable files
+    DirExe=fullfile(OutputDir,'0_EXE'); % directory name for executable files
     switch computer
         case {'PCWIN','PCWIN64'} %Windows system
 …
         [tild,msg1]=mkdir(DirExe);
         if ~strcmp(msg1,'')
             errormsg=['cannot create ' DirExe ': ' msg1];%error message for directory creation
+            errormsg=['cannot create ' DirExe ': ' msg1]; % error message for directory creation
             return
         end
 …
         [tild,msg1]=mkdir(DirLog);
         if ~strcmp(msg1,'')
             errormsg=['cannot create ' DirLog ': ' msg1];%error message for directory creation
+            errormsg=['cannot create ' DirLog ': ' msg1]; % error message for directory creation
             return
         end
 …
                         end
                         cmd=[cmd  'exit \n' 'END_MATLAB \n'];
                         fprintf(fid,cmd);%fill the executable file with the  char string cmd
                         fclose(fid);% close the executable file
                         system(['chmod +x ' file_exe_global]);% set the file to executable
+                        fprintf(fid,cmd); % fill the executable file with the  char string cmd
+                        fclose(fid); % close the executable file
+                        system(['chmod +x ' file_exe_global]); % set the file to executable
                     case {'PCWIN','PCWIN64'}
                         cmd=['matlab -automation -logfile ' regexprep(filelog{iprocess},'\\','\\\\')...
 …
                         end
                         cmd=[cmd ';exit"'];
                         fprintf(fid,cmd);%fill the executable file with the  char string cmd
                         fclose(fid);% close the executable file
+                        fprintf(fid,cmd); % fill the executable file with the  char string cmd
+                        fclose(fid); % close the executable file
                 end
                 system([file_exe_global ' &'])% directly execute the command file
 …
                     switch computer
                         case {'GLNX86','GLNXA64','MACI64'}
                             [fid,message]=fopen(batch_file_list{iprocess},'w');% create the executable file
+                            [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
                             if isequal(fid,-1)
                                 errormsg=['creation of .bat file: ' message];
 …
                                 'hostname && date \n '...
                                 'umask 002 \n'...
                                 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
                             system(['chmod +x ' batch_file_list{iprocess}]);% set the file to executable
+                                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
+                            system(['chmod +x ' batch_file_list{iprocess}]); % set the file to executable
                             system([batch_file_list{iprocess} ' &'])% directly execute the command file
                         case {'PCWIN','PCWIN64'}
 …
         %create subdirectory for oar commands
         for iprocess=1:NbProcess
             [fid,message]=fopen(batch_file_list{iprocess},'w');% create the executable file
+            [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
             if isequal(fid,-1)
                 errormsg=['creation of .bat file: ' message];
 …
                     'hostname && date \n '...
                     'umask 002 \n'...
                     ActionFullName ' ' RunTime ' ' filexml{iprocess}];%allow writting access to created files for user group
+                    ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group
             else
                 matlab_ver = ver('MATLAB');
 …
                     'END_MATLAB \n'];
             end
             fprintf(fid,cmd);%fill the executable file with the  char string cmd
             fclose(fid);% close the executable file
             system(['chmod +x ' batch_file_list{iprocess}]);% set the file to executable
+            fprintf(fid,cmd); % fill the executable file with the  char string cmd
+            fclose(fid); % close the executable file
+            system(['chmod +x ' batch_file_list{iprocess}]); % set the file to executable
         end
         DirOAR=fullfile(OutputDir,'0_OAR');
 …
             [tild,msg1]=mkdir(DirOAR);
             if ~strcmp(msg1,'')
                 errormsg=['cannot create ' DirOAR ': ' msg1];%error message for directory creation
+                errormsg=['cannot create ' DirOAR ': ' msg1]; % error message for directory creation
                 return
             end
         end
         % create file containing the list of jobs
         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
+        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
         for iprocess=1:length(batch_file_list)
             fprintf(fid,[batch_file_list{iprocess} '\n']);% write list of exe files
+            fprintf(fid,[batch_file_list{iprocess} '\n']); % write list of exe files
         end
         fclose(fid);
         system(['chmod +x ' filename_joblist]);% set the file to executable
+        system(['chmod +x ' filename_joblist]); % set the file to executable
         filename_log=fullfile(DirLog,'job_list.stdout');%file for output messages of the master oar process
         filename_errors=fullfile(DirLog,'job_list.stderr');%file for error messages of the master oar process
+        filename_log=fullfile(DirLog,'job_list.stdout'); % file for output messages of the master oar process
+        filename_errors=fullfile(DirLog,'job_list.stderr'); % file for error messages of the master oar process
         % the command job_list.txt contains the list of NbProcess independent individual jobs
         % in which the total calculation has been split. Those are written as executable files .sh in the folder /O_EXE.
 …
         % shorter than the wall time: in the time interval 'checkpoint' (WallTimeOneJob) before the end of the allowed duration,
         %  the oar job restarts when an individual job ends.
         JobTime=CPUTime*BlockLength*nbfield_j;% estimated time for one individual job (in minutes)
+        JobTime=CPUTime*BlockLength*nbfield_j; % estimated time for one individual job (in minutes)
         % wall time (in hours ) for each oar job, allowing 10 individual jobs, but limited to 23 h:
         WallTimeTotal=min(23,4*JobTime/60);
         %disp(['WallTimeTotal: ' num2str(WallTimeTotal) ' hours'])
         % estimated time of an individual job (in min), with a margin of error
         WallTimeOneJob=min(4*JobTime+10,WallTimeTotal*60/2);% estimated max time of an individual job for checkpoint
+        WallTimeOneJob=min(4*JobTime+10,WallTimeTotal*60/2); % estimated max time of an individual job for checkpoint
         disp(['WallTimeOneJob: ' num2str(WallTimeOneJob) ' minutes'])
         oar_command=['oarsub -n UVmat_' ActionFullName ' '...
 …
             '-l ' filename_joblist '.log"'];
         fprintf(oar_command);% display  system command on the Matlab command window
+        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
         filename_oarcommand=fullfile(DirOAR,'0_oar_command');% keep track of the command in file '0-OAR/0_oar_command'
+        filename_oarcommand=fullfile(DirOAR,'0_oar_command'); % keep track of the command in file '0-OAR/0_oar_command'
         fid=fopen(filename_oarcommand,'w');
         fprintf(fid,oar_command); % store the command
         fprintf(fid,result);% store the result (job ID number)
+        fprintf(fid,result); % store the result (job ID number)
         fclose(fid);
         msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched as  ' num2str(NbProcess) ' processes in cluster: press STATUS to see results'])
 …
     case 'cluster_pbs' % for LMFA Kepler machine
         %create subdirectory for pbs command and log files
         DirPBS=fullfile(OutputDir,'0_PBS'); %todo : common name OAR/PBS
+        DirPBS=fullfile(OutputDir,'0_PBS'); % todo : common name OAR/PBS
         if exist(DirPBS,'dir')% delete the content of the dir 0_LOG to allow new input
             curdir=pwd;
 …
             [tild,msg1]=mkdir(DirPBS);
             if ~strcmp(msg1,'')
                 errormsg=['cannot create ' DirPBS ': ' msg1];%error message for directory creation
+                errormsg=['cannot create ' DirPBS ': ' msg1]; % error message for directory creation
                 return
             end
 …
         max_walltime=3600*20; % 20h max total calculation (cannot exceed 24 h)
         walltime_onejob=1800; % seconds, max estimated time for asingle file index value
         filename_joblist=fullfile(DirPBS,'job_list.txt');%create name of the global executable file
+        filename_joblist=fullfile(DirPBS,'job_list.txt'); % create name of the global executable file
         fid=fopen(filename_joblist,'w');
         for iprocess=1:length(batch_file_list)
             fprintf(fid,[batch_file_list{iprocess} '\n']);% list of exe files
+            fprintf(fid,[batch_file_list{iprocess} '\n']); % list of exe files
         end
         fclose(fid);
         system(['chmod +x ' filename_joblist]);% set the file to executable
+        system(['chmod +x ' filename_joblist]); % set the file to executable
         pbs_command=['qsub -n CIVX '...
             '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
 …
         fprintf(fid,pbs_command);
         fclose(fid);
         fprintf(pbs_command);% display in command line
+        fprintf(pbs_command); % display in command line
         %system(pbs_command);
         msgbox_uvmat('CONFIRMATION',[ActionFullName ' command ready to be launched in cluster'])
 …
             [tild,msg1]=mkdir(DirSGE);
             if ~strcmp(msg1,'')
                 errormsg=['cannot create ' DirSGE ': ' msg1];%error message for directory creation
+                errormsg=['cannot create ' DirSGE ': ' msg1]; % error message for directory creation
                 return
             end
 …
                     '-o ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '...
                     fullfile([DirSGE '/job' num2str(currJobIndex) '.sh'])];
                 fprintf(sge_command);% display in command line
+                fprintf(sge_command); % display in command line
                 [status, result] = system(sge_command);
                 fprintf(result);
 …
     [SUCCESS,MESSAGE,MESSAGEID] = fileattrib (OutputDir)
     if MESSAGE.GroupWrite~=1
     [success,msg] = fileattrib(OutputDir,'+w','g','s');% allow writing access for the group of users, recursively in the folder
+    [success,msg] = fileattrib(OutputDir,'+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 ' OutputDir ':']; msg});%error message for directory creation
+        msgbox_uvmat('WARNING',{['unable to set group write access to ' OutputDir ':']; msg}); % error message for directory creation
     end
     end
 …
 %% clean the output structure by removing unused information
 if isfield(Param,'Pairs')
     Param=rmfield(Param,'Pairs'); %info Pairs not needed for output
+    Param=rmfield(Param,'Pairs'); % info Pairs not needed for output
 end
 if isfield(Param,'InputLine')
 …
 %% get Action name and path
 NbBuiltinAction=get(handles.Action,'UserData'); %nbre of functions initially proposed in the menu ActionName (as defined in the Opening fct of series)
 ActionList=get(handles.ActionName,'String');% list menu fields
+NbBuiltinAction=get(handles.Action,'UserData'); % nbre of functions initially proposed in the menu ActionName (as defined in the Opening fct of series)
+ActionList=get(handles.ActionName,'String'); % list menu fields
 ActionIndex=get(handles.ActionName,'Value');
 if ~isequal(ActionIndex,1)% if we are not just opening series
 …
 end
 ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
 ActionPathList=get(handles.ActionName,'UserData');%list of recorded paths to functions of the list ActionName
+ActionPathList=get(handles.ActionName,'UserData'); % list of recorded paths to functions of the list ActionName
 %% add a new function to the menu if 'more...' has been selected in the menu ActionName
 …
     % insert the choice in the menu ActionName
     ActionIndex=find(strcmp(ActionName,ActionList),1);% look for the selected function in the menu Action
+    ActionIndex=find(strcmp(ActionName,ActionList),1); % look for the selected function in the menu Action
     PathName=regexprep(PathName,'/$','');
     if ~isempty(ActionIndex) && ~strcmp(ActionPathList{ActionIndex},PathName)%compare the path to the existing fct
 …
     if isempty(ActionIndex)%the qselected fct (with selected path) does not exist in the menu
         ActionIndex= length(ActionList);
         ActionList=[ActionList(1:end-1);{ActionName};ActionList(end)];% the selected function is appended in the menu, before the last item 'more...'
+        ActionList=[ActionList(1:end-1);{ActionName};ActionList(end)]; % the selected function is appended in the menu, before the last item 'more...'
          ActionPathList=[ActionPathList; PathName];
     end
 …
     % remove old Action options in the menu (keeping a menu length <nb_builtin_ACTION+5)
     if length(ActionList)>NbBuiltinAction+5; %nb_builtin_ACTION=nbre of functions always remaining in the initial menu
+    if length(ActionList)>NbBuiltinAction+5; % nb_builtin_ACTION=nbre of functions always remaining in the initial menu
         nbremove=length(ActionList)-NbBuiltinAction-5;
         ActionList(NbBuiltinAction+1:end-5)=[];
 …
 %% check the current ActionPath to the selected function
 ActionPath=ActionPathList{ActionIndex};%current recorded path
 set(handles.ActionPath,'String',ActionPath); %show the path to the senlected function
+ActionPath=ActionPathList{ActionIndex}; % current recorded path
+set(handles.ActionPath,'String',ActionPath); % show the path to the senlected function
 %% reinitialise the waitbar
 …
     return
 end
 current_dir=pwd;%current working dir
+current_dir=pwd; % current working dir
 cd(ActionPath)
 h_fun=str2func(ActionName);
 …
 % path_series=which('series');
 % %eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
 % spath=fileparts(which(ActionName)); %spath = current path of the selected function ACTION
+% spath=fileparts(which(ActionName)); % spath = current path of the selected function ACTION
 % if ~exist(ActionPath,'dir')
 %     msgbox_uvmat('ERROR',['The prescribed function path ' ActionPath ' does not exist']);
 …
 %% Activate the Action fct to adapt the configuration of the GUI series and bring specific parameters in SeriesData
 Param=read_GUI_series(handles);% read the parameters from the GUI series
 ParamOut=h_fun(Param);%run the selected Action function to get the relevant input
+Param=read_GUI_series(handles); % read the parameters from the GUI series
+ParamOut=h_fun(Param); % run the selected Action function to get the relevant input
 %% Put the first line of the selected Action fct as tooltip help
 …
 %% Visibility of VelType and VelType_1 menus asked by ActionName
 VelTypeRequest=1;%VelType requested by default
 VelTypeRequest_1=1;%VelType requested by default
+VelTypeRequest=1; % VelType requested by default
+VelTypeRequest_1=1; % VelType requested by default
 if isfield(ParamOut,'VelType')
     VelTypeRequest=ismember(ParamOut.VelType,{'on','one','two'});
 …
 %% Detect the types of input files and set menus and default options in 'VelType'
 SeriesData=get(handles.series,'UserData');% info on the input file series
+SeriesData=get(handles.series,'UserData'); % info on the input file series
 iview_civ=find(strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));
 iview_netcdf=find(strcmp('netcdf',SeriesData.FileType)|strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));% all nc files, icluding civ
 FieldList=get(handles.FieldName,'String');% previous list as default
+iview_netcdf=find(strcmp('netcdf',SeriesData.FileType)|strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType)); % all nc files, icluding civ
+FieldList=get(handles.FieldName,'String'); % previous list as default
 if ~iscell(FieldList),FieldList={FieldList};end
 FieldList_1=get(handles.FieldName_1,'String');% previous list as default
+FieldList_1=get(handles.FieldName_1,'String'); % previous list as default
 if ~iscell(FieldList_1),FieldList_1={FieldList_1};end
 %CheckList=0;% indicate whether FieldName has been updated
 CheckList_1=1;% indicate whether FieldName_1 has been updated
+%CheckList=0; % indicate whether FieldName has been updated
+CheckList_1=1; % indicate whether FieldName_1 has been updated
 handles_coord=[handles.Coord_x handles.Coord_y handles.Coord_z handles.Coord_x_title handles.Coord_y_title handles.Coord_z_title];
 if VelTypeRequest && numel(iview_civ)>=1
 …
     set(handles.VelType,'Visible','on')
     set(handles.VelType_title,'Visible','on')
     FieldList=[set_field_list('U','V');{'C'};{'get_field...'}];%standard menu for civx data
+    FieldList=[set_field_list('U','V');{'C'};{'get_field...'}]; % standard menu for civx data
     %CheckList=1;
     set(handles.FieldName,'Value',1); %velocity vector choice by default
+    set(handles.FieldName,'Value',1); % velocity vector choice by default
     if  VelTypeRequest_1 && numel(iview_civ)>=2
         menu=set_veltype_display(SeriesData.FileInfo{iview_civ(2)}.CivStage,SeriesData.FileType{iview_civ(2)});
 …
         set(handles.VelType_1,'Visible','on')
         set(handles.VelType_title_1,'Visible','on')
         FieldList_1=[set_field_list('U','V');{'C'};{'get_field...'}];%standard menu for civx data
+        FieldList_1=[set_field_list('U','V');{'C'};{'get_field...'}]; % standard menu for civx data
         CheckList_1=1;
         set(handles.FieldName_1,'Value',1); %velocity vector choice by default
+        set(handles.FieldName_1,'Value',1); % velocity vector choice by default
     else
         set(handles.VelType_1,'Visible','off')
 …
         set(handles.FieldName,'Visible','on')
         ListVarName=SeriesData.FileInfo{iview_netcdf(1)}.ListVarName;
         ind_var=get(handles.FieldName,'Value');%indices of previously selected variables
+        ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables
         for ilist=1:numel(ind_var)
             if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
                 FieldList={};% previous choice not consistent with new input field
+                FieldList={}; % previous choice not consistent with new input field
                 set(handles.FieldName,'Value',1)
                 break
 …
         if CheckList_1==0        % not civ input made
             ListVarName=SeriesData.FileInfo{iview_netcdf(2)}.ListVarName;
             ind_var=get(handles.FieldName,'Value');%indices of previously selected variables
+            ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables
             for ilist=1:numel(ind_var)
                 if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
                     FieldList_1={};% previous choice not consistent with new input field
+                    FieldList_1={}; % previous choice not consistent with new input field
                     set(handles.FieldName_1,'Value',1)
                     break
 …
 %% Check whether alphabetical sorting of input Subdir is allowed by the Action fct  (for multiples series entries)
 if isfield(ParamOut,'AllowInputSort')&&isequal(ParamOut.AllowInputSort,'on')&& size(Param.InputTable,1)>1
     [tild,iview]=sort(InputTable(:,2)); %subdirectories sorted in alphabetical order
+    [tild,iview]=sort(InputTable(:,2)); % subdirectories sorted in alphabetical order
     set(handles.InputTable,'Data',InputTable(iview,:));
     MinIndex_i=get(handles.MinIndex_i,'Data');
 …
 %% enable or desable j index visibility
 status_j='on';%default
+status_j='on'; % default
 if isfield(ParamOut,'Desable_j_index')&&isequal(ParamOut.Desable_j_index,'on')
     status_j='off';
 …
     status_j='off'; % no j index needed
 elseif strcmp(get(handles.PairString,'Visible'),'on')
     check_burst=cellfun(@isempty,regexp(get(handles.PairString,'Data'),'^j'));%=0 for burst case, 1 otherwise
+    check_burst=cellfun(@isempty,regexp(get(handles.PairString,'Data'),'^j')); % =0 for burst case, 1 otherwise
     if isempty(find(check_burst, 1))% if all pair string begins by j (burst)
         status_j='off'; % no j index needed for bust case
 …
 %% NbSlice visibility
 %NbSliceVisible='off';%default
+%NbSliceVisible='off'; % default
 if isfield(ParamOut,'NbSlice') && (strcmp(ParamOut.NbSlice,'on')||isnumeric(ParamOut.NbSlice))
     set(handles.num_NbSlice,'Visible','on')
 …
 %% definition of the directory containing the output files
 if  ~(isfield(SeriesData,'ActionName') && strcmp(ActionName,SeriesData.ActionName))
     OutputDirExt='.series'; %default
+    OutputDirExt='.series'; % default
     if isfield(ParamOut,'OutputDirExt')&&~isempty(ParamOut.OutputDirExt)
         OutputDirExt=ParamOut.OutputDirExt;
 …
 end
 OutputDirVisible='off';
 OutputSubDirMode='auto';%default
+OutputSubDirMode='auto'; % default
 SubDirOut='';
 if isfield(ParamOut,'OutputSubDirMode')
 …
 end
 switch OutputSubDirMode
     case 'auto';%default
+    case 'auto'; % default
         OutputDirVisible='on';
         SubDir=InputTable(1:end,2); %set of subdirectories
+        SubDir=InputTable(1:end,2); % set of subdirectories
         SubDirOut=SubDir{1};
         if numel(SubDir)>1
 …
     case 'one'
         OutputDirVisible='on';
         SubDirOut=InputTable{1,2}; %use the first subdir name (+OutputDirExt) as output  subdirectory
+        SubDirOut=InputTable{1,2}; % use the first subdir name (+OutputDirExt) as output  subdirectory
     case 'two'
         OutputDirVisible='on';
         SubDir=InputTable(1:2,2); %set of subdirectories
+        SubDir=InputTable(1:2,2); % set of subdirectories
         SubDirOut=SubDir{1};
         if numel(SubDir)>1
 …
     case 'last'
         OutputDirVisible='on';
         SubDirOut=InputTable{end,2}; %use the last subdir name (+OutputDirExt) as output  subdirectory
+        SubDirOut=InputTable{end,2}; % use the last subdir name (+OutputDirExt) as output  subdirectory
 end
 set(handles.OutputSubDir,'String',SubDirOut)
 …
 %set(handles.CheckOverwrite,'Visible',OutputDirVisible)
 set(handles.OutputDir_title,'Visible',OutputDirVisible)
 SeriesData.ActionName=ActionName;%record ActionName for next use
+SeriesData.ActionName=ActionName; % record ActionName for next use
 %% visibility of the run mode (local or background or cluster)
 if strcmp(OutputSubDirMode,'none')
     RunModeVisible='off';% only local mode available if no output file is produced
+    RunModeVisible='off'; % only local mode available if no output file is produced
 else
     RunModeVisible='on';
 …
     SeriesData=get(handles.series,'UserData');
     % input line for which the field choice is relevant
     iview=find(ismember(SeriesData.FileType,{'netcdf','civx','civdata'}));% all nc files, icluding civ
+    iview=find(ismember(SeriesData.FileType,{'netcdf','civx','civdata'})); % all nc files, icluding civ
     hget_field=findobj(allchild(0),'name','get_field');
     if ~isempty(hget_field)
 …
     InputTable=Param.InputTable(iview,:);
     % 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
+    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
         first_j=Param.IndexRange.first_j;
         last_j=Param.IndexRange.last_j;
 …
 function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
 indsel=ind_i;
 indiff=diff(ind_i); %test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
 indiff=[1 indiff last_i-ind_i(end)+1];%for testing gaps with the imposed bounds
+indiff=diff(ind_i); % test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
+indiff=[1 indiff last_i-ind_i(end)+1]; % for testing gaps with the imposed bounds
 if ~isempty(indiff)
     indiff2=diff(indiff);
     indiffp=[indiff2 1];
     indiffm=[1 indiff2];
     ind_multi_m=find((indiff==0)&(indiffm<0))-1;%indices of first members of multiplets
     ind_multi_p=find((indiff==0)&(indiffp>0));%indices of last members of multiplets
+    ind_multi_m=find((indiff==0)&(indiffm<0))-1; % indices of first members of multiplets
+    ind_multi_p=find((indiff==0)&(indiffp>0)); % indices of last members of multiplets
     %for each multiplet, select the most recent file
     ind_remove=[];
 …
         ind_pairs=ind_multi_m(i):ind_multi_p(i);
         for imulti=1:length(ind_pairs)
             datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date);%dates of creation
         end
         [datenew,indsort2]=sort(datepair); %sort the multiplet by creation date
         ind_s=indsort2(1:end-1);%
         ind_remove=[ind_remove ind_pairs(ind_s)];%remove these indices, leave the last one
+            datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date); % dates of creation
+        end
+        [datenew,indsort2]=sort(datepair); % sort the multiplet by creation date
+        ind_s=indsort2(1:end-1); %
+        ind_remove=[ind_remove ind_pairs(ind_s)]; % remove these indices, leave the last one
     end
 end
 …
 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)
 %------------------------------------------------------------------------
 num_i1=num_i;% set of first image numbers by default
+num_i1=num_i; % set of first image numbers by default
 num_i2=num_i;
 num_j1=num_j;
 …
 % if isequal (NomType,'_1-2_1') || isequal (NomType,'_1-2')
 if isequal(mode,'series(Di)')
     num_i1_line=num_i+ind_shift(3);% set of first image numbers
+    num_i1_line=num_i+ind_shift(3); % set of first image numbers
     num_i2_line=num_i+ind_shift(4);
     % adjust the first and last field number
 …
         num_j2=ind_shift(2)*ones(size(num_i));
     else
         num_j1_col=num_j+ind_shift(1);% set of first image numbers
+        num_j1_col=num_j+ind_shift(1); % set of first image numbers
         num_j2_col=num_j+ind_shift(2);
         % adjust the first field number
 …
 function CheckObject_Callback(hObject, eventdata, handles)
 %------------------------------------------------------------------------
 hset_object=findobj(allchild(0),'tag','set_object');%find the set_object interface handle
+hset_object=findobj(allchild(0),'tag','set_object'); % find the set_object interface handle
 if get(handles.CheckObject,'Value')
     SeriesData=get(handles.series,'UserData');
 …
                 data.ProjMode='none';
             end
             hset_object=set_object(data);% call the set_object interface
+            hset_object=set_object(data); % call the set_object interface
             set(hset_object,'Name','set_object_series')% name to distinguish from set_object used with uvmat
         end
         ProjObject=read_GUI(hset_object);
         set(handles.ProjObject,'String',ProjObject.Name);%display the object name
+        set(handles.ProjObject,'String',ProjObject.Name); % display the object name
         SeriesData=get(handles.series,'UserData');
         SeriesData.ProjObject=ProjObject;
 …
     InputTable=get(handles.InputTable,'Data');
     nbview=size(InputTable,1);
     MaskTable=cell(nbview,1);%default
     ListMask=cell(nbview,1);%default
+    MaskTable=cell(nbview,1); % default
+    ListMask=cell(nbview,1); % default
     MaskData=get(handles.MaskTable,'Data');
     MaskData(size(MaskData,1):nbview,1)=cell(size(MaskData,1):nbview,1);%complement if undefined lines
+    MaskData(size(MaskData,1):nbview,1)=cell(size(MaskData,1):nbview,1); % complement if undefined lines
     for iview=1:nbview
         ListMask{iview,1}=num2str(iview);
 …
             if isempty(MaskData{iview})
                 SubDir=InputTable{iview,2};
                 MaskPath=fullfile(RootPath,[regexprep(SubDir,'\..*','') '.mask']);%take the root part of SubDir, before the first dot '.'
+                MaskPath=fullfile(RootPath,[regexprep(SubDir,'\..*','') '.mask']); % take the root part of SubDir, before the first dot '.'
                 if exist(MaskPath,'dir')
                     ListStruct=dir(MaskPath);%look for a mask file
                     ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray
                     check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files
                     ListFiles=ListCells(1,:);%list of file and dri names
                     ListFiles=ListFiles(~check_dir);%list of file names (excluding dir)
+                    ListStruct=dir(MaskPath); % look for a mask file
+                    ListCells=struct2cell(ListStruct); % transform dir struct to a cell arrray
+                    check_dir=cell2mat(ListCells(4,:)); % =1 for directories, =0 for files
+                    ListFiles=ListCells(1,:); % list of file and dri names
+                    ListFiles=ListFiles(~check_dir); % list of file names (excluding dir)
                     mdetect=0;
                     if ~isempty(ListFiles)
 …
                             end
                             if ~strcmp(MaskFile{ifile},MaskFile{1})
                                 mdetect=0;% cancel detection test in case of multiple masks, use the brower for selection
+                                mdetect=0; % cancel detection test in case of multiple masks, use the brower for selection
                                 break
                             end
 …
 % path_to_uvmat=which ('uvmat');% check the path of uvmat
+% path_to_uvmat=which ('uvmat'); % check the path of uvmat
 % pathelp=fileparts(path_to_uvmat);
 % helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
 …
         return     %browser closed without choice
     end
     [TransformPath,TransformName,TransformExt]=fileparts(FileName);% removes extension .m
+    [TransformPath,TransformName,TransformExt]=fileparts(FileName); % removes extension .m
     if ~strcmp(TransformExt,'.m')
         msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
 …
     end
      % insert the choice in the menu
     TransformIndex=find(strcmp(TransformName,TransformList),1);% look for the selected function in the menu Action
+    TransformIndex=find(strcmp(TransformName,TransformList),1); % look for the selected function in the menu Action
     if isempty(TransformIndex)%the input string does not exist in the menu
         TransformIndex= length(TransformList);
         TransformList=[TransformList(1:end-1);{TransformName};TransformList(end)];% the selected function is appended in the menu, before the last item 'more...'
+        TransformList=[TransformList(1:end-1);{TransformName};TransformList(end)]; % the selected function is appended in the menu, before the last item 'more...'
         set(handles.TransformName,'String',TransformList)
         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'
    dir_perso=prefdir;%personal Matalb directory
+   dir_perso=prefdir; % personal Matalb directory
    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
    if exist(profil_perso,'file')
 …
        TransformPathListUser=TransformPathListUser';
        TransformListUser=TransformListUser';
        save (profil_perso,'TransformPathListUser','TransformListUser','-append'); %store the root name for future opening of uvmat
+       save (profil_perso,'TransformPathListUser','TransformListUser','-append'); % store the root name for future opening of uvmat
    end
 end
 %display the current function path
 set(handles.TransformPath,'String',TransformPathList{TransformIndex}); %show the path to the senlected function
+set(handles.TransformPath,'String',TransformPathList{TransformIndex}); % show the path to the senlected function
 set(handles.TransformName,'UserData',TransformPathList);
 …
         return
     end
     current_dir=pwd;%current working dir
+    current_dir=pwd; % current working dir
     cd(TransformPathList{TransformIndex})
     transform_handle=str2func(TransformName);
     cd(current_dir)
     Field.Action.RUN=0;% indicate that the transform fct is called only to get input param
     DataOut=feval(transform_handle,Field,[]);% execute the transform fct to get the required conditions
+    Field.Action.RUN=0; % indicate that the transform fct is called only to get input param
+    DataOut=feval(transform_handle,Field,[]); % execute the transform fct to get the required conditions
     if isfield(DataOut,'TransformInput')%  used to add transform parameters at selection of the transform fct
         SeriesData=get(handles.series,'UserData');
 …
 display('current series config :')
 evalin('base','Param') %display CurData in the workspace
 commandwindow; %brings the Matlab command window to the front
+commandwindow; % brings the Matlab command window to the front
 %------------------------------------------------------------------------
 …
 %% use a browser to choose the xml file containing the processing config
 InputTable=get(handles.InputTable,'Data');
 oldfile=InputTable{1,1};%current path in InputTable
+oldfile=InputTable{1,1}; % current path in InputTable
 if isempty(oldfile)
     % use a file name stored in prefdir
 …
     end
 end
 filexml=uigetfile_uvmat('pick a xml parameter file',oldfile,'.xml');% get the xml file containing processing parameters
+filexml=uigetfile_uvmat('pick a xml parameter file',oldfile,'.xml'); % get the xml file containing processing parameters
 if isempty(filexml), return, end % quit function if an xml file has not been opened
 %% fill the GUI series with the content of the xml file
 Param=xml2struct(filexml);% read the input xml file as a Matlab structure
+Param=xml2struct(filexml); % read the input xml file as a Matlab structure
 % ask to stop current Action if button RUN is in action (another process is already running)
 …
     end
 end
 Param.Action.RUN=0; %desactivate the input RUN=1
+Param.Action.RUN=0; % desactivate the input RUN=1
 fill_GUI(Param,handles.series)% fill the elements of the GUI series with the input parameters
 …
     set(handles.ActionInput,'Visible','on')
     set(handles.ActionInput,'Value',0)
     Param.ActionInput.ConfigSource=filexml;% record the source of config for future info
+    Param.ActionInput.ConfigSource=filexml; % record the source of config for future info
     SeriesData.ActionInput=Param.ActionInput;
 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
+set(handles.REFRESH,'BackgroundColor',[1 0 1]); % paint REFRESH button in magenta to indicate that it should be activated
 …
         return
     end
     OutputSubDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
+    OutputSubDir=[Param.OutputSubDir Param.OutputDirExt]; % subdirectory for output files
     OutputDir=fullfile(RootPath,OutputSubDir);
     if exist(OutputDir,'dir')
 …
     return
 end
 ListFiles(1)=[];%removes the first line ='.'
+ListFiles(1)=[]; % removes the first line ='.'
 ListDisplay=cell(numel(ListFiles),1);
 testrecent=0;
 …
     ListDisplay{ilist}=ListFiles(ilist).name;
       if ~ListFiles(ilist).isdir && isfield(ListFiles(ilist),'datenum')
             datnum(ilist)=ListFiles(ilist).datenum;%only available in recent matlab versions
+            datnum(ilist)=ListFiles(ilist).datenum; % only available in recent matlab versions
             testrecent=1;
        end
 …
 %% Look at date of creation
 ListDisplay=ListDisplay(datnum~=0);
 datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
+datnum=datnum(datnum~=0); % keep the non zero values corresponding to existing files
 NbOutputFile=[];
 if isempty(datnum)
 …
 %% create the GUI set_pairs
 set(0,'Unit','points')
 ScreenSize=get(0,'ScreenSize');% get the size of the screen, to put the fig on the upper right
 Width=220;% fig width in points (1/72 inch)
+ScreenSize=get(0,'ScreenSize'); % get the size of the screen, to put the fig on the upper right
+Width=220; % fig width in points (1/72 inch)
 Height=min(0.8*ScreenSize(4),300);
 Left=ScreenSize(3)- Width-40; %right edge close to the right, with margin=40
 Bottom=ScreenSize(4)-Height-40; %put fig at top right
+Left=ScreenSize(3)- Width-40; % right edge close to the right, with margin=40
+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');
 …
 TimeUnit=get(handles.TimeUnit,'String');
 PairString=get(handles.PairString,'Data');
 ListViewLines=find(cellfun('isempty',PairString)==0);%find list of non empty pairs
+ListViewLines=find(cellfun('isempty',PairString)==0); % find list of non empty pairs
 ListViewMenu=cell(numel(ListViewLines),1);
 iview=get(handles.PairString,'Value');
 …
 end
 if isempty(iview)
     ListViewValue=numel(ListViewLines);% we work by default on the pair option for the last line which requires pairs
+    ListViewValue=numel(ListViewLines); % we work by default on the pair option for the last line which requires pairs
     iview=ListViewLines(end);
 else
 …
 end
 ref_i=str2num(get(handles.num_first_i,'String'));
 ref_j=1;%default
+ref_j=1; % default
 if strcmp(get(handles.num_first_j,'String'),'Visible')
     ref_j=str2num(get(handles.num_first_j,'String'));
 …
 % first raw of the GUI
 uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.88 0.5 0.1],'BackgroundColor',BackgroundColor,...
     'String','row to edit #','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','right');%title
+    'String','row to edit #','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','right'); % title
 uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.54 0.8 0.3 0.2],'BackgroundColor',[1 1 1],...
     'Callback',@(hObject,eventdata)ListView_Callback(hObject,eventdata),'String',ListViewMenu,'Value',ListViewValue,'FontUnits','points','FontSize',12,'FontWeight','bold',...
 …
 % second raw of the GUI
 uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.79 0.7 0.1],'BackgroundColor',BackgroundColor,...
     'String','mode of index pairing:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left');%title
+    'String','mode of index pairing:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title
 uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.05 0.62 0.9 0.2],'BackgroundColor',[1 1 1],...
     'Callback',@(hObject,eventdata)Mode_Callback(hObject,eventdata),'String',ModeMenu,'Value',ModeValue,'FontUnits','points','FontSize',12,'FontWeight','bold',...
 …
 % third raw
 uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.6 0.7 0.1],'BackgroundColor',BackgroundColor,...
     'String','pair choice:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left');%title
+    'String','pair choice:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title
 uicontrol('Style','listbox','Units','normalized', 'Position', [0.05 0.42 0.9 0.2],'BackgroundColor',[1 1 1],...
     'Callback',@(hObject,eventdata)ListPair_Callback(hObject,eventdata),'String',displ_pair,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
     'Tag','ListPair','TooltipString','''ListPair'': menu for selecting the image pair');
 uicontrol('Style','text','Units','normalized', 'Position', [0.1 0.22 0.8 0.1],'BackgroundColor',BackgroundColor,...
     'String','ref_i           ref_j','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center');%title
+    'String','ref_i           ref_j','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center'); % title
 uicontrol('Style','edit','Units','normalized', 'Position', [0.15 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
     'Callback',@(hObject,eventdata)num_ref_i_Callback(hObject,eventdata),'String',num2str(ref_i),'FontUnits','points','FontSize',12,'FontWeight','bold',...
 …
 function Mode_Callback(hObject,eventdata)
 %% get input info
 hseries=findobj(allchild(0),'tag','series');%handles of the GUI series
 hhseries=guidata(hseries);%handles of the elements in the GUI series
+hseries=findobj(allchild(0),'tag','series'); % handles of the GUI series
+hhseries=guidata(hseries); % handles of the elements in the GUI series
 TimeUnit=get(hhseries.TimeUnit,'String');
 SeriesData=get(hseries,'UserData');
 …
 %% enable j index visibility after the new choice
 status_j='on';%default
+status_j='on'; % default
 if isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)); % case of empty j indices
     status_j='off'; % no j index needed
 elseif strcmp(get(handles.PairString,'Visible'),'on')
     check_burst=cellfun(@isempty,regexp(PairString,'^j'));%=0 for burst case, 1 otherwise
+    check_burst=cellfun(@isempty,regexp(PairString,'^j')); % =0 for burst case, 1 otherwise
     if isempty(find(check_burst, 1))% if all pair string begins by j (burst)
         status_j='off'; % no j index needed for bust case
 …
 function ListPair_Callback(hObject,eventdata)
 %------------------------------------------------------------
 list_pair=get(hObject,'String');%get the menu of image pairs
+list_pair=get(hObject,'String'); % get the menu of image pairs
 if isempty(list_pair)
     string='';
 else
     string=list_pair{get(hObject,'Value')};
    % string=regexprep(string,',.*','');%removes time indication (after ',')
+   % string=regexprep(string,',.*',''); % removes time indication (after ',')
 end
 hseries=findobj(allchild(0),'tag','series');
 …
 iline=str2double(get(handles.InputLine,'String'));
 if size(InputTable,1)>1
     InputTable(iline,:)=[];% suppress the current line if not the first
+    InputTable(iline,:)=[]; % suppress the current line if not the first
     set(handles.InputTable,'Data',InputTable);
 end

Note: See TracChangeset for help on using the changeset viewer.

Context Navigation

Changeset 992

Legend:

trunk/src/compile.m

trunk/src/series.m

Download in other formats: