source: trunk/src/series.m @ 1172

%'series': master function associated to the GUI series.m for analysis field series
%------------------------------------------------------------------------
% function varargout = series(varargin)
% associated with the GUI series.fig
%
%INPUT
% param: structure with input parameters (link with the GUI uvmat)
%      .menu_coord_str: string for the TransformName (menu for coordinate transforms)
%      .menu_coord_val: value for TransformName (menu for coordinate transforms)
%      .FileName: input file name
%      .FileName_1: second input file name
%      .list_field: menu of input fields
%      .index_fields: chosen index
%      .civ1=0 or 1, .interp1,  ... : input civ field type
%

%=======================================================================
% Copyright 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
%   http://www.legi.grenoble-inp.fr
%   Joel.Sommeria - Joel.Sommeria (A) univ-grenoble-alpes.fr
%
%     This file is part of the toolbox UVMAT.
%
%     UVMAT is free software; you can redistribute it and/or modify
%     it under the terms of the GNU General Public License as published
%     by the Free Software Foundation; either version 2 of the license,
%     or (at your option) any later version.
%
%     UVMAT is distributed in the hope that it will be useful,
%     but WITHOUT ANY WARRANTY; without even the implied warranty of
%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
%     GNU General Public License (see LICENSE.txt) for more details.
%=======================================================================

%------------------------------------------------------------------------
%------------------------------------------------------------------------
%  I - MAIN FUNCTION series
%------------------------------------------------------------------------
%------------------------------------------------------------------------
function varargout = series(varargin)

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @series_OpeningFcn, ...
                   'gui_OutputFcn',  @series_OutputFcn, ...
                   'gui_LayoutFcn',  [] , ...
                   'gui_Callback',   []);
if nargin && ischar(varargin{1})
    gui_State.gui_Callback = str2func(varargin{1});
end

if nargout
    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
    gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT

%--------------------------------------------------------------------------
% --- Executes just before series is made visible.
%--------------------------------------------------------------------------
function series_OpeningFcn(hObject, eventdata, handles,Param)

% Choose default command line output for series
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);

%% initial settings
% 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)
%adjust to screen size (reduced by a min margin)
RescaleFactor=min((ScreenSize(3)-80)/Width,(ScreenSize(4)-80)/Height);
if RescaleFactor>1
    RescaleFactor=min(RescaleFactor,1);
end
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)
LowY=round(ScreenSize(4)/2-Height/2); % put at the middle height on the screen
set(hObject,'Units','points')
set(hObject,'Position',[LeftX LowY Width Height])% position and size of the GUI at opening

% settings of table MinIndex_j
set(handles.MinIndex_i,'ColumnFormat',{'numeric'})
set(handles.MinIndex_i,'ColumnEditable',false)
set(handles.MinIndex_i,'ColumnName',{'i min'})
set(handles.MinIndex_i,'Data',[])% initiate Data to double (not cell)

% settings of table MinIndex_j
set(handles.MinIndex_j,'ColumnFormat',{'numeric'})
set(handles.MinIndex_j,'ColumnEditable',false)
set(handles.MinIndex_j,'ColumnName',{'j min'})
set(handles.MinIndex_j,'Data',[])% initiate Data to double (not cell)

% settings of table MaxIndex_i
set(handles.MaxIndex_i,'ColumnFormat',{'numeric'})
set(handles.MaxIndex_i,'ColumnEditable',false)
set(handles.MaxIndex_i,'ColumnName',{'i max'})
set(handles.MaxIndex_i,'Data',[])% initiate Data to double (not cell)

% settings of table MaxIndex_j
set(handles.MaxIndex_j,'ColumnFormat',{'numeric'})
set(handles.MaxIndex_j,'ColumnEditable',false)
set(handles.MaxIndex_j,'ColumnName',{'j max'})
set(handles.MaxIndex_j,'Data',[])% initiate Data to double (not cell)

% settings of table PairString
set(handles.PairString,'ColumnName',{'pairs'})
set(handles.PairString,'ColumnEditable',false)
set(handles.PairString,'ColumnFormat',{'char'})
set(handles.PairString,'Data',{''})

% settings of table MaskTable
%set(handles.MaskTable,'ColumnName',{'mask name'})
set(handles.PairString,'ColumnEditable',false)
set(handles.PairString,'ColumnFormat',{'char'})
set(handles.PairString,'Data',{''})

series_ResizeFcn(hObject, eventdata, handles)%resize table according to series GUI size
set(hObject,'WindowButtonDownFcn',{'mouse_down'})%allows mouse action with right button (zoom for uicontrol display)
set(hObject,'DeleteFcn',{@closefcn})%

% check default input data
if ~exist('Param','var')
    Param=[]; % default
end

%% Read the parameter file series.xml, or created from series.xml.default if it does not exist
SeriesData=[];
[path_series,name,ext]=fileparts(which('series'));% path to the GUI series
xmlfile=fullfile(path_series,'series.xml');
if ~exist(xmlfile,'file')
    [success,message]=copyfile(fullfile(path_series,'series.xml.default'),xmlfile);
    if success==0
        disp(message)
        return
    end
end
if exist(xmlfile,'file')
    SeriesData=xml2struct(xmlfile);% read the xml file containing parameters for series computations
    if ~(isfield(SeriesData,'ClusterParam')&& isfield(SeriesData.ClusterParam,'LaunchCmdFcn'))
        [success,message]=copyfile(xmlfile,fullfile(path_series,'series.xml~'));% backup the file series.xml, not correctly documented
        delete(xmlfile);
        [success,message]=copyfile(fullfile(path_series,'series.xml.default'),xmlfile);% use the defualt series.xml
    end
    SeriesData=xml2struct(xmlfile);% read again the xml file containing parameters for series computations
end

%% list of builtin functions in the menu ActionName
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_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'
ActionExtList={'.m';'.sh';'fluidimage'}; % default choice of extensions (Matlab fct .m or compiled version .sh
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)
if isfield(SeriesData.ClusterParam, 'ExistenceTest')
    oarcommand=SeriesData.ClusterParam.ExistenceTest;
    [s,w]=system(oarcommand); % look for cluster system presence
    if isequal(s,0)% cluster detected
        RunModeList=[RunModeList;{'cluster'}];
        set(handles.MonitorCluster,'Visible','on'); % make visible button for access to Monika
        set(handles.num_CPUTime,'Visible','on'); % make visible button for CPU time estimate for one ref index
        set(handles.num_CPUTime,'String','')% default CPU time undefined
        set(handles.CPUTime_txt,'Visible','on'); % make visible button for CPU time title
    end
    set(handles.RunMode,'String',RunModeList)% display the menu of available run modes, local, background or cluster manager
else
    disp('no cluster availability test in series.xml')
end


%% 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
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
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
dir_perso=prefdir;
profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
if exist(profil_perso,'file')
    h=load (profil_perso);
    %get the list of previous input files in the upper bar menu Open
    if isfield(h,'MenuFile')
        for ifile=1:min(length(h.MenuFile),5)
            set(handles.(['MenuFile_' num2str(ifile)]),'Label',h.MenuFile{ifile});
            set(handles.(['MenuFile_' num2str(ifile+5)]),'Label',h.MenuFile{ifile});
        end
    end
    %get the menu of actions
    if isfield(h,'ActionListUser') && iscell(h.ActionListUser) && isfield(h,'ActionPathListUser') && iscell(h.ActionPathListUser)
        ActionList=[ActionList;h.ActionListUser];
        ActionPathList=[ActionPathList;h.ActionPathListUser(:,1)];
    end
    %get the menu of transform fct
    if isfield(h,'TransformListUser') && iscell(h.TransformListUser) && isfield(h,'TransformPathListUser') && iscell(h.TransformPathListUser)
        TransformList=[TransformList;h.TransformListUser];
        TransformPathList=[TransformPathList;h.TransformPathListUser];
    end
end

%% selection of the input 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
ActionList=ActionList(ActionCheckExist);
set(handles.ActionName,'String',[ActionList;{'more...'}])
set(handles.ActionName,'UserData',ActionPathList)
ActionIndex=[];
if isfield(Param,'ActionName')% copy the selected menu index transferred in Param from uvmat
    ActionIndex=find(strcmp(Param.ActionName,ActionList),1);
end
if isempty(ActionIndex)
    ActionIndex=1;
end
set(handles.ActionName,'Value',ActionIndex)
set(handles.ActionPath,'String',ActionPathList{ActionIndex})
set(handles.ActionExt,'Value',1)
set(handles.ActionExt,'String',ActionExtList)

%% selection of the input transform fct
TransformCheckExist=true(size(TransformList));
for ilist=NbBuiltinTransform+1:numel(TransformList)
    TransformCheckExist(ilist)=exist(fullfile(TransformPathList{ilist},[TransformList{ilist} '.m']),'file');
end
TransformPathList=TransformPathList(TransformCheckExist);
TransformList=TransformList(TransformCheckExist);
set(handles.TransformName,'String',[TransformList;{'more...'}])
set(handles.TransformName,'UserData',TransformPathList)
TransformIndex=[];
if isfield(Param,'TransformName')% copy the selected menu index transferred in Param from uvmat
    TransformIndex=find(strcmp(Param.TransformName,TransformList),1);
end
if isempty(TransformIndex)
    TransformIndex=1;
end
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)
    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')
    if isfield(Param.Coordinates,'Coord_x')
        set(handles.Coord_x,'String',Param.Coordinates.Coord_x)
    end
    if isfield(Param.Coordinates,'Coord_y')
        set(handles.Coord_y,'String',Param.Coordinates.Coord_y)
    end
    if isfield(Param.Coordinates,'Coord_z')
        set(handles.Coord_z,'String',Param.Coordinates.Coord_z)
    end
end

%% introduce the input file name(s) if defined from input Param,
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}];
    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
    end
    TimeTable=[{Param.InputFile.TimeName},{[]},{[]},{[]},{[]}];
    if isfield(Param.InputFile,'RootPath_1')
        InputTable=[InputTable;[{Param.InputFile.RootPath_1},{Param.InputFile.SubDir_1},{Param.InputFile.RootFile_1},{Param.InputFile.NomType_1},{Param.InputFile.FileExt_1}]];
        TimeTable=[TimeTable; [{Param.InputFile.TimeName_1},{[]},{[]},{[]},{[]}]];
    end
    set(handles.InputTable,'Data',InputTable)

    %% define the default path for the output files
    [InputPath,Device,DeviceExt]=fileparts(InputTable{1,1});
    [InputPath,Experiment,ExperimentExt]=fileparts(InputPath);
    set(handles.Device,'String',[Device DeviceExt])
    set(handles.Experiment,'String',[Experiment ExperimentExt])
    if ~isempty(regexp(InputTable{1,1},'(^http://)|(^https://)'))
    set(handles.OutputPathBrowse,'Value',1)% an output folder needs to be specified for OpenDAP data
    end

    %update the output path if needed
    if ~(isfield(SeriesData,'InputPath') && strcmp(SeriesData.InputPath,InputPath))
    if get(handles.OutputPathBrowse,'Value')==1  % fix the output path in manual mode
        OutputPathOld=get(handles.OutputPath,'String');
        OutputPath=uigetdir(OutputPathOld,'pick a root folder for output data');
        set(handles.OutputPath,'String',OutputPath)
    else %reproduce the input path for output
        set(handles.OutputPath,'String',InputPath)
    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)
        i1=1;
    end
    if isempty(i2)
        i2=i1;
    end
    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)
        j1=1;
    end
    if isempty(j2)
        j2=j1;
    end
    ref_j=floor((j1+j2)/2); % reference image number corresponding to the file
    SeriesData.ref_i=ref_i;
    SeriesData.ref_j=ref_j;
    set(handles.series,'UserData',SeriesData)
    update_rootinfo(handles,Param.HiddenData.i1_series{1},Param.HiddenData.i2_series{1},Param.HiddenData.j1_series{1},Param.HiddenData.j2_series{1},...
        Param.HiddenData.FileInfo{1},Param.HiddenData.MovieObject{1},1)
    if isfield(Param,'FileName_1')
        %         display_file_name(handles,Param,2)
        update_rootinfo(handles,Param.HiddenData.i1_series{2},Param.HiddenData.i2_series{2},Param.HiddenData.j1_series{2},Param.HiddenData.j2_series{2},...
            Param.HiddenData.FileInfo{2},Param.HiddenData.MovieObject{2},2)
    end
    %% 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
end
if isfield(Param,'incr_i')
    set(handles.num_incr_i,'String',num2str(Param.incr_i))
else
    set(handles.num_incr_i,'String','1')
end
if isfield(Param,'incr_j')
    set(handles.num_incr_j,'String',num2str(Param.incr_j))
else
    set(handles.num_incr_j,'String','1')
end

%------------------------------------------------------------------------
% --- Outputs from this function are returned to the command line.
function varargout = series_OutputFcn(hObject, eventdata, handles)
%------------------------------------------------------------------------
varargout{1} = handles.output;

%------------------------------------------------------------------------
% --- executed when closing uvmat: delete or desactivate the associated figures if exist
function closefcn(gcbo,eventdata)
%------------------------------------------------------------------------

% delete set_object_series if detected
hh=findobj(allchild(0),'name','view_object_series');
if ~isempty(hh)
    delete(hh)
end
hh=findobj(allchild(0),'name','edit_object_series');
if ~isempty(hh)
    delete(hh)
end

%delete the bowser if detected
hh=findobj(allchild(0),'tag','browser');
if ~isempty(hh)
    delete(hh)
end


%------------------------------------------------------------------------
%------------------------------------------------------------------------
%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
% 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
%------------------------------------------------------------------------
%------------------------------------------------------------------------
% --- fct activated by the browser under 'Open'
%------------------------------------------------------------------------
function MenuBrowse_Callback(hObject, eventdata, handles)
%% look for the previously opened file 'oldfile'
InputTable=get(handles.InputTable,'Data');
oldfile=InputTable{1,1};
if isempty(oldfile)
    % use a file name stored in prefdir
    dir_perso=prefdir;
    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
    if exist(profil_perso,'file')
        h=load (profil_perso);
        if isfield(h,'RootPath') && ischar(h.RootPath)
            oldfile=h.RootPath;
        end
    end
end
%% launch the browser
fileinput=uigetfile_uvmat('pick an input file in the series',oldfile);
hh=dir(fileinput);
if numel(hh)>1
    msgbox_uvmat('ERROR','invalid input, probably a broken link');
else
    if ~isempty(fileinput)
        display_file_name(handles,fileinput,'one')
    end
end

% --------------------------------------------------------------------
function MenuBrowseAppend_Callback(hObject, eventdata, handles)

%% look for the previously opened file 'oldfile'
InputTable=get(handles.InputTable,'Data');
RootPathCell=InputTable(:,1);
if isempty(RootPathCell{1})% no input file in the table
     MenuBrowse_Callback(hObject, eventdata, handles)%refresh the input table, not append
     return
end
SubDirCell=InputTable(:,2);
oldfile=fullfile(RootPathCell{1},SubDirCell{1});

%% use a file name stored in prefdir
dir_perso=prefdir;
profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
if exist(profil_perso,'file')
    h=load (profil_perso);
    if isfield(h,'RootPath') && ischar(h.RootPath)
        oldfile=h.RootPath;
    end
end

%% launch the browser
fileinput=uigetfile_uvmat('pick a file to append in the input table',oldfile);
hh=dir(fileinput);
if numel(hh)>1
    msgbox_uvmat('ERROR','invalid input, probably a broken link');
else
    if ~isempty(fileinput)
        display_file_name(handles,fileinput,'append')
    end
end

%------------------------------------------------------------------------
% --- fct activated by selecting a previous file under the menu Open
%------------------------------------------------------------------------
function MenuFile_Callback(hObject, eventdata, handles)

errormsg=display_file_name(handles,get(hObject,'Label'),'one');
if ~isempty(errormsg)
    set(hObject,'Label','')
    MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
        {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
    for ifile=1:numel(MenuFile)
        set(handles.(['MenuFile_' num2str(ifile)]),'Label',MenuFile{ifile});
    end
end

%------------------------------------------------------------------------
% --- fct activated by selecting a previous file under the menu Open/append
%------------------------------------------------------------------------
function MenuFile_append_Callback(hObject, eventdata, handles)

InputTable=get(handles.InputTable,'Data');
if isempty(InputTable{1,1})% no input file in the table
    display_file_name(handles,get(hObject,'Label'),'one') %refresh the input table, not append
else
    display_file_name(handles,get(hObject,'Label'),'append')% append the selected file to the current list of InputTable
end

%------------------------------------------------------------------------
% --- fct activated by the browser under 'Open campaign/Browse...'
%------------------------------------------------------------------------
function MenuBrowseCampaign_Callback(hObject, eventdata, handles)

%% look for the previously opened file 'oldfile'
InputTable=get(handles.InputTable,'Data');
if ~isempty(InputTable)
oldfile=[InputTable{1,1} InputTable{1,2}];
else
    % use a file name stored in prefdir
    dir_perso=prefdir;
    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
    if exist(profil_perso,'file')
        h=load (profil_perso);
        if isfield(h,'MenuCampaign') && ~isempty(h.MenuCampaign)&& ischar(h.MenuCampaign{1})
            oldfile=h.MenuCampaign{1};
        end
    end
end
InputTable{1,1}='...';
set(handles.InputTable,'Data',InputTable)
browse_data(oldfile,'on','on'); % open the GUI browse_data to get select a campaign dir, experiment and device



% --- Executes when selected cell(s) is changed in InputTable.
function InputTable_CellSelectionCallback(hObject, eventdata, handles)
iline=[];
if ~isempty(eventdata.Indices)
    iline=eventdata.Indices(1);
end
set(handles.InputLine,'String',num2str(iline));

%------------------------------------------------------------------------
% --- 'key_press_fcn:' function activated when a key is pressed on the keyboard
%------------------------------------------------------------------------
function InputTable_KeyPressFcn(hObject, eventdata, handles)
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
if ~isempty(xx)
    switch xx
        case 31 %downward arrow
            InputTable=get(handles.InputTable,'Data');
            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
                set(handles.InputTable,'Data',InputTable);
            end
        case 127  %key 'Suppress'
            ClearLine_Callback(hObject, eventdata, handles)
    end
end

%------------------------------------------------------------------------
% --- Executes on button press in REFRESH.
function REFRESH_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
check_input_file_series(handles)

%% enable field and veltype menus, in accordance with the current action
ActionInput_Callback([],[], handles)

%------------------------------------------------------------------------
% --- check the input file series.
function check_input_file_series(handles)
%------------------------------------------------------------------------
InputTable=get(handles.InputTable,'Data');%read the table of input file series
set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
drawnow
empty_line=false(size(InputTable,1),1);
for iline=1:size(InputTable,1)
    empty_line(iline)= isempty(cell2mat(InputTable(iline,1:3)));%check the empty lines in the input table
end
if ~isempty(find(empty_line,1))%removes the empty lines in the table
    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
        set(handles.(ListTable{ilist}),'Data',Table);
    end
    set(handles.series,'UserData',[])%refresh the stored info
end
nbview=size(InputTable,1);
for iview=1:nbview
    RootPath=fullfile(InputTable{iview,1},InputTable{iview,2});
    if ~exist(RootPath,'dir')
        i1_series=[];
        RootFile='';
    else %scan the input folder
        InputTable{iview,3}=regexprep(InputTable{iview,3},'^/','');%suppress '/' at the beginning of the input name
        i1=str2double(get(handles.num_first_i,'String'));
        j1=str2double(get(handles.num_first_j,'String'));
        j2=[];%default
        PairString=get(handles.PairString,'Data');
        if numel(PairString)>=iview
                r=regexp(PairString{iview},'(?<num1>\d+)-(?<num2>\d+)' ,'names');
                if ~isempty(r)
                j1=str2double(r.num1);
                j2=str2double(r.num2);
                end
        end
        InputFile=fullfile_uvmat('','',InputTable{iview,3},InputTable{iview,5},InputTable{iview,4},i1,[],j1,j2);
        [RootPath,~,RootFile,i1_series,i2_series,j1_series,j2_series,~,FileInfo,MovieObject]=...
                find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),InputFile);
    end
    % if no file is found, open a browser
    if isempty(RootFile)&& isempty(i1_series)
        fileinput=uigetfile_uvmat(['wrong input at line ' num2str(iview) ':pick a new input file'],RootPath);
        if isempty(fileinput)
            set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  back to red color
            return
        else
            display_file_name(handles,fileinput,iview)% update the table of input file series, then call update_rootinfo
        end
    else
       update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview)
    end
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
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
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

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
set(handles.MaxIndex_j,'Data',MaxIndex_j_table(1:nbview,:));
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
set(handles.TimeTable,'Data',TimeTable(1:nbview,:));

%% set length of waitbar
displ_time(handles)
set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (indicate activation finished)
set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch'



%------------------------------------------------------------------------
% --- Function called when a new file is opened, either by series_OpeningFcn or by the browser
%------------------------------------------------------------------------
% INPUT:
% handles: handles of elements in the GUI
% Param: structure of input parameters, including  input file name and path
% iview: line index in the input table
%       or 'one': refresh the list
%         '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;
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')
    errormsg=['input file ' fileinput  ' does not exist'];
    msgbox_uvmat('ERROR',errormsg)
    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (refresh still needed)
    return
end

%% detect root name, nomenclature and indices in the input file name:
[FilePath,FileName,FileExt]=fileparts(fileinput);
%%%%%%%%%%%%%%%%%%
%TODO: case of input by uvmat: do not check agai the input series %%%%%%%
%%%%%%%%%%%%%%%%%%%
% detect the file type, get the movie object if relevant, and look for the corresponding file series:
% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
FileType=FileInfo.FileType;
if isempty(RootFile)&&isempty(i1_series)
    errormsg='no input file in the series';
    msgbox_uvmat('ERROR',errormsg)
    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (end of activation)
    return
end
if strcmp(FileType,'txt')
    edit(fileinput)
    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to  magenta color (end of activation)
    return
elseif strcmp(FileType,'xml')
    editxml(fileinput)
    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
     return
elseif strcmp(FileType,'figure')
    open(fileinput)
    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
     return
end

%% enable other menus and uicontrols
set(handles.RUN, 'Enable','On')
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


%% fill the list of file series
InputTable=get(handles.InputTable,'Data');
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
elseif strcmp(iview,'one') % refresh the list of  input  file series
    iview=1; % the first line in InputTable becomes the current line
    InputTable={'','','','',''};
    set(handles.TimeTable,'Data',[{''},{[]},{[]},{[]},{[]}])
    set(handles.MinIndex_i,'Data',[])
    set(handles.MaxIndex_i,'Data',[])
    set(handles.MinIndex_j,'Data',[])
    set(handles.MaxIndex_j,'Data',[])
    set(handles.PairString,'Data',{''})
    SeriesData.CheckPair=0; % reset the list of input lines with pairs
    SeriesData.i1_series={};
    SeriesData.i2_series={};
    SeriesData.j1_series={};
    SeriesData.j2_series={};
    SeriesData.FileType={};
    SeriesData.FileInfo={};
    SeriesData.Time={};
end
if isfield(SeriesData,'i1_series')
    SeriesData.i1_series(iview+1:end)=[];
    SeriesData.i2_series(iview+1:end)=[];
    SeriesData.j1_series(iview+1:end)=[];
    SeriesData.j2_series(iview+1:end)=[];
    SeriesData.FileType(iview+1:end)=[];
    SeriesData.FileInfo(iview+1:end)=[];
    SeriesData.Time(iview+1:end)=[];
end
InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
if iview >1
    set(handles.InputLine,'String',num2str(iview))
end
set(handles.InputTable,'Data',InputTable)

%% determine the selected reference field indices for pair display
if isempty(i1)
    i1=1;
end
if isempty(i2)
    i2=i1;
end
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)
    j1=1;
end
if isempty(j2)
    j2=j1;
end
ref_j=floor((j1+j2)/2); % reference image number corresponding to the file
SeriesData.ref_i=ref_i;
SeriesData.ref_j=ref_j;

%% update first and last indices if they do not exist
Param=read_GUI(handles.series);
first_j=[];
if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
last_j=[];
if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
PairString='';
if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
[i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
if ~exist(FirstFileName,'file')
    set(handles.num_first_i,'String',num2str(ref_i))
    set(handles.num_first_j,'String',num2str(ref_j))
end
[i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString);
LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
if ~exist(LastFileName,'file')
    set(handles.num_last_i,'String',num2str(ref_i))
    set(handles.num_last_j,'String',num2str(ref_j))
end

%% update the list of recent files in the menubar and save it for future opening
MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
str_find=strcmp(fileinput,MenuFile);
if isempty(find(str_find,1))
    MenuFile=[{fileinput};MenuFile]; % insert the current file if not already in the list
end
for ifile=1:min(length(MenuFile),5)
    ffname=['MenuFile_' num2str(ifile)];
    set(handles.(ffname),'Label',MenuFile{ifile});
end
dir_perso=prefdir;
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
else
    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.Ref_i1=i1;
SeriesData.Ref_i2=i2;
SeriesData.Ref_j1=j1;
SeriesData.Ref_j2=j2;

%% define the path for the output files
[InputPath,Device,DeviceExt]=fileparts(InputTable{1,1});
[InputPath,Experiment,ExperimentExt]=fileparts(InputPath);
set(handles.Device,'String',[Device DeviceExt])
set(handles.Experiment,'String',[Experiment ExperimentExt])
if ~isempty(regexp(InputTable{1,1},'(^http://)|(^https://)', 'once'))
    set(handles.OutputPathBrowse,'Value',1)% an output folder needs to be specified for OpenDAP data
end

%update the output path if needed
if ~(isfield(SeriesData,'InputPath') && strcmp(SeriesData.InputPath,InputPath))
    if get(handles.OutputPathBrowse,'Value')==1  % fix the output path in manual mode
        OutputPathOld=get(handles.OutputPath,'String');
        OutputPath=uigetdir(OutputPathOld,'pick a root folder for output data');
        set(handles.OutputPath,'String',OutputPath)
    else %reproduce the input path for output
        set(handles.OutputPath,'String',InputPath)
    end
    SeriesData.InputPath=InputPath;
end

set(handles.series,'UserData',SeriesData)

set(handles.InputTable,'BackgroundColor',[1 1 1])

%% 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
ActionName_Callback([],[], handles)

%% set length of waitbar
displ_time(handles)

set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (end of activation)

%------------------------------------------------------------------------
% --- Update information about a new field series (indices to scan, timing,
%     calibration from an xml file
function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,VideoObject,iview)
%------------------------------------------------------------------------
InputTable=get(handles.InputTable,'Data');

%% make the j indices visible if relevant
if (isempty(j1_series)|| ~isempty(j2_series))% no j series or j1-j2 pair
    enable_j(handles,'off');
else
   enable_j(handles,'on')%%%%remark: put series with j index at the end in the case of a list
end

%% 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
    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)
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
     MinIndex_i=find(ref_i, 1 )-1;
     MaxIndex_i=find(ref_i, 1, 'last' )-1;
     MaxIndex_j=find(ref_j, 1, 'last' )-1;
     MinIndex_j=find(ref_j, 1 )-1;
    diff_j_max=diff(ref_j);
    diff_i_max=diff(ref_i);
    if ~isempty(diff_i_max) && isequal (diff_i_max,diff_i_max(1)*ones(size(diff_i_max)))
        set(handles.num_incr_i,'String',num2str(diff_i_max(1)))% detect an increment to dispaly by default
    end
    if ~isempty(diff_j_max) && isequal (diff_j_max,diff_j_max(1)*ones(size(diff_j_max)))
        set(handles.num_incr_j,'String',num2str(diff_j_max(1)))
    end
end
if isequal(MinIndex_i,-1)
    MinIndex_i=0;
end
if isequal(MinIndex_j,-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
if ~isempty(MinIndex_i)&&~isempty(MaxIndex_i)
    MinIndex_i_table(iview,1)=MinIndex_i;
    MaxIndex_i_table(iview,1)=MaxIndex_i;
end
if ~isempty(MinIndex_j)&&~isempty(MaxIndex_j)
    MinIndex_j_table(iview,1)=MinIndex_j;
    MaxIndex_j_table(iview,1)=MaxIndex_j;
end
set(handles.MinIndex_i,'Data',MinIndex_i_table)%display the min indices in the table MinIndex
set(handles.MinIndex_j,'Data',MinIndex_j_table)%display the max indices in the table MaxIndex
set(handles.MaxIndex_i,'Data',MaxIndex_i_table)%display the min indices in the table MinIndex
set(handles.MaxIndex_j,'Data',MaxIndex_j_table)%display the max indices in the table MaxIndex


SeriesData=get(handles.series,'UserData');

%% 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
ref_i=1;
if isfield(SeriesData,'ref_i')
    ref_i=SeriesData.ref_i;
end
if isempty(first_i)
    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)
end
% j index,  compare input to min index j
first_j=str2num(get(handles.num_first_j,'String'));
ref_j=1;
if isfield(SeriesData,'ref_j')
    ref_j=SeriesData.ref_j;
end
if isempty(first_j)
    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)
elseif first_j >MaxIndex_j
    first_j=MaxIndex_j; % first_j set to the max j index (restricted by oter input lines)
end
% i index, compare input to max index i
last_i=str2num(get(handles.num_last_i,'String'));
if isempty(last_i)
    last_i=ref_i;
elseif last_i > MaxIndex_i
    last_i=MaxIndex_i;
elseif last_i<first_i
    last_i=first_i;
end
% j index, compare input to max index j
last_j=str2num(get(handles.num_last_j,'String'));
if isempty(last_j)
    last_j=ref_j;
elseif last_j>MaxIndex_j
    last_j=MaxIndex_j;
elseif last_j<first_j
    last_j=first_j;
end
set(handles.num_first_i,'String',num2str(first_i));
set(handles.num_first_j,'String',num2str(first_j));
set(handles.num_last_i,'String',num2str(last_i));
set(handles.num_last_j,'String',num2str(last_j));

%% number of slices set by 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')
    NbSlice=str2double(get(handles.num_NbSlice,'String'));
end

%% default time settings
TimeUnit='';
% read  value set by the first series for the append mode (iwiew >1)
if iview>1
    TimeUnit=get(handles.TimeUnit,'String');
end
TimeName='';
Time=[]; % default
TimeMin=[];
TimeFirst=[];
TimeLast=[];
TimeMax=[];

%%  read image documentation file if found
XmlData=[];
check_calib=0;
XmlFileName=find_imadoc(InputTable{iview,1},InputTable{iview,2});
if ~isempty(XmlFileName)
    [XmlData,errormsg]=imadoc2struct(XmlFileName);
    if ~isempty(errormsg)
        msgbox_uvmat('WARNING',['error in reading ' XmlFileName ': ' errormsg]);
    end
    % read time if available
    if isfield(XmlData,'Time')
        Time=XmlData.Time;
        TimeName='xml';
    end
    if isfield(XmlData,'Camera')
        if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
            if iview>1 && ~isempty(TimeUnit) && ~strcmp(TimeUnit,XmlData.Camera.TimeUnit)
                msgbox_uvmat('WARNING','inconsistent time unit with the first field series');
            end
            TimeUnit=XmlData.Camera.TimeUnit;
        end
    end
    % number of slices
    if isfield(XmlData,'TranslationMotor')&& isfield(XmlData.TranslationMotor,'NbSlice')
        NbSlice_motor=XmlData.TranslationMotor.NbSlice;
        if ~isempty(NbSlice) && ~isequal(NbSlice_motor,NbSlice)
                msgbox_uvmat('WARNING','inconsistent Z numbers of Z indices');
        else
            NbSlice=NbSlice_motor;
        end
    end
end
if ~isempty(NbSlice)
set(handles.num_NbSlice,'String',num2str(NbSlice))
set(handles.num_NbSlice,'Visible','on')
end

%% read timing  from the current file (prioritary)
if ~isempty(VideoObject)% case of movies
    imainfo=get(VideoObject);
    if isfield(imainfo,'NumFrames')
        imainfo.NumberOfFrames=imainfo.NumFrames;
    end
    if isempty(j1_series) % frame index along i
        Time=zeros(imainfo.NumberOfFrames+1,2);
        Time(:,2)=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)';
    else
        Time=[0;ones(size(i1_series,3)-1,1)]*(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate);
    end
    TimeName='video';
end


%% determine the min and max times: case of Netcdf files will be treated later in FieldName_Callback
if ~isempty(TimeName)
    if size(Time)<[MaxIndex_i+1 MaxIndex_j+1]
       msgbox_uvmat('WARNING',['incomplete time info in ' XmlFileName]);
    end
    TimeMin=Time(MinIndex_i+1,MinIndex_j+1);
    if size(Time)>=[first_i+1 first_j+1]
        TimeFirst=Time(first_i+1,first_j+1);
    end
    if size(Time)>=[last_i+1 last_j+1]
        TimeLast=Time(last_i+1,last_j+1);
    end
    if size(Time)>=[MaxIndex_i+1 MaxIndex_j+1]
        TimeMax=Time(MaxIndex_i+1,MaxIndex_j+1);
    end
end

%% update the time table
TimeTable=get(handles.TimeTable,'Data');
TimeTable{iview,1}=TimeName;
TimeTable{iview,2}=TimeMin;
TimeTable{iview,3}=TimeFirst;
TimeTable{iview,4}=TimeLast;
TimeTable{iview,5}=TimeMax;
set(handles.TimeTable,'Data',TimeTable)

%% update the series info in 'UserData'
SeriesData.i1_series{iview}=i1_series;
SeriesData.i2_series{iview}=i2_series;
SeriesData.j1_series{iview}=j1_series;
SeriesData.j2_series{iview}=j2_series;
SeriesData.FileType{iview}=FileInfo.FileType;
SeriesData.FileInfo{iview}=FileInfo;
SeriesData.Time{iview}=Time;

SeriesData.TimeName=TimeName;

if check_calib
    SeriesData.GeometryCalib{iview}=XmlData.GeometryCalib;
end
set(handles.series,'UserData',SeriesData)

%% update pair menus
hset_pair=findobj(allchild(0),'Tag','set_pairs');
if ~isempty(hset_pair), delete(hset_pair); end % delete the GUI set_pair if opened
CheckPair= ~isempty(i2_series)||~isempty(j2_series); % check whether index pairs need to be defined
PairString=get(handles.PairString,'Data');
if CheckPair% if pairs need to be display for line iview
    [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series);
    Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,ModeMenu{ModeValue},Time,TimeUnit,ref_i,ref_j,TimeName,InputTable(iview,:),FileInfo);
    PairString{iview,1}=Menu{1};
else
    PairString{iview,1}=''; % no pair for #iview
end
set(handles.PairString,'Data',PairString)
if isempty(find(cellfun('isempty',get(handles.PairString,'Data'))==0, 1))% if all lines of pairs are empty
    set(handles.PairString,'Visible','off')
    set(handles.SetPairs,'Visible','off')
else
    set(handles.PairString,'Visible','on')
    set(handles.SetPairs,'Visible','on')
end


%% display the set of existing files as an image with black bands for gaps showing gaps in the series
set(handles.FileStatus,'Units','pixels')
Position=get(handles.FileStatus,'Position');
set(handles.FileStatus,'Units','normalized')
%xI=0.5:Position(3)-0.5;
nbview=numel(SeriesData.i1_series);
j_max=cell(1,nbview);
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
    if ~isempty(j_max{iline})
    MaxIndex_i(iline)=find(j_max{iline}, 1, 'last' )-1; % max ref index i
    MinIndex_i(iline)=find(j_max{iline}, 1 )-1; % min ref index i
    end
end
MinIndex_i=min(MinIndex_i);
MaxIndex_i=max(MaxIndex_i);
range_index=MaxIndex_i-MinIndex_i+1;
range_y=max(1,floor(Position(4)/nbview));
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
for iline=1:nbview
    ind_y=1+(iline-1)*range_y:iline*range_y;
    LineData=zeros(size(file_indices));
    file_select=file_indices(file_indices<=numel(j_max{iline}));
    ind_select=file_indices<=numel(j_max{iline});
    LineData(ind_select)=j_max{iline}(file_select)~=0;
    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
set(handles.FileStatus,'CData',CData);

%-----------------------------------------------------------guide -------------
%------------------------------------------------------------------------
%  III - FUNCTIONS ASSOCIATED TO THE FRAME IndexRange
%------------------------------------------------------------------------


% ---- determine the menu to put in mode and advice a default choice
%------------------------------------------------------------------------
function [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series)
%------------------------------------------------------------------------
ModeMenu={''};
if isempty(j2_series)% no j pair
    ModeValue=1;
    if ~isempty(i2_series)
        ModeMenu={'series(Di)'}; % pair menu with only option Di
    end
else %existence of j pairs
    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
    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
    if MaxIndex_j==MinIndex_j
        ModeValue=1;
        ModeMenu={'bursts'};
    elseif MaxIndex_i==MinIndex_i
        ModeValue=1;
        ModeMenu={'series(Dj)'};
    else
        ModeMenu={'bursts';'series(Dj)'};
        if (MaxIndex_j-MinIndex_j)>10
            ModeValue=2; % set mode to series(Dj) if more than 10 j values
        else
            ModeValue=1;
        end
    end
end


%------------------------------------------------------------------------
%fill the menu of possible pairs as input
function displ_pair=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo)
%------------------------------------------------------------------------
displ_pair={};
if isempty(TimeUnit)
    dtunit='e-03';
else
    dtunit=['m' TimeUnit];
end
switch mode
    case 'series(Di)'
        diff_i=i2_series-i1_series;
        min_diff=min(diff_i(diff_i>0));
        max_diff=max(diff_i(diff_i>0));
        for ipair=min_diff:max_diff
            if ~isempty(find(diff_i==ipair,1))% if the considered difference exists as input
                pair_string=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
                if size(time,1)>=ref_i+ceil(ipair/2)
                    if ref_i<=floor(ipair/2)
                        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);
                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
                end
                displ_pair=[displ_pair;{pair_string}];
            end
        end
        if ~isempty(displ_pair)
            displ_pair=[displ_pair;{'Di=*|*'}];
        end
    case 'series(Dj)'
        if isempty(j2_series)
            msgbox_uvmat('ERROR','no j1-j2 pair available')
            return
        end
        diff_j=j2_series-j1_series;
        min_diff=min(diff_j(diff_j>0));
        max_diff=max(diff_j(diff_j>0));
        for ipair=min_diff:max_diff
            if numel(diff_j(diff_j==ipair))>0
                pair_string=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
                if ~isempty(time)
                    if ref_j<=floor(ipair/2)
                        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));
                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
                end
                displ_pair=[displ_pair;{pair_string}];
            end
        end
        if ~isempty(displ_pair)
            displ_pair=[displ_pair;{'Dj=*|*'}];
        end
    case 'bursts'
        if isempty(j2_series)
            msgbox_uvmat('ERROR','no j1-j2 pair available')
            return
        end
        %diff_j=j2_series-j1_series;
        min_j1=min(j1_series(j1_series>0));
        max_j1=max(j1_series(j1_series>0));
        min_j2=min(j2_series(j2_series>0));
        max_j2=max(j2_series(j2_series>0));
        for pair1=min_j1:min(max_j1,min_j1+20)
            for pair2=min_j2:min(max_j2,min_j2+20)
                if numel(j1_series(j1_series==pair1))>0 && numel(j2_series(j2_series==pair2))>0
                    pair_string=['j= ' num2str(pair1) '-' num2str(pair2)];
                    [TimeValue,DtValue]=get_time(ref_i,[],pair_string,InputTable,FileInfo,TimeName,'Dt');
                    %Dt=time(ref_i,pair2+1)-time(ref_i,pair1+1);
                    pair_string=[pair_string ', Dt=' num2str(DtValue) ' ' dtunit];
                    displ_pair=[displ_pair;{pair_string}];
                end
            end
        end
        if ~isempty(displ_pair)
            displ_pair=[displ_pair;{'j=*-*'}];
        end
end

%------------------------------------------------------------------------
function num_first_i_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
num_last_i_Callback(hObject, eventdata, handles)

%------------------------------------------------------------------------
function num_last_i_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
SeriesData=get(handles.series,'UserData');
if ~isfield(SeriesData,'Time')
    SeriesData.Time{1}=[];
end
displ_time(handles);

%------------------------------------------------------------------------
function num_first_j_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
 num_last_j_Callback(hObject, eventdata, handles)

%------------------------------------------------------------------------
function num_last_j_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
SeriesData=get(handles.series,'UserData');
if ~isfield(SeriesData,'Time')
    SeriesData.Time{1}=[];
end
displ_time(handles);

%------------------------------------------------------------------------
% ---- find the times corresponding to the first and last indices of a series
function displ_time(handles)
%------------------------------------------------------------------------
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_j_1=[];ref_j_2=[];
if strcmp(get(handles.num_first_j,'Visible'),'on')
ref_j_1=str2num(get(handles.num_first_j,'String'));
ref_j_2=str2num(get(handles.num_last_j,'String'));
end
[i1_1,i2_1,j1_1,j2_1] = get_file_index(ref_i_1,ref_j_1,PairString);
[i1_2,i2_2,j1_2,j2_2] = get_file_index(ref_i_2,ref_j_2,PairString);
TimeTable=get(handles.TimeTable,'Data');
%%%%%%
%TODO: read time in netcdf file, see ActionName_Callback
%%%%%%%
%Pairs=get(handles.PairString,'Data');
for iview=1:size(TimeTable,1)
    if numel(SeriesData.Time)<iview
        break
    end
    TimeTable{iview,3}=[];
    TimeTable{iview,4}=[];
    if size(SeriesData.Time{iview},1)>=i2_2+1 && (isempty(ref_j_1)||size(SeriesData.Time{iview},2)>=j2_2+1)
        if isempty(ref_j_1)
            time_first=(SeriesData.Time{iview}(i1_1+1,2)+SeriesData.Time{iview}(i2_1+1,2))/2;
            time_last=(SeriesData.Time{iview}(i1_2+1,2)+SeriesData.Time{iview}(i2_2+1,2))/2;
        else
            time_first=(SeriesData.Time{iview}(i1_1+1,j1_1+1)+SeriesData.Time{iview}(i2_1+1,j2_1+1))/2;
            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
    end
end
set(handles.TimeTable,'Data',TimeTable)

%% set the waitbar position with respect to the min and max in the series
MinIndex_i=min(get(handles.MinIndex_i,'Data'));
MaxIndex_i=max(get(handles.MaxIndex_i,'Data'));
pos_first=(ref_i_1-MinIndex_i)/(MaxIndex_i-MinIndex_i+1);
pos_last=(ref_i_2-MinIndex_i+1)/(MaxIndex_i-MinIndex_i+1);
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_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
set(handles.Waitbar,'Position',Position)
update_waitbar(handles.Waitbar,0)

%------------------------------------------------------------------------
% --- Executes when selected cell(s) is changed in PairString.
function PairString_CellSelectionCallback(hObject, eventdata, handles)
%------------------------------------------------------------------------
if numel(eventdata.Indices)>=1
    PairString=get(hObject,'Data');
    if ~isempty(PairString{eventdata.Indices(1)})
        SetPairs_Callback(hObject, eventdata.Indices(1), handles)
    end
end


%-----------------------------------
function enable_j(handles,state)
set(handles.j_txt,'Visible',state)
set(handles.num_first_j,'Visible',state)
set(handles.num_last_j,'Visible',state)
set(handles.num_incr_j,'Visible',state)
set(handles.MinIndex_j,'Visible',state)
set(handles.MaxIndex_j,'Visible',state)


%%%%%%%%%%%%%%%%%%%%
%%  MAIN ActionName FUNCTIONS
%%%%%%%%%%%%%%%%%%%%
%------------------------------------------------------------------------
% --- Executes on button press in RUN.
%------------------------------------------------------------------------
function RUN_Callback(hObject, eventdata, handles)

%% settings of the button RUN
if ~isequal(get(handles.ActionInput,'BackgroundColor'),[1 0 0])
    msgbox_uvmat('ERROR','first activate the button ActionInput')
    return
end
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
drawnow
set(handles.status,'Value',0)% desable status display if relevant
status_Callback([], eventdata, handles)

%% launch action
errormsg=launch_action(handles);
if ~isempty(errormsg)
     msgbox_uvmat('ERROR',errormsg)
end

%% reset the GUI series
update_waitbar(handles.Waitbar,1); % put the waitbar to end position to indicate launching is finished
set(handles.RUN, 'Enable','On')
set(handles.RUN,'BackgroundColor',[1 0 0])
set(handles.RUN, 'Value',0)

%------------------------------------------------------------------------
% --- called by RUN_Callback
%------------------------------------------------------------------------
% The calculations are launched in three different ways:
% RunMode='local': calculation on the local Matlab session, will prevent other actions during that time.
% RunMode='background': calculation on the local computer, but in a new Matlab session (with no graphic output).
% 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
% 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
% so that a job is optimum length AdvisedJobCPUTime), and the total job number in any case smaller
% 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.

function errormsg=launch_action(handles)
errormsg=''; % default

%% read the data on the GUI series
Param=read_GUI_series(handles); % displayed parameters
SeriesData=get(handles.series,'UserData'); % hidden parameters
if isfield(SeriesData,'TransformInput')
    Param.TransformInput=SeriesData.TransformInput;
end
if isfield(SeriesData,'ProjObject')
    Param.ProjObject=SeriesData.ProjObject;
end
if ~isfield(SeriesData,'i1_series')
    errormsg='The input field series needs to be refreshed: press REFRESH';
    return
end
if isfield(Param,'InputFields')&& isfield(Param.InputFields,'FieldName')&& isequal(Param.InputFields.FieldName,'add_field...')
    errormsg='input field name(s) not defined, select add_field...';
    return
end
[status,result]=system(['svn info ' Param.Action.ActionPath]);
if status==0
    t=regexp(result,'R.vision\s*:\s*(?<rev>\d+)','names');%detect 'revision' or 'Revision' in the text
    if ~isempty(t)
        Param.UvmatRevision=t.rev; %version nbre of the current package
    end
end

%% select the Action mode, 'local', 'background' or 'cluster' (if available)
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
    Param.RunMode=RunMode; % keep track of the mode
end
ActionExt='.m'; % default
if isfield(Param.Action,'ActionExt')
    ActionExt=Param.Action.ActionExt; % '.m', '.sh' (compiled)  or 'fluidimage' (Python)
    Param.Action=rmfield(Param.Action,'ActionExt'); % remove from the recorded xml file to avoid interference during ImportConfig
end
ActionName=Param.Action.ActionName;
ActionPath=Param.Action.ActionPath;
path_series=fileparts(which('series'));

%% create the Action fct handle if RunMode option = 'local'
if strcmp(RunMode,'local')
    current_dir=pwd; % current working dir
    cd(ActionPath)
    h_fun=str2func(ActionName);% create the function handle for the function ActionName
    cd(current_dir)
end

%% Get  parameters from series.xml
errormsg=''; % default error message
ActionFullName=fullfile(get(handles.ActionPath,'String'),ActionName);

%% If a compiled version has been selected (ext .sh) check wether it needs to be recompiled
if strcmp(ActionExt,'.sh')
    TransformPath='';
    if isfield(SeriesData,'TransformPath')
        TransformPath=SeriesData.TransformPath;
        if isfield(SeriesData,'TransformList')
            TransformList=get(handles.TransformName,'String');
            TransformIndex=get(handles.TransformName,'Value');
            TransformName=TransformList{TransformIndex};
            if ~ismember(TransformName,SeriesData.TransformList)
                TransformPath='';
            end
        end
    end
    if ~isempty(TransformPath)&&...
          ~strcmp(TransformPath,get(handles.TransformPath,'String'))% if the transform is not in paths set for compilation
        msgbox_uvmat('ERROR', 'compilation not available for this transform function, select .m')
        return
    end
    set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
    set(handles.ActionExt,'BackgroundColor',[1 1 0])
    [mcrmajor, mcrminor] = mcrversion;
    MCRROOT = ['MCRROOT',int2str(mcrmajor),int2str(mcrminor)];
    RunTime = getenv('MCRROOT'); % Just variable MCRROOT with no version in it's name
    if strcmp(RunTime,'')
        RunTime = getenv(MCRROOT); % Use specialize MCRROOT with version
    end
    ActionNameVersion=[ActionName '_' MCRROOT];
    ActionFullName=fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']);
    % compile the .m file if the .sh file does not exist yet
    if ~exist(ActionFullName,'file')
        answer=msgbox_uvmat('INPUT_Y-N','compiled version has not been created: compile now?');
        if strcmp(answer,'Yes')
            set(handles.ActionExt,'BackgroundColor',[1 1 0])
            path_uvmat=fileparts(which('series'));
            currentdir=pwd;
            cd(get(handles.ActionPath,'String'))% go to the directory of Action
            addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
            compile(ActionName,TransformPath)
            cd(currentdir)
        else
            errormsg='Action launch interrupted';
            return
        end
    else
        sh_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']));
        m_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.m']));
        if isfield(m_file_info,'datenum') && m_file_info.datenum>sh_file_info.datenum
            set(handles.ActionExt,'BackgroundColor',[1 1 0])
            drawnow
            answer=msgbox_uvmat('INPUT_Y-N',[ActionNameVersion '.sh needs to be updated: recompile now?']);
            if strcmp(answer,'Yes')
                path_uvmat=fileparts(which('series'));
                currentdir=pwd;
                cd(get(handles.ActionPath,'String'))% go to the directory of Action
                addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
                addpath(fullfile(path_uvmat,'transform_field'))% add the path to transform functions to run the fct 'compile'
                compile(ActionName,TransformPath)
                cd(currentdir)
            end
        end
    end

    set(handles.ActionExt,'BackgroundColor',[1 1 1])
     set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch
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.
if ~isfield(Param.IndexRange,'NbSlice')
    Param.IndexRange.NbSlice=[];
end
OutputPath=get(handles.OutputPath,'String');

%% Look for processing on multiple experiments set by the GUI browse_data
NbExp=1;% initiate the number of experiments set by the GUI browse_data, =1 otherwise
if get(handles.Replicate,'Value')
    hh=findobj(allchild(0),'Tag','browse_data');
    if isempty(hh)
        set(handles.Replicate,'Value',0)
    else
        set(handles.Replicate,'BackgroundColor',[1 1 0])%paint Relicate button in yellow
        BrowseData=guidata(hh);
        SourceDir=get(BrowseData.SourceDir,'String');
        ListExp=get(BrowseData.ListExperiments,'String');
        ExpIndices=get(BrowseData.ListExperiments,'Value');
        ListExp=ListExp(ExpIndices);
        ListDevices=get(BrowseData.ListDevices,'String');
        DeviceIndices=get(BrowseData.ListDevices,'Value');
        ListDevices=ListDevices(DeviceIndices);
        ListDataSeries=get(BrowseData.DataSeries,'String');
        DataSeriesIndices=get(BrowseData.DataSeries,'Value');
        ListDataSeries=ListDataSeries(DataSeriesIndices);
        NbExp=0; % counter of the number of experiments set by the GUI browse_data
        for iexp=1:numel(ListExp)
            if ~isempty(regexp(ListExp{iexp},'^\+/'))% if it is a folder
                for idevice=1:numel(ListDevices)
                    if ~isempty(regexp(ListDevices{idevice},'^\+/'))% if it is a folder
                        for isubdir=1:numel(ListDataSeries)
                            if ~isempty(regexp(ListDataSeries{isubdir},'^\+/'))% if it is a folder
                                lpath= fullfile(SourceDir,regexprep(ListExp{iexp},'^\+/',''),...
                                    regexprep(ListDevices{idevice},'^\+/',''));
                                lpathout= fullfile(OutputPath,regexprep(ListExp{iexp},'^\+/',''),...
                                    regexprep(ListDevices{idevice},'^\+/',''));
                                ldir= regexprep(ListDataSeries{isubdir},'^\+/','');
                                if exist(fullfile(lpath,ldir),'dir')
                                    NbExp=NbExp+1;
                                    ExpIndex(NbExp)=ExpIndices(iexp);
                                    DeviceIndex(NbExp)=DeviceIndices(idevice);
                                    ListPath{NbExp}=lpath;
                                    ListPathOut{NbExp}=lpathout;
                                    ListDeviceOut{NbExp}=regexprep(ListDevices{idevice},'^\+/','');
                                    ListExpOut{NbExp}=regexprep(ListExp{iexp},'^\+/','');
                                    ListSubdir{NbExp}=ldir;
                                end
                            end
                        end
                    end
                end
                %                 end
            end
        end
        answer=msgbox_uvmat('INPUT_Y-N-Cancel',['replicate the processing on ' num2str(NbExp) ' data series']);
        if strcmp(answer,'Cancel')||strcmp(answer,'No')
            return
        end
    end
end

%%%%%%%%%%%%%%%%%%% LOOP ON EXPERIMENTS POSSIBLY SET BY THE GUI browse_data, NbExp=1 otherwise %%%%%%%%%

for iexp=1:NbExp
    if get(handles.Replicate,'Value')
        if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action
            disp('program stopped by user')
            return
        end
        set(BrowseData.ListExperiments,'Value',ExpIndex(iexp))
        set(BrowseData.ListDevices,'Value',DeviceIndex(iexp))
        Param.InputTable(:,1)=ListPath(:,iexp);
        Param.InputTable(:,2)=ListSubdir(:,iexp);
        OutputSubDir=unique(ListSubdir(:,iexp));
        Param.OutputSubDir=OutputSubDir{1};
        if numel(OutputSubDir)>1% case
            for iout=2:numel(OutputSubDir)
                Param.OutputSubDir=[Param.OutputSubDir '-' OutputSubDir{iout}];
            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='';
    answer='';
    if isfield(Param,'OutputSubDir')&& isfield(Param,'OutputDirExt')% possibly update the output dir if it already exists
        PathOut=get(handles.OutputPath,'String');
        if ~exist(PathOut,'dir') % test if  the dir  already exist
            PathOut=uigetdir(PathOut,'pick the output root path');
            set(handles.OutputPath,'String',PathOut);
        end
        if get(handles.Replicate,'Value')
        PathExpOut=fileparts(ListPath{iexp});
        PathExpDeviceOut=ListPath{iexp};
        else
            PathExpOut=fullfile(PathOut,get(handles.Experiment,'String'));
            PathExpDeviceOut=fullfile(PathExpOut,get(handles.Device,'String'))
        end
        if ~exist(PathExpOut,'dir')
            [tild,msg1]=mkdir(PathExpOut);
            if ~strcmp(msg1,'')
                errormsg=['cannot create ' PathExpOut ': ' msg1]; % error message for directory creation
                return
            end
        end
        if ~exist(PathExpDeviceOut,'dir')
            [tild,msg1]=mkdir(PathExpDeviceOut);
            if ~strcmp(msg1,'')
                errormsg=['cannot create ' PathExpDeviceOut ': ' msg1]; % error message for directory creation
                return
            end
        end

        SubDirOut=[Param.OutputSubDir Param.OutputDirExt];
        SubDirOutNew=SubDirOut;
        detect=exist(fullfile(PathExpDeviceOut,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')
            CheckOverwrite=Param.CheckOverwrite;% will overwrite previous data if it is equal to 1
        end
        while detect
            if CheckOverwrite
                comment=', possibly overwrite previous data';
            else
                comment=', will complement existing result files (no overwriting)';
            end
            answer=msgbox_uvmat('INPUT_Y-N-Cancel',['use existing ouput directory: ' fullfile(PathExpDeviceOut,SubDirOutNew) comment]);
            if strcmp(answer,'Cancel')
                break
            elseif strcmp(answer,'Yes')
                detect=0;
                check_create=0;
            else
                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(PathExpDeviceOut,SubDirOutNew),'dir'); % test if  the dir  already exists
                check_create=1;
            end
        end
        if strcmp(answer,'Cancel')
            continue
        end
        Param.OutputDirExt=regexprep(SubDirOutNew,['^' Param.OutputSubDir],'');
        Param.OutputRootFile=Param.InputTable{1,3}; % the first sorted RootFile taken for output
        OutputDir=fullfile(PathExpDeviceOut,[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
                return
            end
        end

    elseif isfield(Param,'ActionInput')&&isfield(Param.ActionInput,'LogPath')% custom definition of the output dir
        OutputDir=Param.ActionInput.LogPath;
    end
    if isfield(Param,'OutputSubDir')&& isfield(Param,'OutputDirExt')
        set(handles.OutputSubDir,'String',Param.OutputSubDir)
        set(handles.OutputDirExt,'String',Param.OutputDirExt)
        drawnow
    end
    if get(handles.Replicate,'Value')
        set(handles.InputTable,'Data',Param.InputTable)
        set(handles.OutputPath,'String',OutputPath)
         set(handles.Experiment,'String',ListExpOut{iexp})
        set(handles.Device,'String',ListDeviceOut{iexp})
        Param.Experiment=ListExpOut{iexp};
        Param.Device=ListDeviceOut{iexp};
        check_input_file_series(handles)
    end
    DirXml=fullfile(OutputDir,'0_XML');
    if ~exist(DirXml,'dir')
        [~,msg1]=mkdir(DirXml);
        if ~strcmp(msg1,'')
            errormsg=['cannot create ' DirXml ': ' msg1]; % error message for directory creation
            return
        end
        [success,msg] = fileattrib(DirXml,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
        if success==0
            msgbox_uvmat('WARNING',{['unable to set group write access to ' DirXml ':']; msg}); % error message for directory creation
        end
    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
    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;
        incr_i=Param.IndexRange.incr_i;
        last_i=Param.IndexRange.last_i;
    end
    if isfield(Param.IndexRange,'incr_j')
        first_j=Param.IndexRange.first_j;
        last_j=Param.IndexRange.last_j;
        incr_j=Param.IndexRange.incr_j;
    end
    if last_i < first_i || last_j < first_j
        errormsg= 'series/Run_Callback:last field index must be larger or equal to the first one';
        return
    end
    %incr_i must be defined, =1 by default, if NbSlice is active
    if isempty(incr_i)&& ~isempty(Param.IndexRange.NbSlice)
        incr_i=1;
        set(handles.num_incr_i,'String','1')
    end
    % case of no increment i defined: processing is done on the available files found in i1_series
    if isempty(incr_i)
        if isempty(incr_j)
            [ref_j,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
            ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
            ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
            ref_j=ref_j-1;
            ref_i=ref_i-1;
        else
            ref_j=first_j:incr_j:last_j;
            [tild,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
            ref_i=ref_i-1;
            ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
        end
        % increment i is defined: processing is done on first_i:incr_i:last_i;
    else
        ref_i=first_i:incr_i:last_i;
        if isempty(incr_j)% automatic finding of the existing j indices
            [ref_j,tild]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
            ref_j=ref_j-1;
            ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
        else
            ref_j=first_j:incr_j:last_j;
        end
    end
    nbfield_j=numel(ref_j); % number of j indices
    BlockLength=numel(ref_i); % by default, job involves the full set of i field indicesNbProcess
    NbProcess=1;
    NbCore=1;
    switch RunMode
        case 'cluster'
            if (isfield(Param.Action, 'CPUTime') && ~isempty(Param.Action.CPUTime) && isnumeric(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
            else
                answer=msgbox_uvmat('INPUT_TXT','estimate the CPU time(in minutes) for each value of index i:' ,'');
                CPUTime=str2num(answer);
                set(handles.num_CPUTime,'String',answer)
                Param.Action.CPUTime=CPUTime;
            end
            if isfield(SeriesData.ClusterParam,'JobNumberMax')
                JobNumberMax=SeriesData.ClusterParam.JobNumberMax;
            else
                disp('ClusterParam.JobNumberMax not documented in series.xml, set to 500 by default')
                JobNumberMax=500;
            end
            if isfield(SeriesData.ClusterParam,'JobCPUTimeAdvised')
                JobCPUTimeAdvised=SeriesData.ClusterParam.JobCPUTimeAdvised;
            else
                disp('ClusterParam.JobCPUTimeAdvised not documented in series.xml, set to 120 minutes by default')
                JobCPUTimeAdvised=120;
            end
            if isempty(Param.IndexRange.NbSlice)% if NbSlice is not defined
                BlockLength= ceil(JobCPUTimeAdvised/(CPUTime*nbfield_j)); % iterations are grouped in sets with length BlockLength  such that the typical CPU time of a job is JobCPUTimeAdvised.
                BlockLength=max(BlockLength,ceil(numel(ref_i)*NbExp/JobNumberMax)); % possibly increase the BlockLength to have less than MaxJobNumber 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
            end
            
            %         %proposed number of cores to reserve in the cluster
             if isfield(SeriesData.ClusterParam,'NbCoreAdvised')
                NbCoreAdvised=SeriesData.ClusterParam.NbCoreAdvised;
            else
                disp('ClusterParam.NbCoreAdvised not documented in series.xml, set to 16 by default')
                NbCoreAdvised=16;
             end
                if isfield(SeriesData.ClusterParam,'NbCoreMax')
                NbCoreMax=min(NbProcess,SeriesData.ClusterParam.NbCoreMax);% reduces the number of cores if it exceeds the number of processes
            else
                disp('ClusterParam.NbCoreMax not documented in series.xml, set to 36 by default')
                NbCoreMax=min(NbProcess,36);
                end
            if NbCoreMax~=1
                if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
                    warning_string=', preferably use .sh option to save Matlab licences';
                else
                    warning_string=')';
                end
                answer=msgbox_uvmat('INPUT_TXT',['Number of cores (limited to ' num2str(NbCoreMax) warning_string],num2str(NbCoreAdvised));
                if isempty(answer)||strcmp(answer,'Cancel')
                    errormsg='Action launch interrupted by user';
                    return
                end
                NbCore=str2double(answer);
                if NbCore > NbCoreMax
                    NbCore=NbCoreMax;
                end
            end
        otherwise
            if ~isempty(Param.IndexRange.NbSlice)
                NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
            end
    end

    %% record nbre of output files and starting time for computation for status
    StatusData=get(handles.status,'UserData');
    if isfield(StatusData,'OutputFileMode')
        switch StatusData.OutputFileMode
            case 'NbInput'
                StatusData.NbOutputFile=numel(ref_i)*nbfield_j;
            case 'NbInput_i'
                StatusData.NbOutputFile=numel(ref_i);
            case 'NbSlice'
                StatusData.NbOutputFile=str2num(get(handles.num_NbSlice,'String'));
        end
    end
    StatusData.TimeStart=now;
    set(handles.status,'UserData',StatusData)

    %% case of a function in Python
    if strcmp(ActionExt, 'fluidimage')
        fprintf([
            '\n' ...
            '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n' ...
            'The computation should be done by fluidimage (https://fluidimage.readthedocs.io).\n' ...
            'Warning: Fluidimage parameters will be guessed from UVmat parameters but \n' ...
            'there is no direct correspondance between UVMAT and fluidimage parameters.\n' ...
            'Please report issues here https://foss.heptapod.net/fluiddyn/fluidimage/-/issues\n' ...
            '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n'])
        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
    extxml=cell(1,NbProcess); % initialisation of the set of labels used for the files documenting each process
    for iprocess=1:NbProcess
        extxml{iprocess}='.xml';
    end
    for iprocess=1:NbProcess
        if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action
            disp('program stopped by user')
            return
        end
        Param.IndexRange.incr_slice=incr_i;
        if isempty(Param.IndexRange.NbSlice)
            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
                break
            end
            Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1);
        else %multislices (then incr_i is not empty)
            Param.IndexRange.first_i= first_i+iprocess-1;
            Param.IndexRange.incr_slice=incr_i*Param.IndexRange.NbSlice;
        end
        for ilist=1:size(Param.InputTable,1)
            Param.InputTable{ilist,1}=regexprep(Param.InputTable{ilist,1},'\','/'); % correct path name for PCWIN system
        end

        if isfield(Param,'OutputSubDir')
            t=struct2xml(Param);
            t=set(t,1,'name','Series');
            extxml{iprocess}=fullfile_uvmat('','',Param.InputTable{1,3},'.xml',OutputNomType,...
                Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
            filexml{iprocess}=fullfile(OutputDir,'0_XML',extxml{iprocess});
            try
                save(t, filexml{iprocess}); % save the xml file containing the processing parameters
            catch ME
                if ~strcmp (RunMode,'local')
                    errormsg=['error writting ' filexml{iprocess} ': ' ME.message];
                    return
                end
            end
        end
        if strcmp (RunMode,'local')
            switch ActionExt
                case '.m'
                    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
                        case {'GLNX86','GLNXA64','MACI64'}%Linux  system
                            system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]);
                    end
            end
        end
    end

    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
        switch computer
            case {'PCWIN','PCWIN64'} %Windows system
                ExeExt='.bat';
            case {'GLNX86','GLNXA64','MACI64'}%Linux  system
                ExeExt='.sh';
        end
        %create subdirectory for executable files
        if ~exist(DirExe,'dir')
            [tild,msg1]=mkdir(DirExe);
            if ~strcmp(msg1,'')
                errormsg=['cannot create ' DirExe ': ' msg1]; % error message for directory creation
                return
            end
            [success,msg] = fileattrib(DirExe,'+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 ' DirExe ':']; msg}); % error message for directory creation
            end
        end
        %create subdirectory for log files
        DirLog=fullfile(OutputDir,'0_LOG');
        if ~exist(DirLog,'dir')
            [tild,msg1]=mkdir(DirLog);
            if ~strcmp(msg1,'')
                errormsg=['cannot create ' DirLog ': ' msg1]; % error message for directory creation
                return
            end
            [success,msg] = fileattrib(DirLog,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
            if success==0
                msgbox_uvmat('WARNING',{['unable to set group write access to ' DirLog ':']; msg}); % error message for directory creation
            end
        end

        %create the executable and log file names
        file_exe_global=fullfile_uvmat('','',Param.InputTable{1,3},ExeExt,OutputNomType,...
            first_i,last_i,first_j,last_j);
        file_exe_global=fullfile(OutputDir,'0_EXE',file_exe_global);
        filelog_global=fullfile_uvmat('','',Param.InputTable{1,3},'.log',OutputNomType,...
            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$',ExeExt)); % executable file names
            filelog{iprocess}=fullfile(OutputDir,'0_LOG',regexprep(extxml{iprocess},'.xml$','.log'));% corresponding log file names
        end
    end

    %% launch the executable files for background or cluster processing

    switch RunMode

        case 'background'
            [fid,message]=fopen(file_exe_global,'w');
            if isequal(fid,-1)
                errormsg=['creation of ' file_exe_global ':' message];
                return
            end
            switch ActionExt
                case '.m'% Matlab function
                    switch computer
                        case {'GLNX86','GLNXA64','MACI64'}
                            cmd=command_launch_matlab(filelog_global,path_series,Param.Action.ActionPath,Param.Action.ActionName,filexml,'background');
                            fprintf(fid,cmd); % fill the executable file with the  char string cmd
                            fclose(fid); % close the executable filefilelog_global
                            system(['chmod +x ' file_exe_global]); % set the file to executable
                        case {'PCWIN','PCWIN64'}
                            cmd=['matlab -automation -logfile ' regexprep(filelog{iprocess},'\\','\\\\')...
                                ' -r "addpath(''' regexprep(path_series,'\\','\\\\') ''');'...
                                'addpath(''' regexprep(Param.Action.ActionPath,'\\','\\\\') ''');'];
                            for iprocess=1:NbProcess
                                cmd=[cmd '' Param.Action.ActionName  '( ''' regexprep(filexml{iprocess},'\\','\\\\') ''');']
                            end
                            cmd=[cmd ';exit"'];
                            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
                case '.sh' % compiled Matlab function
                    for iprocess=1:NbProcess
                        switch computer
                            case {'GLNX86','GLNXA64','MACI64'}
                                [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
                                if isequal(fid,-1)
                                    errormsg=['creation of .bat file: ' message];
                                    return
                                end
                                cmd=['#!/bin/bash \n '...
                                    '#$ -cwd \n '...
                                    '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
                                system([batch_file_list{iprocess} ' &'])% directly execute the command file
                            case {'PCWIN','PCWIN64'}
                                msgbox_uvmat('ERROR','option for compiled Matlab functions not implemented for Windows system')
                                return
                        end
                    end
                    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
            for iprocess=1:NbProcess
                [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
                if isequal(fid,-1)
                    errormsg=['creation of .bat file: ' message];
                    return
                end
                if  strcmp(ActionExt,'.sh')
                    cmd=['#!/bin/bash \n '...
                        '#$ -cwd \n '...
                        'hostname && date \n '...
                        'umask 002 \n'...
                        ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group
                else
                    cmd=command_launch_matlab(filelog_global,path_series,Param.Action.ActionPath,Param.Action.ActionName,filexml{iprocess},'cluster');
 
                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
            end
            DIR_CLUSTER=fullfile(OutputDir,'0_CLUSTER');
            if exist(DIR_CLUSTER,'dir')% delete the content of the dir 0_LOG to allow new input
                curdir=pwd;
                cd(DIR_CLUSTER)
                delete('*')
                cd(curdir)
            else
                [tild,msg1]=mkdir(DIR_CLUSTER);
                if ~strcmp(msg1,'')
                    errormsg=['cannot create ' DIR_CLUSTER ': ' msg1]; % error message for directory creation
                    return
                end
            end
            % create file containing the list of jobs
            ListProcess=fullfile(DIR_CLUSTER,'job_list.txt'); % name of the file containing the list of executables
            [fid,errormsg]=fopen(ListProcess,'w'); % open it for writting
            if isempty(errormsg)
            for iprocess=1:length(batch_file_list)
                fprintf(fid,[batch_file_list{iprocess} '\n']); % write list of exe files
            end
            fclose(fid);
            system(['chmod +x ' ListProcess]); % set the file to executable
            else
                errormsg=['error for writting the executable file:' errormsg];
            end
            CPUTimeProcess=CPUTime*BlockLength*nbfield_j; % estimated CPU time for one individual process (in minutes)
            if isfield(SeriesData.ClusterParam,'LaunchCmdFcn')&& exist(SeriesData.ClusterParam.LaunchCmdFcn,'file')
            LaunchCmdFcn=SeriesData.ClusterParam.LaunchCmdFcn;% command obtained from the function 
            else
                disp('no ClusterParam.LaunchCmdFcn defined in series.xml')
                return
            end
            oar_command=feval(LaunchCmdFcn,ListProcess,ActionFullName,DirLog,NbProcess, NbCore,CPUTimeProcess)
            [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(DIR_CLUSTER,'0_cluster_command'); % keep track of the command in file '0-OAR/0_cluster_command'
            [fid,errormsg]=fopen(filename_oarcommand,'w');
            if ~isempty(errormsg)
                msgbox_uvmat('ERROR',['cannot create ' filename_oarcommand ': ' errormsg])
                return
            end
            fprintf(fid,oar_command); % store the command
            fprintf(fid,result); % store the result (job ID number)
            fclose(fid);
            if status==0
                msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched for ' ExpName ' as ' num2str(NbProcess) ' processes in cluster: press STATUS to see results'])
            else
                msgbox_uvmat('ERROR',result)
            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
            %         if exist(DirPBS,'dir')% delete the content of the dir 0_LOG to allow new input
            %             curdir=pwd;
            %             cd(DirPBS)
            %             delete('*')
            %             cd(curdir)
            %         else
            %             [tild,msg1]=mkdir(DirPBS);
            %             if ~strcmp(msg1,'')
            %                 errormsg=['cannot create ' DirPBS ': ' msg1]; % error message for directory creation
            %                 return
            %             end
            %         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
            %         ListProcess=fullfile(DirPBS,'job_list.txt'); % create name of the global executable file
            %         fid=fopen(ListProcess,'w');
            %         for iprocess=1:length(batch_file_list)
            %             fprintf(fid,[batch_file_list{iprocess} '\n']); % list of exe files
            %         end
            %         fclose(fid);
            %         system(['chmod +x ' ListProcess]); % set the file to executable
            %         pbs_command=['qsub -n CIVX '...
            %             '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
            %             '-l /core=' num2str(NbCore) ','...
            %             'walltime=' datestr(min(1.05*walltime_onejob/86400*max(NbProcess*BlockLength*nbfield_j,NbCore)/NbCore,max_walltime/86400),13) ' '...
            %             '-E ' regexprep(ListProcess,'\.txt\>','.stderr') ' '...
            %             '-O ' regexprep(ListProcess,'\.txt\>','.log') ' '...
            %             extra_qstat ' '...
            %             '"oar-parexec -s -f ' ListProcess ' '...
            %             '-l ' ListProcess '.log"'];
            %         filename_oarcommand=fullfile(DirPBS,'pbs_command');
            %         fid=fopen(filename_oarcommand,'w');
            %         fprintf(fid,pbs_command);
            %         fclose(fid);
            %         fprintf(pbs_command); % display in command line
            %         %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
                curdir=pwd;
                cd(DirSGE)
                delete('*')
                cd(curdir)
            else
                [tild,msg1]=mkdir(DirSGE);
                if ~strcmp(msg1,'')
                    errormsg=['cannot create ' DirSGE ': ' msg1]; % error message for directory creation
                    return
                end
            end
            maxImgsPerJob = ceil(length(batch_file_list)/NbCore);
            disp(['Max number of jobs: ' num2str(NbCore)])
            disp(['Images per job: ' num2str(maxImgsPerJob)])

            iprocess = 1;
            imgsInJob = [];
            currJobIndex = 1;
            done = 0;
            while(~done)
                if(iprocess <= length(batch_file_list))
                    imgsInJob = [imgsInJob, iprocess];
                end
                if((numel(imgsInJob) >= maxImgsPerJob) || (iprocess == length(batch_file_list)))
                    cmd=['#!/bin/sh \n'...
                        '#$ -cwd \n'...
                        'hostname && date\n']
                    for ii=1:numel(imgsInJob)
                        cmd=[cmd ActionFullName ' /softs/matlab ' filexml{imgsInJob(ii)} '\n'];
                    end
                    [fid, message] = fopen([DirSGE '/job' num2str(currJobIndex) '.sh'], 'w');
                    fprintf(fid, cmd);
                    fclose(fid);
                    system(['chmod +x ' DirSGE '/job' num2str(currJobIndex) '.sh'])
                    sge_command=['qsub -N civ_' num2str(currJobIndex) ' '...
                        '-q ' qstat_Queue ' '...
                        '-e ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '...
                        '-o ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '...
                        fullfile([DirSGE '/job' num2str(currJobIndex) '.sh'])];
                    fprintf(sge_command); % display in command line
                    [status, result] = system(sge_command);
                    fprintf(result);
                    currJobIndex = currJobIndex + 1;
                    imgsInJob = [];
                end
                if(iprocess == length(batch_file_list))
                    done = 1;
                end
                iprocess = iprocess + 1;
            end
            msgbox_uvmat('CONFIRMATION',[num2str(currJobIndex-1) ' jobs launched on queue ' qstat_Queue '.'])
        case 'python'
            command = command_launch_python(filexml{iprocess});
            fprintf(['command:\n' command '\n\n'])
            [status, result] = call_command_clean(command);
    end
    if exist(OutputDir,'dir')
        [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
            if success==0
                msgbox_uvmat('WARNING',{['unable to set group write access to ' OutputDir ':']; msg}); % error message for directory creation
            end
        end
    end
end
set(handles.Replicate,'BackgroundColor',[0 1 0])

%------------------------------------------------------------------------
function STOP_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(handles.RUN, 'BusyAction','cancel')
set(handles.RUN,'BackgroundColor',[1 0 0])
set(handles.RUN,'enable','on')
set(handles.RUN, 'Value',0)

%------------------------------------------------------------------------
% --- read parameters from the GUI series
%------------------------------------------------------------------------
function Param=read_GUI_series(handles)

%% read raw parameters from the GUI series
Param=read_GUI(handles.series);

%% clean the output structure by removing unused information
if isfield(Param,'Pairs')
    Param=rmfield(Param,'Pairs'); % info Pairs not needed for output
end
if isfield(Param,'InputLine')
    Param=rmfield(Param,'InputLine');
end
if isfield(Param,'EditObject')
    Param=rmfield(Param,'EditObject');
end
Param.IndexRange.TimeSource=Param.IndexRange.TimeTable{end,1};
Param.IndexRange=rmfield(Param.IndexRange,'TimeTable');
empty_line=false(size(Param.InputTable,1),1);
for iline=1:size(Param.InputTable,1)
    empty_line(iline)=isempty(cell2mat(Param.InputTable(iline,1:3)));
end
Param.InputTable(empty_line,:)=[];

%------------------------------------------------------------------------
% --- Executes on selection change in ActionName.
function ActionName_Callback(hObject, ActionPath, handles)
%------------------------------------------------------------------------

%% stop any ongoing series processing
if isequal(get(handles.RUN,'Value'),1)
    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
    if strcmp(answer,'Yes')
        STOP_Callback(hObject, [], handles)
    else
        return
    end
end
set(handles.ActionName,'BackgroundColor',[1 1 0])
huigetfile=findobj(allchild(0),'tag','status_display');
if ~isempty(huigetfile)
    delete(huigetfile)
end
drawnow

%% 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
ActionIndex=get(handles.ActionName,'Value');
if ~isequal(ActionIndex,1)% if we are not just opening series
    InputTable=get(handles.InputTable,'Data');
    if isempty(InputTable{1,4})
        msgbox_uvmat('ERROR','no input file available: use Open in the menu bar')
        return
    end
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

%% add a new function to the menu if 'more...' has been selected in the menu ActionName
if isequal(ActionName,'more...')
    if ~ischar(ActionPath)
        ActionPath=get(handles.ActionPath,'String');
    end
    [FileName, PathName] = uigetfile( ...
        {'*.m', ' (*.m)';
        '*.m',  '.m files '; ...
        '*.*', 'All Files (*.*)'}, ...
        'Pick a series processing function ',ActionPath);
    if length(FileName)<2
        return
    end
    [~,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
    PathName=regexprep(PathName,'/$','');
    if ~isempty(ActionIndex) && ~strcmp(ActionPathList{ActionIndex},PathName)%compare the path to the existing fct
        ActionIndex=[]; % the selected path is different than the recorded one
    end
    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...'
         ActionPathList=[ActionPathList; PathName];
    end

    % record the file extension and extend the path list if it is a new extension
    ActionExtList=get(handles.ActionExt,'String');
    ActionExtIndex=find(strcmp(ActionExt,ActionExtList), 1);
    if isempty(ActionExtIndex)
        set(handles.ActionExt,'String',[ActionExtList;{ActionExt}])
    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
        nbremove=length(ActionList)-NbBuiltinAction-5;
        ActionList(NbBuiltinAction+1:end-5)=[];
        ActionPathList(NbBuiltinAction+1:end-4,:)=[];
        ActionIndex=ActionIndex-nbremove;
    end

    % record action menu, choice and path
    set(handles.ActionName,'Value',ActionIndex)
    set(handles.ActionName,'String',ActionList)
       set(handles.ActionName,'UserData',ActionPathList);
    set(handles.ActionExt,'Value',ActionExtIndex)

    %record the user defined menu additions in personal file profil_perso
    dir_perso=prefdir;
    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
    if NbBuiltinAction+1<=numel(ActionList)-1
        ActionListUser=ActionList(NbBuiltinAction+1:numel(ActionList)-1);
        ActionPathListUser=ActionPathList(NbBuiltinAction+1:numel(ActionList)-1);
        ActionExtListUser={};
        if numel(ActionExtList)>2
            ActionExtListUser=ActionExtList(3:end);
        end
        if exist(profil_perso,'file')
            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-append')
        else
            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-V6')
        end
    end
end

%% check the current ActionPath to the selected function
ActionPath=ActionPathList{ActionIndex}; % current recorded path
set(handles.ActionPath,'String',ActionPath); % show the path to the selected function

%% reinitialise the waitbar
update_waitbar(handles.Waitbar,0)

%% Put the first line of the selected Action fct as tooltip help
try
    [fid,errormsg] =fopen([fullfile(ActionPath,ActionName) '.m']);
    InputText=textscan(fid,'%s',1,'delimiter','\n');
    fclose(fid);
    set(handles.ActionName,'ToolTipString',InputText{1}{1})% put the first line of the selected function as tooltip help
end
set(handles.ActionName,'BackgroundColor',[1 1 1])
set(handles.ActionInput,'BackgroundColor',[1 0 1])% set ActionInput button to magenta color to indicate that input refr
set(handles.num_CPUTime,'String','')

% --- Executes on button press in ActionInput.
function ActionInput_Callback(hObject, eventdata, handles)

set(handles.ActionInput,'BackgroundColor',[1 1 0])
SeriesData=get(handles.series,'UserData'); % info on the input file series

%% create the function handle for Action
ActionPath=get(handles.ActionPath,'String');
ActionList=get(handles.ActionName,'String');
ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
if ~exist(ActionPath,'dir')
    ActionName_Callback(handles.ActionName, ActionPath, handles)% update the function
    return
end
current_dir=pwd; % current working dir
cd(ActionPath)
h_fun=str2func(ActionName);% create the function handle for the function ActionName
cd(current_dir)

%% 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
Param.Action.RUN=0;% indicate that we are in the mode of parameter input, not program run
Param.SeriesData=SeriesData;% info stored in 'UserData' of the fig 'series'
ParamOut=h_fun(Param); % run the selected Action function to get the relevant input


%% Visibility of VelType and VelType_1 menus asked by ActionName
VelTypeRequest=1; % VelType requested by default
VelTypeRequest_1=1; % VelType requested by default
if isfield(ParamOut,'VelType')
    VelTypeRequest=ismember(ParamOut.VelType,{'on','one','two'});
    VelTypeRequest_1=strcmp( ParamOut.VelType,'two');
end
FieldNameRequest=0;  %hidden by default
FieldNameRequest_1=0;  %hidden by default
if isfield(ParamOut,'FieldName')
    FieldNameRequest=ismember(ParamOut.FieldName,{'on','one','two'});
    FieldNameRequest_1=strcmp( ParamOut.FieldName,'two');
end

%% Detect the types of input files and set menus and default options in 'VelType'
if ~isfield(SeriesData,'FileType')
    SeriesData.FileType={'none'};
end
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
if ~iscell(FieldList),FieldList={FieldList};end
FieldList_1=get(handles.FieldName_1,'String'); % previous list as default
if ~iscell(FieldList_1),FieldList_1={FieldList_1};end
CheckPivData_1=0; % indicate whether FieldName_1 has been updated with civ data, 0 by default
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
    menu=set_veltype_display(SeriesData.FileInfo{iview_civ(1)}.CivStage,SeriesData.FileType{iview_civ(1)});
    set(handles.VelType,'Value',1)% set first choice by default
    set(handles.VelType,'String',[{'*'};menu])
    set(handles.VelType,'Visible','on')
    set(handles.VelType_title,'Visible','on')
    FieldList=set_field_list('U','V'); % standard menu for civx data
    if max(get(handles.FieldName,'Value'))>numel(FieldList)
        set(handles.FieldName,'Value',1); % velocity vector choice by default
    end
    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,'Value',1)% set first choice by default
        set(handles.VelType_1,'String',[{'*'};menu])
        set(handles.VelType_1,'Visible','on')
        set(handles.VelType_title_1,'Visible','on')
        FieldList_1=[set_field_list('U','V');{'C'};{'add_field...'}]; % standard menu for civx data
        CheckPivData_1=1;
        set(handles.FieldName_1,'Value',1); % velocity vector choice by default
    else
        set(handles.VelType_1,'Visible','off')
        set(handles.VelType_title_1,'Visible','off')
    end
else
    set(handles.VelType,'Visible','off')
    set(handles.VelType_title,'Visible','off')
end

%% Detect the types of input files and set menus and default options in 'FieldName'
if (FieldNameRequest || VelTypeRequest) && numel(iview_netcdf)>=1
    set(handles.InputFields,'Visible','on')% set the frame InputFields visible
    if FieldNameRequest && isfield(SeriesData.FileInfo{iview_netcdf(1)},'ListVarName')
        set(handles.FieldName,'Visible','on')
        set(handles.Field_text,'Visible','on')
        ListVarName=SeriesData.FileInfo{iview_netcdf(1)}.ListVarName;
        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), 1))
                FieldList={}; % previous choice not consistent with new input field
                set(handles.FieldName,'Value',1)
                break
            end
        end
        if ~isempty(FieldList)
            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName), 1))||...
                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName), 1))
                FieldList={};
                set(handles.Coord_x,'String','')
                set(handles.Coord_y,'String','')
            end
            Coord_z=get(handles.Coord_z,'String');
            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName), 1))
                FieldList={};
                set(handles.Coord_z,'String','')
            end
        end
    else
        set(handles.FieldName,'Visible','off')
        set(handles.Field_text,'Visible','off')
    end
    set(handles_coord,'Visible','on')
    if isempty(find(strcmp('add_field...',FieldList), 1))
        FieldList=[FieldList;{'add_field...'}];%add 'add_field...' to the menu FieldName if it is not already
    end
    if FieldNameRequest_1 && numel(iview_netcdf)>=2
        set(handles.FieldName_1,'Visible','on')
        set(handles.Field_text_1,'Visible','on')
        if CheckPivData_1==0        % not civ input made
            FieldList_1={'add_field...'};
            ListVarName=SeriesData.FileInfo{iview_netcdf(2)}.ListVarName;
            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), 1))
                    %FieldList_1={}; % previous choice not consistent with new input field
                    set(handles.FieldName_1,'Value',1)
                    break
                end
            end
            warn_coord=0;
            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName), 1))||...
                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName), 1))
                warn_coord=1;
            end
            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName), 1))
                FieldList_1={'add_field...'};
                warn_coord=1;
            end
            if warn_coord
                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)
            set(handles.FieldName_1,'String',FieldList_1)
        end
    else
        set(handles.FieldName_1,'Visible','off')
    end
    if isempty(FieldList)
        set(handles.Field_text,'Visible','off')
        set(handles.FieldName,'Visible','off')
    else
        set(handles.Field_text,'Visible','on')
        set(handles.FieldName,'Visible','on')
        set(handles.FieldName,'String',FieldList)
    end
else
    set(handles.InputFields,'Visible','off')
end

%% Introduce visibility of file overwrite option
if isfield(ParamOut,'CheckOverwriteVisible')&& strcmp(ParamOut.CheckOverwriteVisible,'on')
    set(handles.CheckOverwrite,'Visible','on')
else
    set(handles.CheckOverwrite,'Visible','off')
end

%% 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
    [~,iview]=sort(Param.InputTable(:,2)); % subdirectories sorted in alphabetical order
    set(handles.InputTable,'Data',Param.InputTable(iview,:));
    MinIndex_i=get(handles.MinIndex_i,'Data');
    MinIndex_j=get(handles.MinIndex_j,'Data');
    MaxIndex_i=get(handles.MaxIndex_i,'Data');
    MaxIndex_j=get(handles.MaxIndex_j,'Data');
    set(handles.MinIndex_i,'Data',MinIndex_i(iview,:));
    set(handles.MinIndex_j,'Data',MinIndex_j(iview,:));
    set(handles.MaxIndex_i,'Data',MaxIndex_i(iview,:));
    set(handles.MaxIndex_j,'Data',MaxIndex_j(iview,:));
    TimeTable=get(handles.TimeTable,'Data');
    if size(TimeTable,1)<size(Param.InputTable,1)%if the time table is not complete, copy the missing lines from the previous ones
        for iline=size(TimeTable,1)+1:size(Param.InputTable,1)
            TimeTable(iline,:)=TimeTable(iline-1,:);
        end
    end
    set(handles.TimeTable,'Data',TimeTable(iview,:));% sort the time tables
    PairString=get(handles.PairString,'Data');
    set(handles.PairString,'Data',PairString(iview,:));
end

%% Impose the whole input file index range if requested
if ~isfield(ParamOut,'WholeIndexRange')
    ParamOut.WholeIndexRange='off';
end
if ~isfield(ParamOut,'IndexRange_j')
    ParamOut.IndexRange_j='on';% accept Index_j as input by default
end
if strcmp(ParamOut.WholeIndexRange,'on')
    MinIndex_i=get(handles.MinIndex_i,'Data');
    MaxIndex_i=get(handles.MaxIndex_i,'Data');
    set(handles.num_first_i,'String',num2str(MinIndex_i(1)))% set first as the min index (for the first line)
    set(handles.num_last_i,'String',num2str(MaxIndex_i(1)))% set last as the max index (for the first line)
    set(handles.num_incr_i,'String','1')
else
    first_i=1;last_i=1;
    if isfield(Param.IndexRange,'first_i')
        first_i=Param.IndexRange.first_i;
        last_i=Param.IndexRange.last_i;
    end
end
if strcmp(ParamOut.WholeIndexRange,'on')||strcmp(ParamOut.IndexRange_j,'whole')
    MinIndex_j=get(handles.MinIndex_j,'Data');
    MaxIndex_j=get(handles.MaxIndex_j,'Data');
    set(handles.num_first_j,'String',num2str(MinIndex_j(1)))% set first as the min index (for the first line)
    set(handles.num_last_j,'String',num2str(MaxIndex_j(1)))% set last as the max index (for the first line)
    set(handles.num_incr_j,'String','1')
else  % check index ranges
    first_j=1;last_j=1;
    if isfield(Param.IndexRange,'first_j')
        first_j=Param.IndexRange.first_j;
        last_j=Param.IndexRange.last_j;
    end
    if last_i < first_i || last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
            set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end
end
num_first_i_Callback(hObject, eventdata, handles)
num_first_j_Callback(hObject, eventdata, handles)

%% enable or desable j index visibility
if strcmp(ParamOut.IndexRange_j,'off')%do not show the j index
    enable_j(handles,'off')
else% show j index if relevant in the input series
    if isfield(SeriesData,'j1_series')
    j1_series=SeriesData.j1_series;
    for iview=1:size(j1_series,1)
        if ~isempty(j1_series{iview})
            enable_j(handles,'on')
            break
        end
    end
    end
end

%% NbSlice visibility
if isfield(ParamOut,'NbSlice') && (strcmp(ParamOut.NbSlice,'on')||isnumeric(ParamOut.NbSlice))
    set(handles.num_NbSlice,'Visible','on')
    set(handles.NbSlice_title,'Visible','on')
    if isnumeric(ParamOut.NbSlice)
        set(handles.num_NbSlice,'String',num2str(ParamOut.NbSlice))
    end
else
    set(handles.num_NbSlice,'Visible','off')
    set(handles.NbSlice_title,'Visible','off')
end
if isfield(ParamOut,'NbSlice') && isnumeric(ParamOut.NbSlice)
    set(handles.num_NbSlice,'String',num2str(ParamOut.NbSlice))
    set(handles.num_NbSlice,'Enable','off'); % NbSlice set by the activation of the Action function
else
    set(handles.num_NbSlice,'Enable','on'); % NbSlice can be modified on the GUI series
end

%% Visibility of FieldTransform menu
FieldTransformVisible='off';  %hidden by default
if isfield(ParamOut,'FieldTransform')
    if ~strcmp(ParamOut.FieldTransform,'off')
    FieldTransformVisible='on';
    end
    if iscell(ParamOut.FieldTransform)
        SeriesData.TransformList=ParamOut.FieldTransform;
    end
    TransformName_Callback([],[], handles)
end
set(handles.FieldTransform,'Visible',FieldTransformVisible)
if isfield(ParamOut,'TransformPath')% record the path of transform function requested for compilation
    set(handles.TransformPath,'UserData',ParamOut.TransformPath)
else
    set(handles.TransformPath,'UserData',[])
end

%% Visibility of projection object
ProjObjectVisible='off';  %hidden by default
if isfield(ParamOut,'ProjObject')
    ProjObjectVisible=ParamOut.ProjObject;
end
set(handles.CheckObject,'Visible',ProjObjectVisible)
if ~get(handles.CheckObject,'Value')
    ProjObjectVisible='off';
end
set(handles.ProjObjectName,'Visible',ProjObjectVisible)
set(handles.DeleteObject,'Visible',ProjObjectVisible)
set(handles.ViewObject,'Visible',ProjObjectVisible)
set(handles.EditObject,'Visible',ProjObjectVisible)

%% Visibility of mask input
MaskVisible='off';  %hidden by default
if isfield(ParamOut,'Mask')
    MaskVisible=ParamOut.Mask;
end
set(handles.CheckMask,'Visible',MaskVisible);
set(handles.MaskTable,'Visible',MaskVisible);

%% Setting of expected iteration time
if isfield(ParamOut,'CPUTime')
    set(handles.num_CPUTime,'String',num2str(ParamOut.CPUTime));
end

%% definition of the path for the output files
InputTable=get(handles.InputTable,'Data');
[OutputPath,Device,DeviceExt]=fileparts(InputTable{1,1});
[~,Experiment,ExperimentExt]=fileparts(OutputPath);
set(handles.Device,'String',[Device DeviceExt])
set(handles.Device,'Visible','on')
set(handles.Device_title,'Visible','on')
set(handles.Experiment,'String',[Experiment ExperimentExt])
set(handles.Experiment,'Visible','on')
set(handles.Experiment_title,'Visible','on')
set(handles.Experiment_title,'Visible','on')
set(handles.OutputPath,'Visible','on')
set(handles.OutputPathBrowse,'Visible','on')

%% definition of the subdirectory containing the output files
if  ~(isfield(SeriesData,'ActionName') && strcmp(ActionName,SeriesData.ActionName))
    OutputDirExt='.series'; % default
    if isfield(ParamOut,'OutputDirExt')&&~isempty(ParamOut.OutputDirExt)
        OutputDirExt=ParamOut.OutputDirExt;
    end
    set(handles.OutputDirExt,'String',OutputDirExt)
end
OutputDirVisible='off';
OutputSubDirMode='auto'; % default
SubDirOut='';
if isfield(ParamOut,'OutputSubDirMode')
    OutputSubDirMode=ParamOut.OutputSubDirMode;
end
switch OutputSubDirMode
    case 'auto' % default
        OutputDirVisible='on';
        SubDir=InputTable(1:end,2); % set of subdirectories
        SubDirOut=SubDir{1};
        if numel(SubDir)>1
            for ilist=2:numel(SubDir)
                SubDirOut=[SubDirOut '-' regexprep(SubDir{ilist},'^/','')];
            end
        end
    case 'one'
        OutputDirVisible='on';
        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
        SubDirOut=SubDir{1};
        if numel(SubDir)>1
                SubDirOut=[SubDirOut '-' regexprep(SubDir{2},'^/','')];
        end
    case 'last'
        OutputDirVisible='on';
        SubDirOut=InputTable{end,2}; % use the last subdir name (+OutputDirExt) as output  subdirectory
end
set(handles.OutputSubDir,'String',SubDirOut)
set(handles.OutputSubDir,'BackgroundColor',[1 1 1])% set edit box to white color to indicate refreshment
set(handles.OutputDirExt,'Visible',OutputDirVisible)
set(handles.OutputSubDir,'Visible',OutputDirVisible)
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
else
    RunModeVisible='on';
end
set(handles.RunMode,'Visible',RunModeVisible)
set(handles.ActionExt,'Visible',RunModeVisible)
set(handles.RunMode_title,'Visible',RunModeVisible)
set(handles.ActionExt_title,'Visible',RunModeVisible)


%% Expected nbre of output files
if isfield(ParamOut,'OutputFileMode')
    StatusData.OutputFileMode=ParamOut.OutputFileMode;
    set(handles.status,'UserData',StatusData)
end

%% definition of an additional parameter set, determined by an ancillary GUI
if isfield(ParamOut,'ActionInput')
    ParamOut.ActionInput.Program=ActionName; % record the program in ActionInput
    SeriesData.ActionInput=ParamOut.ActionInput;
else
    if isfield(SeriesData,'ActionInput')
        SeriesData=rmfield(SeriesData,'ActionInput');
    end
end
set(handles.series,'UserData',SeriesData)
set(handles.ActionInput,'BackgroundColor',[1 0 0])


%------------------------------------------------------------------------
% --- Executes on button press in RefreshField.
function RefreshField_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(handles.FieldName,'String',{'add_field...'});
set(handles.FieldName,'Value',1);
FieldName_Callback(hObject, eventdata, handles)


%------------------------------------------------------------------------
% --- Executes on selection change in FieldName.
function FieldName_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
FieldListInit=get(handles.FieldName,'String');
field_index=get(handles.FieldName,'Value');
field=FieldListInit{field_index(1)};
if isequal(field,'add_field...')
    FieldListInit(field_index(1))=[];
    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
    hget_field=findobj(allchild(0),'name','get_field');
    if ~isempty(hget_field)
        delete(hget_field)%delete opened versions of get_field
    end
    Param=read_GUI(handles.series);
    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=Param.IndexRange.first_j;
        last_j=Param.IndexRange.last_j;
        MinIndex_j=Param.IndexRange.MinIndex_j(iview);
        MaxIndex_j=Param.IndexRange.MaxIndex_j(iview);
    end
    PairString='';
    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString{iview}; end
    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
    LineIndex=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);
    end
    FirstFileName=fullfile_uvmat(InputTable{LineIndex,1},InputTable{LineIndex,2},InputTable{LineIndex,3},...
        InputTable{LineIndex,5},InputTable{LineIndex,4},i1,i2,j1,j2);
    if exist(FirstFileName,'file') || ~isempty(regexp(InputTable{LineIndex,1},'^http'))
        ParamIn.Title='get_field: pick input variables and coordinates for series processing';
        ParamIn.SeriesInput=1;
        GetFieldData=get_field(FirstFileName,ParamIn);
        FieldList={};
        if isfield(GetFieldData,'FieldOption')% if a field has been selected
        switch GetFieldData.FieldOption
            case 'vectors'
                UName=GetFieldData.PanelVectors.vector_x;
                VName=GetFieldData.PanelVectors.vector_y;
                YName={GetFieldData.Coordinates.Coord_y};
                FieldList={['vec(' UName ',' VName ')'];...
                    ['norm(' UName ',' VName ')'];...
                    UName;VName};
                set(handles.VelType,'Visible','off')
            case {'scalar'}
                FieldList=GetFieldData.PanelScalar.scalar;
                YName={GetFieldData.Coordinates.Coord_y};
                if ischar(FieldList)
                    FieldList={FieldList};
                end
                set(handles.VelType,'Visible','off')
            case 'civdata...'
                FieldList=[set_field_list('U','V') ;{'C'}];
                set(handles.FieldName,'Value',1) % set menu to 'velocity
                XName='X';
                YName='y';
                set(handles.VelType,'Visible','on')
        end
        set(handles.FieldName,'Value',1)
        set(handles.FieldName,'String',[FieldListInit; FieldList; {'add_field...'}]);
        if ~strcmp(GetFieldData.FieldOption,'civdata...')
           if ~isempty(regexp(FieldList{1},'^vec'))
                set(handles.FieldName,'Value',1)
           else
                set(handles.FieldName,'Value',1:numel(FieldList))%select all input fields by default
           end
            XName=GetFieldData.Coordinates.Coord_x;
            YName=GetFieldData.Coordinates.Coord_y;
            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
            % get the time info
            TimeTable=get(handles.TimeTable,'Data');
            switch TimeNameStr
                case 'file index'
                    TimeName='';
                case 'attribute'
                    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,5}=get_time(Param.IndexRange.MaxIndex_i(LineIndex),MaxIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Max time
                case 'variable'
                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
                    set(handles.NomType,'String','*')
                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
                    set(handles.FileIndex,'String','')
                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
                case 'matrix_index'
                    TimeName=['dim:' GetFieldData.Time.TimeName];
                    set(handles.NomType,'String','*')
                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
                    set(handles.FileIndex,'String','')
                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
            end
            TimeTable{LineIndex,1}=TimeName;
            set(handles.TimeTable,'Data',TimeTable);
        end
        set(handles.Coord_x,'String',XName)
        set(handles.Coord_y,'String',YName)
        set(handles.Coord_x,'Visible','on')
        set(handles.Coord_y,'Visible','on')
        end
    else
        msgbox_uvmat('ERROR',[FirstFileName ' does not exist'])
    end
end


function [TimeValue,DtValue]=get_time(ref_i,ref_j,PairString,InputTable,FileInfo,TimeName,DtName)
[i1,i2,j1,j2] = get_file_index(ref_i,ref_j,PairString);
FileName=fullfile_uvmat(InputTable{1},InputTable{2},InputTable{3},InputTable{5},InputTable{4},i1,i2,j1,j2);
%Data=nc2struct(FileName,[]);
TimeValue=[];
DtValue=[];
switch FileInfo.FileType
    case 'civdata'
    Data=nc2struct(FileName,[]);
    if ismember(TimeName,{'civ1','filter1'})
        if isfield(Data,'Civ1_Time')
        TimeValue=Data.Civ1_Time;
        end
        if isfield(Data,'Civ1_Dt')
        DtValue=Data.Civ1_Dt;
        end
    else
        if isfield(Data,'Civ2_Time')
        TimeValue=Data.Civ2_Time;
        end
        if isfield(Data,'Civ2_Dt')
        DtValue=Data.Civ2_Dt;
        end
    end
    case 'pivdata_fluidimage'
      TimeValue=ref_i;%default
      DtValue=1;%default
    case 'netcdf'
        Data=nc2struct(FileName,[]);
    if ~isempty(TimeName)&& isfield(Data,TimeName)
        TimeValue=Data.(TimeName);
    end
    if exist('DtName','var') && isfield(Data,DtName)
        DtValue=Data.(DtName);
    end
end

%------------------------------------------------------------------------
% --- Executes on selection change in FieldName_1.
function FieldName_1_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
field_str=get(handles.FieldName_1,'String');
field_index=get(handles.FieldName_1,'Value');
field=field_str{field_index(1)};
if strcmp(field,'add_field...')
    %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)
        delete(hget_field)%delete opened versions of get_field
    end
    Param=read_GUI(handles.series);
    InputTable=Param.InputTable(2,:);
    % check the existence of the first file in the series
    first_j=[];
    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
    if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
    PairString='';
    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
    FirstFileName=fullfile_uvmat(Param.InputTable{2,1},Param.InputTable{2,2},Param.InputTable{2,3},...
        Param.InputTable{2,5},Param.InputTable{2,4},i1,i2,j1,j2);
    if exist(FirstFileName,'file')
        ParamIn.SeriesInput=1;
        GetFieldData=get_field(FirstFileName,ParamIn);
        FieldList={};
        switch GetFieldData.FieldOption
            case 'vectors'
                UName=GetFieldData.PanelVectors.vector_x;
                VName=GetFieldData.PanelVectors.vector_y;
                FieldList={['vec(' UName ',' VName ')'];...
                    ['norm(' UName ',' VName ')'];...
                    UName;VName};
            case {'scalar','pick variables'}
                FieldList=GetFieldData.PanelScalar.scalar;
                if ischar(FieldList)
                    FieldList={FieldList};
                end
            case '1D plot'

            case 'civdata...'
                FieldList=set_field_list('U','V','C');
                set(handles.FieldName,'Value',2) % set menu to 'velocity
        end
        set(handles.FieldName_1,'Value',1)
        set(handles.FieldName_1,'String',[FieldList; {'add_field...'}]);
    end
end


%%%%%%%%%%%%%
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
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
    %for each multiplet, select the most recent file
    ind_remove=[];
    for i=1:length(ind_multi_m)
        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
    end
end

%------------------------------------------------------------------------
% --- 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)
%------------------------------------------------------------------------
num_i1=num_i; % set of first image numbers by default
num_i2=num_i;
num_j1=num_j;
num_j2=num_j;
num_i_out=num_i;
num_j_out=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_i2_line=num_i+ind_shift(4);
    % adjust the first and last field number
        indsel=find(num_i1_line >= 1);
    num_i_out=num_i(indsel);
    num_i1_line=num_i1_line(indsel);
    num_i2_line=num_i2_line(indsel);
    num_j1=meshgrid(num_j,ones(size(num_i1_line)));
    num_j2=meshgrid(num_j,ones(size(num_i1_line)));
    [xx,num_i1]=meshgrid(num_j,num_i1_line);
    [xx,num_i2]=meshgrid(num_j,num_i2_line);
elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts')
    if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
        num_j1=ind_shift(1)*ones(size(num_i));
        num_j2=ind_shift(2)*ones(size(num_i));
    else
        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
        indsel=find((num_j1_col >= 1));
        num_j_out=num_j(indsel);
        num_j1_col=num_j1_col(indsel);
        num_j2_col=num_j2_col(indsel);
        [num_i1,num_j1]=meshgrid(num_i,num_j1_col);
        [num_i2,num_j2]=meshgrid(num_i,num_j2_col);
    end
end

%------------------------------------------------------------------------
% --- Executes on button press in CheckObject.
function CheckObject_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
hset_object=findobj(allchild(0),'tag','set_object'); % find the set_object interface handle
if get(handles.CheckObject,'Value')
    SeriesData=get(handles.series,'UserData');
    if isfield(SeriesData,'ProjObject') && ~isempty(SeriesData.ProjObject)% a projection object is already loaded in the GUI series
        set(handles.ViewObject,'Value',1)
        ViewObject_Callback(hObject, eventdata, handles)
    else
        if ishandle(hset_object)% a projection object is already displayed in a GUI set_object
            uistack(hset_object,'top')% show the GUI set_object if opened
        else
            %get the object file
            InputTable=get(handles.InputTable,'Data');
            defaultname=InputTable{1,1};
            if isempty(defaultname)
                defaultname={''};
            end
            fileinput=uigetfile_uvmat('pick a xml object file (or use uvmat to create it)',defaultname,'.xml');
            if isempty(fileinput)% exit if no object file is selected
                set(handles.CheckObject,'Value',0)
                return
            end
            %read the file
            data=xml2struct(fileinput);
            if ~isfield(data,'Type')
                msgbox_uvmat('ERROR',[fileinput ' is not an object xml file'])
                set(handles.CheckObject,'Value',0)
                return
            end
            if ~isfield(data,'ProjMode')
                data.ProjMode='none';
            end
            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.ProjObjectName,'String',ProjObject.Name); % display the object name
        SeriesData=get(handles.series,'UserData');
        SeriesData.ProjObject=ProjObject;
        set(handles.series,'UserData',SeriesData);
    end
    set(handles.EditObject,'Visible','on');
    set(handles.DeleteObject,'Visible','on');
    set(handles.ViewObject,'Visible','on');
    set(handles.ProjObjectName,'Visible','on');
else
    set(handles.EditObject,'Visible','off');
    set(handles.DeleteObject,'Visible','off');
    set(handles.ViewObject,'Visible','off');
    if ~ishandle(hset_object)
        set(handles.ViewObject,'Value',0);
    end
    set(handles.ProjObjectName,'Visible','off');
end

%------------------------------------------------------------------------
% --- Executes on button press in ViewObject.
%------------------------------------------------------------------------
function ViewObject_Callback(hObject, eventdata, handles)

UserData=get(handles.series,'UserData');
hset_object=findobj(allchild(0),'Tag','set_object');
if ~isempty(hset_object)
    delete(hset_object)% refresh set_object if already opened
end
hset_object=set_object(UserData.ProjObject);
set(hset_object,'Name','view_object_series')


%------------------------------------------------------------------------
% --- Executes on button press in EditObject.
function EditObject_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
if get(handles.EditObject,'Value')
    set(handles.ViewObject,'Value',0)
    UserData=get(handles.series,'UserData');
    if isfield(UserData,'ProjObject')
    hset_object=set_object(UserData.ProjObject);
    set(hset_object,'Name','edit_object_series')
    set(get(hset_object,'Children'),'Enable','on')
    else
        msgbox_uvmat('ERROR','no projection object available');
    end
else
    hset_object=findobj(allchild(0),'Tag','set_object');
    if ~isempty(hset_object)
        set(get(hset_object,'Children'),'Enable','off')
    end
end

%------------------------------------------------------------------------
% --- Executes on button press in DeleteObject.
function DeleteObject_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
SeriesData=get(handles.series,'UserData');
SeriesData.ProjObject=[];
set(handles.series,'UserData',SeriesData)
set(handles.ProjObjectName,'String','')
set(handles.ProjObjectName,'Visible','off')
set(handles.CheckObject,'Value',0)
set(handles.ViewObject,'Visible','off')
set(handles.EditObject,'Visible','off')
hset_object=findobj(allchild(0),'name','set_object_series');
if ~isempty(hset_object)
    delete(hset_object)
end
set(handles.DeleteObject,'Visible','off')

%------------------------------------------------------------------------
% --- Executed when CheckMask is activated
%------------------------------------------------------------------------
function CheckMask_Callback(hObject, eventdata, handles)


if get(handles.CheckMask,'Value')
    set(handles.DeleteMask,'Visible','on')
    Param=read_GUI_series(handles); % displayed parameters
    NbView=size(Param.InputTable,1);
    MaskTable=cell(NbView,2);
    
    RootPath=Param.InputTable{1,1};
    first_j=[];% note that the function will propose to cover the whole range of indices
    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
    last_j=[];
    if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
    PairString='';
    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
    %checkmask=zeros(NbView,1);
    for iview=1:NbView
        checkmask=0;
        FirstFileName=fullfile_uvmat(Param.InputTable{iview,1},Param.InputTable{iview,2},Param.InputTable{iview,3},...
            Param.InputTable{iview,5},Param.InputTable{iview,4},i1,i2,j1,j2);
        
        [FileInfo,VideoObject]=get_file_info(FirstFileName);
        
        
%         Data=nc2struct(FirstFileName);
        if isfield(Data,'Civ2_Mask')
            if exist(Data.Civ2_Mask,'file')
            MaskTable{iview,1}=Data.Civ2_Mask;
            checkmask=1; 
            end
        end
        if ~checkmask
            MaskTable{iview,1}=uigetfile_uvmat('select a mask file:',Param.InputTable{iview,1},'image');
        end
    end
    for iview=1:NbView
        [Path,Name]=fileparts(MaskTable{iview,1});
        Name=regexprep(Name,'_\d+','');
        maskfiles=dir(fullfile(Path,[Name '_*.png']));%look for mask files        
        if ~isempty(maskfiles)
            for ilist=1:numel(maskfiles)
                r=regexp(maskfiles(ilist).name,'_(?<num1>\d+)','names');%look for burst pairs
                index(ilist)=str2double(r.num1);
            end
            MaskTable{iview,2}=max(index);
        end
    end
    set(handles.MaskTable,'Data',MaskTable)
    set(handles.CheckMask,'Value',0)
end
%       
% if ~isempty(NewMask)
%     if isempty(MaskList)
%         MaskList={NewMask};
%     else
%     MaskList={MaskList;NewMask};
%     end
%     set(handles.Mask,'String',MaskList)
% end
% end
% %     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
%     for iview=1:nbview
%         ListMask{iview,1}=num2str(iview);
%         RootPath=InputTable{iview,1};
%         if ~isempty(RootPath)
%             if isempty(MaskData{iview})
%                 SubDir=InputTable{iview,2};
%                 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)
%                     mdetect=0;
%                     if ~isempty(ListFiles)
%                         for ifile=1:numel(ListFiles)
%                             [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileType]=find_file_series(MaskPath,ListFiles{ifile},0);
%                             if strcmp(MaskFileType,'image') && isempty(i2_series) && isempty(j2_series)
%                                 mdetect=1;
%                                 MaskName=ListFiles{ifile};
%                             end
%                             if ~strcmp(MaskFile{ifile},MaskFile{1})
%                                 mdetect=0; % cancel detection test in case of multiple masks, use the brower for selection
%                                 break
%                             end
%                         end
%                     end
%                     if mdetect==1
%                         MaskName=fullfile(MaskPath,'mask_1.png');
%                     else
%                         MaskName=uigetfile_uvmat('select a mask file:',MaskPath,'image');
%                     end
%                 else
%                     MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
%                 end
%                 MaskTable{iview,1}=MaskName ;
%                 ListMask{iview,1}=num2str(iview);
%             end
%         end
%     end
%     set(handles.MaskTable,'Data',MaskTable)
%     set(handles.MaskTable,'Visible','on')
%     set(handles.MaskBrowse,'Visible','on')
%     set(handles.ListMask,'Visible','on')
%     set(handles.ListMask,'String',ListMask)
%     set(handles.ListMask,'Value',1)



%------------------------------------------------------------------------
% --- Executes when selected cell(s) is changed in MaskTable.
%------------------------------------------------------------------------
function MaskTable_CellSelectionCallback(hObject, eventdata, handles)

if numel(eventdata.Indices)>=1
set(handles.ListMask,'Value',eventdata.Indices(1))
end

%-------------------------------------------------------------------
function MenuHelp_Callback(hObject, eventdata, handles)
%-------------------------------------------------------------------


% path_to_uvmat=which ('uvmat'); % check the path of uvmat
% pathelp=fileparts(path_to_uvmat);
% helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
% if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
% else
%     addpath (fullfile(pathelp,'uvmat_doc'))
%     web([helpfile '#series'])
% end

%-------------------------------------------------------------------
% --- Executes on selection change in TransformName.
function TransformName_Callback(hObject, eventdata, handles)
%----------------------------------------------------------------------
TransformList=get(handles.TransformName,'String');
TransformIndex=get(handles.TransformName,'Value');
TransformName=TransformList{TransformIndex};
TransformPathList=get(handles.TransformName,'UserData');
nb_builtin_transform=4;

%% browse transform functions with the input menu option more...
if isequal(TransformName,'more...')% browse transform functions
    FileName=uigetfile_uvmat('Pick a transform function',get(handles.TransformPath,'String'),'.m');
    if isempty(FileName)
        return     %browser closed without choice
    end
    [TransformPath,TransformName,TransformExt]=fileparts(FileName); % removes extension .m
    if ~strcmp(TransformExt,'.m')
        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
        return
    end
     % insert the choice in the menu
    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...'
        set(handles.TransformName,'String',TransformList)
        TransformPathList=[TransformPathList;{TransformPath}];
    else% the input function already exist, we update its path (possibly new)
        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
   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
   if exist(profil_perso,'file')
       for ilist=nb_builtin_transform+1:numel(TransformPathList)
           TransformListUser{ilist-nb_builtin_transform}=TransformList{ilist};
           TransformPathListUser{ilist-nb_builtin_transform}=TransformPathList{ilist};
       end
       TransformPathListUser=TransformPathListUser';
       TransformListUser=TransformListUser';
       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.TransformName,'UserData',TransformPathList);

%% create the function handle of the selected fct
if ~isempty(TransformName)
    if ~exist(TransformPathList{TransformIndex},'dir')
        msgbox_uvmat('ERROR',['The prescribed transform function path ' TransformPathList{TransformIndex} ' does not exist']);
        return
    end
    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
    SeriesData=get(handles.series,'UserData');
    ParamIn=[];
    if isfield(SeriesData,'TransformInput')
        ParamIn.TransformInput=SeriesData.TransformInput;
    end
    DataOut=feval(transform_handle,Field,ParamIn);% execute the transform fct to get its input parameters
    if isfield(DataOut,'TransformInput')%  used to add transform parameters at selection of the transform fct
        SeriesData.TransformInput=DataOut.TransformInput;
        set(handles.series,'UserData',SeriesData)
    end
end

%------------------------------------------------------------------------
% --- fct activated by the upper bar menu ExportConfig
%------------------------------------------------------------------------
function MenuDisplayConfig_Callback(hObject, eventdata, handles)

global Param
Param=read_GUI_series(handles);
evalin('base','global Param')%make CurData global in the workspace
display('current series config :')
evalin('base','Param') %display CurData in the workspace
commandwindow; % brings the Matlab command window to the front

%------------------------------------------------------------------------
% --- fct activated by the upper bar menu InportConfig: import
%     menu settings from an xml file (stored in /0_XML for each run)
%------------------------------------------------------------------------
function MenuImportConfig_Callback(hObject, eventdata, handles)

%% 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
if isempty(oldfile)
    % use a file name stored in prefdir
    dir_perso=prefdir;
    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
    if exist(profil_perso,'file')
        h=load (profil_perso);
        if isfield(h,'RootPath') && ischar(h.RootPath)
            oldfile=h.RootPath;
        end
    end
end
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,RootTag,errormsg]=xml2struct(filexml); % read the input xml file as a Matlab structure
if ~isempty(errormsg)
    msgbox_uvmat('ERROR',errormsg);
    return
end
% ask to stop current Action if button RUN is in action (another process is already running)
if isequal(get(handles.RUN,'Value'),1)
    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
    if strcmp(answer,'Yes')
        STOP_Callback(hObject, eventdata, handles)
    else
        return
    end
end
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
SeriesData=get(handles.series,'UserData');
if isfield(Param,'InputFields')
    ListField=Param.InputFields.FieldName;
    if ischar(ListField),ListField={ListField}; end
    set(handles.FieldName,'String',[ListField;{'add_field...'}])
     set(handles.FieldName,'Value',1:numel(ListField))
     set(handles.FieldName,'Visible','on')
end
if isfield(Param,'ActionInput')%  introduce  parameters specific to an Action fct, for instance PIV parameters
%     set(handles.ActionInput,'Visible','on')
%     set(handles.ActionInput,'Value',0)
    Param.ActionInput.ConfigSource=filexml; % record the source of config for future info
    SeriesData.ActionInput=Param.ActionInput;
end
if isfield(Param,'TransformInput')%  introduce  parameters specific to a transform fct
    SeriesData.TransformInput=Param.TransformInput;
end
if isfield(Param,'ProjObject') %introduce projection object if relevant
    SeriesData.ProjObject=Param.ProjObject;
end
set(handles.series,'UserData',SeriesData)
if isfield(Param,'CheckObject') && isequal(Param.CheckObject,1)
    set(handles.ProjObjectName,'String',Param.ProjObject.Name)
    set(handles.ViewObject,'Visible','on')
    set(handles.EditObject,'Visible','on')
    set(handles.DeleteObject,'Visible','on')
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.REFRESH,'BackgroundColor',[1 0 1]); % paint REFRESH button in magenta to indicate that it should be activated


%------------------------------------------------------------------------
% --- Executes when the GUI series is resized.
%------------------------------------------------------------------------
function series_ResizeFcn(hObject, eventdata, handles)

%% input table
set(handles.InputTable,'Unit','pixel')
Pos=get(handles.InputTable,'Position');
set(handles.InputTable,'Unit','normalized')
ColumnWidth=round([0.5 0.14 0.14 0.14 0.08]*(Pos(3)-52));
ColumnWidth=num2cell(ColumnWidth);
set(handles.InputTable,'ColumnWidth',ColumnWidth)

%% MaskTable
set(handles.MaskTable,'Unit','pixel')
Pos=get(handles.MaskTable,'Position');
set(handles.MaskTable,'Unit','normalized')
ColumnWidth=round([0.9 0.1]*(Pos(3)-52));
ColumnWidth=num2cell(ColumnWidth);
set(handles.MaskTable,'ColumnWidth',ColumnWidth)

%% MinIndex_j and MaxIndex_i
unit=get(handles.MinIndex_i,'Unit');
set(handles.MinIndex_i,'Unit','pixel')
Pos=get(handles.MinIndex_i,'Position');
set(handles.MinIndex_i,'Unit',unit)
set(handles.MinIndex_i,'ColumnWidth',{Pos(3)-18})
set(handles.MaxIndex_i,'ColumnWidth',{Pos(3)-18})
set(handles.MinIndex_j,'ColumnWidth',{Pos(3)-18})
set(handles.MaxIndex_j,'ColumnWidth',{Pos(3)-18})

%% TimeTable
set(handles.TimeTable,'Unit','pixel')
Pos=get(handles.TimeTable,'Position');
set(handles.TimeTable,'Unit','normalized')
% ColumnWidth=get(handles.TimeTable,'ColumnWidth');
ColumnWidth=num2cell(floor([0.2 0.2 0.2 0.2 0.2]*(Pos(3)-20)));
set(handles.TimeTable,'ColumnWidth',ColumnWidth)


%% PairString
set(handles.PairString,'Unit','pixel')
Pos=get(handles.PairString,'Position');
set(handles.PairString,'Unit','normalized')
set(handles.PairString,'ColumnWidth',{Pos(3)-5})

%% MaskTable
% % set(handles.MaskTable,'Unit','pixel')
% % Pos=get(handles.MaskTable,'Position');
% % set(handles.MaskTable,'Unit','normalized')
% % set(handles.MaskTable,'ColumnWidth',{Pos(3)-5})

%------------------------------------------------------------------------
% --- Executes on button press in status.
%------------------------------------------------------------------------
function status_Callback(hObject, eventdata, handles)

if get(handles.status,'Value')
    set(handles.status,'BackgroundColor',[1 1 0])
    drawnow
    Param=read_GUI(handles.series);
    RootPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device);
    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])
        return
    end
    OutputSubDir=[Param.OutputSubDir Param.OutputDirExt]; % subdirectory for output files
    OutputDir=fullfile(RootPath,OutputSubDir);
    if exist(OutputDir,'dir')
        uigetfile_uvmat('status_display',OutputDir)
    else
        msgbox_uvmat('ERROR','output folder not created yet: calculation did not start')
        set(handles.status,'BackgroundColor',[0 1 0])
    end
else
    %% delete current display fig if selection is off
    set(handles.status,'BackgroundColor',[0 1 0])
    hfig=findobj(allchild(0),'name','status_display');
    if ~isempty(hfig)
        delete(hfig)
    end
    return
end


%------------------------------------------------------------------------
% launched by selecting a file on the list
%------------------------------------------------------------------------
function view_file(hObject, eventdata)

list=get(hObject,'String');
index=get(hObject,'Value');
rootroot=get(hObject,'UserData');
selectname=list{index};
ind_dot=regexp(selectname,'\.\.\.');
if ~isempty(ind_dot)
    selectname=selectname(1:ind_dot-1);
end
FullSelectName=fullfile(rootroot,selectname);
if exist(FullSelectName,'dir')% a directory has been selected
    ListFiles=dir(FullSelectName);
    ListDisplay=cell(numel(ListFiles),1);
    for ilist=2:numel(ListDisplay)% suppress the first line '.'
        ListDisplay{ilist-1}=ListFiles(ilist).name;
    end
    set(hObject,'Value',1)
    set(hObject,'String',ListDisplay)
    if strcmp(selectname,'..')
        FullSelectName=fileparts(fileparts(FullSelectName));
    end
    set(hObject,'UserData',FullSelectName)
    hfig=get(hObject,'parent');
    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);
    if strcmp(FileInfo.FileType,'txt')
        edit(FullSelectName)
    elseif strcmp(FileInfo.FileType,'xml')
        editxml(FullSelectName)
    else
        uvmat(FullSelectName)
    end
    set(gcbo,'Value',1)
end


%------------------------------------------------------------------------
% launched by refreshing the status figure
%------------------------------------------------------------------------
function refresh_GUI(hfig)

htitlebox=findobj(hfig,'tag','titlebox');
hlist=findobj(hfig,'tag','list');
hseries=findobj(allchild(0),'tag','series');
hstatus=findobj(hseries,'tag','status');
StatusData=get(hstatus,'UserData');
OutputDir=get(htitlebox,'String');
if ischar(OutputDir),OutputDir={OutputDir};end
ListFiles=dir(OutputDir{1});
if numel(ListFiles)<1
    return
end
ListFiles(1)=[]; % removes the first line ='.'
ListDisplay=cell(numel(ListFiles),1);
testrecent=0;
datnum=zeros(numel(ListDisplay),1);
for ilist=1:numel(ListDisplay)
    ListDisplay{ilist}=ListFiles(ilist).name;
      if ~ListFiles(ilist).isdir && isfield(ListFiles(ilist),'datenum')
            datnum(ilist)=ListFiles(ilist).datenum; % only available in recent matlab versions
            testrecent=1;
       end
end
set(hlist,'String',ListDisplay)

%% Look at date of creation
ListDisplay=ListDisplay(datnum~=0);
datnum=datnum(datnum~=0); % keep the non zero values corresponding to existing files
NbOutputFile=[];
if isempty(datnum)
    if testrecent
        message='no civ result created yet';
    else
        message='';
    end
else
    [first,indfirst]=min(datnum);
    [last,indlast]=max(datnum);
    NbOutputFile_str='?';
    NbOutputFile=[];
    if isfield(StatusData,'NbOutputFile')
        NbOutputFile=StatusData.NbOutputFile;
        NbOutputFile_str=num2str(NbOutputFile);
    end
    message={[num2str(numel(datnum)) ' file(s) done over ' NbOutputFile_str] ;['oldest modification:  ' ListDisplay{indfirst} ' : ' datestr(first)];...
        ['latest modification:  ' ListDisplay{indlast} ' : ' datestr(last)]};
end
set(htitlebox,'String', [OutputDir{1};message])

%% update the waitbar
hwaitbar=findobj(hfig,'tag','waitbar');
if ~isempty(NbOutputFile)
    BarPosition=get(hwaitbar,'Position');
    BarPosition(3)=0.9*numel(datnum)/NbOutputFile;
    set(hwaitbar,'Position',BarPosition)
end

%------------------------------------------------------------------------
% --- Executes on selection change in ActionExt.
%------------------------------------------------------------------------
function ActionExt_Callback(hObject, eventdata, handles)

ActionExtList=get(handles.ActionExt,'String');
ActionExt=ActionExtList{get(handles.ActionExt,'Value')};
if strcmp(ActionExt,'fluidimage')
    set(handles.RunMode,'Value',2)
end


function num_NbSlice_Callback(hObject, eventdata, handles)
NbSlice=str2num(get(handles.num_NbSlice,'String'));

%------------------------------------------------------------------------
% --- set the visibility of relevant velocity type menus:
function menu=set_veltype_display(Civ,FileType)
%------------------------------------------------------------------------
if ~exist('FileType','var')
    FileType='civx';
end
switch FileType
    case 'civx'
        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
        if isequal(Civ,0)
            imax=0;
        elseif isequal(Civ,1) || isequal(Civ,2)
            imax=1;
        elseif isequal(Civ,3)
            imax=3;
        elseif isequal(Civ,4) || isequal(Civ,5)
            imax=4;
        elseif isequal(Civ,6) %patch2
            imax=6;
        end
    case 'civdata'
        menu={'civ1';'filter1';'civ2';'filter2'};
        if isequal(Civ,0)
            imax=0;
        elseif isequal(Civ,1) || isequal(Civ,2)
            imax=1;
        elseif isequal(Civ,3)
            imax=2;
        elseif isequal(Civ,4) || isequal(Civ,5)
            imax=3;
        else%if isequal(Civ,6) %patch2
            imax=4;
        end
end
menu=menu(1:imax);


% --- Executes on mouse motion over figure - except title and menu.
% function series_WindowButtonMotionFcn(hObject, eventdata, handles)
% set(hObject,'Pointer','arrow');


% --- Executes on button press in SetPairs.
function SetPairs_Callback(hObject, eventdata, handles)

%% delete previous occurrence of 'set_pairs'
hfig=findobj(allchild(0),'Tag','set_pairs');
if ~isempty(hfig)
delete(hfig)
end

%% 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)
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
hfig=findobj(allchild(0),'Tag','set_slice');
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');
SeriesData=get(handles.series,'UserData');
TimeUnit=get(handles.TimeUnit,'String');
PairString=get(handles.PairString,'Data');
ListViewLines=find(cellfun('isempty',PairString)==0); % find list of non empty pairs
ListViewMenu=cell(numel(ListViewLines),1);
%iview=get(handles.PairString,'Value');
iview=[];
for ilist=1:numel(ListViewLines)
    ListViewMenu{ilist}=num2str(ListViewLines(ilist));
end
if isempty(iview)
    ListViewValue=numel(ListViewLines); % we work by default on the pair option for the last line which requires pairs
    iview=ListViewLines(end);
else
    ListViewValue=find(ListViewLines==iview);
end
ref_i=str2num(get(handles.num_first_i,'String'));
ref_j=1; % default
if strcmp(get(handles.num_first_j,'String'),'Visible')
    ref_j=str2num(get(handles.num_first_j,'String'));
end
[ModeMenu,ModeValue]=update_mode(SeriesData.i1_series{1},SeriesData.i2_series{1},SeriesData.j2_series{1});
InputTable=get(handles.InputTable,'Data');
displ_pair=update_listpair(SeriesData.i1_series{1},SeriesData.i2_series{1},SeriesData.j1_series{1},SeriesData.j2_series{1},ModeMenu{ModeValue},...
                                                 SeriesData.Time{1},TimeUnit,ref_i,ref_j,SeriesData.TimeName,InputTable,SeriesData.FileInfo{1});
for iline=1:size(InputTable,1)
    viewcell{iline}=num2str(iline);
end
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
% 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
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',viewcell,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
    'Tag','ListView','TooltipString','''ListView'':choice of the file series w for pair display');
% 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
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',...
    'Tag','Mode','TooltipString','''Mode'': choice of the image pair mode');
% 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
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
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',...
    'Tag','num_ref_i','TooltipString','''num_ref_i'': reference field index i used to display dt in ''list_pair_civ''');
uicontrol('Style','edit','Units','normalized', 'Position', [0.55 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
    'Callback',@(hObject,eventdata)num_ref_j_Callback(hObject,eventdata),'String',num2str(ref_j),'FontUnits','points','FontSize',12,'FontWeight','bold',...
    'Tag','num_ref_j','TooltipString','''num_ref_j'': reference field index i used to display dt in ''list_pair_civ''');
uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.01 0.01 0.3 0.12],'BackgroundColor',[0 1 0],...
    'Callback',@(hObject,eventdata)OK_Callback(hObject,eventdata),'String','OK','FontUnits','points','FontSize',12,'FontWeight','bold',...
    'Tag','OK','TooltipString','''OK'': validate the choice');
%  last raw  of the GUI: pushbuttons
% uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.35 0.01 0.3 0.15],'BackgroundColor',[0 1 0],'String','OK','Callback',@(hObject,eventdata)OK_Callback(hObject,eventdata),...
%     'FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''OK'': apply the output to the current field series in uvmat');
drawnow

%------------------------------------------------------------------------
function ListView_Callback(hObject,eventdata)
Mode_Callback(hObject,eventdata)

%------------------------------------------------------------------------
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
TimeUnit=get(hhseries.TimeUnit,'String');
SeriesData=get(hseries,'UserData');
mode_list=get(hObject,'String');
mode=mode_list{get(hObject,'Value')};
hListView=findobj(get(hObject,'parent'),'Tag','ListView');
iview=get(hListView,'Value');
i1_series=SeriesData.i1_series{iview};
i2_series=SeriesData.i2_series{iview};
j1_series=SeriesData.j1_series{iview};
j2_series=SeriesData.j2_series{iview};

%% enable j index visibility after the new choice

if strcmp(mode,'series(Dj)')
   status_j='on'; % default
else
       status_j='off'; % no j index needed for bust case
end
enable_j(hhseries,status_j) % no j index needed

%% get the reference indices for the time interval Dt
href_i=findobj(get(hObject,'parent'),'Tag','ref_i');
ref_i=[];ref_j=[];
if strcmp(get(href_i,'Visible'),'on')
    ref_i=str2num(get(href_i,'String'));
end
if isempty(ref_i)
    ref_i=1;
end
if isempty(ref_j)
    ref_j=1;
end

%% update the menu ListPair
Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,SeriesData.Time{iview},TimeUnit,ref_i,ref_j,SeriesData.FileInfo);
hlist_pairs=findobj(get(hObject,'parent'),'Tag','ListPair');
set(hlist_pairs,'Value',1)% set the first choice by default in ListPair
set(hlist_pairs,'String',Menu)% set the menu in ListPair
ListPair_Callback(hlist_pairs,[])% apply the default choice in ListPair

%-------------------------------------------------------------
% --- Executes on selection in ListPair.
function ListPair_Callback(hObject,eventdata)
%------------------------------------------------------------
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 ',')
end
hseries=findobj(allchild(0),'tag','series');
hPairString=findobj(hseries,'tag','PairString');
PairString=get(hPairString,'Data');
hListView=findobj(get(hObject,'parent'),'Tag','ListView');
iview=get(hListView,'Value');
PairString{iview,1}=string;
% report the selected pair string to the table PairString
set(hPairString,'Data',PairString)


%------------------------------------------------------------------------
function num_ref_i_Callback(hObject, eventdata)
%------------------------------------------------------------------------
Mode_Callback([],[])

%------------------------------------------------------------------------
function num_ref_j_Callback(hObject, eventdata)
%------------------------------------------------------------------------
Mode_Callback([],[])

%------------------------------------------------------------------------
function OK_Callback(hObject, eventdata)
%------------------------------------------------------------------------
delete(get(hObject,'parent'))


%------------------------------------------------------------------------
% --- Executes on button press in ClearLine.
%------------------------------------------------------------------------
function ClearLine_Callback(hObject, eventdata, handles)
InputTable=get(handles.InputTable,'Data');
iline=str2double(get(handles.InputLine,'String'));
if size(InputTable,1)>1
    InputTable(iline,:)=[]; % suppress the current line if not the first
    set(handles.InputTable,'Data',InputTable);
end
set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refr


% --- Executes on button press in MonitorCluster.
function MonitorCluster_Callback(hObject, eventdata, handles)

[rr,ss]=system('oarstat |grep N=UVmat');% check the list of jobs launched with uvmat
if isempty(ss)
   disp( 'no job presently submitted with uvmat')
else
    disp('format: R/W=run/wait, time lapsed, R=nbre of cores,W=walltime')
    disp(ss)
end


function OutputSubDir_Callback(hObject, eventdata, handles)
set(handles.OutputSubDir,'BackgroundColor',[1 1 1])


% --- Executes on button press in CheckOverwrite.
function CheckOverwrite_Callback(hObject, eventdata, handles)

% --- Executes on button press in TestCPUTime.
function TestCPUTime_Callback(hObject, eventdata, handles)
% hObject    handle to TestCPUTime (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)


% --- Executes on button press in DiskQuota.
function DiskQuota_Callback(hObject, eventdata, handles)
SeriesData=get(handles.series,'UserData');
system(SeriesData.DiskQuotaCmd)


% --- Executes on button press in Replicate.
function Replicate_Callback(hObject, eventdata, handles)
if get(handles.Replicate,'Value')
    InputTable=get(handles.InputTable,'Data');
    for ilist=1:size(InputTable,1)
        InputDir{ilist}=fullfile(InputTable{ilist,1},InputTable{ilist,2});
    end
    browse_data(InputDir)
else
    hh=findobj(allchild(0),'Tag','browse_data');
    if ~isempty(hh)
        delete(hh)
    end
end




function OutputPath_Callback(hObject, eventdata, handles)


function Experiment_Callback(hObject, eventdata, handles)


function Device_Callback(hObject, eventdata, handles)


% --- Executes on button press in OutputPathBrowse.
function OutputPathBrowse_Callback(hObject, eventdata, handles)
CheckValue=get(handles.OutputPathBrowse,'Value');
if CheckValue
OutputPath=uigetdir(get(handles.OutputPath,'String'));
set(handles.OutputPath,'String',OutputPath)
else
    InputTable=get(handles.InputTable,'Data');
    set(handles.OutputPath,'String',InputTable{1,1})
end



% --- Executes on button press in DeleteMask.
function DeleteMask_Callback(hObject, eventdata, handles)
set(handles.MaskTable,'Data',{})