source: trunk/src/series.m @ 771

%'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
%
%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
%  Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org.
%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
%     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 (file UVMAT/COPYING.txt) for more details.
%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

%------------------------------------------------------------------------
%------------------------------------------------------------------------
%  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(handles.InputTable,'KeyPressFcn',{@key_press_fcn,handles})%set keyboard action function (allow action on uvmat when set_object is in front)
set(hObject,'DeleteFcn',{@closefcn})%

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

%% list of builtin functions in the mebu ActionName
ActionList={'check_data_files';'aver_stat';'time_series';'civ_series';'merge_proj'};% WARNING: fits with nb_builtin_ACTION=4 in ActionName_callback
NbBuiltinAction=numel(ActionList);
[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'};% default choice of extensions (Matlab fct .m or compiled version .sh
ActionPathList=cell(NbBuiltinAction,numel(ActionExtList));%initiate the cell matrix of Action fct paths
ActionPathList(:)={path_series_fct}; %set the default path to series fcts to all list members
RunModeList={'local';'background'};% default choice of extensions (Matlab fct .m or compiled version .sh)
[s,w]=system('oarstat');% look for cluster system 'oar'
if isequal(s,0)
    RunModeList=[RunModeList;{'cluster_oar'}];
end
[s,w]=system('qstat');% look for cluster system 'sge'
if isequal(s,0)
    RunModeList=[RunModeList;{'cluster_sge'}];
end
set(handles.RunMode,'String',RunModeList)

%% list of builtin transform functions in the mebu 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

%% 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 list of previous camapigns in the upper bar menu Open campaign
    if isfield(h,'MenuCampaign')
        for ifile=1:min(length(h.MenuCampaign),5)
            set(handles.(['MenuCampaign_' num2str(ifile)]),'Label',h.MenuCampaign{ifile});
        end
    end
    %get the menu of actions
    if isfield(h,'ActionExtListUser') && iscell(h.ActionExtListUser)
        ActionExtList=[ActionExtList; h.ActionExtListUser];
    end 
    if isfield(h,'ActionListUser') && iscell(h.ActionListUser) && isfield(h,'ActionPathListUser') && iscell(h.ActionPathListUser)
        ActionList=[ActionList;h.ActionListUser];
        ActionPathList=[ActionPathList;h.ActionPathListUser];
    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,'Coord_x_str') && ischar(Param.Coord_x_str)
        set(handles.Coord_x,'String',Param.Coord_x_str);% list menu fields
%     set(handles.Coord_x,'Value',Param.Coord_x_val);% selected string index
end
if isfield(Param,'Coord_y_str')&& ischar(Param.Coord_y_str)
        set(handles.Coord_y,'String',Param.Coord_y_str);% list menu fields
%     set(handles.Coord_y,'Value',Param.Coord_y_val);% selected string index
end

%% introduce the input file name(s) if defined from input Param, TODO: avoid the file checking if Param.i1_series defined
if isfield(Param,'FileName')&&~isempty(Param.FileName)
    InputTable={};
    set(handles.InputTable,'Data',InputTable)
    display_file_name(handles,Param,'one')%refresh the input table
    if isfield(Param,'FileName_1')
        Param.FileName=Param.FileName_1;
        display_file_name(handles,Param,2)
    end
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))
end
if isfield(Param,'incr_j')
    set(handles.num_incr_j,'String',num2str(Param.incr_j))
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'
%------------------------------------------------------------------------ 
function MenuBrowseCampaign_Callback(hObject, eventdata, handles)

set(handles.MenuOpenCampaign,'ForegroundColor',[1 1 0])
drawnow
InputTable=get(handles.InputTable,'Data');
RootPath=InputTable{1,1};
CampaignPath=fileparts(fileparts(RootPath));
DirFull=uigetfile_uvmat('define this path as the Campaign folder:',CampaignPath,'uigetdir');
if ~ischar(DirFull)|| ~exist(DirFull,'dir')
    return
end
OutPut=browse_data(DirFull);% open the GUI browse_data to get select a campaign dir, experiment and device
if ~isfield(OutPut,'Campaign')
    return
end
DirName=fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.DataSeries{1});
ListStruct=dir(DirName); %list files and the dir DataSeries
% select the first appropriate file in the dir
FileName='';
for ilist=1:numel(ListStruct)
    if ~isequal(ListStruct(ilist).isdir,1)%look for files, not dir
        FileName=ListStruct(ilist).name;
        FileType=get_file_type(fullfile(DirName,FileName));
        switch FileType
            case {'image','multimage','civx','civdata','netcdf'}
                break
        end
    end
end
if isempty(FileName)
    msgbox_uvmat('ERROR',['no appropriate input file in the DataSeries folder ' fullfile(DirName)])
    return
end

%% update the list of campaigns in the menubar
MenuCampaign=[{get(handles.MenuCampaign_1,'Label')};{get(handles.MenuCampaign_2,'Label')};...
    {get(handles.MenuCampaign_3,'Label')};{get(handles.MenuCampaign_4,'Label')};{get(handles.MenuCampaign_5,'Label')}];
check_dir=isempty(find(strcmp(DirFull,MenuCampaign)));
if check_dir %insert the new campaign in the list if it is not found
    MenuCampaign(end)=[]; %suppress the last item
    MenuCampaign=[{DirFull};MenuCampaign];%insert the new campaign
    for ilist=1:numel(MenuCampaign)
        set(handles.(['MenuCampaign_' num2str(ilist)]),'Label',MenuCampaign{ilist})
    end
    % save the list for future opening:
    dir_perso=prefdir;
    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
    if exist(profil_perso,'file')
        save (profil_perso,'MenuCampaign','RootPath','-append'); %store the file names for future opening of uvmat
    else
        save (profil_perso,'MenuCampaign','RootPath','-V6'); %store the file names for future opening of uvmat
    end
end

%% display the selected field and related information
if get(handles.CheckAppend,'Value')
    display_file_name(handles,fullfile(DirName,FileName),'append')
else
    display_file_name(handles,fullfile(DirName,FileName),'one')
end
set(handles.MenuOpenCampaign,'ForegroundColor',[0 0 0])

% --------------------------------------------------------------------
function MenuCampaign_Callback(hObject, eventdata, handles)
% -------------------------------------------------------------------- 
set(handles.MenuOpenCampaign,'ForegroundColor',[1 1 0])
OutPut=browse_data(get(hObject,'Label'));% open the GUI browse_data to get select a campaign dir, experiment and device
if ~isfield(OutPut,'Campaign')
    return
end
DirName=fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.DataSeries{1});
hdir=dir(DirName); %list files and dirs
for ilist=1:numel(hdir)
    if ~isequal(hdir(ilist).isdir,1)%look for files, not dir
        FileName=hdir(ilist).name;
        FileType=get_file_type(fullfile(DirName,FileName));
        switch FileType
            case {'image','multimage','civx','civdata','netcdf'}
            break
        end
    end
end
if get(handles.CheckAppend,'Value')
    display_file_name(handles,fullfile(DirName,FileName),'append')
else
    display_file_name(handles,fullfile(DirName,FileName),'one')
end
set(handles.MenuOpenCampaign,'ForegroundColor',[0 0 0])



%------------------------------------------------------------------------
% --- Executes when entered data in editable cell(s) in InputTable.
function InputTable_CellEditCallback(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.REFRESH_title,'Visible','on')
iview=eventdata.Indices(1);
view_set=get(handles.REFRESH,'UserData');
if isempty(find(view_set==iview))
    set(handles.REFRESH,'UserData',[view_set iview])
end
%% enable other menus and uicontrols
set(handles.MenuOpenCampaign,'Enable','on')
set(handles.MenuCampaign_1,'Enable','on')
set(handles.MenuCampaign_2,'Enable','on')
set(handles.MenuCampaign_3,'Enable','on')
set(handles.MenuCampaign_4,'Enable','on')
set(handles.MenuCampaign_5,'Enable','on')
set(handles.RUN, 'Enable','On')
set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red 

%------------------------------------------------------------------------
% --- 'key_press_fcn:' function activated when a key is pressed on the keyboard
%------------------------------------------------------------------------
function key_press_fcn(hObject,eventdata,handles)

xx=double(get(handles.series,'CurrentCharacter')); %get the keyboard character
if ismember(xx,[8 127 31])%backspace or delete, or downward
    InputTable=get(handles.InputTable,'Data');
    iline=get(handles.InputTable,'UserData');
            if isequal(xx, 31)
                if isequal(iline,size(InputTable,1))% arrow downward
                InputTable=[InputTable;cell(1,size(InputTable,2))];
                end
            else
    InputTable(iline,:)=[];% suppress the current line 
            end
    set(handles.InputTable,'Data',InputTable);
end


%------------------------------------------------------------------------
% --- Executes on button press in REFRESH.
function REFRESH_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
InputTable=get(handles.InputTable,'Data');
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)));
end
InputTable(empty_line,:)=[];%remove empty lines
set(handles.InputTable,'Data',InputTable)
for iview=1:size(InputTable,1)
    RootPath=fullfile(InputTable{iview,1},InputTable{iview,2});
    if ~exist(RootPath,'dir')
        i1_series=[];
        RootPath=fileparts(RootPath); %will try the upper folder
    else %scan the input folder
        [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,FileInfo,MovieObject]=...
            find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}]);
    end
    % if no file is found, open a browser
    if 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)
        end
    else
       update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,FileInfo,MovieObject,iview)
    end
end
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
function errormsg=display_file_name(handles,Param,iview)
%------------------------------------------------------------------------  
%
% INPUT:
% handles: handles of elements in the GUI
% fileinput: input file name, including path
% iview: line index in the input table
%       or 'one': refresh the list
%         'append': add a new line to the input table
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 ~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 seies %%%%%%%
%%%%%%%%%%%%%%%%%%%
% 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,FileType,FileInfo,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
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.MenuOpenCampaign,'Enable','on')
set(handles.MenuCampaign_1,'Enable','on')
set(handles.MenuCampaign_2,'Enable','on')
set(handles.MenuCampaign_3,'Enable','on')
set(handles.MenuCampaign_4,'Enable','on')
set(handles.MenuCampaign_5,'Enable','on')
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
    InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
elseif strcmp(iview,'one') % refresh the list of  input  file series
    iview=1; %the first line in InputTable becomes the current line
    InputTable={'','','','',''};
    InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
    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.ListView,'Value',1)
    set(handles.ListView,'String',{'1'})
    set(handles.PairString,'Data',{''})
    SeriesData.i1_series={};
    SeriesData.i2_series={};
    SeriesData.j1_series={};
    SeriesData.j2_series={};
    SeriesData.FileType={};
    SeriesData.FileInfo={};
    SeriesData.Time={};
end
nbview=size(InputTable,1);
set(handles.ListView,'String',mat2cell((1:nbview)',ones(nbview,1)))
set(handles.ListView,'Value',iview)
SeriesData.ListViewValue=iview;
SeriesData.ListViewMenu=mat2cell((1:nbview)',ones(nbview,1));
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
% set(handles.num_ref_j,'String',num2str(ref_j)); 
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)
    eval(['set(handles.MenuFile_' num2str(ifile) ',''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;
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,FileType,FileInfo,MovieObject,iview);
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,FileType,FileInfo,VideoObject,iview)
%------------------------------------------------------------------------
InputTable=get(handles.InputTable,'Data');

%% 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=min(find(ref_i))-1;
     MaxIndex_i=max(find(ref_i))-1;
     MaxIndex_j=max(find(ref_j))-1;
     MinIndex_j=min(find(ref_j))-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

%% 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
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=str2num(get(handles.num_ref_j,'String'));%index j given by the input field
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=1;%default
% read  value set by the first series for the checkappend mode (iwiew >1)
if iview>1 && strcmp(get(handles.num_NbSlice,'Visible'),'on')
    NbSlice=str2num(get(handles.num_NbSlice,'String'));
end

%% default time unit
TimeUnit='';
% read  value set by the first series for the checkappend mode (iwiew >1)
if iview>1 
    TimeUnit=get(handles.TimeUnit,'String');
end
TimeSource='';
Time=[];%default

%%  read image documentation file if found
XmlData=[];
check_calib=0;
XmlFileName=find_imadoc(InputTable{iview,1},InputTable{iview,2},InputTable{iview,3},InputTable{iview,5});
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;
        TimeSource='xml';
    end
    if isfield(XmlData,'Camera')
        if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
            if iview>1 && ~isempty(NbSlice) && ~strcmp(NbSlice,XmlData.Camera.NbSlice)
                msgbox_uvmat('WARNING','inconsistent number of slices with the first field series');
            end
            NbSlice=XmlData.Camera.NbSlice;% Nbre of slices from camera
        end
        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,'GeometryCalib')
        check_calib=1;
        if isfield(XmlData.GeometryCalib,'SliceCoord')
            siz=size(XmlData.GeometryCalib.SliceCoord);
            if siz(1)>1
                if iview>1 && ~isempty(NbSlice) && ~strcmp(NbSlice,siz(1))
                    msgbox_uvmat('WARNING','inconsistent number of Z indices with the first field series');
                end
                NbSlice=siz(1);
            end
        end
    end
    set(handles.num_NbSlice,'String',num2str(NbSlice))
end

%% read timing and total frame number from the current file (movie files) if not already set by the xml file (prioritary)
InputTable=get(handles.InputTable,'Data');

% case of movies
if isempty(Time)
    if ~isempty(VideoObject)
        imainfo=get(VideoObject);
        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
        TimeSource='video';
    end
end

%% update time table
if ~isempty(Time)
    TimeTable=get(handles.TimeTable,'Data');
    TimeTable{iview,1}=Time(MinIndex_i+1,MinIndex_j+1);
    if size(Time)>=[first_i+1 first_j+1]
        TimeTable{iview,2}=Time(first_i+1,first_j+1);
    end
    if size(Time)>=[last_i+1 last_j+1]
        TimeTable{iview,3}=Time(last_i+1,last_j+1);
    end
    if size(Time)>=[MaxIndex_i+1 MaxIndex_j+1];
        TimeTable{iview,4}=Time(MaxIndex_i+1,MaxIndex_j+1);
    end
    set(handles.TimeTable,'Data',TimeTable)
end

%% update the series info in 'UserData'
SeriesData=get(handles.series,'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}=FileType;
SeriesData.FileInfo{iview}=FileInfo;
SeriesData.Time{iview}=Time;
if ~isempty(TimeSource)
    SeriesData.TimeSource=TimeSource;
end
% if ~isempty(TimeUnit)
%     SeriesData.TimeUnit=TimeUnit;
% end
if check_calib
    SeriesData.GeometryCalib{iview}=XmlData.GeometryCalib;
end
set(handles.series,'UserData',SeriesData)

%% update pair menus
ListView=get(handles.ListView,'String');
ListView{iview}=num2str(iview);
set(handles.ListView,'String',ListView);
set(handles.ListView,'Value',iview)
update_mode(handles,i1_series,i2_series,j1_series,j2_series,Time)

%% enable j index visibility
status_j='on';%default
if isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)); % case of empty j indices
    status_j='off'; % no j index needed
elseif strcmp(get(handles.PairString,'Visible'),'on')
    PairString=get(handles.PairString,'Data');
    check_burst=cellfun(@isempty,regexp(PairString,'^j'));%=0 for burst case, 1 otherwise
    if isempty(find(check_burst, 1))% if all pair string begins by j (burst)
        status_j='off'; % no j index needed for bust case
    end
end
enable_j(handles,status_j) % no j index needed

%% display the set of existing files as an image
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 iview=1:nbview
    pair_max=squeeze(max(SeriesData.i1_series{iview},[],1)); %max on pair index
    j_max{iview}=max(pair_max,[],1);%max on j index
    if ~isempty(j_max{iview})
    MaxIndex_i(iview)=max(find(j_max{iview}))-1;% max ref index i
    MinIndex_i(iview)=min(find(j_max{iview}))-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 iview=1:nbview
    ind_y=1+(iview-1)*range_y:iview*range_y;
    LineData=zeros(size(file_indices));
    file_select=file_indices(file_indices<=numel(j_max{iview}));
    ind_select=find(file_indices<=numel(j_max{iview}));
    LineData(ind_select)=j_max{iview}(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);

%% check for pair display
check_pairs=0;
for iview=1:numel(SeriesData.i2_series)
    if ~isempty(SeriesData.i2_series{iview})||~isempty(SeriesData.j2_series{iview})
        check_pairs=1;
    end
end
if check_pairs
%     set(handles.Pairs,'Visible','on')
    set(handles.PairString,'Visible','on')
    set(handles.SetPairs,'Visible','on')
else
%     set(handles.Pairs,'Visible','off')
    set(handles.PairString,'Visible','off')
    set(handles.SetPairs,'Visible','off')
end


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

%% set length of waitbar
displ_time(handles)

%% set default options in menu 'Fields'
switch FileType
    case {'civx','civdata'}
        FieldList=[set_field_list('U','V');{'C'}];%standard menu for civx data
%         set(handles.Coord_x,'Value',1);
        set(handles.Coord_x,'String','X');
%         set(handles.Coord_y,'Value',1);
        set(handles.Coord_y,'String','Y');
    case 'netcdf'
        ind_x=find(strcmp(get(handles.Coord_x,'String'),FileInfo.ListVarName));
        if isempty(ind_x)
            FieldList={};% new kind of file opened, we need to pick variables with get_field...
            set(handles.Coord_x,'String','')
            set(handles.Coord_y,'String','')
        else
            FileInfo.ListVarName(ind_x)=[];%remove coord-x from the list of variables to display
            ind_y=find(strcmp(get(handles.Coord_y,'String'),FileInfo.ListVarName));
            if isempty(ind_y)
            FieldList={};% new kind of file opened, we need to pick variables with get_field...
            set(handles.Coord_x,'String','')
            set(handles.Coord_y,'String','')
            else
                FileInfo.ListVarName(ind_y)=[];%remove coord-y from the list of variables to display
                FieldList=(FileInfo.ListVarName)';
            end
        end  
    otherwise
        set(handles.FieldName,'Value',1) % set menu to 'image'
        set(handles.FieldName,'String',{'image'})
        set(handles.Coord_x,'String','AX');
        set(handles.Coord_y,'String','AY');
end
if ismember(FileType,{'civx','civdata','netcdf'})
    PrevMenu=get(handles.FieldName,'String');
    PrevMenu=PrevMenu(get(handles.FieldName,'Value'));
    FieldValue=[];
    for ilist=1:numel(PrevMenu)
        index_menu=find(strcmp(PrevMenu{ilist},FieldList));
        if ~isempty(index_menu)
            FieldValue=[FieldValue index_menu];
        end
    end
    if isempty(FieldValue)
        FieldValue=1;
    end
    set(handles.FieldName,'Value',FieldValue)
    set(handles.FieldName,'String',[FieldList;{'get_field...'}])
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)
%------------------------------------------------------------------------
first_j=str2num(get(handles.num_first_j,'String'));
last_j=str2num(get(handles.num_last_j,'String'));
ref_j=ceil((first_j+last_j)/2);
set(handles.num_ref_j,'String', num2str(ref_j))
num_ref_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');

%Pairs=get(handles.PairString,'Data');
for iview=1:size(TimeTable,1)
    if size(SeriesData.Time,1)<iview
        break
    end
    TimeTable{iview,2}=[];
    TimeTable{iview,3}=[];
    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,2}=time_first; %TODO: take into account pairs
        TimeTable{iview,3}=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
set(handles.ListView,'Value',eventdata.Indices(1))% detect the selected raw index
ListView_Callback ([],[],handles) % update the list of available pairs
end

%------------------------------------------------------------------------
%------------------------------------------------------------------------
%  III - FUNCTIONS ASSOCIATED TO THE FRAME SET PAIRS
%------------------------------------------------------------------------
%------------------------------------------------------------------------
% --- Executes on selection change in ListView.
function ListView_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------    
SeriesData=get(handles.series,'UserData');
i2_series=[];
j2_series=[];
iview=get(handles.ListView,'Value');
if ~isempty(SeriesData.i2_series{iview})
    i2_series=SeriesData.i2_series{iview};
end
if ~isempty(SeriesData.j2_series{iview})
    j2_series=SeriesData.j2_series{iview};
end
update_mode(handles,SeriesData.i1_series{iview},SeriesData.i2_series{iview},...
    SeriesData.j1_series{iview},SeriesData.j2_series{iview},SeriesData.Time{iview})

%------------------------------------------------------------------------
% --- Executes on button press in mode.
function mode_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------       
SeriesData=get(handles.series,'UserData');
iview=get(handles.ListView,'Value');
mode_list=get(handles.mode,'String');
mode=mode_list{get(handles.mode,'Value')};
if isequal(mode,'bursts')
    enable_i(handles,'On')
    enable_j(handles,'Off') %do not display j index scanning in burst mode (j is fixed by the burst choice)
else
    enable_i(handles,'On')
    enable_j(handles,'Off')
end
fill_ListPair(handles,SeriesData.i1_series{iview},SeriesData.i2_series{iview},...
    SeriesData.j1_series{iview},SeriesData.j2_series{iview},SeriesData.Time{iview})
ListPairs_Callback([],[],handles)

%-------------------------------------------------------------
% --- Executes on selection in ListPairs.
function ListPairs_Callback(hObject,eventdata,handles)
%------------------------------------------------------------
list_pair=get(handles.ListPairs,'String');%get the menu of image pairs
if isempty(list_pair)
    string='';
else
    string=list_pair{get(handles.ListPairs,'Value')};
    string=regexprep(string,',.*','');%removes time indication (after ',')
end
PairString=get(handles.PairString,'Data');
iview=get(handles.ListView,'Value');
PairString{iview,1}=string;
% report the selected pair string to the table PairString
set(handles.PairString,'Data',PairString)


%------------------------------------------------------------------------
function update_mode(handles,i1_series,i2_series,j1_series,j2_series,time)
%------------------------------------------------------------------------    
% check_burst=0;
ModeMenu={''};
if isempty(j2_series)% no j pair
    ModeValue=1;
    if isempty(i2_series)
        set(handles.mode,'String',{''})% no pair menu to display
    else   
        set(handles.mode,'Value',1)
        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=max(find(j_max))-1;% max ref index i
    MinIndex_i=min(find(j_max))-1;% min ref index i
    i_max=max(pair_max,[],2);
    MaxIndex_j=max(find(i_max))-1;% max ref index i
    MinIndex_j=min(find(i_max))-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

set(handles.mode,'String',ModeMenu)
set(handles.mode,'Value',ModeValue)
SeriesData=get(handles.series,'UserData');
SeriesData.ModeMenu=ModeMenu;
SeriesData.ModeValue=ModeValue;
set(handles.series,'UserData',SeriesData)
fill_ListPair(handles,i1_series,i2_series,j1_series,j2_series,time)
ListPairs_Callback([],[],handles)

%--------------------------------------------------------------
% determine the menu for pairstring depending on existing netcdf files 
% with the reference indices num_ref_i and num_ref_j
%----------------------------------------------------------------
function fill_ListPair(handles,i1_series,i2_series,j1_series,j2_series,time)

mode_list=get(handles.mode,'String');
mode=mode_list{get(handles.mode,'Value')};
ref_i=str2num(get(handles.num_ref_i,'String'));
if isempty(ref_i)
    ref_i=1;
end
if strcmp(get(handles.num_ref_j,'Visible'),'on')
    ref_j=str2num(get(handles.num_ref_j,'String'));
    if isempty(ref_j)
        ref_j=1;
    end
else
    ref_j=1;
end
TimeUnit=get(handles.TimeUnit,'String');
if length(TimeUnit)>=1
    dtunit=['m' TimeUnit];
else
    dtunit='e-03';
end

displ_pair={};
if strcmp(mode,'series(Di)') 
    if isempty(i2_series)
        msgbox_uvmat('ERROR','no i1-i2 pair available')
        return
    end
    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 numel(diff_i(diff_i==ipair))>0
            pair_string=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
            if ~isempty(time) 
                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
elseif strcmp(mode,'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
elseif strcmp(mode,'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
            displ_pair=[displ_pair;{['j= ' num2str(pair1) '-' num2str(pair2)]}];
        end
        end
    end
    if ~isempty(displ_pair)
        displ_pair=[displ_pair;{'j=*-*'}];
    end
end
set(handles.num_ref_i,'String',num2str(ref_i)) % update ref_i and ref_j 
set(handles.num_ref_j,'String',num2str(ref_j))

%% display list of pairstring
SeriesData=get(handles.series,'UserData');
displ_pair_list=get(handles.ListPairs,'String');
NewVal=[];
if ~isempty(displ_pair_list)
Val=get(handles.ListPairs,'Value');
NewVal=find(strcmp(displ_pair_list{Val},displ_pair),1);% look at the previous display in the new menu displ_pï¿œir
end
if ~isempty(NewVal)
    set(handles.ListPairs,'Value',NewVal)
    SeriesData.ListPairsValue=NewVal;
else
    set(handles.ListPairs,'Value',1)
    SeriesData.ListPairsValue=1;
end
set(handles.ListPairs,'String',displ_pair)
SeriesData.ListPairsMenu=displ_pair;
set(handles.series,'UserData',SeriesData);

%-------------------------------------
function enable_i(handles,state)
set(handles.i_txt,'Visible',state)
set(handles.num_first_i,'Visible',state)
set(handles.num_last_i,'Visible',state)
set(handles.num_incr_i,'Visible',state)
set(handles.num_ref_i,'Visible',state)
set(handles.ref_i_text,'Visible',state)

%-----------------------------------
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.num_ref_j,'Visible',state)
set(handles.ref_j_text,'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)

%% read the data on the GUI series
Param=read_GUI_series(handles);%displayed parameters
SeriesData=get(handles.series,'UserData');%hidden parameters
if ~isfield(SeriesData,'i1_series')
    msgbox_uvmat('ERROR','The input field series needs to be refreshed: press REFRESH')
    return
end
if isfield(Param,'InputFields')&& isequal(Param.InputFields.FieldName,'get_field...')
    msgbox_uvmat('ERROR','input field name(s) not defined, select get_field...')
    return
end

%% settings of the button RUN
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(hObject, eventdata, handles)

%% 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
end
ActionExt='.m';%default
if isfield(Param.Action,'ActionExt')
    ActionExt=Param.Action.ActionExt;% '.m' or '.sh' (compiled)
    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')
    if ~isequal(ActionPath,path_series)
        eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
        if ~exist(ActionPath,'dir')
            msgbox_uvmat('ERROR',['The prescribed function path ' ActionPath ' does not exist']);
            return
        end
        if ~isequal(spath,ActionPath)
            addpath(ActionPath)% add the prescribed path if not the current one
        end
    end
    eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
    if ~isequal(ActionPath,path_series)
        rmpath(ActionPath)% add the prescribed path if not the current one
    end
end

%% Get RunTime code from the file PARAM.xml (needed to run compiled functions)
errormsg='';%default error message
xmlfile=fullfile(path_series,'PARAM.xml');
test_batch=0;%default: ,no batch mode available
if ~exist(xmlfile,'file')
    [success,message]=copyfile(fullfile(path_series,'PARAM.xml.default'),xmlfile);
end
RunTime='';
if strcmp(ActionExt,'.sh')
    if exist(xmlfile,'file')
        s=xml2struct(xmlfile);
        if strcmp(RunMode,'cluster_oar') && isfield(s,'BatchParam')
            if isfield(s.BatchParam,'RunTime')
                RunTime=s.BatchParam.RunTime;
            end
            if isfield(s.BatchParam,'NbCore')
                NbCore=s.BatchParam.NbCore;
            end
        elseif (strcmp(RunMode,'background')||strcmp(RunMode,'local')) && isfield(s,'RunParam')
            if isfield(s.RunParam,'RunTime')
                RunTime=s.RunParam.RunTime;
            end
            if isfield(s.RunParam,'NbCore')
                NbCore=s.RunParam.NbCore;
            end
        end
    end
    if isempty(RunTime) && strcmp(RunMode,'cluster_oar')
        msgbox_uvmat('ERROR','RunTime name not found in PARAM.xml, compiled version .sh cannot run on cluster')
        return
    end
end

%% If a compiled version has been selected (ext .sh) check weather it needs to be recompiled
if strcmp(ActionExt,'.sh')
    TransformPath='';
    if ~isempty(get(handles.ActionExt,'UserData'))
        TransformPath=get(handles.ActionExt,'UserData');
    end
    set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
    set(handles.ActionExt,'BackgroundColor',[1 1 0])
    ActionFullName=fullfile(get(handles.ActionPath,'String'),[ActionName '.sh']);
    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)
        end       
    else
        sh_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.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',[ActionName '.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 uvmat 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
switch RunMode
    case {'local','background'}
        NbCore=1;% no need to split the calculation
    case 'cluster_oar'
        if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
            NbCore=1;% one core used only (limitation of Matlab licences)
            msgbox_uvmat('WARNING','Number of cores =1: select the compiled version civ_matlab.sh for multi-core processing');
            extra_oar='';
        else
            answer=inputdlg({'Number of cores (max 36)','extra oar options'},'oarsub parameter',1,{'12',''});
            NbCore=str2double(answer{1});
            extra_oar=answer{2};
        end
end
if ~isfield(Param.IndexRange,'NbSlice')
    Param.IndexRange.NbSlice=[];
end
if isempty(Param.IndexRange.NbSlice)
    NbProcess=NbCore;% choose one process per core
else
    NbProcess=Param.IndexRange.NbSlice;% the nbre of run processes is equal to the number of slices
    NbCore=min(NbCore,NbProcess);% at least one process per core
end

%% create the output data directory if needed
if isfield(Param,'OutputSubDir')
    SubDirOut=[get(handles.OutputSubDir,'String') Param.OutputDirExt];
    SubDirOutNew=SubDirOut;
    detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir');% test if  the dir  already exist
    check_create=1; %need to create the result directory by default
    while detect
        answer=msgbox_uvmat('INPUT_Y-N',['use existing ouput directory: ' fullfile(Param.InputTable{1,1},SubDirOutNew) ', possibly delete previous data']);
        if strcmp(answer,'Cancel')
            errormsg='Cancel';
            return
        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(Param.InputTable{1,1},SubDirOutNew),'dir');% test if  the dir  already exists
            check_create=1;
        end
    end
    Param.OutputDirExt=regexprep(SubDirOutNew,Param.OutputSubDir,'');
    Param.OutputRootFile=Param.InputTable{1,3};% the first sorted RootFile taken for output
    set(handles.OutputDirExt,'String',Param.OutputDirExt)
    OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]);% full name (with path) of output directory
    if check_create    % create output directory if it does not exist
        [tild,msg1]=mkdir(OutputDir);
        if ~strcmp(msg1,'')
            msgbox_uvmat('ERROR',['cannot create ' OutputDir ': ' msg1]);%error message for directory creation
            return
        end
        [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 ':']; msg1});%error message for directory creation
            return
        end
    end
    OutputNomType=nomtype2pair(Param.InputTable{1,4});% nomenclature for output files
    DirXml=fullfile(OutputDir,'0_XML');
    if ~exist(DirXml,'dir')
        [tild,msg1]=mkdir(DirXml);
        if ~strcmp(msg1,'')
            msgbox_uvmat('ERROR',['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 ':']; msg1});%error message for directory creation
            return
        end
    end
end
        
%% get the set of reference field indices
first_i=1;
last_i=1;
incr_i=1;
first_j=1;
last_j=1;
incr_j=1;
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,'first_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 
    msgbox_uvmat('ERROR', 'series/Run_Callback:last field index must be larger or equal to the first one')
    set(handles.RUN, 'Enable','On'),
    set(handles.RUN,'BackgroundColor',[1 0 0])
    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
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
else
    ref_i=first_i:incr_i:last_i;
    if isempty(incr_j)
        [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
BlockLength=ceil(numel(ref_i)/NbProcess);
nbfield_j=numel(ref_j);

%% 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)

%% direct processing on the current Matlab session
if strcmp (RunMode,'local')
    for iprocess=1:NbProcess
        if isempty(Param.IndexRange.NbSlice)
            %Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;
            Param.IndexRange.first_i=ref_i(1+(iprocess-1)*BlockLength);
            if Param.IndexRange.first_i>last_i
                break
            end
            Param.IndexRange.last_i=min(ref_i(iprocess*BlockLength),last_i);
            %Param.IndexRange.last_i=min(first_i+(iprocess)*BlockLength*incr_i-1,last_i);
        else %multislices (then incr_i is not empty)
             Param.IndexRange.first_i= first_i+incr_i*(iprocess-1);
             Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice;
        end
        if isfield(Param,'OutputSubDir')
        t=struct2xml(Param);
        t=set(t,1,'name','Series');
        filexml=fullfile_uvmat(DirXml,'',Param.InputTable{1,3},'.xml',OutputNomType,...
            Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
        save(t,filexml);
        end
        switch ActionExt
            case '.m'
                h_fun(Param);
            case '.sh'
                switch computer
                    case {'PCWIN','PCWIN64'} %Windows system
                        filexml=regexprep(filexml,'\\','\\\\');% add '\' so that '\' are left as characters
                        system([fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml]);% TODO: adapt to DOS system
                    case {'GLNX86','GLNXA64','MACI64'}%Linux  system
                        system([fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml]);
                end
        end
    end
elseif strcmp(get(handles.OutputDirExt,'Visible'),'off')
    msgbox_uvmat('ERROR',['no output file for Action ' ActionName ', use run mode = local']);% a output dir is needed for background option
    return
else
    %% 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
    DirBat=fullfile(OutputDir,'0_EXE');
    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(DirBat,'dir')
        [tild,msg1]=mkdir(DirBat);
        if ~strcmp(msg1,'')
            msgbox_uvmat('ERROR',['cannot create ' DirBat ': ' msg1]);%error message for directory creation
            return
        end
    end
    %create subdirectory for log files
    DirLog=fullfile(OutputDir,'0_LOG');
    if ~exist(DirLog,'dir')
        [tild,msg1]=mkdir(DirLog);
        if ~strcmp(msg1,'')
            msgbox_uvmat('ERROR',['cannot create ' DirLog ': ' msg1]);%error message for directory creation
            return
        end
    end
    for iprocess=1:NbProcess
        if isempty(Param.IndexRange.NbSlice)% process by blocks of i index
            Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;
            if Param.IndexRange.first_i>last_i
                NbProcess=iprocess-1;
                break% leave the loop, we are at the end of the calculation
            end
            Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1);
        else% process by slices of i index if NbSlice is defined, computation in a single process if NbSlice =1
            Param.IndexRange.first_i= first_i+iprocess-1;
            Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice;
        end
        
        % create, fill and save the xml parameter file
        t=struct2xml(Param);
        t=set(t,1,'name','Series');
        filexml=fullfile_uvmat(DirXml,'',Param.InputTable{1,3},'.xml',OutputNomType,...
            Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
        save(t,filexml);% save the parameter file
        
        %create the executable file
         filebat=fullfile_uvmat(DirBat,'',Param.InputTable{1,3},ExeExt,OutputNomType,...
           Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
        batch_file_list{iprocess}=filebat;
        [fid,message]=fopen(filebat,'w');% create the executable file
        if isequal(fid,-1)
            msgbox_uvmat('ERROR', ['creation of .bat file: ' message]);
            return
        end
        
        % set the log file name
        filelog=fullfile_uvmat(DirLog,'',Param.InputTable{1,3},'.log',OutputNomType,...
            Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
        
        % fill and save the executable file
        switch ActionExt
            case '.m'% Matlab function
                switch computer
                    case {'GLNX86','GLNXA64','MACI64'}
                        cmd=[...
                            '#!/bin/bash \n'...
                            '. /etc/sysprofile \n'...
                            'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog ''' <<END_MATLAB \n'...
                            'addpath(''' path_series '''); \n'...
                            'addpath(''' Param.Action.ActionPath '''); \n'...
                            '' Param.Action.ActionName  '( ''' filexml '''); \n'...
                            'exit \n'...
                            'END_MATLAB \n'];
                        fprintf(fid,cmd);%fill the executable file with the  char string cmd
                        fclose(fid);% close the executable file
                        system(['chmod +x ' filebat]);% set the file to executable
                    case {'PCWIN','PCWIN64'}
                        text_matlabscript=['matlab -automation -logfile ' regexprep(filelog,'\\','\\\\')...
                            ' -r "addpath(''' regexprep(path_series,'\\','\\\\') ''');'...
                            'addpath(''' regexprep(Param.Action.ActionPath,'\\','\\\\') ''');'...
                            '' Param.Action.ActionName  '( ''' regexprep(filexml,'\\','\\\\') ''');exit"'];
                        fprintf(fid,text_matlabscript);%fill the executable file with the  char string cmd
                        fclose(fid);% close the executable file
                end
            case '.sh' % compiled Matlab function
                switch computer
                    case {'GLNX86','GLNXA64','MACI64'}
                        cmd=['#!/bin/bash \n '...
                            '#$ -cwd \n '...
                            'hostname && date \n '...
                            'umask 002 \n'...
                            fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml];%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 ' filebat]);% set the file to executable
                        
                    case {'PCWIN','PCWIN64'}    
                        fprintf(fid,cmd);
                        fclose(fid);
                end
        end
    end
end

%% launch the executable files for background or cluster processing
switch RunMode
    case 'background'
        for iprocess=1:NbProcess
            system([batch_file_list{iprocess} ' &'])% directly execute the command file for each process
            msgbox_uvmat('CONFIRMATION',[ActionName 'launched in background: press STATUS to see results'])
        end
    case 'cluster_oar' % option 'oar-parexec' used
        %create subdirectory for oar command and log files
        DirOAR=fullfile(OutputDir,'0_OAR');
        if exist(DirOAR,'dir')% delete the content of the dir 0_OAR to allow new input
            curdir=pwd;
            cd(DirOAR)
            delete('*')
            cd(curdir)
        else
            [tild,msg1]=mkdir(DirOAR);
            if ~strcmp(msg1,'')
                msgbox_uvmat('ERROR',['cannot create ' DirOAR ': ' msg1]);%error message for directory creation
                return
            end
        end
        max_walltime=3600*12; % 12h max total calculation 
        walltime_onejob=600;%seconds, max estimated time for asingle file index value
        filename_joblist=fullfile(DirOAR,'job_list.txt');%create name of the global executable file
        fid=fopen(filename_joblist,'w');
        for p=1:length(batch_file_list)
            fprintf(fid,[batch_file_list{p} '\n']);% list of exe files 
        end
        fclose(fid);
        system(['chmod +x ' filename_joblist]);% set the file to executable
        oar_command=['oarsub -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(filename_joblist,'\.txt\>','.stderr') ' '...
            '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '...
            extra_oar ' '...
            '"oar-parexec -s -f ' filename_joblist ' '...
            '-l ' filename_joblist '.log"\n'];
        filename_oarcommand=fullfile(DirOAR,'oar_command');
        fid=fopen(filename_oarcommand,'w');
        fprintf(fid,oar_command);
        fclose(fid);
        fprintf(oar_command);% display in command line
        system(oar_command);  
        msgbox_uvmat('CONFIRMATION',[ActionName ' launched in cluster: press STATUS to see results'])
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)

%------------------------------------------------------------------------
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
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, eventdata, 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, eventdata, 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
nb_builtin_ACTION=4; %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...')
    [FileName, PathName] = uigetfile( ...
        {'*.m', ' (*.m)';
        '*.m',  '.m files '; ...
        '*.*', 'All Files (*.*)'}, ...
        'Pick a series processing function ',get(handles.ActionPath,'String'));
    if length(FileName)<2
        return
    end
    [ActionPath,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
    if isempty(ActionIndex)%the input string 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...'
        set(handles.ActionName,'String',ActionList)
    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}])
        ActionExtIndex=numel(ActionExtList)+1;
        ActionPathNew=cell(size(ActionPathList,1),1);%new column of ActionPath
        ActionPathList=[ActionPathList ActionPathNew];
    end
    set(handles.ActionName,'UserData',ActionPathList);

    % remove old Action options in the menu (keeping a menu length <nb_builtin_ACTION+5)
    if length(ActionList)>nb_builtin_ACTION+5; %nb_builtin=nbre of functions always remaining in the initial menu
        nbremove=length(ActionList)-nb_builtin_ACTION-5;
        ActionList(nb_builtin_ACTION+1:end-5)=[];
        ActionPathList(nb_builtin_ACTION+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.ActionExt,'Value',ActionExtIndex)
    ActionPathList{ActionIndex,ActionExtIndex}=PathName;
        
    %record the user defined menu additions in personal file profil_perso
    dir_perso=prefdir;
    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
    if nb_builtin_ACTION+1<=numel(ActionList)-1
        ActionListUser=ActionList(nb_builtin_ACTION+1:numel(ActionList)-1);
        ActionPathListUser=ActionPathList(nb_builtin_ACTION+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 senlected function

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

%% create the function handle for Action
path_series=which('series');
if ~isequal(ActionPath,path_series)
    eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
    if ~exist(ActionPath,'dir')
        errormsg=['The prescribed function path ' ActionPath ' does not exist'];
        return
    end
    if ~isequal(spath,ActionPath)
        addpath(ActionPath)% add the prescribed path if not the current one
    end
end
eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
if ~isequal(ActionPath,path_series)
        rmpath(ActionPath)% add the prescribed path if not the current one    
end

%% Activate the Action fct
Param=read_GUI_series(handles);% read the parameters from the GUI series
ParamOut=h_fun(Param);%run the selected Action function to get the relevant input

%% Put the first line of the selected Action fct as tooltip help
try
    [fid,errormsg] =fopen([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

%% Detect the types of input files
SeriesData=get(handles.series,'UserData');% info on the input file series
iview_civ=[];nb_netcdf=0;
if ~isempty(SeriesData)&&isfield(SeriesData,'FileType')
    iview_civ=find(strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));
    nb_netcdf=numel(find(strcmp('netcdf',SeriesData.FileType)));
end
if numel(iview_civ)>=1 && ~isempty(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])
    if 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])
    end
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
    [tild,iview]=sort(InputTable(:,2)); %subdirectories sorted in alphabetical order
    set(handles.InputTable,'Data',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');
    set(handles.TimeTable,'Data',TimeTable(iview,:));
    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')&&isequal(ParamOut.WholeIndexRange,'on')
    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.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')
    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_i=1;last_i=1;first_j=1;last_j=1;
    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,'first_j')
        first_j=Param.IndexRange.first_j;
       % incr_j=Param.IndexRange.incr_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

%% desable j index if if set by the civ_input GUI
if isfield(ParamOut,'Desable_j_index')&&isequal(ParamOut.Desable_j_index,'on')
    set(handles.num_first_j,'Enable','off')
    set(handles.num_last_j,'Enable','off')
    set(handles.num_incr_j,'Enable','off')
    set(handles.num_incr_j,'String','')
else
   set(handles.num_first_j,'Enable','on')
    set(handles.num_last_j,'Enable','on')
    set(handles.num_incr_j,'Enable','on')
end

%% NbSlice visibility
NbSliceVisible='off';%default
if isfield(ParamOut,'NbSlice') && isequal(ParamOut.NbSlice,'on')
    NbSliceVisible='on';
    set(handles.num_NbProcess,'String',get(handles.num_NbSlice,'String'))% the nbre of processes is imposed as the nbre of slices
else
    set(handles.num_NbProcess,'String','')% free nbre of processes 
end
set(handles.num_NbSlice,'Visible',NbSliceVisible)
set(handles.NbSlice_title,'Visible',NbSliceVisible)

%% Visibility of VelType and VelType_1 menus
VelTypeVisible='off';  %hidden by default
VelType_1Visible='off';
InputFieldsVisible='off';%visibility of the frame Fields
if isfield(ParamOut,'VelType')
    if strcmp( ParamOut.VelType,'on')||strcmp(ParamOut.VelType,'one')||strcmp( ParamOut.VelType,'two')
        if numel(iview_civ)>=1
            VelTypeVisible='on';
            InputFieldsVisible='on';
        end
    end
    if strcmp( ParamOut.VelType,'two')
        if numel(iview_civ)>=2
            VelType_1Visible='on';
        end
    end
end
set(handles.VelType,'Visible',VelTypeVisible)
set(handles.VelType_text,'Visible',VelTypeVisible);
set(handles.VelType_1,'Visible',VelType_1Visible)
set(handles.VelType_text_1,'Visible',VelType_1Visible);

%% Visibility of FieldName and FieldName_1 menus
FieldNameVisible='off';  %hidden by default
FieldName_1Visible='off';  %hidden by default
if isfield(ParamOut,'FieldName')
    if strcmp( ParamOut.FieldName,'on') || strcmp(ParamOut.FieldName,'one')||strcmp( ParamOut.FieldName,'two')
        if (numel(iview_civ)+nb_netcdf)>=1
            InputFieldsVisible='on';
            FieldNameVisible='on';
        end
    end
    if strcmp( ParamOut.FieldName,'two')
        if (numel(iview_civ)+nb_netcdf)>=1
            FieldName_1Visible='on';
        end
    end
end
set(handles.InputFields,'Visible',InputFieldsVisible)
set(handles.FieldName,'Visible',FieldNameVisible) % test for MenuBorser
set(handles.FieldName_1,'Visible',FieldName_1Visible)

%% Visibility of FieldTransform menu
FieldTransformVisible='off';  %hidden by default
if isfield(ParamOut,'FieldTransform')
    FieldTransformVisible=ParamOut.FieldTransform;  
    TransformName_Callback([],[], handles)
end
set(handles.FieldTransform,'Visible',FieldTransformVisible)
if isfield(ParamOut,'TransformPath')
    set(handles.ActionExt,'UserData',ParamOut.TransformPath)
else
    set(handles.ActionExt,'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.ProjObject,'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.Mask,'Visible',MaskVisible)
set(handles.CheckMask,'Visible',MaskVisible);

%% definition of the directory containing the output files 
OutputDirVisible='off';
if isfield(ParamOut,'OutputDirExt')&&~isempty(ParamOut.OutputDirExt)
    OutputSubDirMode='all';%default
    if isfield(ParamOut,'OutputSubDirMode')
        OutputSubDirMode=ParamOut.OutputSubDirMode;
    end
    set(handles.OutputDirExt,'String',ParamOut.OutputDirExt)
    OutputDirVisible='on';
    SubDir=InputTable(1:end,2); %set of subdirectories sorted in alphabetical order
    if strcmp(OutputSubDirMode,'last')
        SubDirOut=SubDir{end};
    else
        SubDirOut=SubDir{1};
        if ~strcmp(OutputSubDirMode,'first')  && numel(SubDir)>1
            for ilist=2:numel(SubDir)
                SubDirOut=[SubDirOut '-' SubDir{ilist}];
            end
        end
    end
    set(handles.OutputSubDir,'String',SubDirOut)
end
set(handles.OutputDirExt,'Visible',OutputDirVisible)
set(handles.OutputSubDir,'Visible',OutputDirVisible)
set(handles.OutputDir_title,'Visible',OutputDirVisible)
set(handles.RunMode,'Visible',OutputDirVisible)
set(handles.ActionExt,'Visible',OutputDirVisible)
set(handles.RunMode_title,'Visible',OutputDirVisible)
set(handles.ActionExt_title,'Visible',OutputDirVisible)


%% 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')
%     set(handles.ActionInput,'Visible','on')
%     set(handles.ActionInput_title,'Visible','on')
    set(handles.ActionInput,'Visible','on')
 %   set(handles.ActionInput,'Value',0)
%     set(handles.ActionInput,'String',ActionName)
    ParamOut.ActionInput.Program=ActionName; % record the program in ActionInput
    SeriesData.ActionInput=ParamOut.ActionInput;
else
%     set(handles.ActionInput,'Visible','off')
%     set(handles.ActionInput_title,'Visible','off')
    set(handles.ActionInput,'Visible','off')
    if isfield(SeriesData,'ActionInput')
    SeriesData=rmfield(SeriesData,'ActionInput');
    end
end   
set(handles.series,'UserData',SeriesData)
set(handles.ActionName,'BackgroundColor',[1 1 1])

%------------------------------------------------------------------------
% --- Executes on button press in ActionInput.
function ActionInput_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
% if get(handles.ActionInput,'Value')
ActionName_Callback(hObject, eventdata, handles)
% end

%------------------------------------------------------------------------
% --- Executes on selection change in FieldName.
function FieldName_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
field_str=get(handles.FieldName,'String');
field_index=get(handles.FieldName,'Value');
field=field_str{field_index(1)};
if isequal(field,'get_field...')
    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);
    Param.InputTable=Param.InputTable(1,:);
    % 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
    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')
        ParamIn.Title='get_field: pick input variables and coordinates for series processing';
        ParamIn.SeriesInput=1;
        GetFieldData=get_field(FirstFileName,ParamIn);
        FieldList={};
        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};
            case {'scalar'}
                FieldList=GetFieldData.PanelScalar.scalar;
                YName={GetFieldData.Coordinates.Coord_y};
                if ischar(FieldList)
                    FieldList={FieldList};
                end
            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',[FieldList; {'get_field...'}]);
        if ~strcmp(GetFieldData.FieldOption,'civdata...')
            set(handles.FieldName,'Value',1:numel(FieldList))%select all input fields by default
            set(handles.VelType,'visible','off')
            XName=GetFieldData.Coordinates.Coord_x;
            YName=GetFieldData.Coordinates.Coord_y;
            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
            switch TimeNameStr
                case 'file index'
                    set(handles.TimeName,'String','');
                case 'attribute'
                    set(handles.TimeName,'String',['att:' GetFieldData.Time.TimeName]);
                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'
                    set(handles.TimeName,'String',['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
        end
        set(handles.Coord_x,'String',XName)
        set(handles.Coord_y,'String',YName)
    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 isequal(field,'get_field...')
    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);
    Param.InputTable=Param.InputTable(1,:);
    % 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{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')
        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
        if ~strcmp(GetFieldData.FieldOption,'civdata...')
            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
            switch TimeNameStr
                case 'file index'
                    set(handles.TimeName,'String','');
                case 'attribute'
                    set(handles.TimeName,'String',['att:' GetFieldData.Time.TimeName]);
                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'
                    set(handles.TimeName,'String',['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
        end
        set(handles.FieldName_1,'Value',1)
        set(handles.FieldName_1,'String',[FieldList; {'get_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)
        set(handles.ViewObject,'Value',1)
        ViewObject_Callback(hObject, eventdata, handles)
    else
        if ishandle(hset_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.ProjObject,'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.ProjObject,'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.ProjObject,'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');
    hset_object=set_object(UserData.ProjObject);
    set(hset_object,'Name','edit_object_series')
    set(get(hset_object,'Children'),'Enable','on')
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.ProjObject,'String','')
set(handles.ProjObject,'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')
    InputTable=get(handles.InputTable,'Data');
    nbview=size(InputTable,1);
    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)
else
    set(handles.MaskTable,'Visible','off')
    set(handles.MaskBrowse,'Visible','off')
    set(handles.ListMask,'Visible','off')
end

%------------------------------------------------------------------------
% --- Executes on button press in MaskBrowse.
%------------------------------------------------------------------------
function MaskBrowse_Callback(hObject, eventdata, handles)

InputTable=get(handles.InputTable,'Data');
iview=get(handles.ListMask,'Value');
RootPath=InputTable{iview,1};
MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
if ~isempty(MaskName)
    MaskTable=get(handles.MaskTable,'Data');
    MaskTable{iview,1}=MaskName ;
    set(handles.MaskTable,'Data',MaskTable)
end

%------------------------------------------------------------------------
% --- 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;
if isequal(TransformName,'more...');     
    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);

%------------------------------------------------------------------------
% --- fct activated by the upper bar menu ExportConfig
%------------------------------------------------------------------------
function MenuExportConfig_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)
% SeriesData=get(handles.series,'UserData');
% if isfield(SeriesData,'RefFile')
%     oldfile=SeriesData.RefFile{1};
% end
%% use a strating file name for browserr
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
filexml=uigetfile_uvmat('pick a xml parameter file',oldfile,'.xml');% get the xml file containing processing parameters
%proceed only if a file has been introduced by the browser
if ~isempty(filexml)
    Param=xml2struct(filexml);% read the input xml file as a Matlab structure
    % ask to stop current Action if button RUN is in action (another process is already running)
    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;
        set(handles.FieldName,'String',[ListField;{'get-field...'}])
         set(handles.FieldName,'Value',1:numel(ListField))
    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)
        SeriesData.ActionInput=Param.ActionInput;
    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.ProjObject,'String',Param.ProjObject.Name)
        set(handles.ViewObject,'Visible','on')
        set(handles.EditObject,'Visible','on')
        set(handles.DeleteObject,'Visible','on')
    else     
        set(handles.ProjObject,'String','')
        set(handles.ProjObject,'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
end

%------------------------------------------------------------------------
% --- 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)

%% 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([0.25 0.25 0.25 0.25]*(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=Param.InputTable{1,1};
    if ~isfield(Param,'OutputSubDir')   
        msgbox_uvmat('ERROR','no directory defined for output files')
        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
    FileType=get_file_type(FullSelectName);
    if strcmp(FileType,'txt')
        edit(FullSelectName)
    elseif strcmp(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')};
ActionList=get(handles.ActionName,'String');
ActionName=ActionList{get(handles.ActionName,'Value')};
% TransformPath='';
% if ~isempty(get(handles.ActionExt,'UserData'))
%     TransformPath=get(handles.ActionExt,'UserData');
% end
% if strcmp(ActionExt,'.sh')
%     set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
%     set(handles.ActionExt,'BackgroundColor',[1 1 0])
%     ActionFullName=fullfile(get(handles.ActionPath,'String'),[ActionName '.sh']);
%     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(get(handles.TransformPath,'String'))
%             addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
%            % addpath(fullfile(path_uvmat,'transform_field'))% add the path to uvmat to run the fct 'compile'
%             compile(ActionName,TransformPath)
%             cd(currentdir)
%         end       
%     else
%         sh_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.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',[ActionName '.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(get(handles.TransformPath,'String'))
%                 addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
%                 addpath(fullfile(path_uvmat,'transform_field'))% add the path to uvmat 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


function num_NbProcess_Callback(hObject, eventdata, handles)


function num_NbSlice_Callback(hObject, eventdata, handles)
NbSlice=str2num(get(handles.num_NbSlice,'String'));
set(handles.num_NbProcess,'String',num2str(NbSlice))

%------------------------------------------------------------------------
% --- 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;
        elseif 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)

%% 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');
hh=0.14; % box height (relative)
ii=0.01; % gap between uicontrols

ww=0.9; % box width (relative)
SeriesData=get(handles.series,'UserData');
% 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],'tag','ListView','BackgroundColor',[1 1 1],...
    'String',SeriesData.ListViewMenu,'Value',SeriesData.ListViewValue,'FontUnits','points','FontSize',12,'FontWeight','bold','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 ww 0.2],'tag','Mode','BackgroundColor',[1 1 1],'Callback',@(hObject,eventdata)ModeMenu_Callback(hObject,eventdata),...
    'String',SeriesData.ModeMenu,'Value',SeriesData.ModeValue,'FontUnits','points','FontSize',12,'FontWeight','bold','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 ww 0.2],'tag','ListPairs','BackgroundColor',[1 1 1],'Callback',@(hObject,eventdata)ListPairsMenu_Callback(hObject,eventdata),...
    'String',SeriesData.ListPairsMenu,'Value',SeriesData.ListPairsValue,'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''ListPairs'': 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],'tag','num_ref_i','BackgroundColor',[1 1 1],'Callback',@(hObject,eventdata)num_ref_i_Callback(hObject,eventdata),...
    'String',num2str(SeriesData.ref_i),'FontUnits','points','FontSize',12,'FontWeight','bold','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],'tag','num_ref_j','BackgroundColor',[1 1 1],'Callback',@(hObject,eventdata)num_ref_j_Callback(hObject,eventdata),...
    'String',num2str(SeriesData.ref_j),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_ref_j'': reference field index i used to display dt in ''list_pair_civ''');
%  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 ModeMenu_Callback(hObject,eventdata)
hseries=findobj(allchild(0),'tag','series');
hhseries=guidata(hseries);
SeriesData=get(hseries,'UserData');
hListView=findobj(get(hObject,'parent'),'Tag','ListView');
iview=get(hListView,'Value');
hMode=findobj(get(hObject,'parent'),'Tag','Mode');
mode_list=get(hMode,'String');
mode=mode_list{get(hMode,'Value')};
if isequal(mode,'bursts')
    enable_i(hhseries,'On')
    enable_j(hhseries,'Off') %do not display j index scanning in burst mode (j is fixed by the burst choice)
else
    enable_i(hhseries,'On')
    enable_j(hhseries,'Off')
end
fill_ListPair(hhseries,SeriesData.i1_series{iview},SeriesData.i2_series{iview},...
    SeriesData.j1_series{iview},SeriesData.j2_series{iview},SeriesData.Time{iview})
ListPairs_Callback([],[],hhseries)

%-------------------------------------------------------------
% --- Executes on selection in ListPairs.
function ListPairsMenu_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)
%------------------------------------------------------------------------
hMode=findobj(get(hObject,'parent'),'Tag','Mode');
mode_list=get(hMode,'String');
mode=mode_list{get(hMode,'Value')};
hseries=findobj(allchild(0),'tag','series');
hhseries=guidata(hseries);
SeriesData=get(hseries,'UserData');
hListView=findobj(get(hObject,'parent'),'Tag','ListView');
iview=get(hListView,'Value');
fill_ListPair(hhseries,SeriesData.i1_series{iview},SeriesData.i2_series{iview},...
    SeriesData.j1_series{iview},SeriesData.j2_series{iview},SeriesData.Time{iview});% update the menu of pairs depending on the available netcdf files

hListPairs=findobj(get(hObject,'parent'),'Tag','ListPairs');
ListPairsMenu_Callback(hListPairs,eventdata)

%------------------------------------------------------------------------
function num_ref_j_Callback(hObject, eventdata)
%------------------------------------------------------------------------
num_ref_i_Callback(hObject, eventdata)

%-------------------------------------------------------------
% --- Executes on selection in ListPairs.
function OK_Callback(hObject,eventdata)
%------------------------------------------------------------
delete(get(hObject,'parent'))