source: trunk/src/civ.m @ 284

%'civ': function associated with the interface 'civ.fig' for PIV, spline interpolation and stereo PIV (patch)
%------------------------------------------------------------------------
%  provides an interface for the software CIVx
% function varargout = civ(varargin)
% provides an interface for the software CIVx
%
%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
%  Copyright Joel Sommeria, 2011, LEGI / CNRS-UJF-INPG, sommeria@legi.grenoble-inp.fr
%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
function varargout = civ(varargin)
%TODO: search range

% Last Modified by GUIDE v2.5 18-Nov-2011 15:30:17
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
    'gui_Singleton',  gui_Singleton, ...
    'gui_OpeningFcn', @civ_OpeningFcn, ...
    'gui_OutputFcn',  @civ_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 civ is made visible.
function civ_OpeningFcn(hObject, eventdata, handles, param)
%------------------------------------------------------------------------
% This function has no output args, see OutputFcn.
%filebase: root name
%nom_type: nomencalture used ('png_old','_i_j'...)
%list of field numbers to process
%subdir: subdirectory of the opened netcdf file
%ind_opening: operation number advised for beginning (1=checkciv1,2=checkfix1,3=checkpatch1,4=checkciv2,5=checkfix2,6=checkpatch2),
%ind_a_opening ind_b_opening chosen pair from the opened netcdf file
% Choose default command line output for civ
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
set(hObject,'WindowButtonDownFcn',{'mouse_alt_gui',handles}) % allows mouse action with right button (zoom for uicontrol display)
%default initial parameters
filebase=''; % root file name ('filebase'.civ)
ext=[];

%% read names of the .exe file to adjust the interface according to available binaries
%path_uvmat=which('uvmat');% check the path detected for source file uvmat
path_civ=fileparts(which('civ')); %path to civ
addpath (path_civ) ; %add the path to UVMAT, (useful in case of change of working directory after civ has been s opened in the working directory)
errormsg=[];%default error message
xmlfile='PARAM.xml';
if exist(xmlfile,'file')
    try
        t=xmltree(xmlfile);
        sparam=convert(t);
    catch
        errormsg={' Unable to read the file PARAM.xml defining the civx binaries:'; lasterr};
        return
    end
else
    errormsg=[xmlfile ' not found: path to civx binaries undefined'];
    return
end
if ~isempty(errormsg)
    msgbox_uvmat('ERROR',errormsg);
end

test_batch=0;%default: ,no batch mode available
if isfield(sparam,'BatchParam') && isfield(sparam.BatchParam,'BatchMode')
    test_batch=strcmp(sparam.BatchParam.BatchMode,'sge'); %sge is currently the only implemented batch mod
end
if test_batch==0
    set(handles.BATCH,'Enable','off')% put the BATCH button in grey (unactivated)
    set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])% put the BATCH button in grey (unactivated)
end
if isfield(sparam.RunParam,'CivBin')
    if ~exist(sparam.RunParam.CivBin,'file')
        sparam.RunParam.CivBin=fullfile(path_civ,sparam.RunParam.CivBin);
    end
else
    sparam.RunParam.CivBin='';
end

%% load the list of previously browsed files in menu Open
 dir_perso=prefdir; % path to the directory .matlab for personal data
 profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmauvmat_perso.mat' in .matlab
 if exist(profil_perso,'file')
      h=load (profil_perso);
      if isfield(h,'MenuFile')
          set(handles.MenuFile_1,'Label',h.MenuFile{1})
          %set(handles.MenuFile_1,'Label',h.MenuFile_1);
      end
%       if isfield(h,'MenuFile_2')
%           set(handles.MenuFile_2,'Label',h.MenuFile_2);
%       end
%       if isfield(h,'MenuFile_3')
%           set(handles.MenuFile_3,'Label',h.MenuFile_3);
%       end
%       if isfield(h,'MenuFile_4')
%           set(handles.MenuFile_4,'Label',h.MenuFile_4);
%       end
%       if isfield(h,'MenuFile_5')
%           set(handles.MenuFile_5,'Label',h.MenuFile_5);
%       end
end

%default input parameters:
num_i1=1; % set of field i numbers
num_i2=1; % set of field i numbers
num_j1=1; % set of field j numbers (fields a)
num_j2=1; % second set of field j numbers (fields b)
%subdir='A'; % subdir for the netcdf result files
ind_opening=0; % proposed operation number (1=civ1,2=fix1,3=patch1,4=civ2,5=fix2,6=patch2)
%load the initial parameters if the interface is started from uvmat
if exist('param','var')&&isstruct(param)% the interface is opened from uvmat
    filebase=param.RootName;
    nom_type_read=param.NomType;
    num_i1=param.num1;
    if isnan(num_i1),num_i1=1;end
    num_i2=param.num2;
    if isnan(num_i2),num_i2=num_i1;end
    num_j1=param.num_a;
    if isnan(num_j1),num_j1=1;end
    num_j2=param.num_b;
    if isnan(num_j2),num_j2=num_j1;end
    subdir=param.SubDir;
    ind_opening=param.IndOpening;
    ext=param.ImaExt;
end
browse.num_i1=num_i1;
browse.num_i2=num_i2;
browse.num_j1=num_j1;
browse.num_j2=num_j2;
if ~isempty(ext) && (~isempty(imformats(ext(2:end)))||strcmpi(ext,'.avi'));%if an image file has been opened by uvmat
    set(handles.ImaExt,'String',ext)
    browse.ext_ima=ext;
    if exist('nom_type_read','var')
        browse.nom_type_ima=nom_type_read; % the image nomenclature is stored
    end
elseif isequal(ext,'.nc')
    if exist('nom_type_read','var')
        browse.nom_type_nc=nom_type_read;% the netcdf  nomenclature is stored
    end
end
set(handles.RootName,'String',filebase);
set(handles.ImaDoc,'String',ext)

%initiate advised operations
enable_civ1(handles,0)
enable_civ2(handles,0)
%enable_pair1(handles,'on')
enable_fix1(handles,0)
enable_patch1(handles,0)
enable_fix2(handles,0)
enable_patch2(handles,0)
set(handles.CheckCiv1,'Value',0)
set(handles.CheckFix1,'Value',0)
set(handles.CheckPatch1,'Value',0)
set(handles.CheckCiv2,'Value',0)
set(handles.CheckFix2,'Value',0)
set(handles.CheckPatch2,'Value',0)
%set(handles.frame_subdirciv2,'BackgroundColor',[0.831 0.816 0.784])
if isequal(ind_opening,1)
    set(handles.CheckCiv1,'Value',1)
    enable_civ1(handles,1)
elseif isequal(ind_opening,2)
    set(handles.CheckFix1,'Value',1)
    enable_fix1(handles,1)
elseif isequal(ind_opening,3)
    set(handles.CheckPatch1,'Value',1)
    enable_patch1(handles,1)
elseif isequal(ind_opening,4)
    set(handles.CheckCiv2,'Value',1)
    enable_civ2(handles,1)
elseif isequal(ind_opening,5)
    set(handles.CheckFix2,'Value',1)
    enable_fix2(handles,1)
    set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
    set(handles.ListPairCiv2,'Enable','On')
    set(handles.ListPairCiv2,'Enable','On')
    enable_pair1(handles,'off')
elseif isequal(ind_opening,6)
    set(handles.CheckPatch2,'Value',1)
    enable_patch2(handles,1)
    set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
    set(handles.ListPairCiv2,'Enable','On')
    enable_pair1(handles,'off')
end

% set the range of fields (1:1 by default) and selected pair
if isequal(num_i2,num_i1)
    num_ref_i=num_i1;
else
    num_ref_i=floor((num_i1+num_i2)/2);
    browse.incr_pair(1)=num_i2-num_i1;
    browse.incr_pair(2)=0;
end
if isequal(num_j1,num_j2)
    if isnan(num_j1)
        num_ref_j=1;
    else
        num_ref_j=num_j1;
    end
else
    num_ref_j=floor((num_j1+num_j2)/2);
    browse.incr_pair(2)=num_j2-num_j1;
end
set(handles.first_i,'String',num2str(num_ref_i));
set(handles.last_i,'String',num2str(num_ref_i));
set(handles.first_j,'String',num2str(num_ref_j));
set(handles.last_j,'String',num2str(num_ref_j));
set(handles.ref_i,'String',num2str(num_ref_i));
set(handles.ref_j,'String',num2str(num_ref_j));
% set(handles.ref_i_civ2,'String',num2str(num_ref_i));
% set(handles.ref_j_civ2,'String',num2str(num_ref_j));
set(handles.RootName,'UserData',browse);
if exist('param','var') && isfield(param,'RootName') && ~isempty(param.RootName)%varargin the interface is opened from uvmat
    RootName_Callback(hObject, eventdata, handles);
end

%------------------------------------------------------------------------
% --- Outputs from this function are returned to the command line.
function varargout = civ_OutputFcn(hObject, eventdata, handles)
%------------------------------------------------------------------------
% varargout  cell array for returning output args (see VARARGOUT);
% hObject    handle to figure
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;

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

%get the input file properties
filebase=get(handles.RootName,'String');
oldfile=''; %default
if isempty(filebase)|| isequal(filebase,'')%loads the previously stored file name and set it as default in the file_input box
    dir_perso=prefdir;
    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
    if exist(profil_perso,'file')
        h=load (profil_perso);
        if isfield(h,'filebase')&& ischar(h.filebase)
            oldfile=h.filebase;
        end
        if isfield(h,'RootPath') && ischar(h.RootPath)
            oldfile=h.RootPath;
        end
    end
else
    oldfile=filebase;
end
ind_opening=1;%default
browse.incr_pair=[0 0]; %default
menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)';
       '*.xml',  '.xml files '; ...
        '*.civ',  '.civ files '; ...
        '*.png','.png image files'; ...
        '*.jpg',' jpeg image files'; ...
        '*.tif','.tif image files'; ...
        '*.avi;*.AVI','.avi movie files'; ...
        '*.nc','.netcdf files'; ...
        '*.*',  'All Files (*.*)'};
[FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file',oldfile);
fileinput=[PathName FileName];%complete file name
sizf=size(fileinput);
if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
[path,name,ext]=fileparts(fileinput);
testeditxml=0;
if isequal(ext,'.xml')
    testeditxml=1;
    t_browse=xmltree(fileinput);
    head_element=get(t_browse,1);
    if isfield(head_element,'name')&& isequal(head_element.name,'ImaDoc')
        testeditxml=0;
    end
end
if testeditxml==1 || isequal(ext,'.xls')
    heditxml=editxml({fileinput});
    set(heditxml,'Tag','browser')
    waitfor(heditxml,'Tag','idle')
    if ~ishandle(heditxml)
        return
    end
    attr=findobj(get(heditxml,'children'),'Tag','CurrentAttributes');
    set(handles.browse,'UserData',fileinput)% store for future opening with browser
    fileinput=get(attr,'UserData');
    if ~exist(fileinput,'file')
        return
    end
end
[RootPath,RootFile,str1,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fileinput);
filebase=fullfile(RootPath,RootFile);
num_i1=str2double(str1);
if isnan(num_i1),num_i1=1;end
num_i2=str2double(str2);
if isnan(num_i2),num_i2=num_i1;end
num_j1=stra2num(str_a);
if isnan(num_j1),num_j1=1;end
num_j2=stra2num(str_b);
if isnan(num_j2),num_j2=num_j1;end
if isequal(get(handles.ListCompareMode,'Value'),1)
    browse=[];%initialisation
else
    browse=get(handlesRootName,'UserData');
end
browse.num_i1=num_i1;
browse.num_i2=num_i2;
browse.num_j1=num_j1;
browse.num_j2=num_j2;
if length(ext)>1 && (~isempty(imformats(ext(2:end)))||strcmpi(ext,'.avi'));%if an image file has been opened by uvmat
    browse.nom_type_ima=nom_type;
    browse.ext_ima=ext;
    set(handles.ImaExt,'String',ext)
end
set(handles.ImaDoc,'String',ext);

%%%%% read the state of the selected netcdf file to advise default operation
if isequal(ext,'.nc')
    browse.nom_type_nc=nom_type;
    ind_opening=2;% propose 'fix' as the default option
    Data=nc2struct(fileinput,'ListGlobalAttribute','CivStage','absolut_time_T0','fix','patch','civ2','fix2');
    if ~isempty(Data.CivStage)%test for civ files
        ind_opening=Data.CivStage;
        set(handles.ListPairMode,'Value',3)
    end
    if ~isempty(Data.absolut_time_T0)%test for civx files
        set(handles.ListPairMode,'Value',1)
        if isfield(Data,'fix') && isequal(Data.fix,1)
            ind_opening=3;
        end
        if isequal(Data.patch,1)
            ind_opening=4;
        end
        if isequal(Data.civ2,1)
            ind_opening=5;
        end
        if  isequal(Data.fix2,1)
            ind_opening=6;
        end
        testciv=1; %TO SUPPRESS WITH NEW VERSION OF CIVX
    else
        ind_opening=3; %GUI used only for patch
        testciv=0;
    end
    set(handles.subdir_civ1,'String',subdir);%set the default subdir directories for installing the .nc results
    set(handles.subdir_civ2,'String',subdir);
    browse.testciv=testciv;
    browse.ind_opening=ind_opening;
end
set(handles.RootName,'String',filebase);
set(handles.ImaDoc,'String',ext);
if ~isempty(num_i1)
    ref_i=num_i1;
    if ~isempty(num_i2)
        ref_i=floor((ref_i+num_i2)/2);% reference image number corresponding to the file
        browse.incr_pair(1)=num_i2-num_i1;
        browse.incr_pair(2)=0;
    end
    set(handles.first_i,'String',num2str(ref_i));
    set(handles.last_i,'String',num2str(ref_i));
    set(handles.ref_i,'String',num2str(ref_i));
%     set(handles.ref_i_civ2,'String',num2str(ref_i))
end
if isempty(num_j1)
    set(handles.ref_j,'String','1');
    set(handles.ref_j_civ2,'String','1');
else
    ref_j=num_j1;
    if ~isempty(num_j2)
        ref_j=floor((num_j1+num_j2)/2);
        browse.incr_pair(2)=num_j2-num_j1;
    end
    set(handles.first_j,'String',num2str(ref_j));
    set(handles.last_j,'String',num2str(ref_j));
    set(handles.ref_j,'String',num2str(ref_j));
%     set(handles.ref_j_civ2,'String',num2str(ref_j));
end

% set default operation options
enable_civ1(handles,0)
enable_civ2(handles,0')
enable_pair1(handles,'on')
enable_fix1(handles,0)
enable_patch1(handles,0)
enable_fix2(handles,0)
enable_patch2(handles,0)
set(handles.CheckCiv1,'Value',0)
set(handles.CheckFix1,'Value',0)
set(handles.CheckPatch1,'Value',0)
set(handles.CheckCiv2,'Value',0)
set(handles.CheckFix2,'Value',0)
set(handles.CheckPatch2,'Value',0)
% set(handles.frame_subdirciv2,'BackgroundColor',[0.831 0.816 0.784])
if isequal(ind_opening,1)
    set(handles.CheckCiv1,'Value',1)
    enable_civ1(handles,'on')
elseif isequal(ind_opening,2)
    set(handles.CheckFix1,'Value',1)
    enable_fix1(handles,'on')
elseif isequal(ind_opening,3)
    set(handles.CheckPatch1,'Value',1)
    enable_patch1(handles)
elseif isequal(ind_opening,4)
    set(handles.CheckCiv2,'Value',1)
    enable_civ2(handles,'on')
elseif isequal(ind_opening,5)
    enable_pair1(handles,'off')
    set(handles.CheckFix2,'Value',1)
    enable_fix2(handles)
    set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
    set(handles.ListPairCiv2,'Enable','On')
    set(handles.ListPairCiv2,'Enable','On')
elseif isequal(ind_opening,6)
    enable_pair1(handles,'off')
    set(handles.CheckPatch2,'Value',1)
    enable_patch2(handles)
    set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
    set(handles.ListPairCiv2,'Enable','On')
end
set(handles.RootName,'UserData',browse);% store information from browser
RootName_Callback(hObject, eventdata, handles);


% -----------------------------------------------------------------------
% --- Open again the file whose name has been recorded in MenuFile_1
function MenuFile_1_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
fileinput=get(handles.MenuFile_1,'Label');
display_file_name(hObject, eventdata, handles,fileinput)

% -----------------------------------------------------------------------
% --- Open again the file whose name has been recorded in MenuFile_2
function MenuFile_2_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
fileinput=get(handles.MenuFile_2,'Label');
display_file_name(hObject, eventdata, handles,fileinput)

% -----------------------------------------------------------------------
% --- Open again the file whose name has been recorded in MenuFile_3
function MenuFile_3_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
fileinput=get(handles.MenuFile_3,'Label');
display_file_name(hObject, eventdata, handles,fileinput)

% -----------------------------------------------------------------------
% --- Open again the file whose name has been recorded in MenuFile_4
function MenuFile_4_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
fileinput=get(handles.MenuFile_4,'Label');
display_file_name(hObject, eventdata, handles,fileinput)

% -----------------------------------------------------------------------
% --- Open again the file whose name has been recorded in MenuFile_5
function MenuFile_5_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
fileinput=get(handles.MenuFile_5,'Label');
display_file_name(hObject, eventdata, handles,fileinput)

%------------------------------------------------------------------------
function ImaDoc_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
RootName_Callback(hObject, eventdata, handles)

%------------------------------------------------------------------------
% --- function activated when a new filebase (image series) is introduced
function RootName_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
filebase=get(handles.RootName,'String');
display_file_name(hObject, eventdata, handles,filebase)

%------------------------------------------------------------------------
function display_file_name(hObject, eventdata, handles,filebase)
%------------------------------------------------------------------------
set(handles.ListCompareMode,'Visible','on')
ext_ima='';%default
nom_type_ima=[];%default
field_count=1;%default
nom_type_nc=[];
time=[];
TimeUnit='frame'; %default
CoordUnit='px';%default
pxcmx_search=[];%default
pxcmy_search=[];%default

ext_imadoc=get(handles.ImaDoc,'String');
browse=get(handles.RootName,'UserData');%default
if isfield(browse,'nom_type_ima')
    nom_type_ima=browse.nom_type_ima;% get an image nomenclature type already determined by an input image name
end 
if isfield(browse,'ext_ima')
    ext_ima=browse.ext_ima;
end
if isfield(browse,'nom_type_nc')
    nom_type_nc=browse.nom_type_nc;% get an image nomenclature type already determined by an input image name
end
if isfield(browse,'num_i1')
    field_count=browse.num_i1;% get an image index type already determined by an input file
end
set(handles.civ,'UserData',[]); %refresh list of previous civ files (for STATUS)

%default first_i and j and increments
first_i=str2double(get(handles.first_i,'String'));%value possibly set by uvmat_Opening
if isnan(first_i)|| first_i < 1
    first_i=1; %default first_i
end
last_i=str2double(get(handles.last_i,'String'));
if isnan(last_i)|| last_i < first_i
    last_i=first_i;  %default last_i
end
first_j=str2double(get(handles.first_j,'String'));
if isnan(first_j)|| first_j < 1
    first_j=1; %default first_j
end
last_j=str2double(get(handles.last_j,'String'));
if isnan(last_j)|| last_j < first_j
    last_j=first_j; %default last_j
end
incr_i=str2double(get(handles.incr_i,'String'));
if isnan(incr_i) || incr_i < 1;
    set(handles.incr_i,'String','1') %default incr_i
end
incr_j=str2double(get(handles.incr_j,'String'));
if isnan(incr_j) || incr_j < 1;
    set(handles.incr_j,'String','1') %default incr_j
end
dt=[];%default
testmode=0;%default
nbfield=[]; %default
nburst=[];%default
pxcmx=1;
pxcmy=1;

%look for an image documentation file
if ~strcmp(ext_imadoc,'.xml') && ~strcmp(ext_imadoc,'.civ')&& ~strcmpi(ext_imadoc,'.avi')
    if exist([filebase '.xml'],'file')
        ext_imadoc='.xml';
    elseif exist([filebase '.civxml'],'file')
        ext_imadoc='.civxml';
    elseif exist([filebase '.civ'],'file')
        ext_imadoc='.civ';
    elseif exist([filebase '.avi'],'file')
        ext_imadoc='.avi';
    elseif exist([filebase '.AVI'],'file')
        ext_imadoc='.AVI';
    end
    set(handles.ImaDoc,'String',ext_imadoc)
end

%%%%%%%%   read image documentation file  %%%%%%%%%%%%%%%%%%%%%%%%%%%
mode=''; %default
set(handles.ImaDoc,'BackgroundColor',[1 1 0])
drawnow
if isequal(ext_imadoc,'.civxml') || isequal(ext_imadoc,'.xml')|| isequal(ext_imadoc,'.civ')
    set(handles.ref_i,'Visible','On')%use a reference index
    set(handles.ref_j,'Visible','On')
elseif isequal(ext_imadoc,'.avi') || isequal(ext_imadoc,'.AVI')
    set(handles.ref_j,'Visible','Off')
else
    set(handles.ref_i,'Visible','Off')
    set(handles.ref_j,'Visible','Off')
end
testima_xml=0;
if isequal(ext_imadoc,'.civxml')%TO ABANDON
    [nbfield,nbfield2,time]=read_civxml([filebase '.civxml']);
    mode='pair j1-j2';
    if isempty(nom_type_ima)% dtermine types by default if not already selected by browser or uvmat
        nom_type_ima='_i_j';
    end
elseif isequal(ext_imadoc,'.xml')
    [XmlData,warntext]=imadoc2struct([filebase '.xml']);
    ext_ima_read=[];
    nom_type_read=[];
    if isfield(XmlData,'Heading')&&isfield(XmlData.Heading','ImageName')&&ischar(XmlData.Heading.ImageName)% get image nom type and extension from the xml file
        [PP,FF,fc,str2,str_a,str_b,ext_ima_read,nom_type_read]=name2display(XmlData.Heading.ImageName);
        fullname=fullfile(fileparts(filebase),XmlData.Heading.ImageName); %full name (including path) of the first image defined by the xmle file,
        if ~exist(fullname,'file')
            msgbox_uvmat('WARNING',['FirstImage ' fullname ' defined in the xml file does not exist'])
        end
    end
    if isfield(XmlData,'Time')
        time=XmlData.Time;
        nbfield=size(time,1);
        nbfield2=size(time,2);
        %transform .Time to a column vector if it is a line vector thenomenclature uses a single index: correct possible bug in xml
        if isequal(nbfield,1) && ~isequal(nbfield2,1)% .Time is a line vector
            if numel(nom_type_read)>=2 && isempty(regexp(nom_type_read(2:end),'\D'))
                time=time';
                nbfield=nbfield2;
                nbfield2=1;
            end
        end
    end
    if isfield(XmlData,'TimeUnit')
        TimeUnit=XmlData.TimeUnit;
    end
    if isfield(XmlData,'Npx')
        npx=XmlData.Npx;
        npy=XmlData.Npy;
    end
    pxcmx_search=1;
    pxcmy_search=1;
    if isfield(XmlData,'GeometryCalib')
        tsai=XmlData.GeometryCalib;
        if isfield(tsai,'f') && isfield(tsai,'Tz') && isfield(tsai,'dpx') && isfield(tsai,'dpy')&& isfield(tsai,'R')
            rot2D=tsai.R(1:2,[1,2]);
            pxcmx_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpx);
            pxcmy_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpy);
        end
        if isfield(tsai,'CoordUnit')
            CoordUnit=tsai.CoordUnit;
        end
    end
elseif strcmp(ext_imadoc,'.civ')% case of .civ image documentation file
    [error,time,TimeUnit,mode,npx,npy]=read_imatext([filebase '.civ']);
    if error==2, msgbox_uvmat('WARNING',['no file ' filebase '.civ']);
    elseif error==1, msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file');
    end
    nom_type_ima='001a';
elseif strcmpi(ext_imadoc,'.avi')
    nom_type_ima='*';
    ext_ima=ext_imadoc;
    set(handles.ListPairMode,'Value',1);
    set(handles.ListPairMode,'String',{'series(Di)'})
    dt=0.04;%default
    if exist([filebase ext_imadoc],'file')==2
        info=aviinfo([filebase ext_imadoc]);%read infos on the avi movie
        dt=1/info.FramesPerSecond;%time interval between successive frames
        nbfield=info.NumFrames;%number of frames
    end
    time=(dt*(0:nbfield-1))';%list of image times
end
if isempty(time)
    set(handles.ImaDoc,'String',''); %xml file not used for timing
end
set(handles.ImaDoc,'BackgroundColor',[1 1 1])

%get the imabe nomenclature type if not defined by the input file nor by the xml file
dirima=[];%default
if isempty(nom_type_ima)
    %look for double image series '_i_j'
    dirima=dir([filebase '_' num2str(first_i) '_' num2str(first_j) '.*']);
    if isempty(dirima)
        % look for images series  with sub marker '_'
        dirima=dir([filebase '_*' num2str(first_i) '.*']);
        if isempty(dirima)
            % look for other images series
            dirima=dir([filebase '*' num2str(first_i) '.*']);
            if isempty(dirima)
                % look for other images series witth letter appendix
                appendix=char(96+first_j);
                dirima=dir([filebase '*' num2str(first_i) appendix '.*']);
            end
        end
    end
end
for ilist=1:numel(dirima)
    [pp,ff,fc,str2,str_a,str_b,ext_list,nom_type_list]=name2display(dirima(ilist).name);
    form=imformats(ext_list(2:end));
    if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
        ext_ima=ext_list;
        nom_type_ima=nom_type_list;
            break
    end
end
% no image documentation file found: look for a series of existing files,images by priority or .nc files
if isempty(nom_type_ima)
    ext_search=ext_imadoc;
    nom_type_search=nom_type_nc;
else
    ext_search=ext_ima;
    nom_type_search=nom_type_ima;
end
if isempty(time) && ~strcmp(nom_type_search,'none') && ~strcmp(nom_type_search,'') && ~strcmp(nom_type_search,'*')
    subdir=get(handles.subdir_civ1,'String');
    incr_pair=[0 0];%default
    if isfield(browse,'incr_pair')
        incr_pair=browse.incr_pair;
    end
    %     nbdetect=0;%test of detected images
    field_i=browse.num_i2;
    imagename=name_generator(filebase,field_i,1,ext_search,nom_type_search);
    imagename_plus='';
    idetect=1;
    while idetect %look for the maximum file number in the series
        imagename_plus=name_generator(filebase,field_i+1,1,ext_search,nom_type_search);
        idetect=(exist(imagename_plus,'file')==2)&& ~strcmp(imagename,imagename_plus);
        if idetect
            field_i=field_i+1;
        end
        %SEE CASE OF NETCDF FILES
        %             nbdetect=nbdetect+(exist(imagename,'file')==2);
    end
    nbfield=field_i;% last detected field number
    field_i=browse.num_i1;%look for the minimum file number in the series
    imagename_min='';
    idetect=1;
    while idetect==1
        imagename_min=name_generator(filebase,field_i-1,1,ext_search,nom_type_search);
        idetect=(exist(imagename_min,'file')==2)&& ~strcmp(imagename,imagename_min);
        if idetect
            field_i=field_i-1;
        end
    end
    first_i=max(field_i,1); 
    if numel(regexp(nom_type_search,'\D'))>=1%two indices i and j
        field_i=browse.num_i1;
        field_j=browse.num_j2;
        imagename=name_generator(filebase,field_i,field_j,ext_search,nom_type_search);
        imagename_plus='';
        jdetect=1;
        while jdetect==1 %look for the maximum file number in the series
            imagename_plus=name_generator(filebase,field_i,field_j+1,ext_search,nom_type_search);
            jdetect=(exist(imagename_plus,'file')==2)&& ~strcmp(imagename,imagename_plus);
            if jdetect
                field_j=field_j+1;
            end
            %SEE CASE OF NETCDF FILES
            %             nbdetect=nbdetect+(exist(imagename,'file')==2);
        end
        nbfield2=field_j;% last detected field number
     end
 
    %determine the set of times and possible intervals for CIV
    %   dt=(1/1000)*str2double(get(handles.dt,'String'));
    time=(0:nbfield-1)';% time=file index -1  by default
    if numel(regexp(nom_type_search,'\D'))>=1%two indices i and j
        [x,y]=meshgrid(0:nbfield2-1,0:nbfield-1);
        time=x+y;
    end
end

if exist('time','var')
    if size(time,1)+size(time,2)>=3 % if there are at least two time values to define dt
        nbfield=size(time,1);
        nbfield2=size(time,2);
        set(handles.ImaDoc,'UserData',time); %store the set of times
        set(handles.dt_unit,'String',['dt in m' TimeUnit]);
%         set(handles.dt_unit_civ2,'String',['dt in m' TimeUnit]);
        set(handles.TimeUnit,'String',TimeUnit);
        set(handles.nb_field,'String',num2str(nbfield));
        set(handles.nb_field2,'String',num2str(nbfield2));
    end
end
set(handles.CoordUnit,'String',CoordUnit)
set(handles.SearchRange,'UserData',[pxcmx_search pxcmy_search]);
% npxy=[npy npx];
set(handles.ImaExt,'String',ext_ima)
set(handles.first_i,'String',num2str(first_i));
set(handles.last_i,'String',num2str(last_i));%
set(handles.first_j,'String',num2str(first_j));
set(handles.last_j,'String',num2str(last_j));%
browse.nom_type_ima=nom_type_ima;
set(handles.RootName,'UserData',browse)% store the nomenclature type

%%  set the menus of image pairs and default selection for civ   %%%%%%%%%%%%%%%%%%%
test_ima_i=numel(nom_type_ima)>1 && isempty(regexp(nom_type_ima(2:end),'\D','once'));%images with single indexing
if test_ima_i || isequal(nom_type_nc,'_i1-i2')||~(exist('nbfield2','var')&&(nbfield2~=1))
    set(handles.ListPairMode,'Value',1)
    set(handles.ListPairMode,'String',{'series(Di)'})   
elseif (nbfield==1)% simple series in j
    set(handles.ListPairMode,'Value',1)
    set(handles.ListPairMode,'String',{'series(Dj)'})
else
    set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)';'series(Di)'})%multiple choice
    if nbfield2 <= 10
        set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' for small burst
    end
end


%% desable status and RUN button
set(handles.RUN, 'Enable','On')
set(handles.RUN,'BackgroundColor',[1 0 0])
set(handles.BATCH,'Enable','On')
set(handles.BATCH,'BackgroundColor',[1 0 0])
if isfield(handles,'status')
set(handles.status,'Value',0);%suppress status display
status_Callback(hObject, eventdata, handles)
end

%% store the root input filename for future opening
dir_perso=prefdir;
profil_perso=fullfile(prefdir,'uvmat_perso.mat');
RootPath=fileparts(filebase);
if exist(profil_perso,'file')
    save (profil_perso,'RootPath','-append'); %store the root name for future opening of uvmat
else
    txt=ver('MATLAB');
    Release=txt.Release;
    relnumb=str2double(Release(3:4));
    if relnumb >= 14
        save (profil_perso,'RootPath','-V6'); %store the root name for future opening of uvmat
    else
        save (profil_perso,'RootPath'); %store the root name for future opening of uvmat
    end
end

%% update the subdir
pathdir=fileparts(filebase);%path to the current xml file
listot=dir(pathdir);
idir=0;
listdir={''};%default
for ilist=1:length(listot)
    if listot(ilist).isdir
        name=listot(ilist).name;
        if ~isequal(name,'.') && ~isequal(name,'..')
            idir=idir+1;
            listdir{idir,1}=listot(ilist).name;
        end
    end
end
set(handles.ListSubdirCiv1,'Value',1)
set(handles.ListSubDirCiv2,'Value',1)
set(handles.ListSubdirCiv1,'String',[listdir;'new...'])
set(handles.ListSubDirCiv2,'String',[listdir;'new...'])
if isempty(listdir)
    dirname=listdir{1};
else
    dirname='CIV'; %default civ directory name
end
set(handles.subdir_civ1,'String',dirname)
set(handles.subdir_civ2,'String',dirname)
%check wether the current subdir exists:
% subdir_civ1=get(handles.subdir_civ1,'String');
% subdir_civ2=get(handles.subdir_civ2,'String');

ListPairMode_Callback(hObject, eventdata, handles)

%------------------------------------------------------------------------
% --- Executes on button press in ListPairMode.
function ListPairMode_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
browse=get(handles.RootName,'UserData');
compare_list=get(handles.ListCompareMode,'String');
val=get(handles.ListCompareMode,'Value');
compare=compare_list{val};
if strcmp(compare,'displacement')
    mode='displacement';
else
    mode_list=get(handles.ListPairMode,'String');
    if ischar(mode_list)
        mode_list={mode_list};
    end
    mode_value=get(handles.ListPairMode,'Value');
    mode=mode_list{mode_value};
end
displ_num=[];%default
ref_i=str2double(get(handles.ref_i,'String'));
% last_i=str2num(get(handles.last_i,'String'));
time=get(handles.ImaDoc,'UserData'); %get the set of times
siztime=size(time);
nbfield=siztime(1);
nbfield2=siztime(2);
indchosen=1;  %%first pair selected by default
if isequal(mode,'pair j1-j2')%| isequal(mode,'st_pair j1-j2')
    dt=1;
    displ='';
    index=0;
    numlist_a=[];
    numlist_B=[];
    %get all the time intervals in bursts
    displ_dt=1;%default
    nbfield2=min(nbfield2,10);%limitate the number of pairs to 10x10
    for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'pair j1-j2' mode
        for numod_b=(numod_a+1):nbfield2
            index=index+1;
            numlist_a(index)=numod_a;
            numlist_b(index)=numod_b;
            if ~isempty(time)
                dt(numod_a,numod_b)=time(ref_i,numod_b)-time(ref_i,numod_a);%first time interval dt
                displ_dt(index)=dt(numod_a,numod_b);
            else
                displ_dt(index)=1;
            end
        end
    end
    [dtsort,indsort]=sort(displ_dt);
    if ~isempty(numlist_a)
        displ_num(1,:)=numlist_a(indsort);
        displ_num(2,:)=numlist_b(indsort);
    end
    displ_num(3,:)=0;
    displ_num(4,:)=0;
    set(handles.jtext,'Visible','Off')
    set(handles.first_j,'Visible','Off')
    set(handles.last_j,'Visible','Off')
    set(handles.incr_j,'Visible','Off')
    set(handles.nb_field2,'Visible','Off')
    set(handles.ref_j,'Visible','Off')
elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)')
    for index=1:min(nbfield2-1,200)
        displ_num(1,index)=-floor(index/2);
        displ_num(2,index)=ceil(index/2);
        displ_num(3,index)=0;
        displ_num(4,index)=0;
    end
    set(handles.jtext,'Visible','On')
    set(handles.first_j,'Visible','On')
    set(handles.last_j,'Visible','On')
    set(handles.incr_j,'Visible','On')
    set(handles.nb_field2,'Visible','On')
    set(handles.ref_j,'Visible','On')
    if nbfield > 1
        set(handles.itext,'Visible','On')
        set(handles.first_i,'Visible','On')
        set(handles.last_i,'Visible','On')
        set(handles.incr_i,'Visible','On')
        set(handles.nb_field,'Visible','On')
        set(handles.ref_i,'Visible','On')
    else
        set(handles.itext,'Visible','Off')
        set(handles.first_i,'Visible','Off')
        set(handles.last_i,'Visible','Off')
        set(handles.incr_i,'Visible','Off')
        set(handles.nb_field,'Visible','Off')
        set(handles.ref_i,'Visible','Off')
    end
elseif isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)')
    for index=1:200%min(nbfield-1,200)
        displ_num(1,index)=0;
        displ_num(2,index)=0;
        displ_num(3,index)=-floor(index/2);
        displ_num(4,index)=ceil(index/2);
    end
    set(handles.itext,'Visible','On')
    set(handles.first_i,'Visible','On')
    set(handles.last_i,'Visible','On')
    set(handles.incr_i,'Visible','On')
    set(handles.nb_field,'Visible','On')
    set(handles.ref_i,'Visible','On')
    if nbfield2 > 1
        set(handles.jtext,'Visible','On')
        set(handles.first_j,'Visible','On')
        set(handles.last_j,'Visible','On')
        set(handles.incr_j,'Visible','On')
        set(handles.nb_field2,'Visible','On')
        set(handles.ref_j,'Visible','On')
    else
        set(handles.jtext,'Visible','Off')
        set(handles.first_j,'Visible','Off')
        set(handles.last_j,'Visible','Off')
        set(handles.incr_j,'Visible','Off')
        set(handles.nb_field2,'Visible','Off')
        set(handles.ref_j,'Visible','Off')
    end
elseif isequal(mode,'displacement')%the pairs have the same indices
    displ_num(1,1)=0;
    displ_num(2,1)=0;
    displ_num(3,1)=0;
    displ_num(4,1)=0;
    if nbfield > 1
        set(handles.itext,'Visible','On')
        set(handles.first_i,'Visible','On')
        set(handles.last_i,'Visible','On')
        set(handles.incr_i,'Visible','On')
        set(handles.nb_field,'Visible','On')
        set(handles.ref_i,'Visible','On')
    else
        set(handles.itext,'Visible','Off')
        set(handles.first_i,'Visible','Off')
        set(handles.last_i,'Visible','Off')
        set(handles.incr_i,'Visible','Off')
        set(handles.nb_field,'Visible','Off')
        set(handles.ref_i,'Visible','Off')
    end
    if nbfield2 > 1
        set(handles.jtext,'Visible','On')
        set(handles.first_j,'Visible','On')
        set(handles.last_j,'Visible','On')
        set(handles.incr_j,'Visible','On')
        set(handles.nb_field2,'Visible','On')
        set(handles.ref_j,'Visible','On')
    else
        set(handles.jtext,'Visible','Off')
        set(handles.first_j,'Visible','Off')
        set(handles.last_j,'Visible','Off')
        set(handles.incr_j,'Visible','Off')
        set(handles.nb_field2,'Visible','Off')
        set(handles.ref_j,'Visible','Off')
    end
end
set(handles.ListPairCiv1,'UserData',displ_num);
find_netcpair_civ1(hObject, eventdata, handles)
find_netcpair_civ2(hObject, eventdata, handles)

%------------------------------------------------------------------------
% determine the menu for checkciv1 pairs depending on existing netcdf file at the middle of
% the field series set by first_i, incr, last_i
function find_netcpair_civ1(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(gcf,'Pointer','watch')
%nomenclature types
filebase=get(handles.RootName,'String');
[filepath,Nme,ext_dir]=fileparts(filebase);
browse=get(handles.RootName,'UserData');
compare_list=get(handles.ListCompareMode,'String');
val=get(handles.ListCompareMode,'Value');
compare=compare_list{val};
if strcmp(compare,'displacement')
    mode='displacement';
else
    mode_list=get(handles.ListPairMode,'String');
    mode_value=get(handles.ListPairMode,'Value');
    if isempty(mode_list)
        return
    end
    mode=mode_list{mode_value};
end

% nomenclature type of the .nc files
nom_type_ima=[];%default
if isfield(browse,'nom_type_ima')
    nom_type_ima=browse.nom_type_ima;
end

%determine nom_type_nc:
nom_type_nc=[];%default
if isfield(browse,'nom_type_nc')
    nom_type_nc=browse.nom_type_nc;
end
if isempty(nom_type_nc)
    [nom_type_nc]=nomtype2pair(nom_type_ima,isequal(mode,'series(Di)'),isequal(mode,'series(Dj)'));
end
browse.nom_type_nc=nom_type_nc;
set(handles.RootName,'UserData',browse)

%reads .nc subdirectoy and image numbers from the interface
subdir_civ1=get(handles.subdir_civ1,'String');%subdirectory subdir_civ1 for the netcdf data
ref_i=str2double(get(handles.ref_i,'String'));
if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
    ref_j=0;
else
    ref_j=str2double(get(handles.ref_j,'String'));
end
time=get(handles.ImaDoc,'UserData');%get the set of times
if isempty(time)
    time=[0 1];
end
dt_unit=1000;%default
displ_num=get(handles.ListPairCiv1,'UserData');

%eliminate the first pairs inconsistent with the position
if isempty(displ_num)
    nbpair=0;
else
    nbpair=length(displ_num(1,:));%nbre of displayed pairs
    if  isequal(mode,'series(Di)')  %| isequal(mode,'st_series(Di)')
        nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index
    elseif  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
        nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index
    end
end
nbpair=min(200,nbpair);%limit the number of displayed pairs to 200

%look for existing processed pairs involving the field at the middle of the series if checkciv1 will not
% be performed, while the result is needed for next steps.
displ_pair={''};
select=ones(size(1:nbpair));%flag for displayed pairs =1 for display
testpair=0;
% case with no checkciv1 operation, netcdf files need to exist for reading
if get(handles.CheckCiv1,'Value')==0 %
    if ~exist(fullfile(filepath,subdir_civ1,ext_dir),'dir')
        msgbox_uvmat('ERROR',['no civ1 file available: subdirectory ' subdir_civ1 ' does not exist']);
        set(handles.ListPairCiv1,'String',{});
        return
    end
    for ipair=1:nbpair
        filename=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,...
            ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1);
        select(ipair)=exist(filename,'file')==2;% put flag to 0 if the file does not exist
    end   
    % case of no displayed pair
    if isequal(select,zeros(size(1:nbpair)))
        if isfield(browse,'incr_pair') && ~isequal(browse.incr_pair,[0 0])
            num_i1=ref_i-floor(browse.incr_pair(1)/2);
            num_i2=ref_i+ceil(browse.incr_pair(1)/2);
            num_j1=ref_j-floor(browse.incr_pair(2)/2);
            num_j2=ref_j+ceil(browse.incr_pair(2)/2);
            filename=name_generator(filebase,num_i1,num_j1,'.nc',nom_type_nc,1,num_i2,num_j2,subdir_civ1);
            select(1)=exist(filename,'file')==2;
            testpair=1;
        else
            if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
                msgbox_uvmat('ERROR',['no civ1 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ1]);
            else
                msgbox_uvmat('ERROR',['no civ1 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ1]);
            end
            set(handles.ListPairCiv1,'String',{''});
            %COMPLETER CAS STEREO
            return
        end
    end
end
if isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)')
    if testpair
        displ_pair{1}=['Di= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
    else
        for ipair=1:nbpair
            if select(ipair)
                if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
                    dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt
                    displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
                else
                    displ_pair{ipair}='...'; %pair not displayed in the menu
                end
            end
        end
    end
elseif isequal(mode,'series(Dj)')%|isequal(mode,'st_series(Dj)')% series on the j index
    if testpair
        displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
    else
        for ipair=1:nbpair
            if select(ipair)
                if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
                    dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt
                    displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
                end
            elseif testpair
                displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(2)/2)) '|' num2str(ceil(browse.incr_pair(2)/2))];
            else
                displ_pair{ipair}='...'; %pair not displayed in the menu
            end
        end
    end
elseif isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')%case of pairs
    for ipair=1:nbpair
        if select(ipair)
            dt=time(ref_i+displ_num(4,ipair),displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),displ_num(1,ipair));%time interval dt
            displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ...
                ' :dt= ' num2str(dt*1000)];
        else
            displ_pair{ipair}='...'; %pair not displayed in the menu
        end
    end
elseif isequal(mode,'displacement')
    displ_pair={'Di=Dj=0'};
end
set(handles.ListPairCiv1,'String',displ_pair');
ichoice=find(select,1);
if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
initial=get(handles.ListPairCiv1,'Value');%initial choice of pair
if initial>nbpair
    set(handles.ListPairCiv1,'Value',ichoice);% first valid pair proposed by default in the menu
end
if numel(select)>=initial && ~isequal(select(initial),1)
    set(handles.ListPairCiv1,'Value',ichoice);% first valid pair proposed by default in the menu
end

%set(handles.ListPairCiv2,'String',displ_pair');
initial=get(handles.ListPairCiv2,'Value');
if initial>length(displ_pair')%|~isequal(select(initial),1)
    if ichoice <= length(displ_pair')
        set(handles.ListPairCiv2,'Value',ichoice);% same pair proposed by default for civ2
    else
        set(handles.ListPairCiv2,'Value',1);% same pair proposed by default for civ2
    end
end
set(handles.ListPairCiv2,'String',displ_pair');
set(gcf,'Pointer','arrow')

%------------------------------------------------------------------------
% determine the menu for checkciv2 pairs depending on the existing netcdf file at the
%middle of the series set by first_i, incr, last_i
function find_netcpair_civ2(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(gcf,'Pointer','watch')
%nomenclature types
filebase=get(handles.RootName,'String');
[filepath,Nme,ext_dir]=fileparts(filebase);
browse=get(handles.RootName,'UserData');
compare_list=get(handles.ListCompareMode,'String');
val=get(handles.ListCompareMode,'Value');
compare=compare_list{val};
if strcmp(compare,'displacement')
    mode='displacement';
else
    mode_list=get(handles.ListPairMode,'String');
    if isempty(mode_list)
        msgbox_uvmat('ERROR','please enter an input image or netcdf file')
        return
    end
    mode_value=get(handles.ListPairMode,'Value');
    mode=mode_list{mode_value};
end

% nomenclature type of the .nc files
nom_type_ima='ima_num';%default
if isfield(browse,'nom_type_ima')
    nom_type_ima=browse.nom_type_ima;
end
nom_type_nc='_i1-i2';%default
if isfield(browse,'nom_type_nc')
    nom_type_nc=browse.nom_type_nc;
end
if isequal(nom_type_ima,'png_old') || isequal(nom_type_ima,'netc_old')|| isequal(nom_type_ima,'raw_SMD')|| isequal(nom_type_nc,'netc_old')
    nom_type_nc='netc_old';%nom_type for the netcdf files
elseif isequal(nom_type_ima,'none')||isequal(nom_type_nc,'none')
    nom_type_nc='none';
elseif isequal(nom_type_ima,'avi')||isequal(nom_type_ima,'_i')||isequal(nom_type_ima,'ima_num')||isequal(nom_type_nc,'_i1-i2')
    nom_type_nc='_i1-i2';
else
    if  isequal(mode,'series(Di)')%|isequal(mode,'st_series(Di)')
        nom_type_nc='_i1-i2_j'; % PIV in volume
    else
        nom_type_nc='_i_j1-j2';
    end
end
browse.nom_type_nc=nom_type_nc;
set(handles.RootName,'UserData',browse)

%reads .nc subdirectory and image numbers from the interface
subdir_civ1=get(handles.subdir_civ1,'String');%subdirectory subdir_civ1 for the netcdf data
subdir_civ2=get(handles.subdir_civ2,'String');%subdirectory subdir_civ2 for the netcdf data
% first_i=str2num(get(handles.first_i,'String'));
% last_i=str2num(get(handles.last_i,'String'));
% incr=str2num(get(handles.incr_i,'String'));
% num1=first_i:incr:last_i;
% if isempty(num1)
%     set(handles.ListPairCiv2,'Value',1);
%     set(handles.ListPairCiv2,'String',{''});
%     return
% end
ref_i=str2double(get(handles.ref_i,'String'));
if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
    ref_j=0;
else
    ref_j=str2double(get(handles.ref_j,'String'));
end
time=get(handles.ImaDoc,'UserData'); %get the set of times
if isempty(time)
    time=[0 1];%default
end
%dt_unit=str2num(get(handles.dt,'String'));% used when there is no image documentation file
%dt_unit=1000;
displ_num=get(handles.ListPairCiv1,'UserData');


%eliminate the first pairs inconsistent with the position
if isempty(displ_num)
    nbpair=0;
else
    nbpair=length(displ_num(1,:));%nbre of displayed pairs
    if  isequal(mode,'series(Di)')% | isequal(mode,'st_series(Di)')
        nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index
    elseif  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
        nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index
    end
end
nbpair=min(200,nbpair);%limit the number of displayed pairs to 200

%look for existing processed pairs involving the field at the middle of the series if checkciv1 will not
% be performed, while the result is needed for next steps.
displ_pair={''}; %default
select=ones(size(1:nbpair));%default =1 for numbers of displayed pairs
if get(handles.CheckCiv2,'Value')==0 & get(handles.CheckCiv1,'Value')==0 & get(handles.CheckFix1,'Value')==0 & get(handles.CheckPatch1,'Value')==0%&...
    if ~exist(fullfile(filepath,subdir_civ2,ext_dir),'dir')
        errordlg(['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist'])
        set(handles.ListPairCiv2,'Value',1);
        set(handles.ListPairCiv2,'String',{''});
        return
    end
    for ipair=1:nbpair
        filename=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,...
            ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1);
        select(ipair)=exist(filename,'file')==2;
    end
    if  isequal(select,zeros(size(1:nbpair)))
        if isfield(browse,'incr_pair')
            num_i1=ref_i-floor(browse.incr_pair(1)/2);
            num_i2=ref_i+floor((browse.incr_pair(1)+1)/2);
            num_j1=ref_j-floor(browse.incr_pair(2)/2);
            num_j2=ref_j+floor((browse.incr_pair(2)+1)/2);
            filename=name_generator(filebase,num_i1,num_j1,'.nc',nom_type_nc,1,num_i2,num_j2,subdir_civ2);
            select(1)=exist(filename,'file')==2;
        else
            if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
                errordlg(['no civ2 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ2])
            else
                errordlg(['no civ2 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ2])
            end
            set(handles.ListPairCiv2,'Value',1);
            set(handles.ListPairCiv2,'String',{''});
            return
        end
    end
end
if isequal(mode,'series(Di)') % | isequal(mode,'st_series(Di)')
    for ipair=1:nbpair
        if select(ipair)
            if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
                dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt
                displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
            end
        else
            displ_pair{ipair}='...'; %pair not displayed in the menu
        end
    end
elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)') % series on the j index
    for ipair=1:nbpair
        if select(ipair)
            if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
                dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt
                displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
            end
        else
            displ_pair{ipair}='...'; %pair not displayed in the menu
        end
    end
elseif isequal(mode,'pair j1-j2')% | isequal(mode,'st_pair j1-j2') %case of pairs
    for ipair=1:nbpair
        if select(ipair)
            dt=time(ref_i+displ_num(4,ipair),displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),displ_num(1,ipair));%time interval dt
            displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ...
                ' :dt= ' num2str(dt*1000)];
        else
            displ_pair{ipair}='...'; %pair not displayed in the menu
        end
    end
elseif isequal(mode,'displacement')
    displ_pair={'Di=Dj=0'};
end
val=get(handles.ListPairCiv2,'Value');
ichoice=find(select,1);
if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
if get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0
    val=ichoice;% first valid pair proposed by default in the menu
end
if val>length(displ_pair')
    set(handles.ListPairCiv2,'Value',1);% first valid pair proposed by default in the menu
else
    set(handles.ListPairCiv2,'Value',val);
end
set(handles.ListPairCiv2,'String',displ_pair');
set(gcf,'Pointer','arrow')




%------------------------------------------------------------------------
% --- Executes on selection change in ListPairCiv1.
function ListPairCiv1_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
%reproduce by default the chosen pair in the checkciv2 menu
list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
index_pair=get(handles.ListPairCiv1,'Value');
displ_num=get(handles.ListPairCiv1,'UserData');
% num_a=displ_num(1,index_pair);
% num_b=displ_num(2,index_pair);
list_pair2=get(handles.ListPairCiv2,'String');%get the menu of image pairs
if index_pair<=length(list_pair2)
    set(handles.ListPairCiv2,'Value',index_pair);
end

%update first_i and last_i according to the chosen image pairs
mode_list=get(handles.ListPairMode,'String');
mode_value=get(handles.ListPairMode,'Value');
mode=mode_list{mode_value};
if isequal(mode,'series(Di)')
    first_i=str2double(get(handles.first_i,'String'));
    last_i=str2double(get(handles.last_i,'String'));
    incr_i=str2double(get(handles.incr_i,'String'));
    num1=first_i:incr_i:last_i;
    lastfield=str2double(get(handles.nb_field,'String'));
    if ~isnan(lastfield)
        test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ...
            (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield);
        num1=num1(test_find);
    end
    set(handles.first_i,'String',num2str(num1(1)));
    set(handles.last_i,'String',num2str(num1(end)));
elseif isequal(mode,'series(Dj)')
    first_j=str2double(get(handles.first_j,'String'));
    last_j=str2double(get(handles.last_j,'String'));
    incr_j=str2double(get(handles.incr_j,'String'));
    num_j=first_j:incr_j:last_j;
    lastfield2=str2double(get(handles.nb_field2,'String'));
    if ~isnan(lastfield2)
        test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2);
        num1=num_j(test_find);
    end
    set(handles.first_j,'String',num2str(num1(1)));
    set(handles.last_j,'String',num2str(num1(end)));
end

%------------------------------------------------------------------------
% --- Executes on selection change in ListPairCiv2.
function ListPairCiv2_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
index_pair=get(handles.ListPairCiv2,'Value');%get the selected position index in the menu

%update first_i and last_i according to the chosen image pairs
mode_list=get(handles.ListPairMode,'String');
mode_value=get(handles.ListPairMode,'Value');
mode=mode_list{mode_value};
if isequal(mode,'series(Di)')
    first_i=str2double(get(handles.first_i,'String'));
    last_i=str2double(get(handles.last_i,'String'));
    incr_i=str2double(get(handles.incr_i,'String'));
    num1=first_i:incr_i:last_i;
    lastfield=str2double(get(handles.nb_field,'String'));
    if ~isnan(lastfield)
        test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ...
            (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield);
        num1=num1(test_find);
    end
    set(handles.first_i,'String',num2str(num1(1)));
    set(handles.last_i,'String',num2str(num1(end)));
elseif isequal(mode,'series(Dj)')
    first_j=str2double(get(handles.first_j,'String'));
    last_j=str2double(get(handles.last_j,'String'));
    incr_j=str2double(get(handles.incr_j,'String'));
    num_j=first_j:incr_j:last_j;
    lastfield2=str2double(get(handles.nb_field2,'String'));
    if ~isnan(lastfield2)
        test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2);
        num1=num_j(test_find);
    end
    set(handles.first_j,'String',num2str(num1(1)));
    set(handles.last_j,'String',num2str(num1(end)));
end

%------------------------------------------------------------------------
% --- Executes on button press in RUN: processing on local computer
function RUN_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(handles.RUN, 'Enable','Off')
set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
batch=0;
errormsg=launch_jobs(hObject, eventdata, handles,batch);
set(handles.RUN, 'Enable','On')
set(handles.RUN,'BackgroundColor',[1 0 0])

% start status callback to visualise results
if ~isempty(errormsg)
    display(errormsg)
    msgbox_uvmat('ERROR',errormsg)
elseif  isfield(handles,'status') %&& ~isequal(get(handles.ListPairMode,'Value'),3)
    set(handles.status,'Value',1);%suppress status display
    status_Callback(hObject, eventdata, handles)
end

%------------------------------------------------------------------------
% --- Executes on button press in BATCH: remote processing
function BATCH_Callback(hObject, eventdata, handles)
% -----------------------------------------------------------------------
set(handles.BATCH, 'Enable','Off')
set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])
batch=1;
errormsg=launch_jobs(hObject, eventdata, handles, batch);
set(handles.BATCH, 'Enable','On')
set(handles.BATCH,'BackgroundColor',[1 0 0])

% start status callback to visualise results
if ~isempty(errormsg)
    display(errormsg)
    msgbox_uvmat('ERROR',errormsg)
elseif isfield(handles,'status')
    set(handles.status,'Value',1);%suppress status display
    status_Callback(hObject, eventdata, handles)
end

%------------------------------------------------------------------------
% --- Lauch command called by RUN and BATCH: remote processing
function errormsg=launch_jobs(hObject, eventdata, handles, batch)
%-----------------------------------------------------------------------
errormsg='';%default

%%read the civ GUI
Param=read_GUI(handles.civ)
%% check the selected list of operations:
operations={'CIV1','FIX1','PATCH1','CIV2','FIX2','PATCH2'};
box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2];

index_first=find(box_test==1,1);
if isempty(index_first)
    errormsg='no selected operation';
    return
end
index_last=find(box_test==1,1,'last');
box_used=box_test(index_first : index_last);
[box_missing,ind_missing]=min(box_used);
if isequal(box_missing,0); %there is a missing step in the sequence of operations
    errormsg=['missing' cell2mat(operations(ind_missing))];
    return
end

%% check mask if selecetd 
%could be included in get_mask callback ?
if isequal(get(handles.CheckMask,'Value'),1)
    maskname=get(handles.txt_MaskName,'String');
    if ~exist(maskname,'file')
        get_mask_civ1_Callback(hObject, eventdata, handles);
    end
end
if isequal(get(handles.CheckMask,'Value'),1)
    maskname=get(handles.txt_MaskName,'String');
    if ~exist(maskname,'file')
        get_mask_fix1_Callback(hObject, eventdata, handles);
    end
end
if isequal(get(handles.CheckMask,'Value'),1)
    maskname=get(handles.txt_Mask,'String');
    if ~exist(maskname,'file')
        get_mask_civ2_Callback(hObject, eventdata, handles);
    end
end
if isequal(get(handles.CheckMask,'Value'),1)
    maskname=get(handles.mask_fix2,'String');
    if ~exist(maskname,'file')
        get_mask_fix2_Callback(hObject, eventdata, handles);
    end
end

%% reinitialise status callback 
if isfield(handles,'status')
    set(handles.status,'Value',0);%suppress status display
    status_Callback(hObject, eventdata, handles)
end

%% set the list of files and check them
display('checking the files...')
[ref_i,ref_j,errormsg]=find_ref_indices(handles);
if ~isempty(errormsg)
    return
end
[filecell,num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2,nom_type_nc,xx,yy,compare]=...
    set_civ_filenames(handles,ref_i,ref_j,box_test);
% ADDED
   [Rootbat,Filebat]=fileparts(filecell.nc.civ1{1,1});%output netcdf file (without extention)
%ADDED 
set(handles.civ,'UserData',filecell);%store for futur use of status callback
if isempty(filecell)% (error message displayed in fct set_civ_filenames)
    return
end
nbfield=numel(num1_civ1);
nbslice=numel(num_a_civ1);

%% read the PARAM.xml file to get the binaries (and batch_mode if batch)
path_civ=fileparts(which('civ')); %path to the source directory of uvmat
xmlfile='PARAM.xml';
if exist(xmlfile,'file')% search parameter xml file in the whole matlab path
    t=xmltree(xmlfile);
    s=convert(t);
else
    errormsg=['no file ' xmlfile];
    return
end

test_interp=0; %eviter les variables test_ (LG)

if batch
    if isfield(s,'BatchParam')
        Param.xml=s.BatchParam;
        if isfield(Param.xml,'BatchMode')
            batch_mode=Param.xml.BatchMode;
            if ~ismember(batch_mode,{'sge','oar'})
                errormsg=['batch mode ' batch_mode ' not supported by UVMAT'];
                return
            end
        end
    else
        errormsg='no batch civ binaries defined in PARAM.xml';
        return
    end
else % run
    if isfield(s,'RunParam')
        Param.xml=s.RunParam;
    else
        msgbox_uvmat('ERROR','no run civ binaries defined in PARAM.xml')
        return
    end
end

%% check batch mode supported
if batch
    switch batch_mode
        case 'sge'
            test_command='qstat';
        case 'oar'
            test_command='oartat';
    end   
    [s,w]=system(test_command);
    if ~isequal(s,0)
        msgbox_uvmat('ERROR',[batch_mode ' batch system not available'])
        return
    end
end

%% check if the binaries exist
if isequal(get(handles.Matlab,'checked'),'on')
    CivMode='Matlab';
else
    CivMode='CivX';
end
binary_list={};
switch CivMode
    case 'CivX'
        binary_list={'Civ1Bin','Civ2Bin','PatchBin','FixBin'};
    case 'CivAll'
        binary_list={'Civ'}
    case 'Matlab'
        if batch
            % vérifier Matlab installé sur le cluster
            % difficile a faire a priori
        end          
end
for bin_name=binary_list
    if isfield(Param.xml,bin_name{1})
        if ~exist(Param.xml.(bin_name{1}),'file')%look for the full path if the file name has been defined with a relative path in PARAM.xml
            fullname=fullfile(path_civ,Param.xml.(bin_name{1}))
            if exist(fullname,'file')
                Param.xml.(bin_name{1})=fullname;
            else
                msgbox_uvmat('ERROR',['Binary ' Param.xml.(bin_name{1}) ' defined in PARAM.xml does not exist'])
                return
            end
        else
            [path,name,ext]=fileparts(Param.xml.(bin_name{1}));
            currentdir=pwd;
            cd(path);
            binpath=pwd;%path of the binary
            Param.xml.(bin_name{1})=fullfile(binpath,[name ext]);
            %                      display(Param.xml.(bin_name{1}));
            cd(currentdir);
        end
        
    end
end

display('files OK, processing...')

%% get checkciv1 parameters
if Param.CheckCiv1
%     Param.Civ1=read_param_civ1(handles,filecell);
end

%% get checkfix1 parameters 
if Param.CheckFix1
    param.fix1=read_param_fix1(handles,filecell);
end

%% get checkpatch1 parameters 
if Param.CheckPatch1
    param.Patch1=read_panel(handles.Patch1);
    %param.checkpatch1=read_param_patch1(handles)
end

%% get checkciv2 parameters:
if Param.CheckCiv2
    param.civ2=read_param_civ2(handles,cell2mat(filecell.ima1.civ2(1,1)));
end

%% get checkfix2 parameters
if Param.CheckFix2
    flagindex2(1)=get(handles.vec_Fmin2_2, 'Value');
    flagindex2(2)=get(handles.vec_F3_2, 'Value');
    flagindex2(3)=get(handles.vec_F4, 'Value');
    thresh_vec2C=str2double(get(handles.thresh_vec2C,'String'));%threshold on image correlation vec_C
    thresh_vel2=str2double(get(handles.thresh_vel2,'String'));%threshold on velocity modulus
    test_mask=get(handles.CheckMask,'Value');
    nbslice_mask=get(handles.mask_fix2,'UserData'); % get the number of slices (= number of masks)
    %%%%%%%%%%%%%COMPLETER LE PROGRAMME FIX AVEC REF FILE ET OPTION inf_sup=2
    %     inf_sup=get(handles.inf_sup2,'Value');
    %     ref=get(handles.ref_fix2,'UserData');
    
    %%%%%%%%%%%%%%%%%%%
end

%% get checkpatch2 parameters
if Param.CheckPatch2==1
    param.Patch2=read_panel(handles.Patch1);
end

%%


%% MAIN LOOP
time=get(handles.ImaDoc,'UserData'); %get the set of times

super_cmd=[];
batch_file_list=[];
    
for ifile=1:nbfield
    for j=1:nbslice
        % initiate system command
        switch CivMode
            case 'CivX'
                if isunix % check: necessaire aussi en RUN?
                    cmd=['#!/bin/bash \n '...
                        '#$ -cwd \n '...
                        'hostname && date \n '...
                        'umask 002 \n'];%allow writting access to created files for user group
                else
                    cmd=[];
                end
            case 'CivAll'
                %         if CivAll
                CivAllxml=xmltree;% xml contents,  all parameters
                CivAllCmd='';
                CivAllxml=set(CivAllxml,1,'name','CivDoc');
        end
        
        
        % define output file name
        if Param.CheckCiv2==1 || Param.CheckFix2==1 || Param.CheckPatch2==1
            OutputFile=filecell.nc.civ2{ifile,j};
        else
            OutputFile=filecell.nc.civ1{ifile,j};
        end
        OutputFile=regexprep(OutputFile,'.nc','');

        
        %CheckCiv1
        if Param.CheckCiv1
            % read image-dependent parameters
            Param.Civ1.filename_ima_a=filecell.ima1.civ1{ifile,j};
            Param.Civ1.filename_ima_b=filecell.ima2.civ1{ifile,j};
            Param.Civ1.Dt=(time(num2_civ1(ifile),num_b_civ1(j))-time(num1_civ1(ifile),num_a_civ1(j)));
            Param.Civ1.T0=((time(num2_civ1(ifile),num_b_civ1(j))+time(num1_civ1(ifile),num_a_civ1(j)))/2);
            Param.Civ1.term_a=num2stra(num_a_civ1(j),nom_type_nc);%UTILITE?
            Param.Civ1.term_b=num2stra(num_b_civ1(j),nom_type_nc);%
Param.Civ1.pxcmx=1; %velocities are expressed in pixel dispalcement
Param.Civ1.pxcmy=1;
% if exist('file_ima','var')
A=imread(filecell.ima1.civ1{1,1});%read the first image to get the size
sizim=size(A);
Param.Civ1.npx=(sizim(2));
Param.Civ1.npy=(sizim(1));
%TODO : civ should not need npx and npy


            
            % read mask parameters
%             dummy=get(handles.CheckMask,'Value');
            if Param.Civ1.CheckMask % the lines below should be changed with the new gui
                %matbe they when check_mask the Maskname is read
                maskdispl=get(handles.txt_MaskName,'String');
                if exist(maskdispl,'file')
                    Param.Civ1.maskname=maskdispl;
                    Param.Civ1.maskflag='y';
                else
                    maskbase=[filecell.filebase '_' maskdispl]; %
                    nbslice_mask=str2double(maskdispl(1:end-4)); %
                    num1_mask=mod(num1_civ1(ifile)-1,nbslice_mask)+1;
                    Param.Civ1.maskname=name_generator(maskbase,num1_mask,1,'.png','_i');
                    if exist(Param.Civ1.maskname,'file')
                        Param.Civ1.maskflag='y';
                    else
                        Param.Civ1.maskname='noFile use default';
                        Param.Civ1.maskflag='n';
                    end
                end
            else
                Param.Civ1.maskname='noFile use default';
                Param.Civ1.maskflag='n';
            end
            
            % read grid parameters=
            
            if Param.Civ1.CheckGrid
                Caram.Civ1.gridflag='y';
                gridname=get(handles.txt_GridName,'String');
                if isequal(gridname(end-3:end),'grid')
                    nbslice_grid=str2double(gridname(1:end-4)); %
                    if ~isnan(nbslice_grid)
                        num1_grid=mod(num1_civ1(ifile)-1,nbslice_grid)+1;
                        Param.Civ1.gridname=[filecell.filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')];
                        if ~exist(Param.Civ1.gridname,'file')
                            msgbox_uvmat('ERROR','grid file absent for civ1')
                        end
                    elseif exist(gridname,'file')
                        Param.Civ1.gridname=gridname;
                    else
                        msgbox_uvmat('ERROR','grid file absent for civ1')
                    end
                end
            else
                Param.Civ1.gridname='noFile use default';
                Param.Civ1.gridflag='n';
            end
            
            switch CivMode
                case 'CivX'
                    cmd=[cmd...
                        cmd_civ1(filecell.nc.civ1{ifile,j},Param) '\n'];
                case 'CivAll'
                    CivAllCmd=[CivAllCmd ' civ1 '];
                    str=CIV1_CMD_Unified(filecell.nc.civ1{ifile,j},'',Param.Civ1);
                    fieldnames=fields(str);
                    [CivAllxml,uid_civ1]=add(CivAllxml,1,'element','civ1');
                    for ilist=1:length(fieldnames)
                        val=eval(['str.' fieldnames{ilist}]);
                        if ischar(val)
                            [CivAllxml,uid_t]=add(CivAllxml,uid_civ1,'element',fieldnames{ilist});
                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
                        end
                    end
            end
        end
        
        % CheckFix1
        if Param.CheckFix1
           switch CivMode
                case 'CivX'
                    if isunix %unix system
                        cmd_FIX=[Param.xml.FixBin ' -f ' filecell.nc.civ1{ifile,j} ' -fi1 ' num2str(param.fix1.flagindex1(1)) ...
                            ' -fi2 ' num2str(param.fix1.flagindex1(2)) ' -fi3 ' num2str(param.fix1.flagindex1(3)) ...
                            ' -threshC ' num2str(param.fix1.thresh_vecC1) ' -threshV ' num2str(param.fix1.thresh_vel1) ' -maskName ' param.fix1.maskname];
                    else %windows system
                        cmd_FIX=['"' Param.xml.FixBin '" -f "' filecell.nc.civ1{ifile,j} '" -fi1 ' num2str(param.fix1.flagindex1(1)) ...
                            ' -fi2 ' num2str(param.fix1.flagindex1(2)) ' -fi3 ' num2str(param.fix1.flagindex1(3)) ...
                            ' -threshC ' num2str(param.fix1.thresh_vecC1) ' -threshV ' num2str(param.fix1.thresh_vel1) ' -maskName "' param.fix1.maskname '"'];
                        cmd_FIX=regexprep(cmd_FIX,'\\','\\\\');
                    end
                    cmd=[cmd cmd_FIX '\n'];
                case 'CivAll'
                    fix1.inputFileName=filecell.nc.civ1{ifile,j} ;
                    fix1.fi1=num2str(param.fix1.flagindex1(1));
                    fix1.fi2=num2str(param.fix1.flagindex1(2));
                    fix1.fi3=num2str(param.fix1.flagindex1(3));
                    fix1.threshC=num2str(param.fix1.thresh_vecC1);
                    fix1.threshV=num2str(param.fix1.thresh_vel1);
                    fieldnames=fields(fix1);
                    [CivAllxml,uid_fix1]=add(CivAllxml,1,'element','fix1');
                    for ilist=1:length(fieldnames)
                        val=eval(['fix1.' fieldnames{ilist}]);
                        if ischar(val)
                            [CivAllxml,uid_t]=add(CivAllxml,uid_fix1,'element',fieldnames{ilist});
                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
                        end
                    end
                    CivAllCmd=[CivAllCmd ' fix1 '];
            end
        end
        
        %CheckPatch1
        if Param.CheckPatch1==1
            switch CivMode
                case 'CivX'
                    cmd_PATCH=cmd_patch(filecell.nc.civ1{ifile,j},param.Patch1,Param.xml.PatchBin);
                    cmd=[cmd cmd_PATCH '\n'];
                case 'CivAll'
                    patch1.inputFileName=filecell.nc.civ1{ifile,j} ;
                    patch1.nopt=subdomain_patch1;
                    patch1.maxdiff=thresh_patch1;
                    patch1.ro=rho_patch1;
                    test_grid=get(handles.get_gridpatch1,'Value');
                    if test_grid
                        patch1.gridflag='y';
                        gridname=get(handles.grid_patch1,'String');
                        if isequal(gridname(end-3:end),'grid')
                            nbslice_grid=str2double(gridname(1:end-4)); %
                            if ~isnan(nbslice_grid)
                                num1_grid=mod(num1_civ1(ifile)-1,nbslice_grid)+1;
                                patch1.gridPatch=[filecell.filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')];
                                if ~exist(patch1.gridPatch,'file')
                                    msgbox_uvmat('ERROR','grid file absent for patch1')
                                end
                            elseif exist(gridname,'file')
                                patch1.gridPatch=gridname;
                            else
                                msgbox_uvmat('ERROR','grid file absent for patch1')
                            end
                        end
                    else
                        patch1.gridPatch='none';
                        patch1.gridflag='n';
                        patch1.m=nx_patch1;
                        patch1.n=ny_patch1;
                    end
                    patch1.convectFlow='n';
                    fieldnames=fields(patch1);
                    [CivAllxml,uid_patch1]=add(CivAllxml,1,'element','patch1');
                    for ilist=1:length(fieldnames)
                        val=eval(['patch1.' fieldnames{ilist}]);
                        if ischar(val)
                            [CivAllxml,uid_t]=add(CivAllxml,uid_patch1,'element',fieldnames{ilist});
                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
                        end
                    end
                    CivAllCmd=[CivAllCmd ' patch1 '];
            end
        end
        if Param.CheckCiv2==1
            param.civ2.filename_ima_a=filecell.ima1.civ2{ifile,j};
            param.civ2.filename_ima_b=filecell.ima2.civ2{ifile,j};
            param.civ2.Dt=num2str(time(num2_civ2(ifile),num_b_civ2(j))-time(num1_civ2(ifile),num_a_civ2(j)));
            param.civ2.T0=num2str((time(num2_civ1(ifile),num_b_civ2(j))+time(num1_civ2(ifile),num_a_civ2(j)))/2);
            param.civ2.term_a=num2stra(num_a_civ2(j),nom_type_nc);
            param.civ2.term_b=num2stra(num_b_civ2(j),nom_type_nc);
            param.civ2.filename_nc1=filecell.nc.civ1{ifile,j};
            param.civ2.filename_nc1(end-2:end)=[]; % remove '.nc'
            test_mask=get(handles.CheckMask,'Value');
            if test_mask==0
                param.civ2.maskname='noFile use default';
                param.civ2.maskflag='n';
            else
                maskdispl=get(handles.txt_Mask,'String');
                if exist(maskdispl,'file')
                    param.civ2.maskname=maskdispl;
                    param.civ2.maskflag='y';
                else
                    maskbase=[filecell.filebase '_' maskdispl]; %
                    nbslice_mask=str2double(maskdispl(1:end-4)); %
                    num1_mask=mod(num1_civ2(ifile)-1,nbslice_mask)+1;
                    param.civ2.maskname=name_generator(maskbase,num1_mask,1,'.png','_i');
                    if exist(param.civ2.maskname,'file')
                        param.civ2.maskflag='y';
                    else
                        param.civ2.maskname='noFile use default';
                        param.civ2.maskflag='n';
                    end
                end
            end
            gridname=get(handles.txt_GridName,'String');
            if numel(gridname)>=4 && isequal(gridname(end-3:end),'grid')
                nbslice_grid=str2double(gridname(1:end-4)); %
                if ~isnan(nbslice_grid)
                    param.civ2.gridflag='y';
                    num1_grid=mod(num1_civ2(ifile)-1,nbslice_grid)+1;
                    param.civ2.gridname=[filecell.filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')];
                    if exist(param.civ2.gridname,'file')
                        param.civ2.gridflag='y';
                    else
                        param.civ2.gridname='noFile use default';
                        param.civ2.gridflag='n';
                    end
                elseif exist(gridname,'file')
                    param.civ2.gridflag='y';
                else
                    param.civ2.gridname='noFile use default';
                    param.civ2.gridflag='n';
                end
            end
            switch CivMode
                case 'CivX'
                    cmd_CIV2=CIV2_CMD(filecell.nc.civ2{ifile,j},param);%creates the cmx file [fullfile(Rootbat,Filebat) '.civ2.cmx]
                    cmd=[cmd cmd_CIV2 '\n'];
                case 'CivAll'
                    CivAllCmd=[CivAllCmd ' civ2 '];
                    str=CIV2_CMD_Unified(filecell.nc.civ2{ifile,j},'',param.civ2);
                    fieldnames=fields(str);
                    [CivAllxml,uid_civ2]=add(CivAllxml,1,'element','civ2');
                    for ilist=1:length(fieldnames)
                        val=eval(['str.' fieldnames{ilist}]);
                        if ischar(val)
                            [CivAllxml,uid_t]=add(CivAllxml,uid_civ2,'element',fieldnames{ilist});
                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
                        end
                    end
            end
        end
        
        % CheckFix2
        if Param.CheckFix2==1
            test_mask=get(handles.CheckMask,'Value');
            if test_mask==0
                maskname=''; %no mask used
            else
                maskdispl=get(handles.mask_fix2,'String');
                maskbase=[filecell.filebase '_' maskdispl]; %
                nbslice_mask=str2double(maskdispl(1:end-4)); %
                num1_mask=mod(num1_civ2(ifile)-1,nbslice_mask)+1;
                maskname =name_generator(maskbase,num1_mask,1,'.png','_i');
            end
            switch CivMode
                case 'CivX'
                    if isunix
                        cmd_FIX=[Param.xml.FixBin ' -f ' filecell.nc.civ2{ifile,j} ' -fi1 ' num2str(flagindex2(1)) ...
                            ' -fi2 ' num2str(flagindex2(2)) ' -fi3 ' num2str(flagindex2(3)) ...
                            ' -threshC ' num2str(thresh_vec2C) ' -threshV ' num2str(thresh_vel2) ' -maskName ' maskname];
                    else
                        cmd_FIX=['"' Param.xml.FixBin '" -f "' filecell.nc.civ2{ifile,j} '" -fi1 ' num2str(flagindex2(1)) ...
                            ' -fi2 ' num2str(flagindex2(2)) ' -fi3 ' num2str(flagindex2(3)) ...
                            ' -threshC ' num2str(thresh_vec2C) ' -threshV ' num2str(thresh_vel2) ' -maskName "' maskname '"'];
                        cmd_FIX=regexprep(cmd_FIX,'\\','\\\\');
                    end
                    cmd=[cmd cmd_FIX '\n'];
                case 'CivAll'
                    fix2.inputFileName=filecell.nc.civ2{ifile,j} ;
                    fix2.fi1=num2str(flagindex2(1));
                    fix2.fi2=num2str(flagindex2(2));
                    fix2.fi3=num2str(flagindex2(3));
                    fix2.threshC=num2str(thresh_vec2C);
                    fix2.threshV=num2str(thresh_vel2);
                    fieldnames=fields(fix2);
                    [CivAllxml,uid_fix2]=add(CivAllxml,1,'element','fix2');
                    for ilist=1:length(fieldnames)
                        val=eval(['fix2.' fieldnames{ilist}]);
                        if ischar(val)
                            [CivAllxml,uid_t]=add(CivAllxml,uid_fix2,'element',fieldnames{ilist});
                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
                        end
                    end
                    CivAllCmd=[CivAllCmd ' fix2 '];
            end
        end
        
        %CheckPatch2
        if Param.CheckPatch2==1
            switch CivMode
                case 'CivX'
                    cmd_PATCH=cmd_patch(filecell.nc.civ2{ifile,j},param.Patch2,Param.xml.PatchBin);
                    cmd=[cmd cmd_PATCH '\n'];
                case 'CivAll'
                    patch2.inputFileName=filecell.nc.civ1{ifile,j} ;
                    patch2.nopt=subdomain_patch2;
                    patch2.maxdiff=thresh_patch2;
                    patch2.ro=rho_patch2;
                    test_grid=get(handles.get_gridpatch2,'Value');
                    if test_grid
                        patch2.gridflag='y';
                        gridname=get(handles.grid_patch2,'String');
                        if isequal(gridname(end-3:end),'grid')
                            nbslice_grid=str2double(gridname(1:end-4)); %
                            if ~isnan(nbslice_grid)
                                num1_grid=mod(num1_civ2(ifile)-1,nbslice_grid)+1;
                                patch2.gridPatch=[filecell.filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')];
                                if ~exist(patch2.gridPatch,'file')
                                    msgbox_uvmat('ERROR','grid file absent for patch2')
                                end
                            elseif exist(gridname,'file')
                                patch2.gridPatch=gridname;
                            else
                                msgbox_uvmat('ERROR','grid file absent for patch2')
                            end
                        end
                    else
                        patch2.gridPatch='none';
                        patch2.gridflag='n';
                        patch2.m=nx_patch2;
                        patch2.n=ny_patch2;
                    end
                    patch2.convectFlow='n';
                    fieldnames=fields(patch2);
                    [CivAllxml,uid_patch2]=add(CivAllxml,1,'element','patch2');
                    for ilist=1:length(fieldnames)
                        val=eval(['patch2.' fieldnames{ilist}]);
                        if ischar(val)
                            [CivAllxml,uid_t]=add(CivAllxml,uid_patch2,'element',fieldnames{ilist});
                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
                        end
                    end
                    CivAllCmd=[CivAllCmd ' patch2 '];
            end
        end
 
        switch CivMode
            case {'CivX','CivAll'}
                if isequal(CivMode,'CivAll')
                    save(CivAllxml,[OutputFile '.xml']);
                    cmd=[cmd sparam.CivBin ' -f ' OutputFile '.xml '  CivAllCmd ' >' OutputFile '.log' '\n'];
                end
                
                % create the .bat file used in run or batch
                filename_bat=[OutputFile '.bat'];
                [fid,message]=fopen(filename_bat,'w');
                if isequal(fid,-1)
                    msgbox_uvmat('ERROR', ['creation of .bat file: ' message])
                    return
                end
                fprintf(fid,cmd);
                fclose(fid);
                
                if isunix
                    system(['chmod +x ' filename_bat]);
                end
                
                batch_file_list{length(batch_file_list)+1}=filename_bat;
                
%                 if batch
%                     switch batch_mode
%                         case 'sge'                            
%                             display(['!qsub -p ' pvalue ' -q civ.q -e ' flname '.errors -o ' flname '.log' ' ' filename_bat]);
%                             eval(  ['!qsub -p ' pvalue ' -q civ.q -e ' flname '.errors -o ' flname '.log' ' ' filename_bat]);
%                         case 'oar'
% %                             eval(  ['!chmod +x ' filename_bat]);
% %                             %eval(  ['!oarsub -n CIVX -l /core=1,walltime=00:10:00  ' filename_bat]);                    
% %                             eval(  ['!oarsub -n CIVX -l "/core=1+{type = ''smalljob''}/licence=1,walltime=00:10:00"   ' filename_bat]);
% 
%                     cmd_str=['sh ' filename_bat];
%                     super_cmd{length(super_cmd)+1}=cmd_str;
%                            
%                     end
%                 else
%                     %% to lauch the jobs locally :
%                     if(isunix)
%                         cmd_str=['. ' filename_bat];
%                     else %case of Windows
%                         cmd_str=['@call "' regexprep(filename_bat,'\\','\\\\') '"'];
%                     end
%                     super_cmd=[super_cmd cmd_str '\n'];
%                     disp(cmd_str);
%                 end
            case 'Matlab'
                drawnow
                if Param.CheckCiv1==1
                    Param.Civ1=Param.Civ1;
                end
                if Param.CheckFix1==1
                    fix1.WarnFlags=[];
                    if get(handles.CheckFmin2,'Value')
                        fix1.WarnFlags=[fix1.WarnFlags -2];
                    end
                    if get(handles.CheckF3,'Value')
                        fix1.WarnFlags=[fix1.WarnFlags 3];
                    end
                    fix1.LowerBoundCorr=thresh_vecC1;
                    if get(handles.inf_sup1,'Value')
                        fix1.UppperBoundVel=thresh_vel1;
                    else
                        fix1.LowerBoundVel=thresh_vel1;
                    end
                    if get(handles.CheckMask,'Value')
                        fix1.MaskName=maskname;
                    end
                    Param.Fix1=fix1;
                end
                if Param.CheckPatch1==1
                    if strcmp(compare,'stereo PIV')
                        filebase_A=filecell.filebase;
                        [pp,ff]=fileparts(filebase_A);
                        filebase_B=fullfile(pp,get(handles.RootName_1,'String'));
                        RUN_STLIN(filecell.ncA.civ1{ifile,j},filecell.nc.civ1{ifile,j},'civ1',filecell.st{ifile,j},...
                            str2num(nx_patch1),str2num(ny_patch1),str2num(thresh_patch1),[filebase_A '.xml'],[filebase_B '.xml'])
                    else
                        Param.Patch1.Rho=rho_patch1;
                        Param.Patch1.Threshold=thresh_patch1;
                        Param.Patch1.SubDomain=subdomain_patch1;
                    end
                end
                if Param.CheckCiv2==1
                    Param.Civ2=param.civ2;
                end
                if Param.CheckFix2==1
                    fix2.WarnFlags=[];
                    if get(handles.vec_Fmin2_2,'Value')
                        fix2.WarnFlags=[fix2.WarnFlags -2];
                    end
                    if get(handles.vec_F4,'Value')
                        fix2.WarnFlags=[fix2.WarnFlags 4];
                    end
                    if get(handles.vec_F3_2,'Value')
                        fix2.WarnFlags=[fix2.WarnFlags 3];
                    end
                    fix2.LowerBoundCorr=thresh_vec2C;
                    if get(handles.inf_sup2,'Value')
                        fix2.UppperBoundVel=thresh_vel2;
                    else
                        fix2.LowerBoundVel=thresh_vel2;
                    end
                    if get(handles.CheckMask,'Value')
                        fix2.MaskName=maskname;
                    end
                    Param.Fix2=fix2;
                end
                if Param.CheckPatch2==1
                    if strcmp(compare,'stereo PIV')
                        filebase_A=filecell.filebase;
                        [pp,ff]=fileparts(filebase_A);
                        filebase_B=fullfile(pp,get(handles.RootName_1,'String'));
                        RUN_STLIN(filecell.ncA.civ2{ifile,j},filecell.nc.civ2{ifile,j},'civ2',filecell.st{ifile,j},...
                            str2num(nx_patch2),str2num(ny_patch2),str2num(thresh_patch2),[filebase_A '.xml'],[filebase_B '.xml'])
                    else
                        Param.Patch2.Rho=rho_patch2;
                        Param.Patch2.Threshold=thresh_patch2;
                        Param.Patch2.SubDomain=subdomain_patch2;
                    end
                end
                if ~strcmp(compare,'stereo PIV')
                    [Data,erromsg]=civ_uvmat(Param,filecell.nc.civ1{ifile,j});
                    if isempty(errormsg)
                        display([filecell.nc.civ1{ifile,j} ' written'])
                    else
                        msgbox_uvmat('ERROR',errormsg)
                    end

                end
        end
    end
end

if batch
    switch batch_mode                        
        case 'sge'
            for p=1:length(batch_file_list)
                cmd=['!qsub -p ' pvalue ' -q civ.q -e ' flname '.errors -o ' flname '.log' ' ' batch_file_list{p}];
                display(cmd);eval(cmd);
            end
        case 'oar_old'
                for p=1:length(batch_file_list)
                    oar_command=['!oarsub -n CIVX -q nicejob '...
                   '-E ' regexprep(batch_file_list{p},'.bat','.errors') ' -O ' regexprep(batch_file_list{p},'.bat','.log ')...
                    '-l "/core=1+{type = ''smalljob''}/licence=1,walltime=00:60:00"   ' batch_file_list{p}];
                display(oar_command);eval(oar_command);
                end
       
           
       case 'oar_perl'
                filename_joblist=fullfile(Rootbat,'job_list.txt');
                fid=fopen(filename_joblist,'w');

                for p=1:length(batch_file_list)
                    oar_command=['oarsub -n CIVX '...
                        '-l "/core=1,walltime=00:10:00"   ' batch_file_list{p}];
                    fprintf(fid,[oar_command '\n']);
                end
                fclose(fid)
                oar_command=['oarsub -t container -n civx-container -l /core=24,walltime=00:35:00 "/fsnet/data/legi/calcul9/home/gostiaux/Documents/MATLAB/uvmat_dev/oar-dispatch -f '...
                    filename_joblist '"'];
                filename_oarcommand=fullfile(Rootbat,'oar_command');
                fid=fopen(filename_oarcommand,'w');
                fprintf(fid,[oar_command '\n']);
                fclose(fid);
%                 display(oar_command);
                eval(['! . ' filename_oarcommand]);

        case 'oar'%'oar_mpi'
                filename_joblist=fullfile(Rootbat,'job_list.txt');
                fid=fopen(filename_joblist,'w');

                for p=1:length(batch_file_list)
                    fprintf(fid,[batch_file_list{p} '\n']);
                end
                fclose(fid)
                
                
%                 oarsub -S ./oar.sub 

                
                

                
            %             for p=0:floor(length(batch_file_list)/6);                
%                 filename_batch_group=fullfile(Rootbat,['job_list_' num2str(p) '.bat']);
%                 fid=fopen(filename_batch_group,'w');
%                 if fid==-1
%                     msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat])
%                     return
%                 end
%                 if p==floor(length(batch_file_list)/6)
%                     kmax=mod(length(batch_file_list),6);
%                 else
%                     kmax=6;
%                 end
%                 for k=1:kmax
%                     fprintf(fid,['sh ' batch_file_list{p*6+k} '\n']);
%                 end
%                 fclose(fid);
%                 system(['chmod +x ' filename_batch_group]);
%                 eval(  ['!oarsub -n CIVX -q nicejob '...
%                     '-E '  flname '.errors -O ' flname '.log '...
%                     '-l "/core=1+{type = ''smalljob''}/licence=1,walltime=00:60:00"   ' filename_batch_group]);
%             end
        case 'oar_new' % to be develloped with Patrick Begou
                filename_joblist=fullfile(Rootbat,'job_list.txt');
                fid=fopen(filename_superbat,'w');
                if fid==-1
                    msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat])
                    return
                end
                for p=1:length(batch_file_list)
                    fprintf(fid,[batch_file_list{p} '\n']);
                end
                fclose(fid);
                walltime=datestr(length(super_cmd)*10/24/60,13);
                eval(  ['!oarsub -n CIVX -q nicejob -l "/core=1+{type = ''smalljob''}/licence=1,walltime=' walltime '"   ' filename_superbat]);
    end
else
    if ~isequal(CivMode,'Matlab')
        filename_superbat=fullfile(Rootbat,'job_list.bat');
        fid=fopen(filename_superbat,'w');
        if fid==-1
            msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat])
            return
        end
        for p=1:length(batch_file_list)
            if isunix
                fprintf(fid,['sh ' batch_file_list{p} '\n']);
            else
                fprintf(fid,['@call "' regexprep(filename_bat,'\\','\\\\') '"' '\n']);
            end
        end
        fclose(fid);
        if(isunix)
            system(['chmod +x ' filename_superbat]);
        end
        system([filename_superbat ' &']);% execute main commmand
    end
    
end


%% save interface state
if isfield(filecell,'nc')
    if isfield(filecell.nc,'civ2')
        fileresu=filecell.nc.civ2{1,1};
    else
        fileresu=filecell.nc.civ1{1,1};
    end
end
[RootPath,RootFile,field_count,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fileresu);
namedoc=fullfile(RootPath,subdir,RootFile);
detect=1;
while detect==1
    namefigfull=[namedoc '.fig'];
    hh=dir(namefigfull);
    if ~isempty(hh)
        detect=1;
        namedoc=[namedoc '.0'];
    else
        detect=0;
    end
end
saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER  .xml)

%Save info in personal profile (initiate browser next time) TODO
MenuFile={};
dir_perso=prefdir;
profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
if exist(profil_perso,'file')
    hh=load (profil_perso);
      if isfield(hh,'MenuFile')
          MenuFile=hh.MenuFile;
      end
      MenuFile=[filecell.ima1.civ1(1,1); MenuFile];
      save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
else
    MenuFile=filecell.ima1.civ1(1,1);
    save (profil_perso,'MenuFile')
end


%------------------------------------------------------------------------
% --- determine the list of reference indices of processing file
function [ref_i,ref_j,errormsg]=find_ref_indices(handles)
%------------------------------------------------------------------------
errormsg=''; %default error message
first_i=str2double(get(handles.first_i,'String'));%first index i
last_i=str2double(get(handles.last_i,'String'));%last index i
incr_i=str2double(get(handles.incr_i,'String'));% increment
if isequal(get(handles.first_j,'Visible'),'on')
    first_j=str2double(get(handles.first_j,'String'));%first index j
    last_j=str2double(get(handles.last_j,'String'));%last index j
    incr_j=str2double(get(handles.incr_j,'String'));% increment
else
    first_j=1;
    last_j=1;
    incr_j=1;
end
ref_i=first_i:incr_i:last_i;% list of i indices (reference values for each pair)
ref_j=first_j:incr_j:last_j;% list of j indices (reference values for each pair)
if isnan(first_i)||isnan(first_j)
    errormsg='first field number not defined';
elseif isnan(last_i)||isnan(last_j)
    errormsg='last field number not defined';
elseif isnan(incr_i)||isnan(incr_j)
    errormsg='increment in field number not defined';
elseif last_i < first_i || last_j < first_j 
    errormsg='last field number must be larger than the first one';
end

%------------------------------------------------------------------------
% --- determine the list of filenames and indices needed for launch_job
function [filecell,num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2,nom_type_nc,file_ref_fix1,file_ref_fix2,compare]=...
    set_civ_filenames(handles,ref_i,ref_j,checkbox)
%------------------------------------------------------------------------
filecell=[];%default

%% get the root names nomenclature and numbers
filebase=get(handles.RootName,'String');

if isempty(filebase)||isequal(filebase,'')
    msgbox_uvmat('ERROR','no input files')
    return
end

%filebase=regexprep(filebase,'\.fsnet','fsnet');% temporary fix for cluster Coriolis
filecell.filebase=filebase;

browse=get(handles.RootName,'UserData');
compare_list=get(handles.ListCompareMode,'String');
val=get(handles.ListCompareMode,'Value');
compare=compare_list{val};
if strcmp(compare,'displacement')
    mode='displacement';
else
    mode_list=get(handles.ListPairMode,'String');
    mode_value=get(handles.ListPairMode,'Value');
    mode=mode_list{mode_value};
end
%time=get(handles.RootName,'UserData'); %get the set of times
ext_ima=get(handles.ImaExt,'String');
nom_type_nc=browse.nom_type_nc;
if isfield(browse,'nom_type_ima')
    nom_type_ima2=browse.nom_type_ima;
end
if isempty(nom_type_ima2),nom_type_ima2='1';end; %default
if isempty(nom_type_nc),nom_type_nc='_i1-i2';end; %default
[num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=...
    find_pair_indices(handles,ref_i,ref_j,mode);
%determine the new filebase for 'displacement' ListPairMode (comparison of two series)
filebase_B=filebase;% root name of the second field series for stereo
if strcmp(compare,'displacement') || strcmp(compare,'stereo PIV')
%     test_disp=1;
    nom_type_ima1=browse.nom_type_ima_1; %nomenclature type of the second file series
    [Path2,Name2]=fileparts(filebase_B);
    Path1=Path2;
    Name1=get(handles.RootName_1,'String');% root name of the first field series for stereo
    filebase_A=fullfile(Path1,Name1);
    if length(Name1)>6
        Name1=Name1(end-5:end);
    end
    if length(Name2)>6
        Name2=Name2(end-5:end);
    end
    filebase_AB=fullfile(Path2,[Name2 '-' Name1]);
else
%     test_disp=0;
    filebase_A=filebase;
    nom_type_ima1=nom_type_ima2;
    filebase_AB=filebase;
end
if strcmp(compare,'displacement')
    filebase_ima1=filebase_A;
    filebase_ima2=filebase_B;
    filebase_nc=filebase_AB; %root name for the result of civ2
else
    filebase_ima1=filebase_B;
    filebase_ima2=filebase_B;
    filebase_nc=filebase_B;
end

%determine reference files for fix:
file_ref_fix1={};%default
file_ref_fix2={};
nbfield=length(num1_civ1);
nbslice=length(num_a_civ1);
if checkbox(2)==1% fix1 performed
    ref=get(handles.ref_fix1,'UserData');%read data on the ref file stored by get_ref_fix1_Callback
    if ~isempty(ref)
        first_i=str2double(get(handles.first_i,'String'));
        last_i=str2double(get(handles.last_i,'String'));
        incr_i=str2double(get(handles.incr_i,'String'));
        first_j=str2double(get(handles.first_j,'String'));
        last_j=str2double(get(handles.last_j,'String'));
        incr_j=str2double(get(handles.incr_j,'String'));
        num_i_ref=first_i:incr_i:last_i;
        num_j_ref=first_j:incr_j:last_j;
        if isequal(mode,'displacement')
            num_i1=num_i_ref;
            num_i2=num_i_ref;
            num_j1=num_j_ref;
            num_j2=num_j_ref;
        elseif isequal(mode,'pair j1-j2')% isequal(mode,'st_pair j1-j2')
            num_i1=num_i_ref;
            num_i2=num_i1;
            num_j1=ref.num_a*ones(size(num_i_ref));
            num_j2=ref.num_b*ones(size(num_i_ref));
        elseif isequal(mode,'series(Di)') % isequal(mode,'st_series(Di)')
            delta1=floor((ref.num2-ref.num1)/2);
            delta2=ceil((ref.num2-ref.num1)/2);
            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
            if isempty(ref.num_a)
                ref.num_a=1;
            end
            num_j1=ref.num_a*ones(size(num_i1));
            num_j2=num_j1;
        elseif isequal(mode,'series(Dj)')%| isequal(mode,'st_series(Dj)')
            delta1=floor((ref.num_b-ref.num_a)/2);
            delta2=ceil((ref.num_b-ref.num_a)/2);
            num_i1=ref.num1*ones(size(num_i_ref));
            num_i2=num_i1;
            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
        end
        for ifile=1:nbfield
            for j=1:nbslice
                file_ref=name_generator(ref.filebase,num_i1(ifile),num_j1(j),'.nc',ref.nom_type,1,num_i2(ifile),num_j2(j),ref.subdir);%
                file_ref_fix1(ifile,j)={file_ref};
                if ~exist(file_ref,'file')
                    msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix1'])
                    filecell=[];
                    return
                end
            end
        end
    end
end

%determine reference files for checkfix2:
if checkbox(5)==1% fix2 performed
    ref=get(handles.ref_fix2,'UserData');
    if ~isempty(ref)
        first_i=str2double(get(handles.first_i,'String'));
        last_i=str2double(get(handles.last_i,'String'));
        incr_i=str2double(get(handles.incr_i,'String'));
        first_j=str2double(get(handles.first_j,'String'));
        last_j=str2double(get(handles.last_j,'String'));
        incr_j=str2double(get(handles.incr_j,'String'));
        num_i_ref=first_i:incr_i:last_i;
        num_j_ref=first_j:incr_j:last_j;
        if isequal(mode,'displacement')
            num_i1=num_i_ref;
            num_i2=num_i_ref;
            num_j1=num_j_ref;
            num_j2=num_j_ref;
        elseif isequal(mode,'pair j1-j2')
            num_i1=num_i_ref;
            num_i2=num_i1;
            num_j1=ref.num_a;
            num_j2=ref.num_b;
        elseif isequal(mode,'series(Di)')
            delta1=floor((ref.num2-ref.num1)/2);
            delta2=ceil((ref.num2-ref.num1)/2);
            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
            num_j1=ref.num_a*ones(size(num_i1));
            num_j2=num_j1;
        elseif isequal(mode,'series(Dj)')
            delta1=floor((ref.num_b-ref.num_a)/2);
            delta2=ceil((ref.num_b-ref.num_a)/2);
            num_i1=ref.num1*ones(size(num_i_ref));
            num_i2=num_i1;
            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
        end
        for ifile=1:nbfield
            for j=1:nbslice
                file_ref=name_generator(ref.filebase,num_i1(ifile),num_j1(j),'.nc',ref.nom_type,1,num_i2(ifile),num_j2(j),ref.subdir);%
                file_ref_fix2(ifile,j)={file_ref};
                if ~exist(file_ref,'file')
                    msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix2'])
                    filecell={};
                    return
                end
            end
        end
    end
end

%check dir
subdir_civ1=get(handles.subdir_civ1,'String');%subdirectory subdir_civ1 for the netcdf output data
subdir_civ2=get(handles.subdir_civ2,'String');
if isequal(subdir_civ1,''),subdir_civ1='CIV'; end% put default subdir
if isequal(subdir_civ2,''),subdir_civ2=subdir_civ1; end% put default subdir
% currentdir=pwd;%store the current working directory
[Path_ima,Name]=fileparts(filebase);%Path of the image files (.civ)
if ~exist(Path_ima,'dir')
    msgbox_uvmat('ERROR',['path to images ' Path_ima ' not found'])
    filecell={};
    return
end
[xx,message]=fileattrib(Path_ima);
if ~isempty(message) && ~isequal(message.UserWrite,1)
    msgbox_uvmat('ERROR',['No writting access to ' Path_ima])
    filecell={};
%     cd(currentdir);
    return
end

%check the existence of the netcdf and image files involved
% %%%%%%%%%%%%  case CheckCiv1 activated   %%%%%%%%%%%%%
if checkbox(1)==1;
    detect=1;
    vers=0;
    subdir_civ1_new=subdir_civ1;
    while detect==1 %create a new subdir if the netcdf files already exist
        for ifile=1:nbfield
            for j=1:nbslice
                filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1_new);
                detect=exist(filename,'file')==2;
                if detect% if a netcdf file already exists
                    indstr=regexp(subdir_civ1_new,'\D');
                    if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number
                        vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1;
                        subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)];
                    else
                        vers=vers+1;
                        subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) '_' num2str(vers)];       
                    end
                    subdir_civ2=subdir_civ1_new;
                    break
                end
                filecell.nc.civ1(ifile,j)={filename};
            end
            if detect% if a netcdf file already exists
                break
            end
        end
  
        %create the new subdir_civ1
        if ~exist(fullfile(Path_ima,subdir_civ1_new),'dir')
%             cd(Path_ima);          
            [xx,msg1]=mkdir(fullfile(Path_ima,subdir_civ1_new));

            if ~strcmp(msg1,'')
                msgbox_uvmat('ERROR',['cannot create ' subdir_civ1_new ': ' msg1])%error message for directory creation
                filecell={};
                return
            elseif isunix          
                [xx,msg2] = fileattrib(fullfile(Path_ima,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g)
                if ~strcmp(msg2,'')
                    msgbox_uvmat('ERROR',['pb of permission for  ' fullfile(Path_ima,subdir_civ1_new) ': ' msg2])%error message for directory creation
                    filecell={};
                    return
                end
            end
%             cd(currentdir);
        end
        if strcmp(compare,'stereo PIV')&&(strcmp(mode,'pair j1-j2')||strcmp(mode,'series(Dj)')||strcmp(mode,'series(Di)'))%check second nc series
            for ifile=1:nbfield
                for j=1:nbslice
                    filename=name_generator(filebase_A,num1_civ1(ifile),num_a_civ1(j),'.nc',nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1_new);%
                    detect=exist(filename,'file')==2;
                    if detect% if a netcdf file already exists
                       indstr=regexp(subdir_civ1_new,'\D');
                       if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number
                           vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1;
                           subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)];
                       else
                           vers=vers+1;
                           subdir_civ1_new=[subdir_civ1_new '_' num2str(vers)];
                       end
                       subdir_civ2=subdir_civ1;
                       break
                    end
                    filecell.ncA.civ1(ifile,j)={filename};
                end
                if detect% if a netcdf file already exists
                    break
                end
            end
            %create the new subdir_civ1
            if ~exist(fullfile(Path_ima,subdir_civ1_new),'dir')
%                    cd(Path_ima);          
                [xx,msg1]=mkdir(fullfile(Path_ima,subdir_civ1_new));
%                             cd(currentdir);
                if ~strcmp(msg1,'')
                    msgbox_uvmat('ERROR',['cannot create ' subdir_civ1_new ': ' msg1])
%                     cd(currentdir)
                    filecell={};
                    return
                else
                    [xx,msg2] = fileattrib(fullfile(Path_ima,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g)
                    if ~strcmp(msg2,'')
                        msgbox_uvmat('ERROR',['pb of permission for ' subdir_civ1_new ': ' msg2])%error message for directory creation
%                         cd(currentdir)
                        filecell={};
                        return
                    end
                end
            end
        end
    end
    subdir_civ1=subdir_civ1_new;
    % get image names
    for ifile=1:nbfield
        for j=1:nbslice
            filename=name_generator(filebase_ima1, num1_civ1(ifile),num_a_civ1(j),ext_ima,nom_type_ima1);
            idetect(j)=exist(filename,'file')==2;
            filecell.ima1.civ1(ifile,j)={filename}; %first image
            filename=name_generator(filebase_ima2, num2_civ1(ifile),num_b_civ1(j),ext_ima,nom_type_ima2);
            idetect_1(j)=exist(filename,'file')==2;
            filecell.ima2.civ1(ifile,j)={filename};%second image
        end
        [idetectmin,indexj]=min(idetect);
        if idetectmin==0,
            msgbox_uvmat('ERROR',[filecell.ima1.civ1{ifile,indexj} ' not found'])
            filecell={};
           % cd(currentdir)
            return
        end
        [idetectmin,indexj]=min(idetect_1);
        if idetectmin==0,
            msgbox_uvmat('ERROR',[filecell.ima2.civ1{ifile,indexj} ' not found'])
            filecell={};
            %cd(currentdir)
            return
        end
    end
    if strcmp(compare,'stereo PIV') && (strcmp(mode,'pair j1-j2') || strcmp(mode,'series(Dj)') || strcmp(mode,'series(Di)'))
        for ifile=1:nbfield
            for j=1:nbslice
                filename=name_generator(filebase_A, num1_civ1(ifile),num_a_civ1(j),ext_ima,nom_type_ima1);
                idetect(j)=exist(filename,'file')==2;
                filecell.imaA1.civ1(ifile,j)={filename} ;%first image
                filename=name_generator(filebase_A, num2_civ1(ifile),num_b_civ1(j),ext_ima,nom_type_ima2);
                idetect_1(j)=exist(filename,'file')==2;
                filecell.imaA2.civ1(ifile,j)={filename};%second image
            end
            [idetectmin,indexj]=min(idetect);
            if idetectmin==0,
                msgbox_uvmat('ERROR',[filecell.imaA1.civ1{ifile,indexj} ' not found'])
                filecell={};
               % cd(currentdir)
                return
            end
            [idetectmin,indexj]=min(idetect_1);
            if idetectmin==0,
                msgbox_uvmat('ERROR',[filecell.imaA2.civ1{ifile,indexj} ' not found'])
                filecell={};
               % cd(currentdir)
                return
            end
        end
    end
    
    %%%%%%%%%%%%%  checkfix1 or checkpatch1 activated but no checkciv1   %%%%%%%%%%%%%
elseif (checkbox(2)==1 || checkbox(3)==1);
    for ifile=1:nbfield
        for j=1:nbslice
            filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',...
                nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
            detect=exist(filename,'file')==2;
            if detect==0
                msgbox_uvmat('ERROR',[filename ' not found'])
                filecell={};
               % cd(currentdir)
                return
            end
            filecell.nc.civ1(ifile,j)={filename};
        end
    end
    if strcmp(compare,'stereo PIV')
        for ifile=1:nbfield
            for j=1:nbslice
                filename=name_generator(filebase_A,num1_civ1(ifile),num_a_civ1(j),'.nc',nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
                filecell.ncA.civ1(ifile,j)={filename};
                if ~exist(filename,'file')
                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
                    set(handles.RUN, 'Enable','On')
                    set(handles.RUN,'BackgroundColor',[1 0 0])
                    filecell={};
                    %cd(currentdir)
                    return
                end
            end
        end
    end
end

%%%%%%%%%%%%%  if checkciv2 performed with pairs different than checkciv1  %%%%%%%%%%%%%
testdiff=0;
if (checkbox(4)==1)&&...
        ((get(handles.ListPairCiv1,'Value')~=get(handles.ListPairCiv2,'Value'))||~strcmp(subdir_civ2,subdir_civ1))
    testdiff=1;
    detect=1;
    vers=0;
    subdir_civ2_new=subdir_civ2;
    while detect==1 %create a new subdir if the netcdf files already exist
        for ifile=1:nbfield
            for j=1:nbslice
                filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2_new);%
                detect=exist(filename,'file')==2;
                if detect% if a netcdf file already exists
                    indstr=regexp(subdir_civ2,'\D');
                    if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
                        vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
                        subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
                    else
                        vers=vers+1;
                        subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
                    end
                    break
                end
                filecell.nc.civ2(ifile,j)={filename};
            end
            if detect% if a netcdf file already exists
                break
            end
        end
        %create the new subdir_civ2_new
        if ~exist(fullfile(Path_ima,subdir_civ2_new),'dir')
            [xx,m2]=mkdir(fullfile(Path_ima,subdir_civ2_new));
            [xx,msg2] = fileattrib(fullfile(Path_ima,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g)
            if ~isequal(m2,'')
                msgbox_uvmat('ERROR',['cannot create ' fullfile(Path_ima,subdir_civ2_new) ': ' m2])
                filecell={};
               % cd(currentdir)
                return
            end
        end
        if strcmp(compare,'stereo PIV')%check second nc series
            for ifile=1:nbfield
                for j=1:nbslice
                    filename=name_generator(filebase_A,num1_civ2(ifile),num_a_civ2(j),'.nc',...
                        nom_type_nc,1,num2_civ2(ifile),num_b_civ1(j),subdir_civ2_new);%
                    detect=exist(filename,'file')==2;
                    if detect% if a netcdf file already exists
                        indstr=regexp(subdir_civ2,'\D');
                        if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
                           vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
                           subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
                        else
                           vers=vers+1;
                           subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
                        end
                        break
                    end
                    filecell.ncA.civ2(ifile,j)={filename};
                end
                if detect% if a netcdf file already exists
                    break
                end
            end
            subdir_civ2=subdir_civ2_new;
            %create the new subdir_civ1
            if ~exist(fullfile(Path_ima,subdir_civ2_new),'dir')
                [xx,m2]=mkdir(subdir_civ2_new);
                 [xx,msg2] = fileattrib(fullfile(Path_ima,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g)
                if ~isequal(m2,'')
                    msgbox_uvmat('ERROR', ['cannot create ' fullfile(Path_ima,subdir_civ2_new) ': ' m2])%error message for directory creation
                  %  cd(currentdir)
                    filecell={};
                    return
                end
            end
        end
    end
    subdir_civ2=subdir_civ2_new;
end
%cd(currentdir);%come back to the current working directory

%%%%%%%%%%%%%  if checkciv2 results are obtained or used  %%%%%%%%%%%%%
if checkbox(4)==1 || checkbox(5)==1 || checkbox(6)==1 %civ2
    %check source netcdf file of checkciv1 estimates
    if checkbox(1)==0; %no civ1 performed
        for ifile=1:nbfield
            for j=1:nbslice
                filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',...
                    nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
                filecell.nc.civ1(ifile,j)={filename};% name of the civ1 file
                if ~exist(filename,'file')
                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
                    filecell={};
                    return
                end
                if ~testdiff % civ2 or patch2 are written in the same file as civ1
                    if checkbox(4)==0 ; %check the existence of civ2 if it is not calculated
                        Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2');
                        if ~isempty(Data.CivStage) && Data.CivStage<4 %test for civ files
                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
                            filecell=[];
                            return
                        elseif isempty(Data.civ2)||isequal(Data.civ2,0)
                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
                            filecell=[];
                            return
                        end
                    elseif checkbox(3)==0; %check the existence of patch if it is not calculated
                        Data=nc2struct(filename,'ListGlobalAttribute','CivStage','patch');
                        if ~isempty(Data.CivStage)
                            if Data.CivStage<3 %test for civ files
                                msgbox_uvmat('ERROR',['no patch data in ' filename])
                                filecell=[];
                                return
                            end
                        elseif isempty(Data.patch)||isequal(Data.patch,0)
                            msgbox_uvmat('ERROR',['no patch data in ' filename])
                            filecell=[];
                            return
                        end
                    end
                end
            end
        end
        if strcmp(compare,'stereo PIV')
            for ifile=1:nbfield
                for j=1:nbslice
                    filename=name_generator(filebase_A,num1_civ2(ifile),num_a_civ2(j),'.nc',...
                        nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
                    filecell.ncA.civ2(ifile,j)={filename};
                    if ~exist(filename,'file')
                        msgbox_uvmat('ERROR',['input file ' filename ' not found'])
                        set(handles.RUN, 'Enable','On')
                        set(handles.RUN,'BackgroundColor',[1 0 0])
                        return
                    end
                end
            end
        end
    end
    
    detect=1;
    %     while detect==1%creates a new subdir if the netcdf files already contain checkciv2 data
    for ifile=1:nbfield
        for j=1:nbslice
            filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',...
                nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);
            detect=exist(filename,'file')==2;
            filecell.nc.civ2(ifile,j)={filename};
        end
    end
    %get first image names for checkciv2
    if checkbox(1)==1 && isequal(num1_civ1,num1_civ2) && isequal(num_a_civ1,num_a_civ2)
        filecell.ima1.civ2=filecell.ima1.civ1;
    elseif checkbox(4)==1
        for ifile=1:nbfield
            for j=1:nbslice
                filename=name_generator(filebase_ima1, num1_civ2(ifile),num_a_civ2(j),ext_ima,nom_type_ima1);
                idetect_2(j)=exist(filename,'file')==2;
                filecell.ima1.civ2(ifile,j)={filename};%first image
            end
            [idetectmin,indexj]=min(idetect_2);
            if idetectmin==0,
                msgbox_uvmat('ERROR',['input image ' filecell.ima1.civ2{ifile,indexj} ' not found'])
                filecell=[];
                return
            end
        end
    end
    
    %get second image names for checkciv2
    if checkbox(1)==1 && isequal(num2_civ1,num2_civ2) && isequal(num_b_civ1,num_b_civ2)
        filecell.ima2.civ2=filecell.ima2.civ1;
    elseif checkbox(4)==1
        for ifile=1:nbfield
            for j=1:nbslice
                filename=name_generator(filebase_ima2, num2_civ2(ifile),num_b_civ2(j),ext_ima,nom_type_ima2);
                idetect_3(j)=exist(filename,'file')==2;
                filecell.ima2.civ2(ifile,j)={filename};%first image
            end
            [idetectmin,indexj]=min(idetect_3);
            if idetectmin==0,
                msgbox_uvmat('ERROR',['input image ' filecell.ima2.civ2{ifile,indexj} ' not found'])
                filecell=[];
                return
            end
        end
    end
end
if (checkbox(5) || checkbox(6)) && ~checkbox(4)  % need to read an existing netcdf civ2 file
    if ~testdiff
        filecell.nc.civ2=filecell.nc.civ1;% file already checked
    else     % check the civ2 files
        for ifile=1:nbfield
            for j=1:nbslice
                filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',...
                    nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
                filecell.nc.civ2(ifile,j)={filename};
                if ~exist(filename,'file')
                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
                    filecell=[];
                    return
                else
                    Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2');
                    if ~isempty(Data.CivStage) && Data.CivStage<4 %test for civ files
                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
                            filecell=[];
                            return
                    elseif isempty(Data.civ2)||isequal(Data.civ2,0)
                        msgbox_uvmat('ERROR',['no civ2 data in ' filename])
                        filecell=[];
                        return
                    end
                end
            end
        end
    end
end

%%%%%%%%%%%%%  if stereo fields are calculated by PATCH %%%%%%%%%%%%%
if strcmp(compare,'stereo PIV')
    if  checkbox(3) && isequal(get(handles.test_stereo1,'Value'),1)
        for ifile=1:nbfield
            for j=1:nbslice
                filename=name_generator(filebase_AB,num1_civ1(ifile),num_a_civ1(j),'.nc',...
                    nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
                filecell.st(ifile,j)={filename};
            end
        end
    end
    if  checkbox(6) && isequal(get(handles.CheckStereo,'Value'),1)
        for ifile=1:nbfield
            for j=1:nbslice
                filename=name_generator(filebase_AB,num1_civ2(ifile),num_a_civ2(j),'.nc',...
                    nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
                filecell.st(ifile,j)={filename};
            end
        end
    end
end
set(handles.subdir_civ1,'String',subdir_civ1);%update the edit box
set(handles.subdir_civ2,'String',subdir_civ2);%update the edit box
browse.nom_type_nc=nom_type_nc;
set(handles.RootName,'UserData',browse); %update the nomenclature type for uvmat


%COPY IMAGES TO THE FORMAT .png IF NEEDED
if isequal(nom_type_ima1,'*')%case of movie files
    nom_type_imanew1='_i';
else
    nom_type_imanew1=nom_type_ima1;
end
if isequal(nom_type_ima2,'*')%case of movie files
    nom_type_imanew2='_i';
else
    nom_type_imanew2=nom_type_ima2;
end
if ~isequal(ext_ima,'.png')
    %%type of image file
    type_ima1='none';%default
    movieobject1=[];%default
    if strcmpi(ext_ima,'.avi')
        hhh=which('mmreader');
        if ~isequal(hhh,'')&& mmreader.isPlatformSupported()% if the mmreader function is found (recent version of matlab)
            type_ima1='movie';
            movieobject1=mmreader([filebase_ima2 ext_ima]);
        else
            type_ima1='avi';
        end
    elseif ischar(ext_ima) && ~isempty(ext_ima(2:end))
        form=imformats(ext_ima(2:end));
        if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
            if isequal(nom_type_ima1,'*');
                type_ima1='multimage';%image series in a single image file
            else
                type_ima1='image';
            end
        end
    end
    type_ima2='none';%default
    movieobject2=[];
    if strcmpi(ext_ima,'.avi')
        hhh=which('mmreader');
        if ~isequal(hhh,'')&& mmreader.isPlatformSupported()% if the mmreader function is found (recent version of matlab)
            type_ima2='movie';
            movieobject2=mmreader([filebase_ima2 ext_ima]);
        else
            type_ima2='avi';
        end
    elseif ischar(ext_ima) && ~isempty(ext_ima(2:end))
        form=imformats(ext_ima(2:end));
        if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
            if isequal(nom_type_ima1,'*');
                type_ima2='multimage';%image series in a single image file
            else
                type_ima2='image';
            end
        end
    end
    %npxy=get(handles.ImaExt,'UserData');
    % %     if numel(npxy)<2
    %
    %         filename=name_generator(filebase_ima1,num1_civ1(1),num_a_civ1(1),ImaExt,nom_type_ima1);
    %         A=imread(filename);
    %         npxy=size(A);
    % %     end
    %     npy=npxy(1);
    %     npx=npxy(2);
    if checkbox(1) %if civ1 is performed
        h = waitbar(0,'copy images to the .png format for civ1');% display a wait bar
        for ifile=1:nbfield
            waitbar(ifile/nbfield);
            for j=1:nbslice
                filename=name_generator(filebase_ima1,num1_civ1(ifile),num_a_civ1(j),'.png',nom_type_imanew1);
                if ~exist(filename,'file')
                    A=read_image(filecell.ima1.civ1{ifile,j},type_ima1,num1_civ1(ifile),movieobject1);
                    imwrite(A,filename,'BitDepth',16);
                end
                filecell.ima1.civ1(ifile,j)={filename};
                filename=name_generator(filebase_ima2, num2_civ1(ifile),num_b_civ1(j),'.png',nom_type_imanew2);
                if ~exist(filename,'file')
                    A=read_image(filecell.ima2.civ1{ifile,j},type_ima2,num2_civ1(ifile),movieobject2);
                    imwrite(A,filename,'BitDepth',16);
                end
                filecell.ima2.civ1(ifile,j)={filename};
            end
        end
        close(h)
    end
    if checkbox(4) %if civ2 is performed
        h = waitbar(0,'copy images to the .png format for civ2');% display a wait bar
        for ifile=1:nbfield
            waitbar(ifile/nbfield);
            for j=1:nbslice
                filename=name_generator(filebase_ima1,num1_civ2(ifile),num_a_civ2(j),'.png',nom_type_imanew1);
                if ~exist(filename,'file')
                    A=read_image(cell2mat(filecell.ima1.civ2(ifile,j)),type_ima2,num1_civ2(ifile));
                    imwrite(A,filename,'BitDepth',16);
                end
                filecell.ima1.civ2(ifile,j)={filename};
                filename=name_generator(filebase_ima2, num2_civ2(ifile),num_b_civ2(j),'.png',nom_type_imanew2);
                if ~exist(filename,'file')
                    A=read_image(cell2mat(filecell.ima2.civ2(ifile,j)),type_ima2,num2_civ2(ifile));
                    imwrite(A,filename,'BitDepth',16);
                end
                filecell.ima2.civ2(ifile,j)={filename};
            end
        end
        close(h);
    end
end

%------------------------------------------------------------------------
% --- determine the list of index pairs of processing file
function [num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=...
    find_pair_indices(handles,ref_i,ref_j,mode)
%------------------------------------------------------------------------

list_civ1=get(handles.ListPairCiv1,'String');
index_civ1=get(handles.ListPairCiv1,'Value');
str_civ1=list_civ1{index_civ1};%string defining the image pairs for civ1
if isempty(str_civ1)||isequal(str_civ1,'')
    msgbox_uvmat('ERROR','no image pair selected for civ1')
    return
end
list_civ2=get(handles.ListPairCiv2,'String');
index_civ2=get(handles.ListPairCiv2,'Value');
if index_civ2>length(list_civ2)
    list_civ2=list_civ1;
    index_civ2=index_civ1;
end
str_civ2=list_civ2{index_civ2};%string defining the image pairs for civ2

if isequal (mode,'series(Di)')
    lastfield=str2double(get(handles.nb_field,'String'));
    num1_civ1=ref_i-floor(index_civ1/2)*ones(size(ref_i));% set of first image numbers
    num2_civ1=ref_i+ceil(index_civ1/2)*ones(size(ref_i));
    num_a_civ1=ref_j;
    num_b_civ1=ref_j;
    num1_civ2=ref_i-floor(index_civ2/2)*ones(size(ref_i));
    num2_civ2=ref_i+ceil(index_civ2/2)*ones(size(ref_i));
    num_a_civ2=ref_j;
    num_b_civ2=ref_j;   
    
    % adjust the first and last field number
    lastfield=str2double(get(handles.nb_field,'String'));
    if isnan(lastfield)
        indsel=find((num1_civ1 >= 1)&(num1_civ2 >= 1));
    else
        indsel=find((num2_civ1 <= lastfield)&(num2_civ2 <= lastfield)&(num1_civ1 >= 1)&(num1_civ2 >= 1));
    end
    if length(indsel)>=1
        firstind=indsel(1);
        lastind=indsel(end);
        set(handles.first_i,'String',num2str(ref_i(firstind)))%update the display of first and last fields
        set(handles.last_i,'String',num2str(ref_i(lastind)))
        ref_i=ref_i(indsel);
        num1_civ1=num1_civ1(indsel);
        num1_civ2=num1_civ2(indsel);
        num2_civ1=num2_civ1(indsel);
        num2_civ2=num2_civ2(indsel);
    end
elseif isequal (mode,'series(Dj)')
    lastfield_j=str2double(get(handles.nb_field2,'String'));
    num1_civ1=ref_i;% set of first image numbers
    num2_civ1=ref_i;
    num_a_civ1=ref_j-floor(index_civ1/2)*ones(size(ref_j));
    num_b_civ1=ref_j+ceil(index_civ1/2)*ones(size(ref_j));
    num1_civ2=ref_i;
    num2_civ2=ref_i;
    num_a_civ2=ref_j-floor(index_civ2/2)*ones(size(ref_j));
    num_b_civ2=ref_j+ceil(index_civ2/2)*ones(size(ref_j));
    % adjust the first and last field number
    if isnan(lastfield_j)
        indsel=find((num_a_civ1 >= 1)&(num_a_civ2 >= 1));
    else
        indsel=find((num_b_civ1 <= lastfield_j)&(num_b_civ2 <= lastfield_j)&(num_a_civ1 >= 1)&(num_a_civ2 >= 1));
    end
    if length(indsel)>=1
        firstind=indsel(1);
        lastind=indsel(end);
        set(handles.first_j,'String',num2str(ref_j(firstind)))%update the display of first and last fields
        set(handles.last_j,'String',num2str(ref_j(lastind)))
        ref_j=ref_j(indsel);
        num_a_civ1=num_a_civ1(indsel);
        num_b_civ1=num_b_civ1(indsel);
        num_a_civ2=num_a_civ2(indsel);
        num_b_civ2=num_b_civ2(indsel);
    end
elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)
    displ_num=get(handles.ListPairCiv1,'UserData');
    num1_civ1=ref_i;
    num2_civ1=ref_i;
    num_a_civ1=displ_num(1,index_civ1);
    num_b_civ1=displ_num(2,index_civ1);
    num1_civ2=ref_i;
    num2_civ2=ref_i;
    num_a_civ2=displ_num(1,index_civ2);
    num_b_civ2=displ_num(2,index_civ2);
elseif isequal(mode,'displacement')
    num1_civ1=ref_i;
    num2_civ1=ref_i;
    num_a_civ1=ref_j;
    num_b_civ1=ref_j;
    num1_civ2=ref_i;
    num2_civ2=ref_i;
    num_a_civ2=ref_j;
    num_b_civ2=ref_j;
end


%------------------------------------------------------------------------
% --- PATCH
function cmd=cmd_patch(filename_nc,Param,PatchBin)
%------------------------------------------------------------------------
namelog=[filename_nc(1:end-3) '_patch.log'];

% if test_interp==0
    if isunix
    cmd=[PatchBin...
        ' -f ' filename_nc ' -m ' num2str(Param.Nx)...
        ' -n ' num2str(Param.Ny) ' -ro ' num2str(Param.SmoothingParam)...
        ' -nopt ' num2str(Param.SubdomainSize) ...
        '  > ' namelog ' 2>&1']; % redirect standard output to the log file
    else
      cmd=['"' Param.xml.PatchBin...
          '" -f "' filename_nc '" -m ' param.Patch1.Nx...
          ' -n ' param.Patch1.Ny ' -ro ' param.Patch1.SmoothParam...
          ' -nopt ' Param.Patch1.SubdomainSize ...
        '  > "' namelog '" 2>&1']; % redirect standard output to the log file
    end
% else %nouveau programme patch
%     cmd=[PatchBin ' -f ' filename_nc ' -m ' nx_patch  ' -n ' ny_patch ' -ro ' rho_patch ...
%         ' -max ' thresh_value ' -nopt ' subdomain_patch  '  > ' namelog ' 2>&1']; % redirect standard output to the log file
% end
cmd=regexprep(cmd,'\\','\\\\');

%------------------------------------------------------------------------
% --- STEREO Interp
function cmd=RUN_STINTERP(stinterpBin,filename_A_nc,filename_B_nc,filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,xmlA,xmlB)
%------------------------------------------------------------------------
namelog=[filename_nc(1:end-3) '_stinterp.log'];
cmd=[stinterpBin ' -f1 ' filename_A_nc  ' -f2 ' filename_B_nc ' -f  ' filename_nc ...
    ' -m ' nx_patch  ' -n ' ny_patch ' -ro ' rho_patch ' -nopt ' subdomain_patch ' -c1 ' xmlA ' -c2 ' xmlB '  -xy  x -Nfy 1024 > ' namelog ' 2>&1']; % redirect standard output to the log file

%------------------------------------------------------------------------
% --- Executes on button press in CheckCiv1.
function CheckCiv1_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
state=get(handles.CheckCiv1,'Value');
enable_civ1(handles,state)
if state
    enable_pair1(handles,'on')
end
find_netcpair_civ1(hObject, eventdata, handles);

%------------------------------------------------------------------------
% --- Executes on button press in CheckFix1.
function CheckFix1_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
enable_fix1(handles,get(handles.CheckFix1,'Value'))

%------------------------------------------------------------------------
% --- Executes on button press in CheckPatch1.
function CheckPatch1_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
enable_patch1(handles,get(handles.CheckPatch1,'Value'))

%------------------------------------------------------------------------
% --- Executes on button press in CheckCiv2.
function CheckCiv2_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
state=get(handles.CheckCiv2,'Value');
enable_civ2(handles,state)
if state
    find_netcpair_civ2(hObject, eventdata, handles)
    enable_pair1(handles,'on')
end

%------------------------------------------------------------------------
% --- Executes on button press in CheckFix2.
function CheckFix2_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
state=get(handles.CheckFix2,'Value');
enable_fix2(handles,state)
if state
    find_netcpair_civ2(hObject, eventdata, handles) % select the available netcdf files
end

%------------------------------------------------------------------------
% --- Executes on button press in CheckPatch2.
function CheckPatch2_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
state=get(handles.CheckPatch2,'Value');
enable_patch2(handles,state)
if state
    find_netcpair_civ2(hObject, eventdata, handles) % select the available netcdf files
end

%------------------------------------------------------------------------
function first_i_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
% last_i_Callback(hObject, eventdata, handles)
first_i=str2double(get(handles.first_i,'String'));
% last_i=str2num(get(handles.last_i,'String'));
% ref_i=ceil((first_i+last_i)/2);
set(handles.ref_i,'String', num2str(first_i))% reference index for pair dt = first index
%set(handles.ref_i_civ2,'String', num2str(first_i))% reference index for pair dt = first index
ref_i_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)

%------------------------------------------------------------------------
function first_j_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
first_j=str2num(get(handles.first_j,'String'));
set(handles.ref_j,'String', num2str(first_j))% reference index for pair dt = first index
ref_j_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)

%------------------------------------------------------------------------
% --- Executes on button press in SearchRange: determine the search range num_Sx,num_Sy
function SearchRange_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
%determine pair numbers
if strcmp(get(handles.umin,'Visible'),'off')
    set(handles.u_title,'Visible','on')
    set(handles.v_title,'Visible','on')
    set(handles.umin,'Visible','on')
    set(handles.umax,'Visible','on')
    set(handles.vmin,'Visible','on')
    set(handles.vmax,'Visible','on')
    set(handles.CoordUnit,'Visible','on')
    set(handles.TimeUnit,'Visible','on')
    set(handles.slash_title,'Visible','on')
    set(handles.min_title,'Visible','on')
    set(handles.max_title,'Visible','on')
    set(handles.unit_title,'Visible','on')
else
    get_search_range(hObject, eventdata, handles)
end

%------------------------------------------------------------------------
% ---  determine the search range num_Sx,num_Sy and shift
function get_search_range(hObject, eventdata, handles)
umin=str2double(get(handles.umin,'String'));
umax=str2double(get(handles.umax,'String'));
vmin=str2double(get(handles.umin,'String'));
vmax=str2double(get(handles.vmax,'String'));
%switch min_title and max_title in case of error
if umax<=umin
    umin_old=umin;
    umin=umax;
    umax=umin_old;
    set(handles.umin,'String', num2str(umin))
    set(handles.umax,'String', num2str(umax))
end
if vmax<=vmin
    vmin_old=vmin;
    vmin=vmax;
    vmax=vmin_old;
    set(handles.vmin,'String', num2str(vmin))
    set(handles.vmax,'String', num2str(vmax))
end   
if ~(isnan(umin)||isnan(umax)||isnan(vmin)||isnan(vmax))
    list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
    index=get(handles.ListPairCiv1,'Value');
    displ_num=get(handles.ListPairCiv1,'UserData');
    time=get(handles.ImaDoc,'UserData'); %get the set of times
    pxcm_xy=get(handles.SearchRange,'UserData');
    pxcmx=pxcm_xy(1);
    pxcmy=pxcm_xy(2);
    mode_list=get(handles.ListPairMode,'String');
    mode_value=get(handles.ListPairMode,'Value');
    mode=mode_list{mode_value};
    if isequal (mode, 'series(Di)' )
        ref_i=str2double(get(handles.ref_i,'String'));
        num1=ref_i-floor(index/2);%  first image numbers
        num2=ref_i+ceil(index/2);
        num_a=1;
        num_b=1;
    elseif isequal (mode, 'series(Dj)')
        num1=1;
        num2=1;
        ref_j=str2double(get(handles.ref_j,'String'));
        num_a=ref_j-floor(index/2);%  first image numbers
        num_b=ref_j+ceil(index/2);
    elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)
        ref_i=str2double(get(handles.ref_i,'String'));
        num1=ref_i;
        num2=ref_i;
        num_a=displ_num(1,index);
        num_b=displ_num(2,index);
    end
    dt=time(num2,num_b)-time(num1,num_a);
    ibx=str2double(get(handles.num_Bx,'String'));
    iby=str2double(get(handles.num_By,'String'));
    umin=dt*pxcmx*umin;
    umax=dt*pxcmx*umax;
    vmin=dt*pxcmy*vmin;
    vmax=dt*pxcmy*vmax;
    shiftx=round((umin+umax)/2);
    shifty=round((vmin+vmax)/2);
    isx=(umax+2-shiftx)*2+ibx;
    isx=2*ceil(isx/2)+1;
    isy=(vmax+2-shifty)*2+iby;
    isy=2*ceil(isy/2)+1;
    set(handles.num_Shiftx,'String',num2str(shiftx));
    set(handles.num_Shifty,'String',num2str(shifty));
    set(handles.num_Sx,'String',num2str(isx));
    set(handles.num_Sy,'String',num2str(isy));
end

%------------------------------------------------------------------------
% --- Executes on carriage return on the subdir checkciv1 edit window
function subdir_civ1_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
subdir=get(handles.subdir_civ1,'String');
set(handles.subdir_civ2,'String',subdir);% set civ2 directory the same as civ1 by default
menu_str=get(handles.ListSubdirCiv1,'String');% read the list of subdirectories for update
ichoice=find(strcmp(subdir,menu_str),1);
if isempty(ichoice)
    ilist=numel(menu_str); %select 'new...' in the menu
else
    ilist=ichoice;
end
set(handles.ListSubdirCiv1,'Value',ilist)% select the selected subdir in the menu
if get(handles.CheckCiv1,'Value')==0
    find_netcpair_civ1(hObject, eventdata, handles); %update the list of available pairs from netcdf files in the new directory
end

%------------------------------------------------------------------------
% --- Executes on carriage return on the subdir checkciv1 edit window
function subdir_civ2_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
subdir=get(handles.subdir_civ1,'String');
menu_str=get(handles.ListSubDirCiv2,'String');% read the list of subdirectories for update
ichoice=find(strcmp(subdir,menu_str),1);
if isempty(ichoice)
    ilist=numel(menu_str); %select 'new...' in the menu
else
    ilist=ichoice;
end
set(handles.ListSubDirCiv2,'Value',ilist)% select the selected subdir in the menu
%update the list of available pairs from netcdf files in the new directory
if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
    find_netcpair_civ2(hObject, eventdata, handles);
end

% %------------------------------------------------------------------------
% % --- Executes on button press in CheckMask: select box for mask option
% function check_Mask_Callback(hObject, eventdata, handles)
% %------------------------------------------------------------------------
% maskval=get(handles.CheckMask,'Value');
% if isequal(maskval,0)
%     set(handles.txt_MaskName,'Visible','off')
% %     set(handles.txt_MaskName,'String','')
% else
%     mask_displ='no mask'; %default
%     filebase=get(handles.RootName,'String');
%     [ nbslice_mask, flag_mask]=get_mask(filebase,handles);
%     if isequal(flag_mask,1)
%         mask_displ=[num2str(nbslice_mask) 'mask'];
%     elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
%         common_path=fileparts(filebase);
%         filebase_a=fullfile(common_path,get(handles.RootName_1,'String'));
%         [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
%         if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice_mask)
%             mask_displ='no mask';
%         end
%     end
%     if isequal(mask_displ,'no mask')
%         [FileName, PathName, filterindex] = uigetfile( ...
%             {'*.png', ' (*.png)';
%             '*.png',  '.png files '; ...
%             '*.*', 'All Files (*.*)'}, ...
%             'Pick a mask file *.png',filebase);
%         mask_displ=fullfile(PathName,FileName);
%         if exist(mask_displ,'file')
%             set(handles.txt_MaskName,'Visible','on')
%             set(handles.txt_MaskName,'String',mask_displ)
% %             mask_displ='no mask';
%         end
%     end
%     if isequal(mask_displ,'no mask')
%         set(handles.CheckMask,'Value',0)
%         set(handles.CheckMask,'Value',0)
%         set(handles.CheckMask,'Value',0)
%         set(handles.CheckMask,'Value',0)
%     else
%         set(handles.CheckMask,'Value',1)
%         set(handles.CheckMask,'Value',1)
%     end
%     set(handles.txt_MaskName,'String',mask_displ)
%     set(handles.txt_MaskName,'String',mask_displ)
%     set(handles.txt_Mask,'String',mask_displ)
%     set(handles.mask_fix2,'String',mask_displ)
% end
% set(handles.CheckMask,'Value',maskval)%update the checkciv2 mask with the same option as checkciv1

%------------------------------------------------------------------------
% --- Executes on button press in CheckMask.
function get_mask_fix1_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
maskval=get(handles.CheckMask,'Value');
if isequal(maskval,0)
    set(handles.txt_MaskName,'String','')
else
    mask_displ='no mask'; %default
    filebase=get(handles.RootName,'String');
    [nbslice, flag_mask]=get_mask(filebase,handles);
    if isequal(flag_mask,1)
        mask_displ=[num2str(nbslice) 'mask'];
    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
        filebase_a=get(handles.RootName_1,'String');
        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
            mask_displ='no mask';
        end
    end
    if isequal(mask_displ,'no mask')
        [FileName, PathName, filterindex] = uigetfile( ...
            {'*.png', ' (*.png)';
            '*.png',  '.png files '; ...
            '*.*', 'All Files (*.*)'}, ...
            'Pick a mask file *.png',filebase);
        mask_displ=fullfile(PathName,FileName);
        if ~exist(mask_displ,'file')
            mask_displ='no mask';
        end
    end
    if isequal(mask_displ,'no mask')
        set(handles.CheckMask,'Value',0)
        set(handles.CheckMask,'Value',0)
        set(handles.CheckMask,'Value',0)
    else
        %set(handles.CheckMask,'Value',1)
        set(handles.CheckMask,'Value',1)
    end
    set(handles.txt_MaskName,'String',mask_displ)
    set(handles.txt_Mask,'String',mask_displ)
    set(handles.mask_fix2,'String',mask_displ)
end

%------------------------------------------------------------------------
% --- Executes on button press in CheckMask: select box for mask option
function get_mask_civ2_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
maskval=get(handles.CheckMask,'Value');
if isequal(maskval,0)
    set(handles.txt_Mask,'String','')
else
    mask_displ='no mask'; %default
    filebase=get(handles.RootName,'String');
    [nbslice, flag_mask]=get_mask(filebase,handles);
    if isequal(flag_mask,1)
        mask_displ=[num2str(nbslice) 'mask'];
    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
        filebase_a=get(handles.RootName_1,'String');
        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
            mask_displ='no mask';
        end
    end
    if isequal(mask_displ,'no mask')
        [FileName, PathName, filterindex] = uigetfile( ...
            {'*.png', ' (*.png)';
            '*.png',  '.png files '; ...
            '*.*', 'All Files (*.*)'}, ...
            'Pick a mask file *.png',filebase);
        mask_displ=fullfile(PathName,FileName);
        if ~exist(mask_displ,'file')
            mask_displ='no mask';
        end
    end
    if isequal(mask_displ,'no mask')
        set(handles.CheckMask,'Value',0)
        set(handles.CheckMask,'Value',0)
    else
        set(handles.CheckMask,'Value',1)
    end
    set(handles.txt_Mask,'String',mask_displ)
    set(handles.mask_fix2,'String',mask_displ)
end

%------------------------------------------------------------------------
% --- Executes on button press in CheckMask.
function get_mask_fix2_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
maskval=get(handles.CheckMask,'Value');
if isequal(maskval,0)
    set(handles.mask_fix2,'String','')
else
    mask_displ='no mask'; %default
    filebase=get(handles.RootName,'String');
    [nbslice, flag_mask]=get_mask(filebase,handles);
    if isequal(flag_mask,1)
        mask_displ=[num2str(nbslice) 'mask'];
    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
        filebase_a=get(handles.RootName_1,'String');
        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
            mask_displ='no mask';
        end
    end
    if isequal(mask_displ,'no mask')
        [FileName, PathName, filterindex] = uigetfile( ...
            {'*.png', ' (*.png)';
            '*.png',  '.png files '; ...
            '*.*', 'All Files (*.*)'}, ...
            'Pick a mask file *.png',filebase);
        mask_displ=fullfile(PathName,FileName);
        if ~exist(mask_displ,'file')
            mask_displ='no mask';
        end
    end
    if isequal(mask_displ,'no mask')
        set(handles.CheckMask,'Value',0)
    end
    set(handles.mask_fix2,'String',mask_displ)
end

%------------------------------------------------------------------------
% --- function called to look for mask files
function [nbslice, flag_mask]=get_mask(filebase,handles)
%------------------------------------------------------------------------
%detect mask files, images with appropriate file base
%[filebase '_' xx 'mask'], xx=nbslice
%flag_mask=1 indicates detection

flag_mask=0;%default
nbslice=1;

% subdir=get(handles.subdir_civ1,'String');
[Path,Name]=fileparts(filebase);
if ~isdir(Path)
    msgbox_uvmat('ERROR','no path for input files')
    return
end
% currentdir=pwd;
% cd(Path);%move in the dir of the root name filebase
maskfiles=dir(fullfile(Path,[Name '_*mask_*.png']));%look for mask files
% cd(currentdir);%come back to the current working directory
if ~isempty(maskfiles)
    %     msgbox_uvmat('ERROR','no mask available, to create it use Tools/Make mask in the upper menu bar of uvmat')
    % else
    flag_mask=1;
    maskname=maskfiles(1).name;% take the first mask file in the list
    [Path2,Name,ext]=fileparts(maskname);
    Namedouble=double(Name);
    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
    ind_mask=findstr('mask',Name);
    i=ind_mask-1;
    while val(i)==0 && i>0
        i=i-1;
    end
    nbslice=str2double(Name(i+1:ind_mask-1));
    if ~isnan(nbslice) && Name(i)=='_'
        flag_mask=1;
    else
        msgbox_uvmat('ERROR',['bad mask file ' Name ext ' found in ' Path2])
        return
        nbslice=1;
    end
end

%------------------------------------------------------------------------
% --- function called to look for grid files
function [nbslice, flag_mask]=get_grid(filebase,handles)
%------------------------------------------------------------------------
flag_mask=0;%default
nbslice=1;
[Path,Name]=fileparts(filebase);
currentdir=pwd;
cd(Path);%move in the dir of the root name filebase
maskfiles=dir([Name '_*grid_*.grid']);%look for mask files
cd(currentdir);%come back to the current working directory
if ~isempty(maskfiles)
    flag_mask=1;
    maskname=maskfiles(1).name;% take the first mask file in the list
    [Path2,Name,ext]=fileparts(maskname);
    Namedouble=double(Name);
    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
    ind_mask=findstr('grid',Name);
    i=ind_mask-1;
    while val(i)==0 && i>0
        i=i-1;
    end
    nbslice=str2double(Name(i+1:ind_mask-1));
    if ~isnan(nbslice) && Name(i)=='_'
        flag_mask=1;
    else
        msgbox_uvmat('ERROR',['bad grid file ' Name ext ' found in ' Path2])
        return
        nbslice=1;
    end
end

%------------------------------------------------------------------------
% --- transform numbers to letters
function str=num2stra(num,nom_type)
%------------------------------------------------------------------------
if isempty(nom_type)
    str='';
elseif strcmp(nom_type(end),'a')
    str=char(96+num);
elseif strcmp(nom_type(end),'A')
    str=char(96+num);
elseif isempty(nom_type(2:end))%a single index
    str='';
else
    str=num2str(num);
end

%------------------------------------------------------------------------
% --- Executes on button press in ListSubdirCiv1.
function ListSubdirCiv1_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
list_subdir_civ1=get(handles.ListSubdirCiv1,'String');
val=get(handles.ListSubdirCiv1,'Value');
subdir=list_subdir_civ1{val};
if strcmp(subdir,'new...')
    subdir='CIV'; %default subdirectory
end
set(handles.subdir_civ1,'String',subdir);
find_netcpair_civ1(hObject, eventdata, handles) 
% end

%------------------------------------------------------------------------
% --- Executes on button press in ListSubDirCiv2.
function ListSubDirCiv2_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
list_subdir_civ2=get(handles.ListSubDirCiv2,'String');
val=get(handles.ListSubDirCiv2,'Value');
subdir=list_subdir_civ2{val};
if strcmp(subdir,'new...')
    subdir='CIV'; %default subdirectory
end
set(handles.subdir_civ2,'String',subdir);
%     set(handles.ListSubDirCiv2,'Value',1);


%------------------------------------------------------------------------
% --- Executes on button press in CheckGrid.
function CheckGrid_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
value=get(hObject,'Value');
hparent=get(hObject,'parent');
hchildren=get(hparent,'children');
handle_txtbox=findobj(hchildren,'tag','txt_GridName');
handle_dx=findobj(hchildren,'tag','num_Dx');
handle_dy=findobj(hchildren,'tag','num_Dy');
testgrid=0;
filegrid='';
if value
    filebase=get(handles.RootName,'String');
    [nbslice, flag_grid]=get_grid(filebase,handles);% look for a grid with appropriate name 
    if isequal(flag_grid,1)
        filegrid=[num2str(nbslice) 'grid'];
        testgrid=1;
    else % browse for a grid 
        filegrid=get(hObject,'UserData');%look for previous grid name stored as UserData
        if exist(filegrid,'file')
            filebase=filegrid;
        end
        [FileName, PathName, filterindex] = uigetfile( ...
            {'*.grid', ' (*.grid)';
            '*.grid',  '.grid files '; ...
            '*.*', 'All Files (*.*)'}, ...
            'Pick a file',filebase);
        filegrid=fullfile(PathName,FileName);
        set(hObject,'UserData',filegrid);%store for future use
        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filegrid,'file'))
            testgrid=1;
        end
    end
end
if testgrid
    set(handle_dx,'Visible','off');
    set(handle_dy,'Visible','off');
    set(handle_txtbox,'Visible','on')
    set(handle_txtbox,'String',filegrid)
else
    set(hObject,'Value',0);
    set(handle_dx,'Visible','on');
    set(handle_dy,'Visible','on');
    set(handle_txtbox,'Visible','off')
end

%% if hObject is on the checkciv1 frame, duplicate action for checkciv2 frame
PanelName=get(hparent,'tag');
if strcmp(PanelName,'panel_Civ1')
    hchildren=get(handles.Civ2,'children');
    handle_checkbox=findobj(hchildren,'tag','check_Grid');
    handle_txtbox=findobj(hchildren,'tag','txt_GridName');
    handle_dx=findobj(hchildren,'tag','num_Dx');
    handle_dy=findobj(hchildren,'tag','num_Dy');
    set(handle_checkbox,'UserData',filegrid);%store for future use
    if testgrid
        set(handle_checkbox,'Value',1);
        set(handle_dx,'Visible','off');
        set(handle_dy,'Visible','off');
        set(handle_txtbox,'Visible','on')
        set(handle_txtbox,'String',filegrid)
    else
        set(handle_checkbox,'Value',0);
        set(handles.CheckGrid,'Value',0);
        set(handle_dx,'Visible','on');
        set(handle_dy,'Visible','on');
        set(handle_txtbox,'Visible','off')
    end 
end
%------------------------------------------------------------------------
% --- Executes on button press in CheckMask.
function CheckMask_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
value=get(hObject,'Value');
testmask=0;
if value
    filebase=get(handles.RootName,'String');
    [nbslice, flag_mask]=get_mask(filebase,handles);% look for a mask with appropriate name 
    if isequal(flag_mask,1)
        filemask=[num2str(nbslice) 'mask'];
        testmask=1;
    else % browse for a mask 
        filemask=get(handles.CheckMask,'UserData');%look for previous mask name stored as UserData
        if exist(filemask,'file')
            filebase=filemask;
        end
        [FileName, PathName, filterindex] = uigetfile( ...
            {'*.png', ' (*.png)';
            '*.png',  '.png files '; ...
            '*.*', 'All Files (*.*)'}, ...
            'Pick a mask file *.png',filebase);
        filemask=fullfile(PathName,FileName);
        set(handles.CheckMask,'UserData',filemask);%store for future use
        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filemask,'file'))
            testmask=1;
        end
    end
end
if testmask
    set(handles.num_Dx,'Visible','off');
    set(handles.num_Dy,'Visible','off');
    set(handles.num_Dx,'Visible','off');
    set(handles.num_Dy,'Visible','off');
    set(handles.txt_MaskName,'Visible','on')
    set(handles.txt_MaskName,'String',filemask)
else
    set(handles.CheckMask,'Value',0);
    set(handles.CheckGrid,'Value',0);
    set(handles.num_Dx,'Visible','on');
    set(handles.num_Dy,'Visible','on');
    set(handles.num_Dx,'Visible','on');
    set(handles.num_Dy,'Visible','on');
    set(handles.txt_MaskName,'Visible','off')
end

%------------------------------------------------------------------------
% --- Executes on button press in CheckGrid.
function browse_gridciv2_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
value=get(handles.CheckGrid,'Value');
if value
    filebase=get(handles.RootName,'String');
    [nbslice, flag_grid]=get_grid(filebase,handles);
    if isequal(flag_grid,1)
        mask_displ=[num2str(nbslice) 'grid'];
        set(handles.txt_GridName,'String',mask_displ)
        set(handles.num_Dx,'Visible','off');
        set(handles.num_Dy,'Visible','off');
    else
        [FileName, PathName, filterindex] = uigetfile( ...
            {'*.grid', ' (*.grid)';
            '*.grid',  '.grid files '; ...
            '*.*', 'All Files (*.*)'}, ...
            'Pick a file',filebase);
        filegrid=fullfile(PathName,FileName);
        if isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filegrid,'file')
            set(handles.CheckGrid,'Value',0);
            set(handles.txt_GridName,'string','');
            set(handles.num_Dx,'Visible','on');
            set(handles.num_Dy,'Visible','on');
            set(handles.txt_GridName,'string','');
        else
            set(handles.txt_GridName,'string',filegrid);
            set(handles.num_Dx,'Visible','off');
            set(handles.num_Dy,'Visible','off');
            set(handles.txt_GridName,'string',filegrid);
        end
    end
else
    set(handles.txt_GridName,'string','');
    set(handles.num_Dx,'Visible','on');
    set(handles.num_Dy,'Visible','on');
    set(handles.txt_GridName,'string','');
end

% % --- Executes on button press in CheckGrid.
% function browse_gridciv2_Callback(hObject, eventdata, handles)
%
% filebase=get(handles.RootName,'String');
% [FileName, PathName, filterindex] = uigetfile( ...
%        {'*.grid', ' (*.grid)';
%         '*.grid',  '.grid files '; ...
%         '*.*', 'All Files (*.*)'}, ...
%         'Pick a file',filebase);
% filegrid=fullfile(PathName,FileName);
% set(handles.txt_GridName,'string',filegrid);
% set(handles.num_Dx,'String',' ');
% set(handles.num_Dy,'String',' ');
% % set(handles.grid_patch2,'string',filegrid);

% --- Executes on button press in get_gridpatch1.
function get_gridpatch1_Callback(hObject, eventdata, handles)
% hObject    handle to get_gridpatch1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

filebase=get(handles.RootName,'String');
[FileName, PathName, filterindex] = uigetfile( ...
    {'*.grid', ' (*.grid)';
    '*.grid',  '.grid files '; ...
    '*.*', 'All Files (*.*)'}, ...
    'Pick a file',filebase);
filegrid=fullfile(PathName,FileName);
set(handles.grid_patch1,'string',filegrid);
% set(handles.grid_patch2,'string',filegrid

%------------------------------------------------------------------------
% --- Executes on button press in get_gridpatch2.
function get_gridpatch2_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------

%------------------------------------------------------------------------
function enable_civ1(handles,state)
%------------------------------------------------------------------------
if state
    RootName=get(handles.RootName,'String');
    if isempty(RootName)
         msgbox_uvmat('ERROR','No input file')
        return
    end
    set(handles.Civ1,'Visible','on')   
    set(handles.PairIndices,'Visible','on')
%     set(handles.frame_civ1,'BackgroundColor',[1 1 0])
%     set(handles.frame_para_civ1,'BackgroundColor',[1 1 0])
%     set(handles.frame_grid_civ1,'BackgroundColor',[1 1 0])
else
    set(handles.Civ1,'Visible','off')  
%     set(handles.frame_civ1,'BackgroundColor',[0.831 0.816 0.784])
%     set(handles.frame_para_civ1,'BackgroundColor',[0.831 0.816 0.784])
%     set(handles.frame_grid_civ1,'BackgroundColor',[0.831 0.816 0.784])
end

% set(handles.num_Bx,'Visible',state)
% set(handles.num_By,'Visible',state)
% set(handles.num_Sx,'Visible',state)
% set(handles.num_Sy,'Visible',state)
% set(handles.num_Shiftx,'Visible',state)
% set(handles.num_Shifty,'Visible',state)
% set(handles.num_Rho,'Visible',state)
% set(handles.num_Dx,'Visible',state)
% set(handles.num_Dy,'Visible',state)
% set(handles.SearchRange,'Visible',state)
% set(handles.u_title,'Visible',state)
% set(handles.v_title,'Visible',state)
% set(handles.min_title,'Visible',state)
% set(handles.max_title,'Visible',state)
% set(handles.umin,'Visible',state)
% set(handles.umax,'Visible',state)
% set(handles.vmin,'Visible',state)
% set(handles.vmax,'Visible',state)
% set(handles.txt_GridName,'Visible',state)
% set(handles.txt_MaskName,'Visible',state)
% set(handles.CheckGrid,'Visible',state)
% set(handles.CheckMask,'Visible',state)
% set(handles.parameters,'Visible',state)
% set(handles.grid,'Visible',state)
% set(handles.num_Dx,'Visible',state)
% set(handles.num_Dy,'Visible',state)
% set(handles.check_Threshold,'Visible',state)
% if isequal(state,'off')
%     set(handles.num_MinIma,'Visible','off')
%     set(handles.num_MaxIma,'Visible','off')
%     set(handles.check_Threshold,'Value',0)
% end
% set(handles.dx_civ1_title,'Visible',state)
% set(handles.dy_civ1_title,'Visible',state)
% set(handles.ImaThreshold_title,'Visible',state)
% set(handles.ib_title,'Visible',state)
% set(handles.is_title,'Visible',state)
% set(handles.shift_title,'Visible',state)
% set(handles.rho_title,'Visible',state)
% set(handles.TestCiv1,'Visible',state)
%set(handles.ListPairMode,'Visible',state)

%------------------------------------------------------------------------
function enable_fix1(handles,state)
%------------------------------------------------------------------------

if isequal(state,0)
    state='off';
end
if isequal(state,1)
    state='on';
    RootName=get(handles.RootName,'String');
    if isempty(RootName)
         msgbox_uvmat('ERROR','No input file')
        return
    end
end
if isequal(state,'on')
    set(handles.Fix1,'Visible','on')
%     set(handles.frame_fix1,'BackgroundColor',[1 1 0])
else
    set(handles.Fix1,'Visible','off')
    %set(handles.frame_fix1,'BackgroundColor',[0.7 0.7 0.7])
end
% % set(handles.REMOVE,'Visible',state)
% set(handles.CheckFmin2,'Visible',state)
% set(handles.CheckF2,'Visible',state)
% set(handles.CheckF3,'Visible',state)
% set(handles.num_MinCorr,'Visible',state)
% set(handles.thresh_vecC_title,'Visible',state)
% set(handles.num_MaxVel,'Visible',state)
% set(handles.thresh_vel_text,'Visible',state)
% set(handles.txt_MaskName,'Visible',state)
% set(handles.CheckMask,'Visible',state)
% set(handles.get_ref_fix1,'Visible',state)
% set(handles.ref_fix1,'Visible',state)
% set(handles.inf_sup1,'Visible',state)
% set(handles.field_ref1,'Visible',state)

%------------------------------------------------------------------------
function enable_patch1(handles,state)
%------------------------------------------------------------------------
if state
    RootName=get(handles.RootName,'String');
    if isempty(RootName)
        msgbox_uvmat('ERROR','No input file')
        return
    end
    set(handles.Patch1,'Visible','on')
else
    set(handles.Patch1,'Visible','off')
end
return
set(handles.frame_patch1,'BackgroundColor',[1 1 0])
set(handles.rho_patch1,'Visible','on')
set(handles.rho_text1,'Visible','on')
if get(handles.ListPairMode,'Value')==2
    set(handles.thresh_patch1,'Visible','on')
    set(handles.thresh_text1,'Visible','on')
end
set(handles.subdomain_patch1,'Visible','on')
set(handles.subdomain_text1,'Visible','on')
set(handles.nx_patch1,'Visible','on')
set(handles.num_Ny,'Visible','on')
set(handles.nx_patch1_title,'Visible','on')
set(handles.ny_patch1_title,'Visible','on')
% if ~isempty(patch_newBin)
set(handles.test_interp,'Visible','off');
stereo_test=get(handles.ListCompareMode,'Value');
if stereo_test==3
    set(handles.test_stereo1,'Visible','on')
end
% end
%set(handles.get_gridpatch1,'Visible','on')
%set(handles.grid_patch1,'string','none');
%set(handles.grid_patch1,'Visible','on')

% %------------------------------------------------------------------------
% function desable_patch1(handles)
% %------------------------------------------------------------------------
% return
% set(handles.frame_patch1,'BackgroundColor',[0.831 0.816 0.784])
% set(handles.rho_patch1,'Visible','off')
% set(handles.rho_text1,'Visible','off')
% set(handles.thresh_patch1,'Visible','off')
% set(handles.thresh_text1,'Visible','off')
% set(handles.subdomain_patch1,'Visible','off')
% set(handles.subdomain_text1,'Visible','off')
% set(handles.nx_patch1,'Visible','off')
% set(handles.num_Ny,'Visible','off')
% set(handles.nx_patch1_title,'Visible','off')
% set(handles.ny_patch1_title,'Visible','off')
% set(handles.test_stereo1,'Visible','off')
% %set(handles.test_interp,'Visible','off')
% %set(handles.get_gridpatch1,'Visible','off')
% %set(handles.grid_patch1,'Visible','off')

%------------------------------------------------------------------------
function enable_civ2(handles,state)
%------------------------------------------------------------------------
if state
    RootName=get(handles.RootName,'String');
    if isempty(RootName)
         msgbox_uvmat('ERROR','No input file')
        return
    end
    set(handles.Civ2,'Visible','on')
else
    set(handles.Civ2,'Visible','off') 
end

% 
% set(handles.ibx_civ2,'Visible',state)
% set(handles.iby_civ2,'Visible',state)
% set(handles.decimal,'Visible',state)
% set(handles.deformation,'Visible',state)
% set(handles.rho_civ2,'Visible',state)
% set(handles.num_Dx,'Visible',state)
% set(handles.num_Dy,'Visible',state)
% set(handles.CheckGrid,'Visible',state)
% set(handles.CheckMask,'Visible',state)
% set(handles.parameters,'Visible',state)
% set(handles.grid,'Visible',state)
% set(handles.parameters_text,'Visible',state)
% set(handles.grid_text,'Visible',state)
% set(handles.txt_GridName,'Visible',state)
% set(handles.txt_Mask,'Visible',state)
% set(handles.dx_civ2_title,'Visible',state)
% set(handles.dy_civ2_title,'Visible',state)
% set(handles.ibx_civ2_text,'Visible',state)
% set(handles.rho_civ2_title,'Visible',state)
% set(handles.ImaThreshold2,'Visible',state)
% set(handles.ImaThreshold_title2,'Visible',state)
% if isequal(state,'off')
%     set(handles.MinIma2,'Visible','off')
%     set(handles.MaxIma2,'Visible','off')
%     set(handles.ImaThreshold2,'Value',0)
%     if isequal(get(handles.CheckFix2,'Value'),0) & isequal(get(handles.CheckPatch2,'Value'),0)
%         set(handles.ListPairCiv2,'Visible','off')
%         set(handles.subdir_civ2,'Visible','off')
%         set(handles.subdir_civ2_text,'Visible','off')
%         set(handles.dt_unit_civ2,'Visible','off')
%         %set(handles.ref_i_civ2,'Visible','off')
%         set(handles.i_ref_civ2_title,'Visible','off')
%         set(handles.j_ref_civ2_title,'Visible','off')
%         set(handles.ref_j_civ2,'Visible','off')
%     end
% else
%     set(handles.ListPairCiv2,'Visible','on')
%     set(handles.subdir_civ2,'Visible','on')
%     set(handles.subdir_civ2_text,'Visible','on')
%     set(handles.dt_unit_civ2,'Visible','on')
%   %  set(handles.ref_i_civ2,'Visible','on')
%     set(handles.i_ref_civ2_title,'Visible','on')
%     set(handles.j_ref_civ2_title,'Visible','on')
%     set(handles.ref_j_civ2,'Visible','on')
% end
% set(handles.rho_civ2_title,'Visible',state)

%------------------------------------------------------------------------
function enable_fix2(handles,state)
%------------------------------------------------------------------------
% if isequal(state,'on')
%     set(handles.Fix2,'Visible','on')  
%     
% %     set(handles.frame_civ2,'BackgroundColor',[1 1 0])
% %     set(handles.frame_para_civ2,'BackgroundColor',[1 1 0])
% %     set(handles.frame_grid_civ2,'BackgroundColor',[1 1 0])
% %     set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
% else
if state
    RootName=get(handles.RootName,'String');
    if isempty(RootName)
         msgbox_uvmat('ERROR','No input file')
        return
    end
    set(handles.Fix2,'Visible','on') 
else
    set(handles.Fix2,'Visible','off') 
end

% set(handles.frame_fix2,'BackgroundColor',[1 1 0])
% set(handles.REMOVE2,'Visible','on')
% set(handles.vec_Fmin2_2,'Visible','on')
% set(handles.vec_F4,'Visible','on')
% set(handles.vec_F3_2,'Visible','on')
% set(handles.thresh_vec2C,'Visible','on')
% set(handles.thresh_vec2C_text,'Visible','on')
% set(handles.thresh_vel2,'Visible','on')
% set(handles.thresh_vel2_text,'Visible','on')
% set(handles.mask_fix2,'Visible','on')
% set(handles.CheckMask,'Visible','on')
% set(handles.ListPairCiv2,'Visible','on')
% set(handles.subdir_civ2,'Visible','on')
% set(handles.subdir_civ2_text,'Visible','on')
% set(handles.get_ref_fix2,'Visible','on')
% set(handles.ref_fix2,'Visible','on')
% set(handles.inf_sup2,'Visible','on')
% set(handles.field_ref2,'Visible','on')

% %------------------------------------------------------------------------
% function desable_fix2(handles)
% %------------------------------------------------------------------------
% set(handles.frame_fix2,'BackgroundColor',[0.831 0.816 0.784])
% set(handles.REMOVE2,'Visible','off')
% set(handles.vec_Fmin2_2,'Visible','off')
% set(handles.vec_F4,'Visible','off')
% set(handles.vec_F3_2,'Visible','off')
% set(handles.thresh_vec2C,'Visible','off')
% set(handles.thresh_vec2C_text,'Visible','off')
% set(handles.thresh_vel2,'Visible','off')
% set(handles.thresh_vel2_text,'Visible','off')
% set(handles.mask_fix2,'Visible','off')
% set(handles.CheckMask,'Visible','off')
% set(handles.get_ref_fix2,'Visible','off')
% set(handles.ref_fix2,'Visible','off')
% set(handles.inf_sup2,'Visible','off')
% set(handles.field_ref2,'Visible','off')
% if isequal(get(handles.CheckCiv2,'Value'),0) & isequal(get(handles.CheckPatch2,'Value'),0)
%     set(handles.ListPairCiv2,'Visible','off')
%     set(handles.subdir_civ2,'Visible','off')
%     set(handles.subdir_civ2_text,'Visible','off')
% end

%------------------------------------------------------------------------
function enable_patch2(handles,state)
%------------------------------------------------------------------------
if state
RootName=get(handles.RootName,'String');
    if isempty(RootName)
         msgbox_uvmat('ERROR','No input file')
        return
    end
    set(handles.Patch2,'Visible','on')
else
set(handles.Patch2,'Visible','off')
end
% set(handles.frame_patch2,'BackgroundColor',[1 1 0])
% set(handles.num_SmoothParam,'Visible','on')
% set(handles.num_SmoothingParam,'Visible','on')
% set(handles.num_MaxDiff,'Visible','on')
% set(handles.thresh_text2,'Visible','on')
% set(handles.num_SubdomainSize,'Visible','on')
% set(handles.subdomain_text2,'Visible','on')
% set(handles.num_Nx,'Visible','on')
% set(handles.num_Ny,'Visible','on')
% set(handles.nx_patch2_title,'Visible','on')
% set(handles.ny_patch2_title,'Visible','on')
% % set(handles.get_gridpatch2,'Visible','on')
% % set(handles.grid_patch2,'Visible','on')
% set(handles.ListPairCiv2,'Visible','on')
% set(handles.subdir_civ2,'Visible','on')
% set(handles.subdir_civ2_text,'Visible','on')
% stereo_test=get(handles.ListCompareMode,'Value');
% if stereo_test==3
%     set(handles.CheckStereo,'Visible','on')
% end

% %------------------------------------------------------------------------
% function desable_patch2(handles)
% %------------------------------------------------------------------------
% %set(handles.checkpatch2,'Visible','off')
% return
% set(handles.frame_patch2,'BackgroundColor',[0.831 0.816 0.784])
% set(handles.num_SmoothParam,'Visible','off')
% set(handles.num_SmoothingParam,'Visible','off')
% set(handles.num_MaxDiff,'Visible','off')
% set(handles.thresh_text2,'Visible','off')
% set(handles.num_SubdomainSize,'Visible','off')
% set(handles.subdomain_text2,'Visible','off')
% set(handles.num_Nx,'Visible','off')
% set(handles.num_Ny,'Visible','off')
% set(handles.nx_patch2_title,'Visible','off')
% set(handles.ny_patch2_title,'Visible','off')
% % set(handles.get_gridpatch2,'Visible','off')
% % set(handles.grid_patch2,'Visible','off')
% if isequal(get(handles.CheckCiv2,'Value'),0) & isequal(get(handles.CheckFix2,'Value'),0)
%     set(handles.ListPairCiv2,'Visible','off')
%     set(handles.subdir_civ2,'Visible','off')
%     set(handles.subdir_civ2_text,'Visible','off')
% end
% set(handles.CheckStereo,'Visible','off')
%------------------------------------------------------------------------
function enable_pair1(handles,state)
%------------------------------------------------------------------------
set(handles.subdir_civ1,'Visible',state)
set(handles.ListSubdirCiv1,'Visible',state)
set(handles.SUBDIR_CIV1_txt,'Visible',state)
%set(handles.frame_subdirciv1,'Visible',state)
set(handles.ListPairCiv1,'Visible',state)
set(handles.PairCiv1_title,'Visible',state)
%set(handles.dt_unit,'Visible',state)
%set(handles.PAIR_frame,'Visible',state)

%------------------------------------------------------------------------
% --- Read the parameters for checkciv1 on the interface
function par=read_param_civ1(handles,filecell)
%------------------------------------------------------------------------
ibx_val=str2double(get(handles.num_Bx,'String'));
par.ibx=num2str(ibx_val);
iby_val=str2double(get(handles.num_By,'String'));
par.iby=num2str(iby_val);
isx=get(handles.num_Sx,'String');
if isnan(str2double(isx)), isx='41'; set(handles.num_Sx,'String','41'), end; %default
if str2double(isx)<ibx_val+8,isx=num2str(ibx_val+8); set(handles.num_Sx,'String',num2str(ibx_val+8)); end
isy=get(handles.num_Sy,'String');
if isnan(str2double(isy)), isy='41'; set(handles.num_Sy,'String','41'), end;%default
if str2double(isy)<iby_val+8,isy=num2str(iby_val+8); set(handles.num_Sy,'String',num2str(iby_val+8)); end
par.isx=get(handles.num_Sx,'String');
par.isy=get(handles.num_Sy,'String');
par.shiftx=get(handles.num_Shiftx,'String');
par.shifty=get(handles.num_Shifty,'String');
if isnan(str2double(par.isx))
    par.isx='41';%default
    set(handles.num_Sx,'String','41');
end
if isnan(str2double(par.isy))
    par.isy='41'; %default
    set(handles.num_Sy,'String','41');
end
if isnan(str2double(par.shiftx))
    par.shiftx='0';%default
    set(handles.num_Shiftx,'String','0');
end
if isnan(str2double(par.shifty))
    par.shifty='0'; %default
    set(handles.num_Shifty,'String','0');
end
par.rho=get(handles.num_Rho,'String');
if isequal(get(handles.num_Rho,'Style'),'popupmenu')
    index=get(handles.num_Rho,'Value');
    par.rho=par.rho{index};
end
dummy=get(handles.num_Dx,'String');
par.dx=dummy{1};
dummy=get(handles.num_Dy,'String');
par.dy=dummy{1};
if isnan(str2double(par.dx))
    if isempty(get(handles.txt_GridName,'String'));
        par.dx='0'; %just read by civ program, not used
    else
        par.dx='20';%default
        set(handles.num_Dx,'String','20');
    end
end
if isnan(str2double(par.dy))
    if isempty(get(handles.txt_GridName,'String'));
        par.dy='0';%just read by civ program, not used
    else
        par.dy='20';%default
        set(handles.dy_civ1_title,'String','20');
    end
end
par.pxcmx='1'; %velocities are expressed in pixel dispalcement
par.pxcmy='1';
% if exist('file_ima','var')
A=imread(filecell.ima1.civ1{1,1});%read the first image to get the size
sizim=size(A);
par.npx=num2str(sizim(2));
par.npy=num2str(sizim(1));
%TODO : civ should not need npx and npy


% end
%time=get(handles.RootName,'UserData'); %get the set of times
dummy=get(handles.txt_GridName,'String');
par.gridname=dummy{1};
par.gridflag='y';
if strcmp(par.gridname,'')|| isempty(par.gridname)
    par.gridname='nogrid';
    par.gridflag='n';
end

%------------------------------------------------------------------------
function par=read_param_fix1(handles,filecell)
%------------------------------------------------------------------------
    par.flagindex1(1)=get(handles.CheckFmin2, 'Value');
    par.flagindex1(2)=get(handles.CheckF3, 'Value');
    par.flagindex1(3)=get(handles.CheckF2, 'Value');
    par.thresh_vecC1=str2double(get(handles.num_MinCorr,'String'));%threshold on image correlation vec_C
    par.thresh_vel1=str2double(get(handles.num_MaxVel,'String'));%threshold on velocity modulus
    par.test_mask=get(handles.CheckMask,'Value');
    par.nbslice_mask=get(handles.txt_MaskName,'UserData'); % get the number of slices (= number of masks)
    %%%%%%%%%%%%%COMPLETER LE PROGRAMME FIX
    %     inf_sup=get(handles.inf_sup1,'Value');80
    %     fileref=get(handles.ref_fix1,'String');
    %     refpath=get(handles.ref_fix1,'UserData');
    %     fileref=fullfile(refpath,fileref);
    par.menu=get(handles.field_ref1,'String');
    par.index=get(handles.field_ref1,'Value');
    if isempty(par.menu)
        par.fieldchoice='';
    else
        par.fieldchoice=menu{index};
        msgbox_uvmat('WARNING','reference field is not used presently with batch, use RUN option')
    end
           if par.test_mask==0
                par.maskname='';
            else
                maskdispl=get(handles.txt_MaskName,'String');
                nbslice_mask=str2double(maskdispl(1:end-4)); %
                num1_mask=mod(num1_civ1(ifile)-1,nbslice_mask)+1;
                maskbase=[filecell.filebase '_' maskdispl];
                par.maskname=name_generator(maskbase,num1_mask,1,'.png','_i');
           end
 
%------------------------------------------------------------------------
function par=read_param_patch1(handles)
%------------------------------------------------------------------------

par.rho_patch=str2double(get(handles.rho_patch1,'String'));
if isnan(par.rho_patch)
    par.rho_patch='1000';
    set(handles.rho_patch1,'String','1')
else
    par.rho_patch=num2str(1000*par.rho_patch);
end
par.nx_patch=get(handles.nx_patch1,'String');
par.ny_patch=get(handles.ny_patch1,'String');
if isnan(str2double(par.nx_patch))
    par.nx_patch='50' ;%default
    set(handles.nx_patch1,'String','50');
end
if isnan(str2double(par.ny_patch))
    par.ny_patch='50' ;%default
    set(handles.ny_patch1,'String','50');
end
par.subdomain_patch=get(handles.subdomain_patch1,'String');
par.thresh_patch=get(handles.thresh_patch1,'String');

           
%------------------------------------------------------------------------
function par=read_param_civ2(handles,file_ima)
%------------------------------------------------------------------------
par.ibx=get(handles.ibx_civ2,'String');
par.iby=get(handles.iby_civ2,'String');
par.rho=get(handles.rho_civ2,'String');
par.decimal=int2str(get(handles.decimal,'Value'));
par.deformation=int2str(get(handles.deformation,'Value'));
par.dx=get(handles.num_Dx,'String');
par.dy=get(handles.num_Dy,'String');
if isnan(str2double(par.dx))
    if isempty(get(handles.txt_GridName,'String'));
        par.dx='0'; %just read by civ program, not used
    else
        par.dx='20';%default
        set(handles.num_Dx,'String','20');
    end
end
if isnan(str2double(par.dy))
    if isempty(get(handles.txt_GridName,'String'));
        par.dy='0';%just read by civ program, not used
    else
        par.dy='20';%default
        set(handles.num_Dy,'String','20');
    end
end
par.pxcmx='1';
par.pxcmy='1';
A=imread(file_ima);%read the first image to get the size
sizim=size(A);
par.npx=num2str(sizim(2));
par.npy=num2str(sizim(1));
%time=get(handles.RootName,'UserData'); %get the set of times
par.gridname=get(handles.txt_GridName,'String');
par.gridflag='y';
if strcmp(par.gridname,'')|| isempty(par.gridname)
    par.gridname='nogrid';
    par.gridflag='n';
end

function cmd_CIV1=CIV1_CMD(filename,param)
%TODO : include filename in par_civ1
%------------------------------------------------------------------------
%pixels per cm and matrix of the image times, read from the .civ file by uvmat

%changes : filename_cmx -> filename ( no extension )

filename=regexprep(filename,'.nc','');

if isequal(Param.Civ1.Dt,'0')
    Param.Civ1.Dt='1' ;%case of 'displacement' mode
end
Param.Civ1.filename_ima_a=regexprep(Param.Civ1.filename_ima_a,'.png','');
Param.Civ1.filename_ima_b=regexprep(Param.Civ1.filename_ima_b,'.png','');
fid=fopen([filename '.civ1.cmx'],'w');
fprintf(fid,['##############   CMX file' '\n' ]);
fprintf(fid,   ['FirstImage ' regexprep(Param.Civ1.filename_ima_a,'\\','\\\\') '\n' ]);% for windows compatibility
fprintf(fid,   ['LastImage  ' regexprep(Param.Civ1.filename_ima_b,'\\','\\\\') '\n' ]);% for windows compatibility
fprintf(fid,  ['XX' '\n' ]);
fprintf(fid,  ['Mask ' Param.Civ1.maskflag '\n' ]);
fprintf(fid,  ['MaskName ' regexprep(Param.Civ1.maskname,'\\','\\\\') '\n' ]);
fprintf(fid,   ['ImageSize ' Param.Civ1.npx ' ' Param.Civ1.npy '\n' ]);   %VERIFIER CAS GENERAL ?
fprintf(fid,   ['CorrelationBoxesSize ' Param.Civ1.ibx ' ' Param.Civ1.iby '\n' ]);
fprintf(fid,   ['SearchBoxeSize ' Param.Civ1.isx ' ' Param.Civ1.isy '\n' ]);
fprintf(fid,   ['RO ' Param.Civ1.rho '\n' ]);
fprintf(fid,   ['GridSpacing ' Param.Civ1.dx ' ' Param.Civ1.dy '\n' ]);
fprintf(fid,   ['XX 1.0' '\n' ]);
fprintf(fid,   ['Dt_TO ' Param.Civ1.Dt ' ' Param.Civ1.T0 '\n' ]);
fprintf(fid,  ['PixCmXY ' Param.Civ1.pxcmx ' ' Param.Civ1.pxcmy '\n' ]);
fprintf(fid,  ['XX 1' '\n' ]);
fprintf(fid,   ['ShiftXY ' Param.Civ1.shiftx ' '  Param.Civ1.shifty '\n' ]);
fprintf(fid,  ['Grid ' Param.Civ1.gridflag '\n' ]);
fprintf(fid,   ['GridName ' regexprep(Param.Civ1.gridname,'\\','\\\\') '\n' ]);
fprintf(fid,   ['XX 85' '\n' ]);
fprintf(fid,   ['XX 1.0' '\n' ]);
fprintf(fid,   ['XX 1.0' '\n' ]);
fprintf(fid,   ['Hart 1' '\n' ]);
fprintf(fid,  [ 'DecimalShift 0' '\n' ]);
fprintf(fid,   ['Deformation 0' '\n' ]);
fprintf(fid,  ['CorrelationMin 0' '\n' ]);
fprintf(fid,   ['IntensityMin 0' '\n' ]);
fprintf(fid,  ['SeuilImage n' '\n' ]);
fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);
fprintf(fid,   ['ImageToUse ' Param.Civ1.term_a ' ' Param.Civ1.term_b '\n' ]); % VERIFIER ?
fprintf(fid,   ['ImageUsedBefore null null' '\n' ]);
fclose(fid);

% cmd_CIV1=[sparam.Civ1Bin ' -f ' filename '.cmx >' filename '.log' ]; % redirect standard output to the log file
% cmd_CIV1=regexprep(cmd_CIV1,'\\','\\\\');
% namelog=regexprep(namelog,'\\','\\\\');
if(isunix)
    cmd_CIV1=['cp -f ' filename '.civ1.cmx ' filename '.cmx'];
    cmd_CIV1=[cmd_CIV1 '\n'...
        Param.xml.Civ1Bin ' -f ' filename '.cmx >' filename '.log' ]; % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx
    cmd_CIV1=[cmd_CIV1 '\n' 'mv ' filename '.log' ' ' filename '.civ1.log' '\n' 'chmod g+w ' filename '.civ1.log' '\n' 'chmod g+w ' filename '.nc'];%rename .log as .civ1.log and set the netcdf result file for group user writting
   % cmd_CIV1=[cmd_CIV1 '\n' 'mv ' filename '.cmx' ' ' filename '.checkciv1.cmx' '\n'];%rename .cmx as .checkciv1.cmx
else %Windows system
%                     flname=regexprep(flname,'\\','\\\\');
%                     cmd=[cmd 'copy /Y "' flname '.checkciv1.cmx" "' flname '.cmx"\n'];
%     filename=regexprep(filename,'\\','\\\\');
    cmd_CIV1=['copy /Y "' filename '.civ1.cmx" "' filename '.cmx"'];% copy the .civ1.cmx parameter file to .cmx
    cmd_CIV1=[cmd_CIV1 '\n "' regexprep(Param.xml.Civ1Bin,'\\','\\\\') '" -f "' filename '.cmx" >"' filename '.log"' ]; % redirect standard output to the log file
%     namelog=regexprep(namelog,'\\','\\\\');
    cmd_CIV1=[cmd_CIV1 '\n ' 'copy /Y "' filename '.log' '" "' filename '.civ1.log"']; %preserve the log file as .civ1.log

    %  cmd_CIV1=[cmd_CIV1 '\n' 'copy /Y "' filename '.cmx' '" "' filename '.checkciv1.cmx"'];
end

%------------------------------------------------------------------------
% --- CheckCiv1  Unified
function xml_civ1_parameters=CIV1_CMD_Unified(filename,namelog,par)
%------------------------------------------------------------------------
%pixels per cm and matrix of the image times, read from the .civ file by uvmat
%global CivBin%name of the executable for checkciv1 calculation

civ1.image1=par.filename_ima_a;
civ1.image2=par.filename_ima_b;
civ1.imageSize_X=par.npx;
civ1.imageSize_Y=par.npy;
civ1.outputFileName=[filename '.nc'];
civ1.correlationBoxesSize_X=par.ibx;
civ1.correlationBoxesSize_Y=par.iby;
civ1.searchBoxesSize_X=par.isx;
civ1.searchBoxesSize_Y=par.isy;
civ1.globalShift_X=par.shiftx;
civ1.globalShift_Y=par.shifty;
civ1.ro=par.rho;
civ1.hart='y';
if isequal(par.gridflag,'y')
    civ1.grid=par.gridname;
else
    civ1.grid='n';
    civ1.gridSpacing_X=par.dx;
    civ1.gridSpacing_Y=par.dy;
end
if isequal(par.maskflag,'y')
    civ1.mask=par.maskname;
end
civ1.dt=par.Dt;
civ1.unit='pixel';
civ1.absolut_time_T0=par.T0;
civ1.pixcmx=par.pxcmx;
civ1.pixcmy=par.pxcmy;
civ1.convectFlow='n';

xml_civ1_parameters=civ1;

%------------------------------------------------------------------------
% --- CheckCiv2  Unified
function civ2=CIV2_CMD_Unified(filename,namelog,par)
%------------------------------------------------------------------------
%pixels per cm and matrix of the image times, read from the .civ file by uvmat
%global CivBin%name of the executable for checkciv1 calculation

filename=regexprep(filename,'.nc','');

civ2.image1=par.filename_ima_a;
civ2.image2=par.filename_ima_b;
civ2.imageSize_X=par.npx;
civ2.imageSize_Y=par.npy;
civ2.inputFileName=[par.filename_nc1 '.nc'];
civ2.outputFileName=[filename '.nc'];
civ2.correlationBoxesSize_X=par.ibx;
civ2.correlationBoxesSize_Y=par.iby;
civ2.ro=par.rho;
%checkciv2.decimalShift=par.decimal;
%checkciv2.deformation=par.deformation;
if isequal(par.decimal,'1')
    civ2.decimalShift='y';
else
    civ2.decimalShift='n';
end
if isequal(par.deformation,'1')
    civ2.deformation='y';
else
    civ2.deformation='n';
end
if isequal(par.gridflag,'y')
    civ2.grid=par.gridname;
else
    civ2.grid='n';
    civ2.gridSpacing_X=par.dx;
    civ2.gridSpacing_Y=par.dy;
end
civ2.gridSpacing_X='10';
civ2.gridSpacing_Y='10';%NOTE: faut mettre gridSpacing pourque ca tourne, meme si c'est la grille qui est utilisee
if isequal(par.maskflag,'y')
    civ2.mask=par.maskname;
else
    civ2.mask='n';
end
civ2.dt=par.Dt;
civ2.unit='pixel';
civ2.absolut_time_T0=par.T0;
civ2.pixcmx=par.pxcmx;
civ2.pixcmy=par.pxcmy;
civ2.convectFlow='n';
civ2.pixcmx=par.pxcmx;
civ2.pixcmy=par.pxcmy;
civ2.convectFlow='n';

%------------------------------------------------------------------------
% --- CheckCiv2  CheckCiv2  CheckCiv2 CheckCiv2
function cmd_CIV2=CIV2_CMD(filename,param)
%------------------------------------------------------------------------
%pixels per cm and matrix of the image times, read from the .civ file by uvmat
% global civ2Bin sge%name of the executable for checkciv1 calculation
filename=regexprep(filename,'.nc','');
if isequal(param.civ2.Dt,'0')
    param.civ2.Dt='1' ;%case of 'displacement' mode
end
param.civ2.filename_ima_a=regexprep(param.civ2.filename_ima_a,'.png','');
param.civ2.filename_ima_b=regexprep(param.civ2.filename_ima_b,'.png','');% bug : .png appears two times ?
[fid,errormsg]=fopen([filename '.civ2.cmx'],'w');
if isequal(fid,-1)
    msgbox_uvmat('ERROR',errormsg)
    cmd_CIV2='';
    return
end
fprintf(fid,['##############   CMX file' '\n' ]);
fprintf(fid,   ['FirstImage ' regexprep(param.civ2.filename_ima_a,'\\','\\\\') '\n' ]);% for windows compatibility
fprintf(fid,   ['LastImage  ' regexprep(param.civ2.filename_ima_b,'\\','\\\\') '\n' ]);% for windows compatibility
fprintf(fid,  ['XX' '\n' ]);
fprintf(fid, ['Mask ' param.civ2.maskflag '\n' ]);
fprintf(fid, ['MaskName ' regexprep(param.civ2.maskname,'\\','\\\\') '\n' ]);% for windows compatibility
fprintf(fid, ['ImageSize ' param.civ2.npx ' ' param.civ2.npy '\n' ]);   %VERIFIER CAS GENERAL ?
fprintf(fid, ['CorrelationBoxesSize ' param.civ2.ibx ' ' param.civ2.iby '\n' ]);
fprintf(fid, ['SearchBoxeSize ' param.civ2.ibx ' ' param.civ2.iby '\n']);
fprintf(fid, ['RO ' param.civ2.rho '\n']);
fprintf(fid, ['GridSpacing ' param.civ2.dx ' ' param.civ2.dy '\n']);
fprintf(fid, ['XX 1.0' '\n' ]);
fprintf(fid, ['Dt_TO ' param.civ2.Dt ' ' param.civ2.T0 '\n' ]);
fprintf(fid, ['PixCmXY ' param.civ2.pxcmx ' ' param.civ2.pxcmy '\n' ]);
fprintf(fid, ['XX 1' '\n' ]);
fprintf(fid, 'ShiftXY 0 0\n');
fprintf(fid, ['Grid ' param.civ2.gridflag '\n' ]);
fprintf(fid, ['GridName ' regexprep(param.civ2.gridname,'\\','\\\\') '\n']);
fprintf(fid, ['XX 85' '\n' ]);
fprintf(fid, ['XX 1.0' '\n' ]);
fprintf(fid, ['XX 1.0' '\n' ]);
fprintf(fid, ['Hart 1' '\n' ]);
fprintf(fid, ['DecimalShift ' param.civ2.decimal '\n']);
fprintf(fid, ['Deformation ' param.civ2.deformation '\n']);
fprintf(fid,  ['CorrelationMin 0' '\n' ]);
fprintf(fid,   ['IntensityMin 0' '\n' ]);
fprintf(fid,  ['SeuilImage n' '\n' ]);
fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);
fprintf(fid,   ['ImageToUse ' param.civ2.term_a ' ' param.civ2.term_b '\n' ]); % VERIFIER ?
fprintf(fid, ['ImageUsedBefore ' regexprep(param.civ2.filename_nc1,'\\','\\\\') '\n']);
fclose(fid);

if(isunix)
    cmd_CIV2=['cp -f ' filename '.civ2.cmx ' filename '.cmx\n'];
    cmd_CIV2=[cmd_CIV2 Param.xml.Civ2Bin ' -f ' filename  '.cmx >' filename '.log' ]; % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx
    cmd_CIV2=[cmd_CIV2 '\n' 'mv ' filename '.log' ' ' filename '.civ2.log' '\n' 'chmod g+w ' filename '.nc'];%preserve the log file as .civ2.log
%    cmd_CIV2=[cmd_CIV2 '\n' 'mv ' filename '.cmx' ' ' filename '.checkciv2.cmx' '\n'];%rename .cmx as .checkciv2.cmx, the result file is named [filename '.nc'] by CIVx

else 
    filename=regexprep(filename,'\\','\\\\');
    cmd_CIV2=['copy /Y "' filename '.civ2.cmx" "' filename '.cmx"'];
    cmd_CIV2=[cmd_CIV2 '\n "' regexprep(Param.xml.Civ2Bin,'\\','\\\\') '" -f "' filename  '.cmx" >"' filename '.log"' ]; % redirect standard output to the log file
    cmd_CIV2=[cmd_CIV2 '\n ' 'copy /Y "' filename '.log' '" "' filename '.civ2.log"'];
 %    cmd_CIV2=[cmd_CIV2 '\n' 'copy /Y "' filename '.cmx' '" "' filename '.checkciv2.cmx"'];
end


%------------------------------------------------------------------------
%--read images and convert them to the uint16 format used for PIV
function A=read_image(filename,type_ima,num,movieobject)
%------------------------------------------------------------------------
%num is the view number needed for an avi movie
switch type_ima
    case 'movie'
        A=read(movieobject,num);
    case 'avi'
        mov=aviread(filename,num);
        A=frame2im(mov(1));
    case 'multimage'
        A=imread(filename,num);
    case 'image'
        A=imread(filename);
end
siz=size(A);
if length(siz)==3;%color images
    A=sum(double(A),3);
    A=uint16(A);
end

%------------------------------------------------------------------------
function ref_i_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
mode_list=get(handles.ListPairMode,'String');
mode_value=get(handles.ListPairMode,'Value');
mode=mode_list{mode_value};
find_netcpair_civ1(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files
if isequal(mode,'series(Di)') || ...% we do patch2 only
        (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
    find_netcpair_civ2(hObject, eventdata, handles);
end

%------------------------------------------------------------------------
function ref_j_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
mode_list=get(handles.ListPairMode,'String');
mode_value=get(handles.ListPairMode,'Value');
mode=mode_list{mode_value};
if isequal(get(handles.CheckCiv1,'Value'),0)|| isequal(mode,'series(Dj)')
    find_netcpair_civ1(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files
end
if isequal(mode,'series(Dj)') || ...
        (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
    find_netcpair_civ2(hObject, eventdata, handles);
end

%------------------------------------------------------------------------
function ref_i_civ2_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
mode_list=get(handles.ListPairMode,'String');
mode_value=get(handles.ListPairMode,'Value');
mode=mode_list{mode_value};
find_netcpair_civ2(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files

%------------------------------------------------------------------------
function ref_j_civ2_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
mode_list=get(handles.ListPairMode,'String');
mode_value=get(handles.ListPairMode,'Value');
mode=mode_list{mode_value};
if  isequal(mode,'series(Dj)')
    find_netcpair_civ2(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files
end

%------------------------------------------------------------------------
% --- Executes on button press in ListCompareMode.
function ListCompareMode_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
test=get(handles.ListCompareMode,'Value');
if test==2 || test==3 % case 'dispalcemen' or 'stereo PIV'
    filebase=get(handles.RootName,'String');
    browse=get(handlesRootName,'Userdata');
    browse.nom_type_ima1=browse.nom_type_ima;
    set(handlesRootName,'UserData',browse);
    set(handles.sub_txt,'Visible','on')
    set(handles.RootName_1,'Visible','On');%mkes the second file input window visible
    mode_store=get(handles.ListPairMode,'String');%get the present 'mode'
    set(handles.ListCompareMode,'UserData',mode_store);%store the mode display
    set(handles.ListPairMode,'Visible','off')
    if test==2
        set(handles.ListPairMode,'Visible','off')
        set(handles.ListPairMode,'Value',1) % mode 'civX' selected by default
    else
        set(handles.ListPairMode,'Visible','on')
        set(handles.ListPairMode,'Value',3) % mode 'Matlab' selected for stereo 
    end
    
    %% menuopen an image file with the browser
    ind_opening=1;%default
    browse.incr_pair=[0 0]; %default
    oldfile=get(handles.RootName,'String');
     menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)';
       '*.xml',  '.xml files '; ...
        '*.civ',  '.civ files '; ...
        '*.png','.png image files'; ...
        '*.jpg',' jpeg image files'; ...
        '*.tif','.tif image files'; ...
        '*.avi;*.AVI','.avi movie files'; ...
        '*.nc','.netcdf files'; ...
        '*.*',  'All Files (*.*)'};
    [FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file of the second series',oldfile);
    fileinput=[PathName FileName];%complete file name
    sizf=size(fileinput);
    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
    [path,name,ext]=fileparts(fileinput);
    [path1]=fileparts(filebase);
    if isunix
        [status,path]=system(['readlink ' path])
        [status,path1]=system(['readlink ' path1])% look for the true path in case of symbolic paths
    end
    if ~strcmp(path1,path)
        msgbox_uvmat('ERROR','The second image series must be in the same directory as the first one')
        return
     end
%     set(handles.RootName_1,'String',name);
    [RootPath,RootFile,field_count,str2,str_a,str_b,xx,nom_type,subdir]=name2display(name);
    set(handles.RootName_1,'String',RootFile);
    browse=get(handlesRootName,'UserData');
    browse.nom_type_ima_1=nom_type;
    set(handlesRootName,'UserData',browse)
    
    %check image extension
    if ~strcmp(ext,get(handles.ImaExt,'String'))
        msgbox_uvmat('ERROR','The second image series must have the same extension name as the first one')
        return
    end
    
    %% check coincidence of image sizes
%     ref_i=get(handles.ref_i,'string');
%     ref_j=get(handles.ref_j,'string');
%     [filecell,num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2,nom_type_nc]=set_civ_filenames(handles,ref_i,ref_j,[1 0 0 0 0 0]);
%     A=imread(filecell.ima1.checkciv1{1});
%     A_1=imread(fileinput);
%     npxy=size(A);
%     npxy_1=size(A_1);
%     if ~isequal(size(A),size(A_1))
%         msgbox_uvmat('ERROR','The two input image series do not have the same size')
%         return
%     end
else
    set(handles.ListPairMode,'Visible','on')
    set(handles.RootName_1,'Visible','Off');
    set(handles.sub_txt,'Visible','off')
    set(handles.RootName_1,'String',[]);
    mode_store=get(handles.ListCompareMode,'UserData');
    set(handles.ListPairMode,'Value',1)
    set(handles.ListPairMode,'String',mode_store)
    set(handles.test_stereo1,'Value',0)
    set(handles.CheckStereo,'Value',0)
    set(handles.ListPairMode,'Value',1) % mode 'civX' selected by default
end
if test==3 && get(handles.CheckPatch1,'Value')
    set(handles.test_stereo1,'Visible','on')
else
    set(handles.test_stereo1,'Visible','off')
end
if test==3 && get(handles.CheckPatch2,'Value')
    set(handles.CheckStereo,'Visible','on')
else
    set(handles.CheckStereo,'Visible','off')
end
mode_Callback(hObject, eventdata, handles)

%------------------------------------------------------------------------
% --- Executes on button press in get_ref_fix1.
function get_ref_fix1_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
filebase=get(handles.RootName,'String');
[FileName, PathName, filterindex] = uigetfile( ...
    {'*.nc', ' (*.nc)';
    '*.nc',  'netcdf files '; ...
    '*.*', 'All Files (*.*)'}, ...
    'Pick a file',filebase);

fileinput=[PathName FileName];
sizf=size(fileinput);
if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
ref.filebase=fullfile(Path,File);
ref.num_a=stra2num(str_a);
ref.num_b=stra2num(str_b);
ref.num1=str2double(field_count);
ref.num2=str2double(str2);
browse=[];%initialisation
if ~isequal(ref.ext,'.nc')
    msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
    return
end
set(handles.ref_fix1,'String',[fullfile(ref.subdir,File) '....nc']);
set(handles.ref_fix1,'UserData',ref)
menu_field{1}='civ1';
Data=nc2struct(fileinput,[]);
if isfield(Data,'patch') && isequal(Data.patch,1)
    menu_field{2}='filter1';
end
if isfield(Data,'civ2') && isequal(Data.civ2,1)
    menu_field{3}='civ2';
end
if isfield(Data,'patch2') && isequal(Data.patch2,1)
    menu_field{4}='filter2';
end
set(handles.field_ref1,'String',menu_field);
set(handles.field_ref1,'Value',length(menu_field));
set(handles.inf_sup1,'Value',2);
set(handles.num_MaxVel,'String','1');%default threshold
set(handles.ref_fix1,'Enable','on')

%------------------------------------------------------------------------
% --- Executes on button press in get_ref_fix2.
function get_ref_fix2_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
if isequal(get(handles.get_ref_fix2,'Value'),1)
    filebase=get(handles.RootName,'String');
    [FileName, PathName, filterindex] = uigetfile( ...
        {'*.nc', ' (*.nc)';
        '*.nc',  'netcdf files '; ...
        '*.*', 'All Files (*.*)'}, ...
        'Pick a file',filebase);
    fileinput=[PathName FileName];
    sizf=size(fileinput);
    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
    [Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
    ref.filebase=fullfile(Path,File);
    ref.num_a=stra2num(str_a);
    ref.num_b=stra2num(str_b);
    ref.num1=str2num(field_count);
    ref.num2=str2num(str2);
    browse=[];%initialisation
    if ~isequal(ref.ext,'.nc')
        msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
        return
    end
    set(handles.ref_fix2,'String',[fullfile(ref.subdir,File) '....nc']);
    set(handles.ref_fix2,'UserData',ref)
    menu_field{1}='civ1';
    Data=nc2struct(fileinput,[]);
    if isfield(Data,'patch') & isequal(Data.patch,1)
        menu_field{2}='filter1';
    end
    if isfield(Data,'civ2') & isequal(Data.civ2,1)
        menu_field{3}='civ2';
    end
    if isfield(Data,'patch2') & isequal(Data.patch2,1)
        menu_field{4}='filter2';
    end
    set(handles.field_ref2,'String',menu_field);
    set(handles.field_ref2,'Value',length(menu_field));
    set(handles.inf_sup2,'Value',2);
    set(handles.thresh_vel2,'String','1');%default threshold
    set(handles.ref_fix2,'Enable','on')
    set(handles.ref_fix2,'Visible','on')
    set(handles.field_ref2,'Visible','on')
else
    set(handles.ref_fix2,'Visible','off')
    set(handles.field_ref2,'Visible','off')
end

%------------------------------------------------------------------------
function ref_fix1_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(handles.inf_sup1,'Value',1);
set(handles.field_ref1,'Value',1)
set(handles.field_ref1,'String',{' '})
set(handles.ref_fix1,'UserData',[]);
set(handles.ref_fix1,'String','');
set(handles.thresh_vel1,'String','0');

%------------------------------------------------------------------------
function ref_fix2_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(handles.inf_sup2,'Value',1);
set(handles.field_ref2,'Value',1)
set(handles.field_ref2,'String',{' '})
set(handles.ref_fix2,'UserData',[]);
set(handles.ref_fix2,'String','');
set(handles.thresh_vel2,'String','0');

%------------------------------------------------------------------------
% --- Executes on button press in test_stereo1.
function test_stereo1_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
if isequal(get(handles.test_stereo1,'Value'),0)
    set(handles.subdomain_patch1,'Visible','on')
    set(handles.rho_patch1,'Visible','on')
else
    set(handles.subdomain_patch1,'Visible','off')
    set(handles.rho_patch1,'Visible','off')
end

%------------------------------------------------------------------------
% --- Executes on button press in CheckStereo.
function StereoCheck_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
if isequal(get(handles.CheckStereo,'Value'),0)
    set(handles.num_SubdomainSize,'Visible','on')
    set(handles.num_SmoothParam,'Visible','on')
else
    set(handles.num_SubdomainSize,'Visible','off')
    set(handles.num_SmoothParam,'Visible','off')
end

%------------------------------------------------------------------------
% --- Executes on button press in check_Threshold.
function ImaThreshold_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
if isequal(get(handles.check_Threshold,'Value'),1)
    set(handles.num_MinIma,'Visible','on')
    set(handles.num_MaxIma,'Visible','on')
else
    set(handles.num_MinIma,'Visible','off')
    set(handles.num_MaxIma,'Visible','off')
end

%------------------------------------------------------------------------
% --- Executes on button press in ImaThreshold2.
function ImaThreshold2_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
if isequal(get(handles.ImaThreshold2,'Value'),1)
    set(handles.MinIma2,'Visible','on')
    set(handles.MaxIma2,'Visible','on')
else
    set(handles.MinIma2,'Visible','off')
    set(handles.MaxIma2,'Visible','off')
end

%------------------------------------------------------------------------
% --- Executes on button press in TestCiv1: display image correlation function
function TestCiv1_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(handles.TestCiv1,'BackgroundColor',[1 1 0])
drawnow
test_civ1=get(handles.TestCiv1,'Value');
if test_civ1
    ref_i=str2double(get(handles.ref_i,'String'));
    if strcmp(get(handles.ref_j,'Visible'),'on')
        ref_j=str2double(get(handles.ref_j,'String'));
    else
        ref_j=1;%default
    end
    [filecell,num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2,nom_type_nc,file_ref_fix1,file_ref_fix2]=...
        set_civ_filenames(handles,ref_i,ref_j,[1 0 0 0 0 0]);
    Data.ListVarName={'ny','nx','A'};
    Data.VarDimName={'ny','nx',{'ny','nx'}};
    Data.A=imread(filecell.ima1.civ1{1});
    Data.ny=[size(Data.A,1) 1];
    Data.nx=[1 size(Data.A,2)];
    par_civ1=read_param_civ1(handles,filecell.ima1.civ1{1});
    par_civ1.filename_ima_a=filecell.ima1.civ1{1};
    par_civ1.filename_ima_b=filecell.ima2.civ1{1};
    par_civ1.T0=0;
    par_civ1.Dt=1;
    Param.Civ1=par_civ1;
    Data=civ_uvmat(Param);
    Data.ListVarName=[Data.ListVarName {'ny','nx','A'}];
    Data.VarDimName=[Data.VarDimName {'ny','nx',{'ny','nx'}}];
    Data.A=imread(filecell.ima1.civ1{1});
    Data.ny=[size(Data.A,1) 1];
    Data.nx=[1 size(Data.A,2)];
    hview_field=view_field(Data);
    set(0,'CurrentFigure',hview_field)
    hhview_field=guihandles(hview_field);
    set(hview_field,'CurrentAxes',hhview_field.axes3)
    ViewData=get(hview_field,'UserData');
    ViewData.CivHandle=handles.civ;% indicate the handle of the civ GUI in view_field
    ViewData.axes3.B=imread(filecell.ima2.civ1{1});%store the second image in the UserData of the GUI view_field
    ViewData.axes3.X=Data.Civ1_X; %keep the set of points in memeory
    ViewData.axes3.Y=Data.Civ1_Y;
    set(hview_field,'UserData',ViewData)
    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
    if isempty(corrfig)
        corrfig=figure;
        set(corrfig,'tag','corrfig')
        set(corrfig,'name','image correlation')
        set(corrfig,'DeleteFcn',{@closeview_field})%
    end
    set(handles.TestCiv1,'BackgroundColor',[1 0 0])
else
    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
    if ~isempty(corrfig)
        delete(corrfig)
    end
    hview_field=findobj(allchild(0),'tag','view_field');% look for view_field    
    if ~isempty(hview_field)
        delete(hview_field)
    end
end

function closeview_field(gcbo,eventdata)
hview_field=findobj(allchild(0),'tag','view_field');% look for view_field    
    if ~isempty(hview_field)
        delete(hview_field)
    end
%-------------------------------------------------------------------
% --- Executes on button press in status.
function status_Callback(hObject, eventdata, handles)
%-------------------------------------------------------------------
val=get(handles.status,'Value');
if val==0
    set(handles.status,'BackgroundColor',[0 1 0])
    hfig=findobj(allchild(0),'name','civ_status');
    if ~isempty(hfig)
        delete(hfig)
    end
    return
end
set(handles.status,'BackgroundColor',[1 1 0])
drawnow
listtype={'civ1','fix1','patch1','civ2','fix2','patch2'};
Param.CheckCiv1=get(handles.CheckCiv1,'Value');
Param.CheckFix1=get(handles.CheckFix1,'Value');
Param.CheckPatch1=get(handles.CheckPatch1,'Value');
Param.CheckCiv2=get(handles.CheckCiv2,'Value');
Param.CheckFix2=get(handles.CheckFix2,'Value');
Param.CheckPatch2=get(handles.CheckPatch2,'Value');
box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2];

option_civ=find(box_test,1,'last');%last selected option (non-zero index of box_test)
filecell=get(handles.civ,'UserData');%retrieve the list of output files expected for PIV
test_new=0;
if ~isfield(filecell,'nc')
    test_new=1;
    [ref_i,ref_j,errormsg]=find_ref_indices(handles);
    if ~isempty(errormsg)
        msgbox_uvmat('ERROR',errormsg)
        return
    end
    filecell=set_civ_filenames(handles,ref_i,ref_j,box_test);%determine the output file expected from the GUI status
end
if ~isequal(box_test(4:6),[0 0 0])
    civ_files=filecell.nc.civ2;%case of civ2 operations
else
    civ_files=filecell.nc.civ1;
end
[root,filename,ext]=fileparts(civ_files{1});
[rootroot,subdir,extdir]=fileparts(root);
hfig=findobj(allchild(0),'name','civ_status');
if isempty(hfig)
    hfig=figure('DeleteFcn',@stop_status);
    set(hfig,'name','civ_status')
    hlist=uicontrol('Style','listbox','Units','normalized', 'Position',[0.05 0.09 0.9 0.71], 'Callback', @open_view_field,'tag','list');
    uicontrol('Style','edit','Units','normalized', 'Position', [0.05 0.87 0.9 0.1],'tag','msgbox','Max',2,'String','checking files...');
    uicontrol('Style','frame','Units','normalized', 'Position', [0.05 0.81 0.9 0.05]);
    uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.7 0.01 0.2 0.07],'String','OK','FontWeight','bold','FontUnits','normalized','FontSize',0.9,'Callback',@close_GUI);
    BarPosition=[0.05 0.81 0.01 0.05];
    hwaitbar=uicontrol('Style','frame','Units','normalized', 'Position',BarPosition ,'BackgroundColor',[1 0 0],'tag','waitbar');
    drawnow
end
% datnum=[];
Tabchar={};
nbfiles=numel(civ_files);
count=0;
testrecent=0;
while count<nbfiles
    count=0;
    datnum=zeros(1,nbfiles);
    for ifile=1:nbfiles
        detect=exist(civ_files{ifile},'file'); % check the existence of the file
        option=0;
        if detect==0
            option_str='not created';
        else
            datfile=dir(civ_files{ifile});
            if isfield(datfile,'datenum')
                datnum(ifile)=datfile.datenum;%only available in recent matlab versions
                testrecent=1;
            end
            filefound(ifile)={datfile.name};
            lastfield='';
            % check the content  netcdf file
            Data=nc2struct(civ_files{ifile},'ListGlobalAttribute','patch2','fix2','civ2','patch','fix');
            if ~isempty(Data.patch2) && isequal(Data.patch2,1)
                option=6;
                option_str='patch2';
            elseif ~isempty(Data.fix2) && isequal(Data.fix2,1)
                option=5;
                option_str='fix2';
            elseif ~isempty(Data.civ2) && isequal(Data.civ2,1);
                option=4;
                option_str='civ2';
            elseif ~isempty(Data.patch) && isequal(Data.patch,1);
                option=3;
                option_str='patch1';
            elseif ~isempty(Data.fix) && isequal(Data.fix,1);
                option=2;
                option_str='fix1';
            else
                option=1;
                option_str='civ1';
            end
        end
        if option >= option_civ
            count=count+1;
        end
        [rr,filename,ext]=fileparts(civ_files{ifile});
        Tabchar{ifile,1}=[fullfile([subdir extdir],filename) ext  '...' option_str];
    end
    datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
    if isempty(datnum) 
        if testrecent
            message='no civ result created yet';
        else
            message='';
        end
    else
        datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
        [first,ind]=min(datnum);
        [last,indlast]=max(datnum);
        if test_new
            message='existing file status, no processing launched yet';
        else
        message={[num2str(count) ' file(s) done over ' num2str(nbfiles)] ;['oldest modification:  ' cell2mat(filefound(ind)) ' : ' datestr(first)];...
            ['latest modification:  ' cell2mat(filefound(indlast)) ' : ' datestr(last)]};
        end
    end
    hfig=findobj(allchild(0),'name','civ_status');
    if isempty(hfig)% the status list has been deleted
        return
    else
        hlist=findobj(hfig,'tag','list');
        hmsgbox=findobj(hfig,'tag','msgbox');
        hwaitbar=findobj(hfig,'tag','waitbar');
        set(hlist,'String',Tabchar)
        set(hmsgbox,'String', message)
        if count>0 && ~test_new
            BarPosition(3)=0.9*count/nbfiles;
            set(hwaitbar,'Position',BarPosition)
        end
    end
    set(hlist,'UserData',rootroot)
    pause(10)% wait 10 seconds for next check
end

    
%------------------------------------------------------------------------   
% call 'view_field.fig' to display the  field selected in the list of 'status'
function open_view_field(hObject, eventdata)
%------------------------------------------------------------------------
list=get(hObject,'String');
index=get(hObject,'Value');
rootroot=get(hObject,'UserData');
filename=list{index};
ind_dot=findstr(filename,'...');
filename=filename(1:ind_dot-1);
filename=fullfile(rootroot,filename);
delete(get(hObject,'parent'))%delete the display figure to stop the check process
if exist(filename,'file')%visualise the vel field if it exists
    uvmat(filename)
    set(gcbo,'Value',1)
end

%------------------------------------------------------------------------   
% launched by pressing OK on the status figure
function close_GUI(hObject, eventdata)
%------------------------------------------------------------------------
    delete(gcbf)
    
%------------------------------------------------------------------------   
% launched by deleting the status figure
function stop_status(hObject, eventdata)
%------------------------------------------------------------------------
hciv=findobj(allchild(0),'tag','civ');
hhciv=guidata(hciv);
set(hhciv.status,'value',0) %reset the status uicontrol in the GUI civ
set(hhciv.status,'BackgroundColor',[0 1 0])

%------------------------------------------------------------------------
% % --- Executes on button press in ListPairMode.
% function CivMode_Callback(hObject, eventdata, handles)
% %------------------------------------------------------------------------
% Listprog=get(handles.ListPairMode,'String');
% index=get(handles.ListPairMode,'Value');
% prog=Listprog{index};
% switch prog
%     case 'CivX'
%         set(handles.thresh_patch1,'Visible','off')
%         set(handles.thresh_text1,'Visible','off')
%         set(handles.num_MaxDiff,'Visible','off')
%         set(handles.thresh_text2,'Visible','off')
%         set(handles.num_Rho,'Style','edit')
%         set(handles.num_Rho,'String','1')
%         set(handles.BATCH,'Enable','on')
%     case 'CivAll'
%         if get(handles.CheckPatch1,'Value')
%             set(handles.thresh_patch1,'Visible','on')
%             set(handles.thresh_text1,'Visible','on')
%         end
%         set(handles.num_Rho,'Style','edit')
%         set(handles.num_Rho,'String','1')
%         set(handles.BATCH,'Enable','on')
%     case 'CivUvmat'
%        
% end


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

% Hint: get(hObject,'Value') returns toggle state of CheckStereo



function num_SubdomainSize_Callback(hObject, eventdata, handles)
% hObject    handle to num_SubdomainSize (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of num_SubdomainSize as text
%        str2double(get(hObject,'String')) returns contents of num_SubdomainSize as a double



function num_SmoothingParam_Callback(hObject, eventdata, handles)
% hObject    handle to num_SmoothingParam (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of num_SmoothingParam as text
%        str2double(get(hObject,'String')) returns contents of num_SmoothingParam as a double



function num_MaxDiff_Callback(hObject, eventdata, handles)
% hObject    handle to num_MaxDiff (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of num_MaxDiff as text
%        str2double(get(hObject,'String')) returns contents of num_MaxDiff as a double


function num_Nx_Callback(hObject, eventdata, handles)
% hObject    handle to num_Nx (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of num_Nx as text
%        str2double(get(hObject,'String')) returns contents of num_Nx as a double


function num_Ny_Callback(hObject, eventdata, handles)
% hObject    handle to num_Ny (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of num_Ny as text
%        str2double(get(hObject,'String')) returns contents of num_Ny as a double


% --------------------------------------------------------------------
function MenuHelp_Callback(hObject, eventdata, handles)
path_civ=fileparts(which ('civ'));
helpfile=fullfile(path_civ,'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(path_civ,'uvmat_doc'))
    web([helpfile '#civ'])
end

% --------------------------------------------------------------------
function CivX_Callback(hObject, eventdata, handles)
%set(handles.thresh_patch1,'Visible','off')
set(handles.thresh_text1,'Visible','off')
set(handles.num_MaxDiff,'Visible','off')
set(handles.thresh_text2,'Visible','off')
set(handles.num_Rho,'Style','edit')
set(handles.num_Rho,'String','1')
set(handles.BATCH,'Enable','on')

% --------------------------------------------------------------------
function Matlab_Callback(hObject, eventdata, handles)
set(handles.Matlab,'checked','on')
set(handles.CivX,'checked','off')
if get(handles.CheckPatch1,'Value')
    set(handles.thresh_patch1,'Visible','on')
    set(handles.thresh_text1,'Visible','on')
end
if get(handles.CheckPatch2,'Value')
    set(handles.num_MaxDiff,'Visible','on')
    set(handles.thresh_text2,'Visible','on')
end
set(handles.num_Rho,'Style','popupmenu')
set(handles.num_Rho,'Value',1)
set(handles.num_Rho,'String',{'1';'2'})
set(handles.BATCH,'Enable','off')

% --------------------------------------------------------------------
% --- read a panel with handle 'handle' producing a structure 'struct'
function struct=read_panel(handle)
hchild=get(handle,'children');
for ichild=1:numel(hchild)
    if strcmp(get(hchild(ichild),'Visible'),'on')
        object_style=get(hchild(ichild),'Style');
        tag=get(hchild(ichild),'tag');
        check_input=1;%default
        switch object_style
            case 'edit'
                switch(tag(1:4))
                    case 'num_'
                        input=str2double(get(hchild(ichild),'String'));
                        %deal with undefined input: retrieve the default value stored as UserData
                        if isnan(input)
                            input=get(hchild(ichild),'UserData');
                            set(hchild(ichild),'String',num2str(input))
                        end
                    case 'txt_'
                        input=get(hchild(ichild),'String');
                end
                key=tag(5:end);
            case 'checkbox'
                input=get(hchild(ichild),'Value');
                key=tag(7:end);
            otherwise
                check_input=0;
        end
        if check_input
            eval(['struct.' key '=input;'])
        end
    end
end



function cmd=cmd_civ1(filename,Param)
%TODO : include filename in par_civ1
%------------------------------------------------------------------------
%pixels per cm and matrix of the image times, read from the .civ file by uvmat

%changes : filename_cmx -> filename ( no extension )

filename=regexprep(filename,'.nc','')

if isequal(Param.Civ1.Dt,'0')
    Param.Civ1.Dt='1' ;%case of 'displacement' mode
end
Param.Civ1.filename_ima_a=regexprep(Param.Civ1.filename_ima_a,'.png','');
Param.Civ1.filename_ima_b=regexprep(Param.Civ1.filename_ima_b,'.png','');
fid=fopen([filename '.civ1.cmx'],'w');
fprintf(fid,['##############   CMX file' '\n' ]);
fprintf(fid,   ['FirstImage ' regexprep(Param.Civ1.filename_ima_a,'\\','\\\\') '\n' ]);% for windows compatibility
fprintf(fid,   ['LastImage  ' regexprep(Param.Civ1.filename_ima_b,'\\','\\\\') '\n' ]);% for windows compatibility
fprintf(fid,  ['XX' '\n' ]);
fprintf(fid,  ['Mask ' Param.Civ1.maskflag '\n' ]);
fprintf(fid,  ['MaskName ' regexprep(Param.Civ1.maskname,'\\','\\\\') '\n' ]);
fprintf(fid,   ['ImageSize ' num2str(Param.Civ1.npx) ' ' num2str(Param.Civ1.npy) '\n' ]);   %VERIFIER CAS GENERAL ?
fprintf(fid,   ['CorrelationBoxesSize ' num2str(Param.Civ1.Bx) ' ' num2str(Param.Civ1.By) '\n' ]);
fprintf(fid,   ['SearchBoxeSize ' num2str(Param.Civ1.Sx) ' ' num2str(Param.Civ1.Sy) '\n' ]);
fprintf(fid,   ['RO ' num2str(Param.Civ1.Rho) '\n' ]);
fprintf(fid,   ['GridSpacing ' num2str(Param.Civ1.Dx) ' ' num2str(Param.Civ1.Dy) '\n' ]);
fprintf(fid,   ['XX 1.0' '\n' ]);
fprintf(fid,   ['Dt_TO ' num2str(Param.Civ1.Dt) ' ' num2str(Param.Civ1.T0) '\n' ]);
fprintf(fid,  ['PixCmXY ' num2str(Param.Civ1.pxcmx) ' ' num2str(Param.Civ1.pxcmy) '\n' ]);
fprintf(fid,  ['XX 1' '\n' ]);
fprintf(fid,   ['ShiftXY ' num2str(Param.Civ1.Shiftx) ' '  num2str(Param.Civ1.Shifty) '\n' ]);
fprintf(fid,  ['Grid ' Param.Civ1.gridflag '\n' ]);
fprintf(fid,   ['GridName ' regexprep(Param.Civ1.gridname,'\\','\\\\') '\n' ]);
fprintf(fid,   ['XX 85' '\n' ]);
fprintf(fid,   ['XX 1.0' '\n' ]);
fprintf(fid,   ['XX 1.0' '\n' ]);
fprintf(fid,   ['Hart 1' '\n' ]);
fprintf(fid,  [ 'DecimalShift 0' '\n' ]);
fprintf(fid,   ['Deformation 0' '\n' ]);
fprintf(fid,  ['CorrelationMin 0' '\n' ]);
fprintf(fid,   ['IntensityMin 0' '\n' ]);
fprintf(fid,  ['SeuilImage n' '\n' ]);
fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);
fprintf(fid,   ['ImageToUse ' Param.Civ1.term_a ' ' Param.Civ1.term_b '\n' ]); % VERIFIER ?
fprintf(fid,   ['ImageUsedBefore null null' '\n' ]);
fclose(fid);

% cmd_CIV1=[sparam.Civ1Bin ' -f ' filename '.cmx >' filename '.log' ]; % redirect standard output to the log file
% cmd_CIV1=regexprep(cmd_CIV1,'\\','\\\\');
% namelog=regexprep(namelog,'\\','\\\\');
if(isunix)
    cmd=['cp -f ' filename '.civ1.cmx ' filename '.cmx \n '];% the cmx file gives the name to the nc file
    cmd=[cmd Param.xml.Civ1Bin ' -f ' filename '.cmx >' filename '.civ1.log \n ' ]; % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx
%     cmd=[cmd '\n' 'mv ' filename '.log' ' ' filename '.civ1.log' '\n' 'chmod g+w ' filename '.civ1.log' '\n' 'chmod g+w ' filename '.nc'];%rename .log as .civ1.log and set the netcdf result file for group user writting
%    cmd=[cmd '\n' 'mv ' filename '.cmx' ' ' filename '.civ1.cmx' '\n'];%rename .cmx as .civ1.cmx
    cmd=[cmd 'rm ' filename '.cmx'];
else %Windows system
    filename=regexprep(filename,'\\','\\\\');
    cmd=['copy /Y "' filename '.civ1.cmx" "' filename '.cmx" \n '];
    cmd=[cmd '"' regexprep(Param.xml.Civ1Bin,'\\','\\\\')...
        '" -f "' filename '.cmx" >"' filename '.civ1.log" \n ' ]; % redirect standard output to the log file
%     namelog=regexprep(namelog,'\\','\\\\');
%     cmd=[cmd '\n ' 'copy /Y "' filename '.log' '" "' filename '.civ1.log"']; %preserve the log file as .civ1.log
    cmd=[cmd 'del "' filename '.cmx'];
end