source: trunk/src/uvmat.m @ 441

%'uvmat': function associated with the GUI 'uvmat.fig' for images and data field visualization 
%------------------------------------------------------------------------
% function huvmat=uvmat(input)
%
%OUTPUT
% huvmat=current handles of the GUI uvmat.fig
%%
%
%INPUT:
% input: input file name (if character chain), or input image matrix to
% visualize, or Matlab structure representing  netcdf fields (with fields
% ListVarName....)
%
%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
%  Copyright Joel Sommeria,  2008, LEGI / CNRS-UJF-INPG, joel.sommeria@legi.grenoble-inp.fr.
%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
%     This open 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 (open UVMAT/COPYING.txt) for more details.
%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
%
% Information stored on the interface:
%    'Strings' of all edit boxes and menus: get(handles.Tag,'String')
%    'Values' of all menus and toggle buttons: get(handles.Tag,'Value')
%     Matlab structure called UvData stored as 'UserData' of the figure uvmat.fig,(can be obtained by right mouse click on the interface).
%          It contains the following fields:
%     - Fixed specifiacation of plotting figures and axes (defined bu uvmat_OpeningFcn) 
%          .PosColorbar: [0.8210 0.4710 0.0190 0.4450]; specified position of the colorbar on figures
%     - Information read in the documentation open of a series (activated by RootPath_Callback) :
%          .XmlData, with fields:
%               .Time: matrix of times of the images with index i and j
%               .GeometryCalib: [1x1 struct]
%     - Information defined from the interface:
%           .NewSeries: =1 when the first view of a new field series is displayed, else 0
%           .filename:(char string)
%           .FieldName: (char string) main field selected('image', 'velocity'...)
%           .CName: (char string)name of the scalar used for vector colors
%          .MovieObject{1}: movie object representing an input movie
%          .MovieObject{2}: idem for a second input series (_1)
%          .filename_1 : last second input file name (to deal with a constant second input without reading again the file)
%          .ZMin, .ZMax: range of the z coordinate
%..... to complement
%     - Information on  projection objects
%           .Object: {[1x1 struct]}
%           .CurrentObjectIndex: index of the projection object .Object currently selected for editing
%     -Information on the current field (Field{i})
%            .Txt : text information to display (e.g. error message)
%            .NbDim: number of dimensions (=0 by default)
%            .NbCoord: number of vector components
%            .CoordType: expresses the type of coordinate ('px' for image, 'sig' for instruments, or 'phys')
%            .dt: time interval for the corresponding image pair
%            .Mesh: estimated typical distance between vectors
%            .ZMax:
%            .ZMin: 
%            .X, .Y, .Z: set of vector coordinates 
%            .U,.V,.W: corresponding set of vector components
%            .F: corresponding set of warning flags
%            .FF: corresponding set of false flags, =0 for good vectors
%            .C: corresponding values of the scalar used for vector color
%             (.X, .Y, .Z,.U,.V,.W,.F,.FF,.C are matlab vectors of the same length,
%                     equal to the number of vectors stored in the input open)
%            .CName: name of the scalar .C
%            .CType: type of the scalar .C, setting how the scalar is obtained (see 'Scalars' below)
%            .A image or scalar 
%            .AX: vector of dimension 2 representing the first and last values
%              of the X coordinates for the image or scalar known on a regular grid,
%              or vector of dimension .A for a scaler defined on irregular grid.
%            .AY: same as .AX along the Y direction
%            .AName: name of the scalar, ='image' for an image

% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%   DATA FLOW  (for run0_Callback) %%%%%%%%%%%%%%%%%%%%:
%
%
% 1) Input filenames are determined by MenuBrowse (first field), MenuBrowse_1
% (second field), or by the stored file names under  Browse, or as an input of uvmat. 
% 2) These functions call 'display_file_name.m' which detects the file series, and fills the file index boxes
% 3) Then 'update_rootinfo.m' Updates information about a new field series (indices to scan, timing, calibration from an xml file)
% 4) Then fields are opened and visualised by the main sub-function 'refresh_field.m'
% The function first reads the name of the input file from the edit boxes  of the GUI
% A second input file can be introduced for file comparison
% It then reads the input file(s) with the appropriate function, read for
% images, read_civxdata.m for CIVx PIV data, nc2struct for other netcdf
% files.
%               Main input open   second input open(_1)        second image (pair animation) 
%            |                 |                             
%            |                 |                                                
%                     Field{1}         Field{2}               
%                                                                         |
% coord transform (phys.m) or other user defined  fct acting on Field{i}  |
%                                                                   Field{i}
%                                                                    |
% calc_field.m: calculate scalar or other derived fields (vort, div..).
%
% sub_field.m: combine the input Field{i} in a single set of fields (vector + scalar):
%              Field{i=1->3}.X --> UvData.X                          |
%                                                                    |
%                                                                 UvData
%                                                                    |
% plot histograms of the whole  field
% proj_field.m: project the set of fields on the current projection objects defined by UvData.Object
%                                                                    |                                                                          |
%                                                                ObjectData
%                                                                    |
% plot_field.m: plot the projected fields and store them as          |
% UvData.axes3                                        |
%                                                                    |
%                                                                AxeData
%
%%%%%%%%%%%%%%    SCALARS: %%%%%%%%%%%%??%%%
% scalars are displayed either as an image or countour plot, either as a color of
% velocity vectors. The scalar values in the first case is represented by
% UvData.Field.A, and by UvData.Field.C in the second case. The corresponding set of X
% and Y coordinates are represented by UvData.Field.AX and UvData.Field.AY, and .X and
% .Y for C (the same as velocity vectors). If A is a nxxny matrix (scalar
% on a regtular grid), then .AX andf.AY contains only two elements, represneting the
% coordinates of the four image corners. The scalar name is represented by
% the strings .AName and/or .CName.
% If the scalar exists in an input open (image or scalar stored under its
% name in a netcdf open), it is directly read at the level of Field{1}or Field{2}.
% Else only its name AName is recorded in Field{i}, and its field is then calculated 
%by the fuction calc_scal after the coordinate transform or after projection on an edit_object
     
% Properties attached to plotting figures (standard Matlab properties):
%    'CurrentAxes'= gca or get(gcf,'CurrentAxes');
%    'CurrentPoint'=get(gcf,'CurrentPoint'): figure coordinates of the point over which the mouse is positioned
%    'CurrentCharacter'=get(gcf,'CurrentCharacter'): last character typed  over the figure where the mouse is positioned
%    'WindowButtonMotionFcn': function permanently called by mouse motion over the figure
%    'KeyPressFcn': function called by pressing a key on the key board 
%    'WindowButtonDownFcn':  function called by pressing the mouse over the  figure
%    'WindowButtonUpFcn': function called by releasing  the mouse pressure over the  figure

% Properties attached to plotting axes:
%    'CurrentPoint'=get(gca,'CurrentPoint'); (standard Matlab) same as for the figure, but position in plot coordinates.
%     AxeData:=get(gca,'UserData');
%     AxeData.Drawing  = create: create a new object 
%                       = deform: modify an existing object by moving its defining create
%                      = off: no current drawing action
%                     = translate: translate an existing object
%                    = calibration: move a calibration point
%                    = CheckZoom: isolate a subregion for CheckZoom in=1 if an object is being currently drawn, 0 else (set to 0 by releasing mouse button)
%            .CurrentOrigin: Origin of a curently drawn edit_object
%            .CurrentLine: currently drawn menuline (A REVOIR)
%            .CurrentObject: handle of the currently drawn edit_object
%            .CurrentRectZoom: current rectangle used for CheckZoom

% Properties attached to projection objects (create, menuline, menuplane...):
%    'Tag'='proj_object': for all projection objects
%    ObjectData.Type=...: style of projection object:
%              .ProjMode
%              .Coord: defines the position of the object
%              .XMin,YMin....
%              .XMax,YMax....
%              .DX,DY,DZ
%              .Phi, .Theta, .Psi : Euler angles
%              .X,.Y,.U,.V.... : field data projected on the object
%              .IndexObj: index in the list of UvData.Object
           %during plotting
%               .plotaxes: handles of the current axes used to plot the  result of field projection on the object
%               .plothandle: vector of handle(s) of the object graphic represnetation in all the opened plotting axes
% To each projection object #iobj, corresponds an axis
% Object{iobj}.plotaxes and nbobj representation graphs  Object{iobj}.plothandles(:) (where nbobj is the
% nbre of current objects opened in uvmat. Note that Object{iobj}.plothandles(iobj)=[] : an object is not represented in its own projection field;

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

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',          mfilename, ...
                   'gui_Singleton',     gui_Singleton, ...
                   'gui_OpeningFcn',    @uvmat_OpeningFcn, ...
                   'gui_OutputFcn',     @uvmat_OutputFcn, ...
                   'gui_LayoutFcn',     [], ...
                   'gui_Callback',      []);
if nargin && ischar(varargin{1})&& ~isempty(regexp(varargin{1},'_Callback','once'))
    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 the GUI uvmat is made visible.
function uvmat_OpeningFcn(hObject, eventdata, handles, input )
%------------------------------------------------------------------------

%% Choose default command menuline output for uvmat (standard GUI)
handles.output = hObject;

%% Update handles structure (standard GUI)
guidata(hObject, handles);

%% check the path and date of modification of all functions in uvmat
path_to_uvmat=which ('uvmat');% check the path detected for source file uvmat
[errormsg,date_str,svn_info]=check_files;%check the path of the functions called by uvmat.m
date_str=['last modification: ' date_str];


%% set the position of colorbar and ancillary GUIs:
set(hObject,'Units','Normalized')
movegui(hObject,'center')
UvData.OpenParam.PosColorbar=[0.805 0.022 0.019 0.445];
UvData.OpenParam.SetObjectOrigin=[-0.05 -0.03]; %position for set_object
UvData.OpenParam.SetObjectSize=[0.3 0.7];
UvData.OpenParam.CalOrigin=[0.95 -0.03];%position for geometry_calib (TO IMPROVE)
UvData.OpenParam.CalSize=[0.28 1];
UvData.axes3=[];%initiate the record of plotted field
UvData.axes2=[];
UvData.axes1=[];
AxeData.LimEditBox=1; %initialise AxeData
set(handles.axes3,'UserData',AxeData)

%% set functions for the mouse and keyboard
% set(handles.histo_u,'NextPlot','replacechildren');
% set(handles.histo_v,'NextPlot','replacechildren');
set(hObject,'KeyPressFcn',{'keyboard_callback',handles})%set keyboard action function
set(hObject,'WindowButtonMotionFcn',{'mouse_motion',handles})%set mouse action functio
set(hObject,'WindowButtonDownFcn',{'mouse_down'})%set mouse click action function
set(hObject,'WindowButtonUpFcn',{'mouse_up',handles}) 
set(hObject,'DeleteFcn',{@closefcn})%

%% refresh projection plane
% UvData.Object{1}.ProjMode='projection';%main plotting plane
% UvData.Object{1}.DisplayHandle.uvmat=handles.axes3;
% UvData.Object{1}.DisplayHandle.view_field=[];
set(handles.ListObject,'Value',1)% default: empty projection objectproj_field
set(handles.ListObject,'String',{'plane'})
set(handles.ListObject_1,'Value',1)% default: empty projection objectproj_field
set(handles.ListObject_1,'String',{'plane'})
set(handles.Fields,'Value',1)
set(handles.Fields,'string',{''})

%% TRANSFORM menu: builtin fcts
menu_str={'';'phys';'px';'phys_polar'};
UvData.OpenParam.NbBuiltin=numel(menu_str); %number of functions
path_uvmat=fileparts(which('uvmat'));
addpath (path_uvmat) ; %add the path to UVMAT, (useful in case of change of working directory after civ has been s opened in the working directory)
addpath(fullfile(path_uvmat,'transform_field'))%add the path to transform functions,
fct_handle{1,1}=[];
testexist=zeros(size(menu_str'));%default
testexist(1)=1;
for ilist=2:length(menu_str)
    if exist(menu_str{ilist},'file')
        fct_handle{ilist,1}=str2func(menu_str{ilist});
        testexist(ilist)=1;
    else
        testexist(ilist)=0;
    end
end
rmpath(fullfile(path_uvmat,'transform_field'))

%% load the list of previously browsed files in menus Open and Open_1
 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')
          for ifile=1:min(length(h.MenuFile),5)
              eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',h.MenuFile{ifile});'])
               eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',h.MenuFile{ifile});'])
          end
      end
      if isfield(h,'transform_fct') && iscell(h.transform_fct)
         for ilist=1:length(h.transform_fct);
             if exist(h.transform_fct{ilist},'file')
                [path,file]=fileparts(h.transform_fct{ilist});
                addpath(path)
                h_func=str2func(file);
                rmpath(path)
                testexist=[testexist 1]; 
             else
                file='';
                h_func=[];
                testexist=[testexist 0]; 
             end
             fct_handle=[fct_handle; {h_func}]; %concatene the list of paths
             menu_str=[menu_str; {file}]; 
         end
      end
 end
menu_str=menu_str(testexist==1);%=menu_str(testexist~=0)
fct_handle=fct_handle(testexist==1);
menu_str=[menu_str;{'more...'}];
set(handles.transform_fct,'String',menu_str)
set(handles.transform_fct,'UserData',fct_handle)% store the list of path in UserData of ACTION

%% case of an input argument for uvmat
testinputfield=0;
inputfile=[];
Field=[];
if exist('input','var')
%     if ~isempty(errormsg)
%         msgbox_uvmat('WARNING',errormsg)
%     end
    if ishandle(handles.UVMAT_title)
        delete(handles.UVMAT_title)
    end   
    if isstruct(input)
        if isfield(input,'InputFile')
            inputfile=input.InputFile;
        end
        if isfield(input,'TimeIndex')
            set(handles.i1,num2str(input.TimeIndex))
        end
        if isfield(input,'FieldsString')
            UvData.FieldsString=input.FieldsString;
        end
    elseif ischar(input)% file name introduced as input
           inputfile=input;
    elseif isnumeric(input)%simple matrix introduced as input
        sizinput=size(input);
        if sizinput(1)<=1 || sizinput(2)<=1
            msgbox_uvmat('ERROR','bad input for uvmat: file name, structure or numerical matrix accepted')
            return
        end
        UvData.Field.ListVarName={'A','coord_y','coord_x'};
        UvData.Field.VarDimName={{'coord_y','coord_x'},'cord_y','coord_x'};
        UvData.Field.A=input;
        UvData.Field.coord_x=[0.5 size(input,2)-0.5];
        UvData.Field.coord_y=[size(input,1)-0.5 0.5];
        testinputfield=1;
    end
else
   if ishandle(handles.UVMAT_title)
       set(handles.UVMAT_title,'String',...
           [{'Copyright  LEGI UMR 5519 /CNRS-UJF-Grenoble INP, 2010'};...
           {'GNU General Public License'};...
           {path_to_uvmat};...
           {date_str};...
           {['SVN revision : ' num2str(svn_info.cur_rev)]};...
           errormsg]);
   end
end
set(handles.uvmat,'UserData',UvData)
if ~isempty(inputfile)
    %%%%% display the input field %%%%%%%
    display_file_name(handles,inputfile)
    %%%%%%%
    testinputfield=1;
end

%% plot input field if exists
if testinputfield
    %delete drawn objects
    hother=findobj(handles.axes3,'Tag','proj_object');%find all the proj objects
    for iobj=1:length(hother)
        delete_object(hother(iobj))
    end  
    if isempty(inputfile)
        errormsg=refresh_field(handles,[],[],[],[],[],[],{Field});
        set(handles.MenuTools,'Enable','on')
        set(handles.OBJECT_txt,'Visible','on')
        set(handles.edit_object,'Visible','on')
%         set(handles.ListObject_1,'Visible','on')
        set(handles.frame_object,'Visible','on')
        if ~isempty(errormsg)
            msgbox_uvmat('ERROR',errormsg)
        end
    end
end

set_vec_col_bar(handles) %update the display of color code for vectors

%------------------------------------------------------------------------
% --- Outputs from this function are returned to the command menuline.
function varargout = uvmat_OutputFcn(hObject, eventdata, handles)
varargout{1} = handles.output;% the only output argument is the handle to the GUI figure

%------------------------------------------------------------------------
% --- executed when closing uvmat: delete or desactivate the associated figures if exist
function closefcn(gcbo,eventdata)
%------------------------------------------------------------------------
hh=findobj(allchild(0),'tag','view_field');
if ~isempty(hh)
    delete(hh)
end
hh=findobj(allchild(0),'tag','geometry_calib');
if ~isempty(hh)
    delete(hh)
end
hh=findobj(allchild(0),'tag','set_object');
if ~isempty(hh)
    hhh=findobj(hh,'tag','PLOT');
    set(hhh,'enable','off')
end

%------------------------------------------------------------------------
%------------------------------------------------------------------------
%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
% automatically sets the global properties when the rootfile name is introduced
% then activate the view-field action if selected
% it is activated either by clicking on the RootPath window or by the 
% browser 
%------------------------------------------------------------------------
%------------------------------------------------------------------------
% --- Executes on the menu Open/Browse...
% search the files, recognize their type according to their name and fill the rootfile input windows
function MenuBrowse_Callback(hObject, eventdata, handles)
[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
oldfile=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
if isempty(oldfile)||isequal(oldfile,'') %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,'MenuFile_1')
                  oldfile=h.MenuFile_1;
             end
         end
end
% [FileName, PathName] = uigetfile( ...
%        {'*.xml;*.xls;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol;*.nc;*.cmx;*.fig;*.log;*.dat;*.bat;', ' (*.xml,*.xls,*.civ,*.jpg ,*.png, .tif, *.avi,*.vol,*.nc,*.cmx,*.fig,*.log,*.dat,*.bat)';
%        '*.xml',  '.xml files '; ...
%         '*.xls',  '.xls files '; ...
%         '*.civ',  '.civ files '; ...
%         '*.jpg',' jpeg image files'; ...
%         '*.png','.png image files'; ...
%         '*.tif','.tif image files'; ...
%         '*.avi;*.AVI','.avi movie files'; ...
%         '*.vol','.volume images (png)'; ...
%         '*.nc','.netcdf files'; ...
%         '*.cdf','.netcdf files'; ...
%         '*.cmx','.cmx text files ';...
%         '*.fig','.fig files (matlab fig)';...
%         '*.log','.log text files ';...
%         '*.dat','.dat text files ';...
%         '*.bat','.bat system command text files';...
%         '*.*',  'All Files (*.*)'}, ...
%         'Pick a file',oldfile);

[FileName, PathName] = uigetfile({'*.*','All Files(*.*)'},'Pick a file',oldfile);
fileinput=[PathName FileName];%complete file name 
sizf=size(fileinput);
if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end

% display the selected field and related information
display_file_name( handles,fileinput)

% -----------------------------------------------------------------------
% --- 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( 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(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(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(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(handles,fileinput)

%------------------------------------------------------------------------
% --- Executes on the menu Open/Browse_1 for the second input field,
%     search the files, recognize their type according to their name and fill the rootfile input windows
function MenuBrowse_1_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
RootPath=get(handles.RootPath,'String');
% [FileName, PathName, filterindex] = uigetfile( ...
%        {'*.xml;*.xls;*.civ;*.jpg;*.png;*.avi;*.AVI;*.nc;*.cmx;*.fig;*.log;*.dat', ' (*.xml,*.xls,*.civ, *.jpg,*.png, *.avi,*.nc,*.cmx ,*.fig,*.log,*.dat)';
%        '*.xml',  '.xml files '; ...
%         '*.xls',  '.xls files '; ...
%         '*.civ',  '.civ files '; ...
%         '*.jpg','.jpg image files'; ...
%         '*.png','.png image files'; ...
%         '*.avi;*.AVI','.avi movie files'; ...
%         '*.nc','.netcdf files'; ...
%         '*.cdf','.netcdf files'; ...
%         '*.cmx','.cmx text files';...
%         '*.cmx2','.cmx2 text files';...
%         '*.fig','.fig files (matlab fig)';...
%         '*.log','.log text files ';...
%         '*.dat','.dat text files ';...
%         '*.*',  'All Files (*.*)'}, ...
%         'Pick a second file for comparison',RootPath);
[FileName, PathName] = uigetfile({'*.*','All Files(*.*)'},'Pick a file',RootPath);
fileinput_1=[PathName FileName];%complete file name 
sizf=size(fileinput_1);
if (~ischar(fileinput_1)||~isequal(sizf(1),1)),return;end

% refresh the current displayed field
set(handles.SubField,'Value',1)
display_file_name(handles,fileinput_1,2)

%update list of recent files in the menubar
MenuFile_1=fileinput_1;
MenuFile_2=get(handles.MenuFile_1,'Label');
MenuFile_3=get(handles.MenuFile_2,'Label');
MenuFile_4=get(handles.MenuFile_3,'Label');
MenuFile_5=get(handles.MenuFile_4,'Label');
set(handles.MenuFile_1,'Label',MenuFile_1)
set(handles.MenuFile_2,'Label',MenuFile_2)
set(handles.MenuFile_3,'Label',MenuFile_3)
set(handles.MenuFile_4,'Label',MenuFile_4)
set(handles.MenuFile_5,'Label',MenuFile_5)
set(handles.MenuFile_1_1,'Label',MenuFile_1)
set(handles.MenuFile_2_1,'Label',MenuFile_2)
set(handles.MenuFile_3_1,'Label',MenuFile_3)
set(handles.MenuFile_4_1,'Label',MenuFile_4)
set(handles.MenuFile_5_1,'Label',MenuFile_5)
dir_perso=prefdir;
profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
if exist(profil_perso,'file')
    save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
else
    txt=ver('MATLAB');
    Release=txt.Release;
    relnumb=str2double(Release(3:4));
    if relnumb >= 14
        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
    else
        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
    end
end

% -----------------------------------------------------------------------
% --- Open again as second field the file whose name has been recorded in MenuFile_1
function MenuFile_1_1_Callback(hObject, eventdata, handles)
% -----------------------------------------------------------------------
fileinput_1=get(handles.MenuFile_1_1,'Label');
set(handles.SubField,'Value',1)
display_file_name(handles,fileinput_1,2)

% -----------------------------------------------------------------------
% --- Open again as second field the file whose name has been recorded in MenuFile_2
function MenuFile_2_1_Callback(hObject, eventdata, handles)
% -----------------------------------------------------------------------
fileinput_1=get(handles.MenuFile_2_1,'Label');
set(handles.SubField,'Value',1)
display_file_name(handles,fileinput_1,2)

% -----------------------------------------------------------------------
% --- Open again as second field the file whose name has been recorded in MenuFile_3
function MenuFile_3_1_Callback(hObject, eventdata, handles)
% -----------------------------------------------------------------------
fileinput_1=get(handles.MenuFile_3_1,'Label');
set(handles.SubField,'Value',1)
display_file_name(handles,fileinput_1,2)

% -----------------------------------------------------------------------
% --- Open again as second field the file whose name has been recorded in MenuFile_4
function MenuFile_4_1_Callback(hObject, eventdata, handles)
% -----------------------------------------------------------------------
fileinput_1=get(handles.MenuFile_4_1,'Label');
set(handles.SubField,'Value',1)
display_file_name(handles,fileinput_1,2)

% -----------------------------------------------------------------------
% --- Open again as second field the file whose name has been recorded in MenuFile_5
function MenuFile_5_1_Callback(hObject, eventdata, handles)
% -----------------------------------------------------------------------
fileinput_1=get(handles.MenuFile_5_1,'Label');
set(handles.SubField,'Value',1)
display_file_name(handles,fileinput_1,2)

%------------------------------------------------------------------------
% --- Called by action in RootPath edit box
function RootPath_Callback(hObject,eventdata,handles)
%------------------------------------------------------------------------
% read the current input file name:
[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
% detect the file type, get the movie object if relevant, and look for the corresponding file series:
[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
% initiate the input file series and refresh the current field view: 
update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,1);

%-----------------------------------------------------------------------
% --- Called by action in RootPath_1 edit box
function RootPath_1_Callback(hObject,eventdata,handles)
% -----------------------------------------------------------------------
% update_rootinfo_1(hObject,eventdata,handles)
[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
% detect the file type, get the movie object if relevant, and look for the corresponding file series:
[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
% initiate the input file series and refresh the current field view: 
update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,2);

%------------------------------------------------------------------------
% --- Called by action in RootFile edit box
function SubDir_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
%refresh the menu of input fields
Fields_Callback(hObject, eventdata, handles);
% refresh the current field view
run0_Callback(hObject, eventdata, handles); 

%------------------------------------------------------------------------
% --- Called by action in RootFile edit box
function RootFile_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
RootPath_Callback(hObject,eventdata,handles)

%-----------------------------------------------------------------------
% --- Called by action in RootFile_1 edit box
function RootFile_1_Callback(hObject, eventdata, handles)
% -----------------------------------------------------------------------
RootPath_1_Callback(hObject,eventdata,handles)

%------------------------------------------------------------------------
% --- Called by action in FileIndex edit box
function FileIndex_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
set(handles.i1,'String',num2str(i1));
set(handles.i2,'String',num2str(i2));
set(handles.j1,'String',num2str(j1));
set(handles.j2,'String',num2str(j2));

% refresh the current field view
run0_Callback(hObject, eventdata, handles)

%------------------------------------------------------------------------
% --- Called by action in FileIndex_1 edit box
function FileIndex_1_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
run0_Callback(hObject, eventdata, handles)

%------------------------------------------------------------------------
% --- Called by action in NomType edit box
function NomType_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
i1=str2num(get(handles.i1,'String'));
i2=str2num(get(handles.i2,'String'));
j1=str2num(get(handles.j1,'String'));
j2=str2num(get(handles.j2,'String'));
FileIndex=fullfile_uvmat('','','','',get(handles.NomType,'String'),i1,i2,j1,j2);
set(handles.FileIndex,'String',FileIndex)
% refresh the current settings and refresh the field view
RootPath_Callback(hObject,eventdata,handles)

%------------------------------------------------------------------------
% --- Called by action in NomType edit box
function NomType_1_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
i1=str2num(get(handles.i1,'String'));
i2=str2num(get(handles.i2,'String'));
j1=str2num(get(handles.j1,'String'));
j2=str2num(get(handles.j2,'String'));
FileIndex=fullfile_uvmat('','','','',get(handles.NomType_1,'String'),i1,i2,j1,j2);
set(handles.FileIndex_1,'String',FileIndex)
% refresh the current settings and refresh the field view
RootPath_1_Callback(hObject,eventdata,handles)

%------------------------------------------------------------------------ 
% --- Fills the edit boxes RootPath, RootFile,NomType...from an input file name 'fileinput'
function display_file_name(handles,fileinput,index)
%------------------------------------------------------------------------
%% look for the input file existence
if ~exist(fileinput,'file')
    msgbox_uvmat('ERROR',['input file ' fileinput  ' does not exist'])
    return
end

%% set the mouse pointer to 'watch'
set(handles.uvmat,'Pointer','watch')
set(handles.RootPath,'BackgroundColor',[1 1 0])
drawnow

%% define the relevant handles for the first field series (index=1) or the second file series (index=2)
if ~exist('index','var')
    index=1;
end
if index==1
    handles_RootPath=handles.RootPath;
    handles_SubDir=handles.SubDir;
    handles_RootFile=handles.RootFile;
    handles_FileIndex=handles.FileIndex;
    handles_NomType=handles.NomType;
    handles_FileExt=handles.FileExt;
elseif index==2
    handles_RootPath=handles.RootPath_1;
    handles_SubDir=handles.SubDir_1;
    handles_RootFile=handles.RootFile_1;
    handles_FileIndex=handles.FileIndex_1;
    handles_NomType=handles.NomType_1;
    handles_FileExt=handles.FileExt_1;
    set(handles.RootPath_1,'Visible','on')
    set(handles.RootFile_1,'Visible','on')
    set(handles.SubDir_1,'Visible','on');
    set(handles.FileIndex_1,'Visible','on');
    set(handles.FileExt_1,'Visible','on');
    set(handles.NomType_1,'Visible','on');
end

%% detect root name, nomenclature and indices in the input file name:
[FilePath,FileName,FileExt]=fileparts(fileinput);
% detect the file type, get the movie object if relevant, and look for the corresponding file series:
% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);

%% open the file or fill the GUI uvmat according to the detected file type
switch FileType
    case ''
        msgbox_uvmat('ERROR','invalid input file type')
    case 'txt'
        edit(fileinput)
    case 'figure'                           %display matlab figure
        hfig=open(fileinput);
        set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
        set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
        set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
    case {'xml','xls'}                % edit xml or Excel files
        editxml(fileinput);
    otherwise
        set(handles_RootPath,'String',RootPath);
        rootname=fullfile(RootPath,SubDir,RootFile);
        set(handles_SubDir,'String',['/' SubDir]);
        set(handles_RootFile,'String',['/' RootFile]); %display the separator
        indices=fileinput(length(rootname)+1:end);
        indices(end-length(FileExt)+1:end)=[]; %remove extension
        set(handles_FileIndex,'String',indices);
        set(handles_NomType,'String',NomType);
        set(handles_FileExt,'String',FileExt);
        if index==1
            % fill file index counters if the first file series is opened
            set(handles.i1,'String',num2str(i1));
            set(handles.i2,'String',num2str(i2));
            set(handles.j1,'String',num2stra(j1,NomType));
            set(handles.j2,'String',num2stra(j2,NomType));
        else %read the current field index if the second file series is opened
            i1=str2num(get(handles.i1,'String'));
            i2=str2num(get(handles.i2,'String'));
            j1=stra2num(get(handles.j1,'String'));
            j2=stra2num(get(handles.j2,'String'));
        end
        
        % synchronise indices of the second  input file if it exists
        if get(handles.SubField,'Value')==1% if the subfield button is activated, update the field numbers
            Input=read_GUI(handles.InputFile);
            if ~isfield(Input,'RootPath_1')||strcmp(Input.RootPath_1,'"')
                Input.RootPath_1=Input.RootPath;
            end
            if ~isfield(Input,'SubDir_1')||strcmp(Input.SubDir_1,'"')
                Input.SubDir_1=Input.SubDir;
            end
            if ~isfield(Input,'RootFile_1')||strcmp(Input.RootFile_1,'"')
                Input.RootFile_1=Input.RootFile;
            end
            if ~isfield(Input,'FileExt_1')||strcmp(Input.FileExt_1,'"')
                Input.FileExt_1=Input.FileExt;
            end
            if ~isfield(Input,'NomType_1')||strcmp(Input.NomType_1,'"')
                Input.NomType_1=Input.NomType;
            end
            %updtate the indices of the second field series to correspond to the newly opened one
            FileName_1=fullfile_uvmat(Input.RootPath_1,Input.SubDir_1,Input.RootFile_1,Input.FileExt_1,Input.NomType_1,i1,i2,j1,j2);
            if exist(FileName_1,'file')
                FileIndex_1=fullfile_uvmat('','','','',Input.NomType_1,i1,i2,j1,j2);
                set(handles.FileIndex_1,'String',FileIndex_1)
            else
                msgbox_uvmat('WARNING','unable to synchronise the indices of the two series')
%                 set(handles.SubField,'Value',0)
%                 SubField_Callback([], [], handles)
            end
        end
        
        %enable other menus
        set(handles.MenuOpen_1,'Enable','on')
        set(handles.MenuFile_1_1,'Enable','on')
        set(handles.MenuFile_2_1,'Enable','on')
        set(handles.MenuFile_3_1,'Enable','on')
        set(handles.MenuFile_4_1,'Enable','on')
        set(handles.MenuFile_5_1,'Enable','on')
        set(handles.MenuExport,'Enable','on')
        set(handles.MenuExportFigure,'Enable','on')
        set(handles.MenuExportMovie,'Enable','on')
        set(handles.MenuTools,'Enable','on')
%         set(handles.OBJECT_txt,'Visible','on')
%         set(handles.edit_object,'Visible','on')
%          set(handles.ListObject_1,'Visible','on')
%          set(handles.ViewObject,'Visible','on')
%         set(handles.frame_object,'Visible','on')
        
        % initiate input file series and refresh the current field view:     
        update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,index);

end

%% set back the mouse pointer to arrow
set(handles.uvmat,'Pointer','arrow')


%------------------------------------------------------------------------
% --- Update information about a new field series (indices to scan, timing,
%     calibration from an xml file, then refresh current plots
function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,VideoObject,index)
%------------------------------------------------------------------------
%% define the relevant handles depending on the index (1=first file series, 2= second file series)
if ~exist('index','var')
    index=1;
end
if index==1
    handles_RootPath=handles.RootPath;
    handles_Fields=handles.Fields;
elseif index==2
    handles_RootPath=handles.RootPath_1;
    handles_Fields=handles.Fields_1;
end

set(handles_RootPath,'BackgroundColor',[1 1 0])
drawnow
set(handles.Fields,'UserData',[])% reinialize data from uvmat opening
UvData=get(handles.uvmat,'UserData');%huvmat=handles of the uvmat interface
UvData.NewSeries=1; %flag for run0: begin a new series
UvData.TestInputFile=1;
UvData.FileType{index}=FileType;
UvData.i1_series{index}=i1_series;
UvData.i2_series{index}=i2_series;
UvData.j1_series{index}=j1_series;
UvData.j2_series{index}=j2_series;
% set(handles.CheckFixPair,'Value',1) % activate by default the comp_input '-'input window
set(handles.FixVelType,'Value',0); %desactivate fixed veltype
if index==1
    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
else
    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
end
FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
FileBase=fullfile(RootPath,RootFile);
if ~exist(FileName,'file')
   msgbox_uvmat('ERROR',['input file ' FileName ' not found']);
    return
end
nbfield=[];%default
nbfield_j=[];%default

%% read timing and total frame number from the current file (movie files) !! may be overrid by xml file
XmlData.Time=[];%default
XmlData.GeometryCalib=[];%default
TimeUnit=[];%default
testima=0; %test for image input
imainfo=[];
ColorType='falsecolor'; %default
hhh=[];
UvData.MovieObject{index}=VideoObject;
if ~isempty(VideoObject)
    imainfo=get(VideoObject);
    testima=1;
    nbfield_j=1;
    TimeUnit='s';
    XmlData.Time=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames-1)/imainfo.FrameRate)';
    % %         nbfield=imainfo.NumberOfFrames;
    set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FrameRate) 'ms']);%display the elementary time interval in millisec
    ColorType='truecolor';
elseif ~isempty(FileExt(2:end))&&(~isempty(imformats(FileExt(2:end))) || isequal(FileExt,'.vol'))%&& isequal(NomType,'*')% multi-frame image
    testima=1;
    if ~isequal(SubDir,'')
        RootFile=get(handles.RootFile,'String');
        imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]);
    else
        imainfo=imfinfo([FileBase FileIndices FileExt]);
    end
    ColorType=imainfo.ColorType;%='truecolor' for color images
    if length(imainfo) >1 %case of image with multiple frames
        nbfield=length(imainfo);
        nbfield_j=1;
    end
end
if isfield(imainfo,'Width') && isfield(imainfo,'Height')
    if length(imainfo)>1
        set(handles.num_Npx,'String',num2str(imainfo(1).Width));%fills nbre of pixels x box
        set(handles.num_Npy,'String',num2str(imainfo(1).Height));%fills nbre of pixels x box
    else
        set(handles.num_Npx,'String',num2str(imainfo.Width));%fills nbre of pixels x box
        set(handles.num_Npy,'String',num2str(imainfo.Height));%fills nbre of pixels x box
    end
else
    set(handles.num_Npx,'String','');%fills nbre of pixels x box
    set(handles.num_Npy,'String','');%fills nbre of pixels x box
end
set(handles.CheckBW,'Value',strcmp(ColorType,'grayscale'))% select handles.CheckBW if grayscale image

%% read parameters (time, geometric calibration..) from a documentation file (.xml advised)
SubDirBase=regexprep(SubDir,'\..*','');%take the root part of SubDir, before the first dot '.'
filexml=fullfile(RootPath,[SubDirBase '.xml']);% new convention: xml above the image dir
if ~exist(filexml,'file')
    filexml=fullfile(RootPath,SubDir,[RootFile '.xml']);%old convention: xml within the image directroy
end
warntext='';%default warning message
NbSlice=1;%default
set(handles.RootPath,'BackgroundColor',[1 1 1])
if exist(filexml,'file')
    set(handles.view_xml,'Visible','on')
    set(handles.view_xml,'BackgroundColor',[1 1 0])
    set(handles.view_xml,'String','view .xml')
    drawnow
    [XmlData,warntext]=imadoc2struct(filexml);
    if ~isempty(warntext)
        msgbox_uvmat('WARNING',warntext)
    end
    if isfield(XmlData,'TimeUnit')
        if isfield(XmlData,'TimeUnit')&& ~isempty(XmlData.TimeUnit)
            TimeUnit=XmlData.TimeUnit;
        end
    end
    set(handles.view_xml,'BackgroundColor',[1 1 1])
    drawnow
    if isfield(XmlData, 'GeometryCalib') && ~isempty(XmlData.GeometryCalib)
        if isfield(XmlData.GeometryCalib,'VolumeScan') && isequal(XmlData.GeometryCalib.VolumeScan,'y')
            set (handles.nb_slice,'String','volume')
        end
        hgeometry_calib=findobj('tag','geometry_calib');
        if ~isempty(hgeometry_calib)
            GUserData=get(hgeometry_calib,'UserData');
            if ~(isfield(GUserData,'XmlInputFile') && strcmp(GUserData.XmlInputFile,filexml))
                answer=msgbox_uvmat('INPUT_Y-N','replace the display of geometry_calib with the new input data?');
                if strcmp(answer,'Yes')
                    geometry_calib(filexml);%diplay the new calibration points and parameters in geometry_calib
                end
            end
        end
    end  
else
    fileciv=fullfile(RootPath,SubDir,[RootFile '.civ']);
    if exist(fileciv,'file')% if .civ file found (very old convention)
        [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext(fileciv);
        GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
        GeometryCalib.Tx=0;
        GeometryCalib.Ty=0;
        GeometryCalib.Tz=1;
        GeometryCalib.dpx=1;
        GeometryCalib.dpy=1;
        GeometryCalib.sx=1;
        GeometryCalib.Cx=0;
        GeometryCalib.Cy=0;
        GeometryCalib.f=1;
        GeometryCalib.kappa1=0;
        GeometryCalib.CoordUnit='cm';
        XmlData.GeometryCalib=GeometryCalib;
        if error==2, warntext=['no file ' fileciv];
        elseif error==1, warntext='inconsistent number of fields in the .civ file';
        end
        set(handles.num_Npx,'String',num2str(npx));%fills nbre of pixels x box
        set(handles.num_Npy,'String',num2str(npy));%fills nbre of pixels y box
        set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box
        set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box
        set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box
        set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box
        set(handles.view_xml,'Visible','on')
        set(handles.view_xml,'String','view .civ')
    else
        set(handles.view_xml,'Visible','off')
    end
end

%% store last index in handles.lat_i and .last_j
nbfield=max(max(i2_series));
if isempty(nbfield)
    nbfield=max(max(i1_series));
end
nbfield_j=max(max(j2_series));
if isempty(nbfield_j)
    nbfield_j=max(max(j1_series));
end
if ~isempty(XmlData.Time)
    %transform .Time to a column vector if it is a line vector the nomenclature uses a single index
    if isequal(size(XmlData.Time,1),1)
%     if isequal(nbfield,1) && ~isequal(nbfield_j,1)% .Time is a line vector
        NomType=get(handles.NomType,'String');
%         if isempty(nbfield_j)
%         if numel(NomType)>=2 &&(strcmp(NomType,'_i')||strcmp(NomType(1:2),'%0')||strcmp(NomType(1:2),'_%'))
            XmlData.Time=(XmlData.Time)';
    end
end
last_i_cell=get(handles.last_i,'String');
if isempty(nbfield)
    last_i_cell{1}='';
else
    last_i_cell{1}=num2str(nbfield);
end
set(handles.last_i,'String',last_i_cell)
last_j_cell=get(handles.last_j,'String');
if isempty(nbfield_j)
     last_j_cell{1}='';
else
     last_j_cell{1}=num2str(nbfield_j);
end
set(handles.last_j,'String',last_j_cell);

%% store geometric calibration in UvData
if isfield(XmlData,'GeometryCalib')
    GeometryCalib=XmlData.GeometryCalib;
    if isempty(GeometryCalib)
        set(handles.pxcm,'String','')
        set(handles.pycm,'String','')
        set(handles.transform_fct,'Value',1); %  no transform by default
    else
        if (isfield(GeometryCalib,'R')&& ~isequal(GeometryCalib.R(2,1),0) && ~isequal(GeometryCalib.R(1,2),0)) ||...
            (isfield(GeometryCalib,'kappa1')&& ~isequal(GeometryCalib.kappa1,0))
            set(handles.pxcm,'String','var')
            set(handles.pycm,'String','var')
        elseif isfield(GeometryCalib,'fx_fy')
            pixcmx=GeometryCalib.fx_fy(1);%*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx);
            pixcmy=GeometryCalib.fx_fy(2);%*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy);
            set(handles.pxcm,'String',num2str(pixcmx))
            set(handles.pycm,'String',num2str(pixcmy))
        end
        if ~get(handles.CheckFixLimits,'Value')
            set(handles.transform_fct,'Value',2); % phys transform by default if fixedLimits is off
        end
        if isfield(GeometryCalib,'SliceCoord')
            
           siz=size(GeometryCalib.SliceCoord);
           if siz(1)>1
               NbSlice=siz(1);
               set(handles.slices,'Visible','on')
               set(handles.slices,'Value',1)
           end
           if isfield(GeometryCalib,'VolumeScan') && isequal(GeometryCalib.VolumeScan,'y')
               set(handles.nb_slice,'String','volume')
           else
               set(handles.nb_slice,'String',num2str(NbSlice))
           end
           slices_Callback([],[], handles)
        end           
    end
end

%% update the data attached to the uvmat interface
if ~isempty(TimeUnit)
    set(handles.time_txt,'String',['time (' TimeUnit ')'])
end
UvData.TimeUnit=TimeUnit;
UvData.XmlData{index}=XmlData;
UvData.NewSeries=1;
% UvData.MovieObject=MovieObject;

%display warning message
if ~isequal(warntext,'')
    msgbox_uvmat('WARNING',warntext);
end

%% set default options in menu 'Fields'
if ~testima
    testcivx=0;
    if isfield(UvData,'FieldsString') && isequal(UvData.FieldsString,{'get_field...'})% field menu defined as input (from get_field)
        set(handles_Fields,'Value',1)
        set(handles_Fields,'String',{'get_field...'})
        UvData=rmfield(UvData,'FieldsString');
    else
        Data=nc2struct(FileName,'ListGlobalAttribute','Conventions','absolut_time_T0','civ');
        if strcmp(Data.Conventions,'uvmat/civdata') ||( ~isempty(Data.absolut_time_T0)&& ~isequal(Data.civ,0))%if the new input is Civx
            FieldList=calc_field;
            set(handles_Fields,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data
            set(handles_Fields,'Value',2) % set menu to 'velocity'
            col_vec=FieldList;
            col_vec(1)=[];%remove 'velocity' option for vector color (must be a scalar)
            testcivx=1;
        end
        if ~testcivx
            set(handles_Fields,'Value',1) % set menu to 'get_field...
            set(handles_Fields,'String',{'get_field...'})
            col_vec={'get_field...'};
        end
        set(handles.ColorScalar,'String',col_vec)
    end
end
set(handles.uvmat,'UserData',UvData)

%% set index navigation options and refresh plots
scan_option='i';%default
state_j='off'; %default
if index==2
    if get(handles.scan_j,'Value')
        scan_option='j'; %keep the scan option for the second fiel series
    end
    if strcmp(get(handles.j1,'Visible'),'on')
        state_j='on';
    end
end
if ~isempty(j1_series) 
        state_j='on';
        if isequal(nbfield,1) &&index==1
            scan_option='j'; %scan j index by default if nbfield=1                
        end 
end
if isequal(scan_option,'i')
     set(handles.scan_i,'Value',1)
     scan_i_Callback([],[], handles); 
else
     set(handles.scan_j,'Value',1)
     scan_j_Callback([],[], handles); 
end
set(handles.scan_j,'Visible',state_j)
set(handles.j1,'Visible',state_j)
set(handles.j2,'Visible',state_j)
set(handles.last_j,'Visible',state_j);
set(handles.frame_j,'Visible',state_j);
set(handles.j_text,'Visible',state_j);
if ~isempty(i2_series)||~isempty(j2_series)
    set(handles.CheckFixPair,'Visible','on')
elseif index==1
    set(handles.CheckFixPair,'Visible','off')
end

%% view the field  
run0_Callback([],[], handles); %view field
mask_test=get(handles.CheckMask,'value');
if mask_test
    MaskData=get(handles.CheckMask,'UserData');
    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
          delete(MaskData.maskhandle)    %delete old mask
    end
    CheckMask_Callback([],[],handles)
end

%% update list of recent files in the menubar and save it for future opening
MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
str_find=strcmp(FileName,MenuFile);
if isempty(find(str_find,1))
    MenuFile=[{FileName};MenuFile];%insert the current file if not already in the list
end
for ifile=1:min(length(MenuFile),5)
    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
    eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',MenuFile{ifile});'])
end
dir_perso=prefdir;
profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
if exist(profil_perso,'file')
    save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
else
    save (profil_perso,'MenuFile','-V6'); %store the file names for future opening of uvmat
end


%------------------------------------------------------------------------
% --- switch file index scanning options scan_i and scan_j in an exclusive way
function scan_i_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
if get(handles.scan_i,'Value')==1
    set(handles.scan_i,'BackgroundColor',[1 1 0])
    set(handles.scan_j,'Value',0)
else
    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
    set(handles.scan_j,'Value',1)
end
scan_j_Callback(hObject, eventdata, handles)

%------------------------------------------------------------------------
% --- switch file index scanning options scan_i and scan_j in an exclusive way
function scan_j_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
if get(handles.scan_j,'Value')==1
    set(handles.scan_j,'BackgroundColor',[1 1 0])
    set(handles.scan_i,'Value',0)
    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
%     NomType=get(handles.NomType,'String');
%     switch NomType
%     case {'_1_1-2','#_ab','%3dab'},% pair with j index
%         set(handles.CheckFixPair,'Visible','on')% option fixed pair on/off made visible (choice of avaible pair with buttons + and - if ='off')
%     otherwise
%         set(handles.CheckFixPair,'Visible','off')
%     end 
else
    set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
    set(handles.scan_i,'Value',1)
    set(handles.scan_i,'BackgroundColor',[1 1 0])
    set(handles.CheckFixPair,'Visible','off')
end

%------------------------------------------------------------------------
function i1_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(handles.i1,'BackgroundColor',[0.7 0.7 0.7])
NomType=get(handles.NomType,'String');
i1=stra2num(get(handles.i1,'String'));
i2=stra2num(get(handles.i2,'String'));
j1=stra2num(get(handles.j1,'String'));
j2=stra2num(get(handles.j2,'String'));
indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
%indices=name_generator('',num1,num_a,'',NomType,1,num2,num_b,'');
set(handles.FileIndex,'String',indices)
set(handles.FileIndex,'BackgroundColor',[0.7 0.7 0.7])
if get(handles.SubField,'Value')==1
    NomType_1=get(handles.NomType_1,'String');
    indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
     %indices=name_generator('',num1,num_a,'',NomType_1,1,num2,num_b,'');
     set(handles.FileIndex_1,'String',indices)
     set(handles.FileIndex_1,'BackgroundColor',[0.7 0.7 0.7])
end

%------------------------------------------------------------------------
function i2_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(handles.i2,'BackgroundColor',[0.7 0.7 0.7])
i1_Callback(hObject, eventdata, handles)

%------------------------------------------------------------------------
function j1_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(handles.j1,'BackgroundColor',[0.7 0.7 0.7])
i1_Callback(hObject, eventdata, handles)

%------------------------------------------------------------------------
function j2_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(handles.j2,'BackgroundColor',[0.7 0.7 0.7])
i1_Callback(hObject, eventdata, handles)

%------------------------------------------------------------------------
function slices_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
if get(handles.slices,'Value')==1
    set(handles.slices,'BackgroundColor',[1 1 0])
    set(handles.nb_slice,'Visible','on')
    set(handles.z_text,'Visible','on')
    set(handles.z_index,'Visible','on')
    nb_slice_Callback(hObject, eventdata, handles)
else
    set(handles.nb_slice,'Visible','off')
    set(handles.slices,'BackgroundColor',[0.7 0.7 0.7])
    set(handles.z_text,'Visible','off')
    set(handles.z_index,'Visible','off') 
    set(handles.masklevel,'Value',1)
    set(handles.masklevel,'String',{'1'})
end

%------------------------------------------------------------------------
function nb_slice_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
nb_slice_str=get(handles.nb_slice,'String');
if isequal(nb_slice_str,'volume')
    num=stra2num(get(handles.j1,'String'));
    last_j=get(handles.last_j,'String');
    nbslice=str2double(last_j{1});
else
    num=str2double(get(handles.i1,'String'));
    nbslice=str2double(get(handles.nb_slice,'String'));
end
z=mod(num-1,nbslice)+1;
set(handles.z_index,'String',num2str(z))
for ilist=1:nbslice
    list_index{ilist,1}=num2str(ilist);
end   
set(handles.masklevel,'String',list_index)
set(handles.masklevel,'Value',z)

%------------------------------------------------------------------------
% --- Executes on button press in view_xml.
function view_xml_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
%[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles);
 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
FileBase=fullfile(RootPath,RootFile);
option=get(handles.view_xml,'String');
if isequal(option,'view .xml')
    FileXml=[FileBase '.xml'];
    heditxml=editxml(FileXml);
end

%------------------------------------------------------------------------
% --- Executes on button press in CheckMask.
function CheckMask_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
%case of view mask selection
if isequal(get(handles.CheckMask,'Value'),1)
   % [FF,RootPath,FileBase]=read_file_boxes(handles);
     [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
     FileBase=fullfile(RootPath,RootFile);
    num_i1=stra2num(get(handles.i1,'String'));
    num_j1=stra2num(get(handles.j1,'String'));
    currentdir=pwd;  
    cd(RootPath);
    maskfiles=dir('*_*mask_*.png');%look for a mask file
    cd(currentdir);%come back to the working directory
    mdetect=0;
    if ~isempty(maskfiles)
        for ilist=1:length(maskfiles)
            maskname=maskfiles(ilist).name;% take the first mask file in the list
            [tild,tild,tild,tild,tild,tild,tild,MaskExt,Mask_NomType{ilist}]=fileparts_uvmat(maskname);
%             [rr,ff,x1,x2,xa,xb,xext,Mask_NomType{ilist}]=name2display(maskname);
             [tild,Name]=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
            nbmask_str=str2num(Name(i+1:ind_mask-1));
            if ~isempty(nbmask_str)
                nbslice(ilist)=nbmask_str; % number of different masks (slices)
            end
        end
        if isequal(min(nbslice),max(nbslice))
            nbslice=nbslice(1);
        else
            msgbox_uvmat('ERROR','several inconsistent mask sets coexist in the current image directory')
            return
        end
        if ~isempty(nbslice) && Name(i)=='_'
            Mask.Base=[FileBase Name(i:ind_mask+3)];
            Mask.NbSlice=nbslice;
            num_i1=mod(num_i1-1,nbslice)+1;
            Mask.NomType=regexprep(Mask_NomType{1},'0','');%remove '0' in nom type for masks
            [RootPath,RootFile]=fileparts(Mask.Base);
            maskname=fullfile_uvmat(RootPath,'',RootFile,'.png',Mask.NomType,num_i1,[],num_j1);
            %maskname=name_generator(Mask.Base,num_i1,num_j1,'.png',Mask.NomType);%
            mdetect=exist(maskname,'file');
            if mdetect
                set(handles.nb_slice,'String',Name(i+1:ind_mask-1));
                set(handles.nb_slice,'BackgroundColor',[1 1 0])
                set(handles.CheckMask,'UserData',Mask);
                set(handles.CheckMask,'BackgroundColor',[1 1 0])
                if nbslice > 1
                    set(handles.slices,'value',1)
                    slices_Callback(hObject, eventdata, handles)
                end
            end
        end
    end
    errormsg=[];%default
    if mdetect==0
        [FileName, PathName, filterindex] = uigetfile( ...
            {'*.png', ' (*.png)';
            '*.png',  '.png files '; ...
            '*.*', 'All Files (*.*)'}, ...
            'Pick a mask file *.png',FileBase);
        maskname=fullfile(PathName,FileName);
        if ~exist(maskname,'file')
            errormsg='no file browsed';
        end
        [RootDir,tild,RootFile,tild,tild,tild,tild,tild,Mask.NomType]=fileparts_uvmat(maskname);
%         [RootDir,RootFile,x1,x2,xa,xb,xext,Mask.NomType]=name2display(maskname);
        Mask.Base=fullfile(RootDir,RootFile);
        Mask.NbSlice=1;
        set(handles.CheckMask,'UserData',Mask);
        set(handles.CheckMask,'BackgroundColor',[1 1 0])
    end
    if isempty(errormsg)
        errormsg=update_mask(handles,num_i1,num_j1);
    end
    if ~isempty(errormsg)
            set(handles.CheckMask,'Value',0)
            set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
     end
else % desactivate mask display
    MaskData=get(handles.CheckMask,'UserData');
    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
          delete(MaskData.maskhandle)    
    end
    set(handles.CheckMask,'UserData',[])    
    UvData=get(handles.uvmat,'UserData');
    if isfield(UvData,'MaskName')
        UvData=rmfield(UvData,'MaskName');
        set(handles.uvmat,'UserData',UvData)
    end
    set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
end

%------------------------------------------------------------------------
function errormsg=update_mask(handles,num_i1,num_j1)
%------------------------------------------------------------------------
errormsg=[];%default
MaskData=get(handles.CheckMask,'UserData');
if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
    uistack(MaskData.maskhandle,'top');
end
num_i1_mask=mod(num_i1-1,MaskData.NbSlice)+1;
[RootPath,RootFile]=fileparts(MaskData.Base);
MaskName=fullfile_uvmat(RootPath,'',RootFile,'.png',MaskData.NomType,num_i1_mask,[],num_j1);
%MaskName=name_generator(MaskData.Base,num_i1_mask,num_j1,'.png',MaskData.NomType);
% huvmat=get(handles.CheckMask,'parent');
UvData=get(handles.uvmat,'UserData');
%update mask image if the mask is new
if ~ (isfield(UvData,'MaskName') && isequal(UvData.MaskName,MaskName)) 
    UvData.MaskName=MaskName; %update the recorded name on UvData
    set(handles.uvmat,'UserData',UvData);
    if ~exist(MaskName,'file')
        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
            delete(MaskData.maskhandle)    
        end
    else
        %read mask image
        Mask.AName='image';
        Mask.A=imread(MaskName);
        npxy=size(Mask.A);
        test_error=0;
        if length(npxy)>2
            errormsg=[MaskName ' is not a grey scale image'];
            return
        elseif ~isa(Mask.A,'uint8')
            errormsg=[MaskName ' is not a 8 bit grey level image'];
            return
        end
        Mask.AX=[0.5 npxy(2)-0.5];
        Mask.AY=[npxy(1)-0.5 0.5 ];
        Mask.CoordUnit='pixel';
        if isequal(get(handles.slices,'Value'),1)
           NbSlice=str2num(get(handles.nb_slice,'String'));
           num_i1=str2num(get(handles.i1,'String')); 
           Mask.ZIndex=mod(num_i1-1,NbSlice)+1;
        end
        %px to phys or other transform on field
         menu_transform=get(handles.transform_fct,'String');
        choice_value=get(handles.transform_fct,'Value');
        transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
        transform_list=get(handles.transform_fct,'UserData');
        transform=transform_list{choice_value};
        if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
            if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
                Calib=UvData.XmlData{1}.GeometryCalib;
                Mask=transform(Mask,UvData.XmlData{1});
            end
        end
        flagmask=Mask.A < 200;
        
        %make brown color image
        imflag(:,:,1)=0.9*flagmask;
        imflag(:,:,2)=0.7*flagmask;
        imflag(:,:,3)=zeros(size(flagmask));
        
        %update mask image
        hmask=[]; %default
        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
            hmask=MaskData.maskhandle;
        end
        if ~isempty(hmask)
            set(hmask,'CData',imflag)    
            set(hmask,'AlphaData',flagmask*0.6)
            set(hmask,'XData',Mask.AX);
            set(hmask,'YData',Mask.AY);
%             uistack(hmask,'top')
        else
            axes(handles.axes3)
            hold on    
            MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*flagmask);
%             set(MaskData.maskhandle,'AlphaData',0.6*flagmask)
            set(handles.CheckMask,'UserData',MaskData)
        end
    end
end

%------------------------------------------------------------------------
%------------------------------------------------------------------------
% III - MAIN REFRESH FUNCTIONS : 'FRAME PLOT'
%------------------------------------------------------------------------

%------------------------------------------------------------------------
% --- Executes on button press in runplus: make one step forward and call
% --- run0. The step forward is along the fields series 1 or 2 depending on 
% --- the scan_i and scan_j check box (exclusive each other)
function runplus_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(handles.runplus,'BackgroundColor',[1 1 0])%paint the command button in yellow
drawnow
%TODO: introduce the option: increment ='*' to move to the next available view
increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
% if isnan(increment)
%     set(handles.increment_scan,'String','1')%default value
%     increment=1;
% end
errormsg=runpm(hObject,eventdata,handles,increment);
if ~isempty(errormsg)
    msgbox_uvmat('ERROR',errormsg);
end
set(handles.runplus,'BackgroundColor',[1 0 0])%paint the command button back to red

%------------------------------------------------------------------------
% --- Executes on button press in runmin: make one step backward and call
% --- run0. The step backward is along the fields series 1 or 2 depending on 
% --- the scan_i and scan_j check box (exclusive each other)
function runmin_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(handles.runmin,'BackgroundColor',[1 1 0])%paint the command button in yellow
drawnow
increment=-str2num(get(handles.increment_scan,'String')); %get the field increment d
% if isnan(increment)
%     set(handles.increment_scan,'String','1')%default value
%     increment=1;
% end
errormsg=runpm(hObject,eventdata,handles,increment);
if ~isempty(errormsg)
    msgbox_uvmat('ERROR',errormsg);
end
set(handles.runmin,'BackgroundColor',[1 0 0])%paint the command button back to red

%------------------------------------------------------------------------
% -- Executes on button press in Movie: make a series of +> steps
function Movie_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(handles.Movie,'BackgroundColor',[1 1 0])%paint the command button in yellow
drawnow
increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
% if isnan(increment)
%     set(handles.increment_scan,'String','1')%default value
%     increment=1;
% end
set(handles.STOP,'Visible','on')
set(handles.speed,'Visible','on')
set(handles.speed_txt,'Visible','on')
set(handles.Movie,'BusyAction','queue')
UvData=get(handles.uvmat,'UserData');

while get(handles.Movie,'Value')==1 && get(handles.speed,'Value')~=0 && isequal(get(handles.Movie,'BusyAction'),'queue') % enable STOP command
        errormsg=runpm(hObject,eventdata,handles,increment);
        if ~isempty(errormsg)
            set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
            return
        end
        pause(1.02-get(handles.speed,'Value'))% wait for next image
end
if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
    UvData.aviobj=close(UvData.aviobj);
   set(handles.uvmat,'UserData',UvData);
end
set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red

%------------------------------------------------------------------------
% -- Executes on button press in Movie: make a series of <- steps
function MovieBackward_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(handles.MovieBackward,'BackgroundColor',[1 1 0])%paint the command button in yellow
drawnow
increment=-str2num(get(handles.increment_scan,'String')); %get the field increment d
set(handles.STOP,'Visible','on')
set(handles.speed,'Visible','on')
set(handles.speed_txt,'Visible','on')
set(handles.MovieBackward,'BusyAction','queue')
UvData=get(handles.uvmat,'UserData');

while get(handles.MovieBackward,'Value')==1 && get(handles.speed,'Value')~=0 && isequal(get(handles.MovieBackward,'BusyAction'),'queue') % enable STOP command
        errormsg=runpm(hObject,eventdata,handles,increment);
        if ~isempty(errormsg)
            set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
            return
        end
        pause(1.02-get(handles.speed,'Value'))% wait for next image
end
if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
    UvData.aviobj=close(UvData.aviobj);
   set(handles.uvmat,'UserData',UvData);
end
set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red

%------------------------------------------------------------------------
function STOP_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(handles.movie_pair,'BusyAction','Cancel')
set(handles.movie_pair,'value',0)
set(handles.Movie,'BusyAction','Cancel')
set(handles.MovieBackward,'BusyAction','Cancel')
set(handles.MenuExportMovie,'BusyAction','Cancel')
set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command buttonback to red
set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red

%------------------------------------------------------------------------
% --- function activated by runplus and run minus
function errormsg=runpm(hObject,eventdata,handles,increment)
%------------------------------------------------------------------------
errormsg='';%default
%% check for movie pair status
movie_status=get(handles.movie_pair,'Value');
if isequal(movie_status,1)
    STOP_Callback(hObject, eventdata, handles)%interrupt movie pair if active
end

%% read the current input file name(s) and field indices
InputFile=read_GUI(handles.InputFile);
InputFile.RootFile=regexprep(InputFile.RootFile,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
InputFile.SubDir=regexprep(InputFile.SubDir,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
FileExt=InputFile.FileExt;
NomType=get(handles.NomType,'String');
i1=str2num(get(handles.i1,'String'));%read the field indices (for movie, it is not given by the file name)
i2=[];%default
if strcmp(get(handles.i2,'Visible'),'on')
    i2=str2num(get(handles.i2,'String'));
end
j1=[];
if strcmp(get(handles.j1,'Visible'),'on')
    j1=stra2num(get(handles.j1,'String'));
end
j2=j1;
if strcmp(get(handles.j2,'Visible'),'on')
    j2=stra2num(get(handles.j2,'String'));
end
sub_value= get(handles.SubField,'Value');
if sub_value % a second input file has been entered 
     [InputFile.RootPath_1,InputFile.SubDir_1,InputFile.RootFile_1,InputFile.FileIndex_1,InputFile.FileExt_1,InputFile.NomType_1]=read_file_boxes_1(handles);   
    [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(InputFile.FileIndex_1);
%     InputFile.NomType_1=get(handles.NomType_1,'String');
else
    filename_1=[];
end   

%% increment (or decrement) the field indices and update the input filename(s)
CheckSearch=0;
if isempty(increment)
    CheckSearch=1;% search for the next available file
    set(handles.CheckFixPair,'Value',0)
end
CheckFixPair=get(handles.CheckFixPair,'Value')||(isempty(i2)&&isempty(j2));

% the pair i1-i2 or j1-j2 is imposed (check box CheckFixPair selected)
if CheckFixPair
    if get(handles.scan_i,'Value')==1% case of scanning along index i
        i1=i1+increment;
        i2=i2+increment;
        if sub_value
            i1_1=i1_1+increment;
            i2_1=i2_1+increment;
        end
    else % case of scanning along index j (burst numbers)
        j1=j1+increment;
        j2=j2+increment;
        if sub_value
            j1_1=j1_1+increment;
            j2_1=j2_1+increment;
        end
    end
    
% the pair i1-i2 or j1-j2 is free (check box CheckFixPair not selected): 
% the list of existing indices recorded in UvData is used
else
    UvData=get(handles.uvmat,'UserData');
    ref_i=i1;
    if ~isempty(i2)
        ref_i=floor((i1+i2)/2);% current reference index i
    end
    ref_j=1;
    if ~isempty(j1)
        ref_j=j1;
        if ~isempty(j2)
            ref_j=floor((j1+j2)/2);% current reference index j
        end
    end
    if ~isempty(increment)
        if get(handles.scan_i,'Value')==1% case of scanning along index i
            ref_i=ref_i+increment;% increment the current reference index i
        else % case of scanning along index j (burst numbers)
            ref_j=ref_j+increment;% increment the current reference index j if scan_j option is used
        end
    else % free increment
        if isequal(get(handles.runplus,'BackgroundColor'),[1 1 0])% if runplus is activated
            step=1;
        else
            step=-1;
        end
        if get(handles.scan_i,'Value')==1% case of scanning along index i
            ref_i=ref_i+step;
            while ref_i>=0  && size(UvData.i1_series{1},1)>=ref_i+1 && UvData.i1_series{1}(ref_i+1,ref_j+1,1)==0
                ref_i=ref_i+step;
            end
        else % case of scanning along index j (burst numbers)
            ref_j=ref_j+step;
            while ref_j>=0  && size(UvData.i1_series{1},2)>=ref_j+1 && UvData.i1_series{1}(ref_i+1,ref_j+1,1)==0
                ref_j=ref_j+step;
            end
        end
    end
    if ref_i<0
        errormsg='minimum i index reached';
    elseif ref_j<0
        errormsg='minimum j index reached';
    elseif ref_i+1>size(UvData.i1_series{1},1)
        errormsg='maximum i index reached';
    elseif ref_j+1>size(UvData.i1_series{1},2)
        errormsg='maximum j index reached';
    end
    if ~isempty(errormsg)
        return
    end
    i1_subseries=UvData.i1_series{1}(ref_i+1,ref_j+1,:);
    i1_subseries=i1_subseries(i1_subseries>0);
    if isempty(i1_subseries)
        errormsg='no next file';
        return
    else
        i1=i1_subseries(end);
    end
    if ~isempty(UvData.i2_series{1})
        i2_subseries=UvData.i2_series{1}(ref_i+1,ref_j+1,:);
        i2_subseries=i2_subseries(i2_subseries>0);
        i2=i2_subseries(end);
    end
    if ~isempty(UvData.j1_series{1})
        j1_subseries=UvData.j1_series{1}(ref_i+1,ref_j+1,:);
        j1_subseries=j1_subseries(j1_subseries>0);
        j1=j1_subseries(end);
    end
    if ~isempty(UvData.j2_series{1})
        j2_subseries=UvData.j2_series{1}(ref_i+1,ref_j+1,:);
        j2_subseries=j2_subseries(j2_subseries>0);
        j2=j2_subseries(end);
    end  
    % case of a second file series
    if numel(UvData.i1_series)>=2
        i1_subseries=UvData.i1_series{2}(ref_i+1,ref_j+1,:);
        i1_subseries=i1_subseries(i1_subseries>0);
        i1_1=i1_subseries(end);
        if ~isempty(UvData.i2_series{2})
            i2_subseries=UvData.i2_series{2}(ref_i+1,ref_j+1,:);
            i2_subseries=i2_subseries(i2_subseries>0);
            i2_1=i2_subseries(end);
        end
        if ~isempty(UvData.j1_series{2})
            j1_subseries=UvData.j1_series{2}(ref_i+1,ref_j+1,:);
            j1_subseries=j1_subseries(j1_subseries>0);
            j1_1=j1_subseries(end);
        end
        if ~isempty(UvData.j2_series{2})
            j2_subseries=UvData.j2_series{2}(ref_i+1,ref_j+1,:);
            j2_subseries=j2_subseries(j2_subseries>0);
            j2_1=j2_subseries(end);
        end
    end
end
filename=fullfile_uvmat(InputFile.RootPath,InputFile.SubDir,InputFile.RootFile,FileExt,NomType,i1,i2,j1,j2);
if sub_value
    filename_1=fullfile_uvmat(InputFile.RootPath_1,InputFile.SubDir_1,InputFile.RootFile_1,InputFile.FileExt_1,InputFile.NomType_1,i1_1,i2_1,j1_1,j2_1);
end

%% refresh plots
errormsg=refresh_field(handles,filename,filename_1,i1,i2,j1,j2);

%% update the index counters if the index move is successfull
if isempty(errormsg) 
    set(handles.i1,'String',num2stra(i1,NomType,1));
    if isequal(i2,i1)
        set(handles.i2,'String','');
    else
        set(handles.i2,'String',num2stra(i2,NomType,1));
    end
    set(handles.j1,'String',num2stra(j1,NomType,2));
    if isequal(j2,j1)
        set(handles.j2,'String','');
    else
        set(handles.j2,'String',num2stra(j2,NomType,2));
    end
    indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
    set(handles.FileIndex,'String',indices);
    if ~isempty(filename_1)
        indices_1=fullfile_uvmat('','','','',InputFile.NomType_1,i1_1,i2_1,j1_1,j2_1);
        set(handles.FileIndex_1,'String',indices_1);
    end
    if isequal(movie_status,1)
        set(handles.movie_pair,'Value',1)
        movie_pair_Callback(hObject, eventdata, handles); %reactivate moviepair if it was activated
    end
end

%------------------------------------------------------------------------
% --- Executes on button press in movie_pair: create an alternating movie with two view
function movie_pair_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
%% stop movie action if the movie_pair button is off
if ~get(handles.movie_pair,'value')
    set(handles.movie_pair,'BusyAction','Cancel')%stop movie pair if button is 'off'
    set(handles.i2,'String','')
    set(handles.j2,'String','')
    return
else
    set(handles.movie_pair,'BusyAction','queue')
end

%% initialisation
set(handles.movie_pair,'BackgroundColor',[1 1 0])%paint the command button in yellow
drawnow
list_fields=get(handles.Fields,'String');% list menu fields
index_fields=get(handles.Fields,'Value');% selected string index
FieldName=list_fields{index_fields}; % selected field
UvData=get(handles.uvmat,'UserData');
if isequal(FieldName,'image')
    test_1=0;
    [RootPath,SubDir,RootFile,FileIndices,Ext]=read_file_boxes(handles);
    NomType=get(handles.NomType,'String');
else
    list_fields=get(handles.Fields_1,'String');% list menu fields
    index_fields=get(handles.Fields_1,'Value');% selected string index
    FieldName=list_fields{index_fields}; % selected field
    if isequal(FieldName,'image')
        test_1=1;
        [RootPath,tild,RootFile,FileIndex_1,Ext,NomType]=read_file_boxes_1(handles);
    else
        msgbox_uvmat('ERROR','an image or movie must be first introduced as input')
        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
        set(handles.movie_pair,'Value',0)
        return
    end
end
num_i1=str2num(get(handles.i1,'String'));
num_j1=stra2num(get(handles.j1,'String'));
num_i2=str2num(get(handles.i2,'String'));
num_j2=stra2num(get(handles.j2,'String'));
if isempty(num_j2)
    if isempty(num_i2)   
        msgbox_uvmat('ERROR', 'a second image index i2 or j2 is needed to show the pair as a movie')
        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
         set(handles.movie_pair,'Value',0)
        return
    else
        num_j2=num_j1;%repeat the index i1 by default
    end
end
if isempty(num_i2)
    num_i2=num_i1;%repeat the index i1 by default
end
% imaname_1=name_generator(filebase,num_i2,num_j2,Ext,NomType);
imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,Ext,NomType,num_i2,[],num_j2);
if ~exist(imaname_1,'file')
      msgbox_uvmat('ERROR',['second input open (-)  ' imaname_1 ' not found']);
      set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
       set(handles.movie_pair,'Value',0)
      return
end

%% read the second image
Field.AName='image';
if test_1
    Field_a=UvData.Field_1;
else
    Field_a=UvData.Field;
end
Field_b.AX=Field_a.AX;
Field_b.AY=Field_a.AY;
% z index
nbslice=str2double(get(handles.nb_slice,'String'));
if ~isempty(nbslice)
    Field_b.ZIndex=mod(num_i2-1,nbslice)+1;
end
Field_b.CoordUnit='pixel';

%% determine the input file type
if (test_1 && isfield(UvData,'MovieObject')&& numel(UvData.MovieObject>=2))||(~test_1 && ~isempty(UvData.MovieObject{1}))
    FileType='movie';
elseif isequal(lower(Ext),'.avi')
    FileType='avi';
elseif isequal(lower(Ext),'.vol')
    FileType='vol';
else 
   form=imformats(Ext(2:end));
   if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
       if isequal(NomType,'*');
           FileType='multimage';
       else
           FileType='image';
       end
   end
end
switch FileType
        case 'movie'
            if test_1
                Field_b.A=read(UvData.MovieObject{2},num_i2);
            else
                Field_b.A=read(UvData.MovieObject{1},num_i2);
            end
        case 'avi'
            mov=aviread(imaname_1,num_i2);
            Field_b.A=frame2im(mov(1));
        case 'vol'
            Field_b.A=imread(imaname_1);
        case 'multimage'
            Field_b.A=imread(imaname_1,num_i2);
        case 'image'
            Field_b.A=imread(imaname_1);
end 
if get(handles.slices,'Value')
    Field.ZIndex=str2double(get(handles.z_index,'String'));
end

%px to phys or other transform on field
menu_transform=get(handles.transform_fct,'String');
choice_value=get(handles.transform_fct,'Value');
transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
transform_list=get(handles.transform_fct,'UserData');
transform=transform_list{choice_value};
if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
    if test_1 && isfield(UvData,'XmlData') && numel(UvData.XmlData)==2 && isfield(UvData.XmlData{2},'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
        Field_a=transform(Field_a,UvData.XmlData{2});%the first field has been stored without transform
        Field_b=transform(Field_b,UvData.XmlData{2});
    elseif ~test_1 && isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'GeometryCalib')%use geometry calib
        Field_b=transform(Field_b,UvData.XmlData{1});
    end
end

 % make movie until movie speed is set to 0 or STOP is activated
hima=findobj(handles.axes3,'Tag','ima');% %handles.axes3 =main plotting window (A GENERALISER)
set(handles.STOP,'Visible','on')
set(handles.speed,'Visible','on')
set(handles.speed_txt,'Visible','on')
while get(handles.speed,'Value')~=0 && isequal(get(handles.movie_pair,'BusyAction'),'queue')%isequal(get(handles.run0,'BusyAction'),'queue'); % enable STOP command
    % read and plot the series of images in non erase mode
    set(hima,'CData',Field_b.A); 
    pause(1.02-get(handles.speed,'Value'));% wait for next image
    set(hima,'CData',Field_a.A);
    pause(1.02-get(handles.speed,'Value'));% wait for next image
end
set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
 set(handles.movie_pair,'Value',0)

%------------------------------------------------------------------------
% --- Executes on button press in run0.
function run0_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
drawnow
[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
filename_1=[];%default
if get(handles.SubField,'Value')
    [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
    filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
end
num_i1=stra2num(get(handles.i1,'String'));
num_i2=stra2num(get(handles.i2,'String'));
num_j1=stra2num(get(handles.j1,'String'));
num_j2=stra2num(get(handles.j2,'String'));

errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2);

if ~isempty(errormsg)
      msgbox_uvmat('ERROR',errormsg);
else
    set(handles.i1,'BackgroundColor',[1 1 1])
    set(handles.i2,'BackgroundColor',[1 1 1])
    set(handles.j1,'BackgroundColor',[1 1 1])
    set(handles.j2,'BackgroundColor',[1 1 1])
    set(handles.FileIndex,'BackgroundColor',[1 1 1])
    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
end    
set(handles.run0,'BackgroundColor',[1 0 0])


%------------------------------------------------------------------------
% --- read the input files and refresh all the plots, including projection.
% OUTPUT: 
%  errormsg: error message char string  =[] by default
% INPUT:
% filename: first input file (=[] in the absence of input file)
% filename_1: second input file (=[] in the asbsenc of secodn input file) 
% num_i1,num_i2,num_j1,num_j2; frame indices
% Field: structure describing an optional input field (then replace the input file)

function errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2,Field)
%------------------------------------------------------------------------

%% initialisation
abstime=[];
abstime_1=[];
dt=[];
if ~exist('Field','var')
    Field={};
end
UvData=get(handles.uvmat,'UserData');
if ishandle(handles.UVMAT_title) %remove title panel on uvmat
    delete(handles.UVMAT_title)
end

%% determine the main input file information for action
FileType=[];%default
if ~exist(filename,'file')
    errormsg=['input file ' filename ' does not exist'];
    return
end
NomType=get(handles.NomType,'String');
% NomType=get(handles.FileIndex,'UserData');
%update the z position index
nbslice_str=get(handles.nb_slice,'String');
if isequal(nbslice_str,'volume')%NOT USED
    z_index=num_j1;
    set(handles.z_index,'String',num2str(z_index))
else
    nbslice=str2num(nbslice_str);
    z_index=mod(num_i1-1,nbslice)+1;
    set(handles.z_index,'String',num2str(z_index))
end
% refresh menu for save_mask if relevant
masknumber=get(handles.masklevel,'String');
if length(masknumber)>=z_index
    set(handles.masklevel,'Value',z_index)
end

%% read the first input field if a filename has been introduced
ParamIn.ColorVar='';%default variable name for vector color
if ~isempty(filename)
    ObjectName=filename;
    FieldName='';%default
    VelType='';%default
%     FileType=UvData.FileType{1};
    switch UvData.FileType{1}
        case {'civx','civdata','netcdf'};
            list_fields=get(handles.Fields,'String');% list menu fields
  %          index_fields=get(handles.Fields,'Value');% selected string index
            FieldName= list_fields{get(handles.Fields,'Value')}; % selected field
            if ~strcmp(FieldName,'get_field...')
                if get(handles.FixVelType,'Value')
                    VelTypeList=get(handles.VelType,'String');
                    VelType=VelTypeList{get(handles.VelType,'Value')};
                end
            end
            if strcmp(FieldName,'velocity')
                list_code=get(handles.ColorCode,'String');% list menu fields
                index_code=get(handles.ColorCode,'Value');% selected string index
                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
                    list_code=get(handles.ColorScalar,'String');% list menu fields
                    index_code=get(handles.ColorScalar,'Value');% selected string index
                    ParamIn.ColorVar= list_code{index_code}; % selected field
                end
            end
        case {'video','mmreader'}
            ObjectName=UvData.MovieObject{1};         
        case 'vol' %TODO: update
            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
                ParamIn.Npy=UvData.XmlData.Npy;
                ParamIn.Npx=UvData.XmlData.Npx;
            else            
                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
                return
            end
    end
    ParamIn.FieldName=FieldName;
    ParamIn.VelType=VelType;
    ParamIn.GUIName='get_field';
    [Field{1},ParamOut,errormsg] = read_field(ObjectName,UvData.FileType{1},ParamIn,num_i1);
    if ~isempty(errormsg)
        errormsg=['error in reading ' filename ': ' errormsg];
        return
    end  
    if isfield(ParamOut,'Npx')&& isfield(ParamOut,'Npy')
        set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
        set(handles.num_Npy,'String',num2str(ParamOut.Npy));
    end
    if isfield(ParamOut,'TimeIndex')% case of time obtained from get_field
        set(handles.i1,'String',num2str(ParamOut.TimeIndex))
    end
    if isfield(ParamOut,'TimeValue')
        Field{1}.Time=ParamOut.TimeValue;% case of time obtained from get_field
    end
end

%% choose and read a second field filename_1 if defined
VelType_1=[];%default
FieldName_1=[];
ParamOut_1=[];
if ~isempty(filename_1)
    if ~exist(filename_1,'file')
        errormsg=['second file ' filename_1 ' does not exist'];
        return
    end
    Name=filename_1;
    switch UvData.FileType{2}
        case {'civx','civdata','netcdf'};
            list_fields=get(handles.Fields_1,'String');% list menu fields
            FieldName_1= list_fields{get(handles.Fields_1,'Value')}; % selected field
            if ~strcmp(FieldName,'get_field...')
                if get(handles.FixVelType,'Value')
                    VelTypeList=get(handles.VelType_1,'String');
                    VelType_1=VelTypeList{get(handles.VelType_1,'Value')};% read the velocity type.
                end
            end
            if strcmp(FieldName_1,'velocity')&& strcmp(get(handles.ColorCode,'Visible'),'on')
                list_code=get(handles.ColorCode,'String');% list menu fields
                index_code=get(handles.ColorCode,'Value');% selected string index
                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
                    list_code=get(handles.ColorScalar,'String');% list menu fields
                    index_code=get(handles.ColorScalar,'Value');% selected string index
                    ParamIn_1.ColorVar= list_code{index_code}; % selected field for vector color display                  
                end
            end
        case {'video','mmreader'}
            Name=UvData.MovieObject{2};
        case 'vol' %TODO: update
            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
                ParamIn_1.Npy=UvData.XmlData.Npy;
                ParamIn_1.Npx=UvData.XmlData.Npx;
            else
                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
                return
            end
    end
    if isequal(get(handles.NomType_1,'Visible'),'on')
    NomType_1=get(handles.NomType_1,'String');
    else
        NomType_1=get(handles.NomType,'String');
    end
    test_keepdata_1=0;% test for keeping the previous stored data if the input files are unchanged
    if ~isequal(NomType_1,'*')%in case of a series of files (not avi movie)
        if isfield(UvData,'filename_1')%&& isfield(UvData,'VelType_1') && isfield(UvData,'FieldName_1')
            test_keepdata_1= strcmp(filename_1,UvData.filename_1) ;%&& strcmp(FieldName_1,UvData.FieldName_1);
        end
    end
    if test_keepdata_1
        Field{2}=UvData.Field_1;% keep the stored field
        ParamOut_1=UvData.ParamOut_1;
    else
        ParamIn_1.FieldName=FieldName_1;
        ParamIn_1.VelType=VelType_1;
        ParamIn_1.GUIName='get_field_1';
        [Field{2},ParamOut_1,errormsg] = read_field(Name,UvData.FileType{2},ParamIn_1,num_i1);
        if ~isempty(errormsg)
            errormsg=['error in reading ' FieldName_1 ' in ' filename_1 ': ' errormsg];
            return
        end
%         UvData.Field_1=Field{2}; %store the second field for possible use at next RUN
    end
end

%% update uvmat interface
if isfield(ParamOut,'Npx')
    set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
    set(handles.num_Npy,'String',num2str(ParamOut.Npy));
elseif isfield(ParamOut_1,'Npx')
    set(handles.num_Npx,'String',num2str(ParamOut_1.Npx));% display image size on the interface
    set(handles.num_Npy,'String',num2str(ParamOut_1.Npy));
end

%% update the display menu for the first velocity type (first menuline)
test_veltype=0;
% if ~isequal(FileType,'netcdf')|| isequal(FieldName,'get_field...')
if (strcmp(UvData.FileType{1},'civx')||strcmp(UvData.FileType{1},'civdata'))&& ~strcmp(FieldName,'get_field...')
    test_veltype=1;
    set(handles.VelType,'Visible','on')
    set(handles.VelType_1,'Visible','on')
    set(handles.FixVelType,'Visible','on')
    menu=set_veltype_display(ParamOut.CivStage,UvData.FileType{1});
    index_menu=strcmp(ParamOut.VelType,menu);%look for VelType in  the menu
    index_val=find(index_menu,1);
    if isempty(index_val)
        index_val=1;
    end
    set(handles.VelType,'Value',index_val)
    if ~get(handles.SubField,'value')
        set(handles.VelType,'String',menu)
        set(handles.VelType_1,'Value',1)
        set(handles.VelType_1,'String',[{''};menu])
    end
else
    set(handles.VelType,'Visible','off')
end
% display the Fields menu from the input file and pick the selected one: 
field_index=strcmp(ParamOut.FieldName,ParamOut.FieldList);
set(handles.Fields,'String',ParamOut.FieldList); %update the field menu
set(handles.Fields,'Value',find(field_index,1))

%% update the display menu for the second velocity type (second menuline)
test_veltype_1=0;
if isempty(filename_1)
    set(handles.Fields_1,'Value',1); %update the field menu
    set(handles.Fields_1,'String',[{''};ParamOut.FieldList]); %update the field menu
elseif ~test_keepdata_1
    if (~strcmp(UvData.FileType{2},'netcdf')&&~strcmp(UvData.FileType{2},'civdata')&&~strcmp(UvData.FileType{2},'civx'))|| isequal(FieldName_1,'get_field...')
        set(handles.VelType_1,'Visible','off')
    else
        test_veltype_1=1;
        set(handles.VelType_1,'Visible','on')
%         if ~get(handles.FixVelType,'Value')
            menu=set_veltype_display(ParamOut_1.CivStage);
            index_menu=strcmp(ParamOut_1.VelType,menu);
            set(handles.VelType_1,'Value',1+find(index_menu,1))
            set(handles.VelType_1,'String',[{''};menu])
%         end
    end
    % update the second field menu: the same quantity
    set(handles.Fields_1,'String',[{''};ParamOut_1.FieldList]); %update the field menu
    % display the Fields menu from the input file and pick the selected one: 
    field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
    set(handles.Fields_1,'Value',find(field_index,1)+1)  
%     % synchronise  with the first menu if the first selection is not 'velocity'
%     if ~strcmp(ParamOut.FieldName,'velocity')
%         field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
%         set(handles.Fields_1,'Value',field_index); %update the field menu
%         ParamOut_1.FieldName=ParamOut.FieldName;
%         set(handles.Fields_1,'String',ParamOut_1.FieldList)
%     end
end
if test_veltype||test_veltype_1
     set(handles.FixVelType,'Visible','on')
else
     set(handles.FixVelType,'Visible','off')
end

% field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
% set(handles.Fields,'String',ParamOut.FieldList); %update the field menu
% set(handles.Fields,'Value',find(field_index,1))
    
%% introduce w as background image by default for a new series (only for nbdim=2)
if ~isfield(UvData,'NewSeries')
    UvData.NewSeries=1;
end
%put W as background image by default if NbDim=2:
if  UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W) && ~isequal(Field{1}.NbDim,3);
        set(handles.SubField,'Value',1);
        set(handles.RootPath_1,'String','"')
        set(handles.RootFile_1,'String','"')
        set(handles.SubDir_1,'String','"');
         indices=fullfile_uvmat('','','','',NomType,num_i1,num_i2,num_j1,num_j2);
        set(handles.FileIndex_1,'String',indices)
        set(handles.FileExt_1,'String','"');
        set(handles.Fields_1,'Visible','on');
        set(handles.Fields_1,'Visible','on');
        set(handles.RootPath_1,'Visible','on')
        set(handles.RootFile_1,'Visible','on')
        set(handles.SubDir_1,'Visible','on');
        set(handles.FileIndex_1,'Visible','on');
        set(handles.FileExt_1,'Visible','on');
        set(handles.Fields_1,'Visible','on');
        Field{1}.AName='w';
end           

%% display time
testimedoc=0;
TimeUnit='';
if isfield(Field{1},'Time')
    abstime=Field{1}.Time;%time read from the netcdf input file 
end
if numel(Field)==2 && isfield(Field{2},'Time')
    abstime_1=Field{2}.Time;%time read from the netcdf input file 
end
if isfield(Field{1},'Dt')
    dt=Field{1}.Dt;%dt read from the netcdf input file
    if isfield(Field{1},'TimeUnit')
       TimeUnit=Field{1}.TimeUnit;
    end
elseif numel(Field)==2 && isfield(Field{2},'Dt')%dt obtained from the second field if not defined in the first
    dt=Field{2}.Dt;%dt read from the netcdf input file
    if isfield(Field{2},'TimeUnit')
       TimeUnit=Field{2}.TimeUnit;
    end
end
% time from xml file overset previous result
if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'Time')
    if isempty(num_i2)||isnan(num_i2)
        num_i2=num_i1;
    end
    if isempty(num_j1)||isnan(num_j1)
        num_j1=1;
    end
    if isempty(num_j2)||isnan(num_j2)
        num_j2=num_j1;
    end
    siz=size(UvData.XmlData{1}.Time);
    if siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
        abstime=(UvData.XmlData{1}.Time(num_i1,num_j1)+UvData.XmlData{1}.Time(num_i2,num_j2))/2;%overset the time read from files
        dt=(UvData.XmlData{1}.Time(num_i2,num_j2)-UvData.XmlData{1}.Time(num_i1,num_j1));
        Field{1}.Dt=dt;
        if isfield(UvData.XmlData{1},'TimeUnit')
            TimeUnit=UvData.XmlData{1}.TimeUnit;
        end
    end
    if numel(UvData.XmlData)==2
        [tild,tild,tild,num_i1,num_i2,num_j1,num_j2]=fileparts_uvmat(['xx' get(handles.FileIndex_1,'String') get(handles.FileExt_1,'String')]);
        if isempty(num_i2)
            num_i2=num_i1;
        end
        if isempty(num_j1)
            num_j1=1;
        end
        if isempty(num_j2)
            num_j2=num_j1;
        end
        siz=size(UvData.XmlData{2}.Time);
        if ~isempty(num_i1) && siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
            abstime_1=(UvData.XmlData{2}.Time(num_i1,num_j1)+UvData.XmlData{2}.Time(num_i2,num_j2))/2;%overset the time read from files
            Field{2}.Dt=(UvData.XmlData{2}.Time(num_i2,num_j2)-UvData.XmlData{2}.Time(num_i1,num_j1));
        end
    end
end
if ~isequal(numel(abstime),1)
    abstime=[];
end
if ~isequal(numel(abstime_1),1)
      abstime_1=[];
end  
set(handles.abs_time,'String',num2str(abstime,4))
set(handles.abs_time_1,'String',num2str(abstime_1,4))
% if testimedoc && isfield(UvData,'dt')
%     dt=UvData.dt;
% end 
if isempty(dt)||isequal(dt,0)
    set(handles.Dt_txt,'String','')
else
    if  isempty(TimeUnit)
        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  10^(-3)'] )
    else
        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  m' TimeUnit] )
    end
end


%% store the current open names, fields and vel types in uvmat interface 
UvData.filename_1=filename_1;

%% apply coordinate transform or other user fct
XmlData=[];%default
XmlData_1=[];%default
if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority
    XmlData=UvData.XmlData{1};
    if numel(UvData.XmlData)==2
        XmlData_1=UvData.XmlData{2};
    end
end
choice_value=get(handles.transform_fct,'Value');
transform_list=get(handles.transform_fct,'UserData');
transform=transform_list{choice_value};%selected function handles
% z index
if ~isempty(filename)
    Field{1}.ZIndex=z_index;
end
if ~isempty(transform)
    if length(Field)>=2
        Field{2}.ZIndex=z_index;
        [Field{1},Field{2}]=transform(Field{1},XmlData,Field{2},XmlData_1);
        if isempty(Field{2})
            Field(2)=[];
        end
    else
        Field{1}=transform(Field{1},XmlData);
    end
    %% update tps in phys coordinates if needed
    if (strcmp(VelType,'filter1')||strcmp(VelType,'filter2'))&& strcmp(UvData.FileType{1},'civdata')&&isfield(Field{1},'U')&& isfield(Field{1},'V')
        Field{1}.X=Field{1}.X(Field{1}.FF==0);
        Field{1}.Y=Field{1}.Y(Field{1}.FF==0);
        Field{1}.U=Field{1}.U(Field{1}.FF==0);
        Field{1}.V=Field{1}.V(Field{1}.FF==0);
        [Field{1}.SubRange,Field{1}.NbSites,Field{1}.Coord_tps,Field{1}.U_tps,Field{1}.V_tps]=filter_tps([Field{1}.X Field{1}.Y],Field{1}.U,Field{1}.V,[],Field{1}.Patch1_SubDomain,0);
    end
    if numel(Field)==2 && ~test_keepdata_1 && isequal(UvData.FileType{2}(1:3),'civ') && ~isequal(ParamOut_1.FieldName,'get_field...')%&&~isempty(FieldName_1)
        %update tps in phys coordinates if needed
        if (strcmp(VelType_1,'filter1')||strcmp(VelType_1,'filter2'))&& strcmp(UvData.FileType{2},'civdata')&&isfield(Field{2},'U')&& isfield(Field{2},'V')
            Field{2}.X=Field{2}.X(Field{2}.FF==0);
            Field{2}.Y=Field{1}.Y(Field{2}.FF==0);
            Field{2}.U=Field{1}.U(Field{2}.FF==0);
            Field{2}.V=Field{1}.V(Field{2}.FF==0);
            [Field{2}.SubRange,Field{2}.NbSites,Field{2}.Coord_tps,Field{2}.U_tps,Field{2}.V_tps]=filter_tps([Field{2}.X Field{2}.Y],Field{2}.U,Field{2}.V,[],1500,0);
        end
    end
end

%% calculate scalar
if ~strcmp(ParamOut.FieldName,'get_field...')&& (strcmp(UvData.FileType{1},'civdata')||strcmp(UvData.FileType{1},'civx'))%&&~strcmp(ParamOut.FieldName,'velocity')&& ~strcmp(ParamOut.FieldName,'get_field...');% ~isequal(ParamOut.CivStage,0)%&&~isempty(FieldName)%
    Field{1}=calc_field([{ParamOut.FieldName} {ParamOut.ColorVar}],Field{1});
end
if numel(Field)==2 && ~strcmp(ParamOut_1.FieldName,'get_field...')&& ~test_keepdata_1 && (strcmp(UvData.FileType{2},'civdata')||strcmp(UvData.FileType{2},'civx'))  &&~strcmp(ParamOut_1.FieldName,'velocity') && ~strcmp(ParamOut_1.FieldName,'get_field...')
     Field{2}=calc_field([{ParamOut_1.FieldName} {ParamOut_1.ColorVar}],Field{2});
end

%% combine the two input fields (e.g. substract velocity fields)
%Field{1}.FieldList=[{ParamOut.FieldName} {ParamOut.ColorVar}];
if numel(Field)==2
%    Field{2}.FieldList=[{ParamOut_1.FieldName} {ParamOut_1.ColorVar}];
   [UvData.Field,errormsg]=sub_field(Field{1},Field{2});  
   UvData.Field_1=Field{2}; %store the second field for possible use at next RUN
   UvData.ParamOut_1=ParamOut_1;
else
   UvData.Field=Field{1};
end
if ~isempty(errormsg)
    errormsg=['error in uvmat/refresh_field/sub_field:' errormsg];
    return
end
%UvData.Field.FieldList={FieldName}; % TODO: to generalise, used for proj_field with tps interpolation

%% analyse input field
test_x=0;
test_z=0;% test for unstructured z coordinate
[errormsg,ListDimName,DimValue,VarDimIndex]=check_field_structure(UvData.Field);% check the input field structure
if ~isempty(errormsg)
    errormsg=['error in uvmat/refresh_field/check_field_structure: ' errormsg];% display error
    return
end
[CellVarIndex,NbDim,VarType,errormsg]=find_field_indices(UvData.Field);% analyse  the input field structure
if ~isempty(errormsg)
    errormsg=['error in uvmat/refresh_field/find_field_indices: ' errormsg];% display error
    return
end
[NbDim,imax]=max(NbDim);% spatial dimension of the input field
if isfield(UvData.Field,'NbDim')
    NbDim=UvData.Field.NbDim;% deal with plane fields containing z coordinates
end

%% get bounds and mesh (needed for mouse action and to open set_object)
if NbDim>1
    XName=''; %default
    YName='';
    %unstructured coordinates
    if ~isempty(VarType{imax}.coord_x)&&~isempty(VarType{imax}.coord_y)
        XName=UvData.Field.ListVarName{VarType{imax}.coord_x};
        YName=UvData.Field.ListVarName{VarType{imax}.coord_y};
        %nbvec=length(UvData.Field.(XName));%nbre of measurement points (e.g. vectors)
        test_x=1;%test for unstructured coordinates
        if ~isempty(VarType{imax}.coord_z)
            ZName=UvData.Field.ListVarName{VarType{imax}.coord_z};
        else
            NbDim=2;
        end
        %structured coordinate
    elseif numel(VarType)>=imax && numel(VarType{imax}.coord)>=NbDim && VarType{imax}.coord(NbDim)>0
        XName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim)};
        if NbDim> 1 && VarType{imax}.coord(NbDim-1)>0
            YName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim-1)}; %structured coordinates
        end
        % VarIndex=CellVarIndex{imax}; % list of variable indices
        DimIndex=VarDimIndex{CellVarIndex{imax}(1)}; %list of dim indices for the variable
        nbpoints_x=DimValue(DimIndex(NbDim));
        XMax=nbpoints_x;%default
        XMin=1;%default
    end
    
    if NbDim==3
        if ~test_x
            ZName=UvData.Field.ListVarName{VarType{imax}.coord(1)};%structured coordinates in 3D
        end
        ZMax=max(UvData.Field.(ZName));
        ZMin=min(UvData.Field.(ZName));
        UvData.Field.ZMax=ZMax;
        UvData.Field.ZMin=ZMin;
        test_z=1;
        if isequal(ZMin,ZMax)%no z dependency
            NbDim=2;
            test_z=0;
        end
    end
    if ~isempty (XName)
        XMax=max(max(UvData.Field.(XName)));
        XMin=min(min(UvData.Field.(XName)));
        UvData.Field.NbDim=NbDim;
        UvData.Field.XMax=XMax;
        UvData.Field.XMin=XMin;
        if NbDim >1&& ~isempty(YName)
            YMax=max(max(UvData.Field.(YName)));
            YMin=min(min(UvData.Field.(YName)));
            UvData.Field.YMax=YMax;
            UvData.Field.YMin=YMin;
        end
        nbvec=length(UvData.Field.(XName));
        if test_x %unstructured coordinates
            if test_z
                UvData.Field.Mesh=((XMax-XMin)*(YMax-YMin)*(ZMax-ZMin))/nbvec;% volume per vector
                UvData.Field.Mesh=(UvData.Field.Mesh)^(1/3);
            else
                UvData.Field.Mesh=sqrt((XMax-XMin)*(YMax-YMin)/nbvec);%2D
            end
        end
    end
    % case of structured coordinates
    if ~test_x
        DX=(XMax-XMin)/(nbpoints_x-1);
        if NbDim >1
            nbpoints_y=DimValue(DimIndex(NbDim-1));
            if isempty(YName)% if the y coordinate is not expressed, it is taken as the matrix index
                DY=1;
                UvData.Field.YMax=nbpoints_y;
                UvData.Field.YMin=1;
            else
                DY=(YMax-YMin)/(nbpoints_y-1);
            end
        end
        if NbDim==3
            nbpoints_z=DimValue(DimIndex(1));
            DZ=(ZMax-ZMin)/(nbpoints_z-1);
            UvData.Field.Mesh=(DX*DY*DZ)^(1/3);
            UvData.Field.ZMax=ZMax;
            UvData.Field.ZMin=ZMin;
        else
            UvData.Field.Mesh=DX;%sqrt(DX*DY);
        end
    end
    % adjust the mesh to a value 1, 2 , 5 *10^n
    ord=10^(floor(log10(UvData.Field.Mesh)));%order of magnitude
    if UvData.Field.Mesh/ord>=5
        UvData.Field.Mesh=5*ord;
    elseif UvData.Field.Mesh/ord>=2
        UvData.Field.Mesh=2*ord;
    else
        UvData.Field.Mesh=ord;
    end
    UvData.Object{1}.Type='plane';%main plotting plane
    UvData.Object{1}.ProjMode='projection';%main plotting plane
    UvData.Object{1}.DisplayHandle.uvmat=[]; %plane not visible in uvmat
    UvData.Object{1}.DisplayHandle.view_field=[]; %plane not visible in uvmat
    
    %% 3D case (menuvolume)
    if NbDim==3% && UvData.NewSeries
        test_set_object=1;
        hset_object=findobj(allchild(0),'tag','set_object');% look for the set_object GUI
        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
        if ~isempty(hset_object) %if set_object is detected
            delete(hset_object);% delete the GUI set_object if it does not fit
        end
        if test_set_object% reinitiate the GUI set_object
            delete_object(1);% delete the current projection object in the list UvData.Object, delete its graphic representations and update the list displayed in handles.ListObject and 2
            UvData.Object{1}.NbDim=NbDim;%test for 3D objects
            UvData.Object{1}.RangeZ=UvData.Field.Mesh;%main plotting plane
            UvData.Object{1}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen
            UvData.Object{1}.Angle=[0 0 0];
            UvData.Object{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR
            UvData.Object{1}.Name='1-PLANE';
            UvData.Object{1}.enable_plot=1;
            set_object(UvData.Object{1},handles,ZBounds);
            set(handles.ListObject,'Value',1);
            set(handles.ListObject,'String',{'1-PLANE'});
            set(handles.edit_object,'Value',1)% put the plane in edit mode to enable the z cursor
            edit_object_Callback([],[], handles)
        end
        %multilevel case (single menuplane in a 3D space)
    elseif isfield(UvData,'Z')
        if isfield(UvData,'CoordType')&& isequal(UvData.CoordType,'phys') && isfield(UvData,'XmlData')
            XmlData=UvData.XmlData{1};
            if isfield(XmlData,'PlanePos')
                UvData.Object{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:);
            end
            if isfield(XmlData,'PlaneAngle')
                siz=size(XmlData.PlaneAngle);
                indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning)
                UvData.Object{1}.PlaneAngle=XmlData.PlaneAngle(indangle,:);
            end
        elseif isfield(UvData,'ZIndex')
            UvData.Object{1}.ZObject=UvData.ZIndex;
        end
    end
end

testnewseries=UvData.NewSeries;
UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback)
set(handles.uvmat,'UserData',UvData)

%% reset the min and max of scalar if only the mask is displayed(TODO: check the need)
% if isfield(UvData,'Mask')&& ~isfield(UvData,'A')
%     set(handles.num_MinA,'String','0')
%     set(handles.num_MaxA,'String','255')
% end

%% usual 1D (x,y) plots
if NbDim<=1
    set(handles.Objects,'Visible','off')
    set(handles.ListObject_1_title,'Visible','off')
    set(handles.ListObject_1,'Visible','off')
    [PlotType,PlotParamOut]=plot_field(UvData.Field,handles.axes3,read_GUI(handles.uvmat));
    write_plot_param(handles,PlotParamOut) %update the auto plot parameters
%     if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
%         ObjectData.Mesh=Field.Mesh; % gives an estimated mesh size (useful for mouse action on the plot)
%     end
    
%% 2D or 3D fields are generally projected
else
    set(handles.Objects,'Visible','on')
    set(handles.ListObject_1_title,'Visible','on')
    set(handles.ListObject_1,'Visible','on')
    
    %% Plot the projections on the selected  projection objects
    % main projection object (uvmat display)
    list_object=get(handles.ListObject_1,'String');
    if isequal(list_object,{''})%refresh list of objects if the menu is empty
        UvData.Object={[]};
        set(handles.ListObject_1,'Value',1)
    end
    IndexObj(1)=get(handles.ListObject_1,'Value');%selected projection object for main view
    if IndexObj(1)> numel(UvData.Object)
        IndexObj(1)=1;%select the first object if the selected one does not exist
        set(handles.ListObject_1,'Value',1)
    end
    IndexObj(2)=get(handles.ListObject,'Value');%selected projection object for main view
    if isequal(IndexObj(2),IndexObj(1))
        IndexObj(2)=[];
    end
    plot_handles{1}=handles;
    if isfield(UvData,'plotaxes')%case of movies
        haxes(1)=UvData.plotaxes;
    else
        haxes(1)=handles.axes3;
    end
    PlotParam{1}=read_GUI(handles.uvmat);
    %default settings if vectors not visible
    if ~isfield(PlotParam{1},'Vectors')
        PlotParam{1}.Vectors.MaxVec=1;
        PlotParam{1}.Vectors.MinVec=0;
        PlotParam{1}.Vectors.CheckFixVecColor=1;
        PlotParam{1}.Vectors.ColCode1=0.33;
        PlotParam{1}.Vectors.ColCode2=0.66;
        PlotParam{1}.Vectors.ColorScalar={'ima_cor'};
        PlotParam{1}.Vectors.ColorCode= {'rgb'};
    end
    PosColorbar{1}=UvData.OpenParam.PosColorbar;%prescribe the colorbar position on the uvmat interface
    
    %% second projection object (view_field display)
    if length( IndexObj)>=2
        view_field_handle=findobj(allchild(0),'tag','view_field');%handles of the view_field GUI
        if ~isempty(view_field_handle)
            plot_handles{2}=guidata(view_field_handle);
            haxes(2)=plot_handles{2}.axes3;
            PlotParam{2}=read_GUI(handles.uvmat);%read plotting parameters on the uvmat interface
            PosColorbar{2}='*'; %TODO: deal with colorbar position on view_field
        end
    end
    
    %% loop on the projection objects: one or two
    
    for imap=1:numel(IndexObj)
        iobj=IndexObj(imap);
        %      if imap==2 || check_proj==0  % field not yet projected) && ~isfield(UvData.Object{iobj},'Type')% case with no projection (only for the first empty object)
        % %          [ObjectData,errormsg]=calc_field(UvData.Field.FieldList,UvData.Field);
        % %      else
        [ObjectData,errormsg]=proj_field(UvData.Field,UvData.Object{iobj});% project field on the object
        %      end
        if ~isempty(errormsg)
            return
        end
        if testnewseries
            PlotParam{imap}.Scalar.CheckBW=[]; %B/W option depends on the input field (image or scalar)
            if isfield(ObjectData,'CoordUnit')
                PlotParam{imap}.Coordinates.CheckFixAspectRatio=1;% set x and y scaling equal if CoordUnit is defined (common unit for x and y)
                PlotParam{imap}.Coordinates.AspectRatio=1; %set aspect ratio to 1
            end
        end
        %use of mask (TODO: check)
        if isfield(ObjectData,'NbDim') && isequal(ObjectData.NbDim,2) && isfield(ObjectData,'Mask') && isfield(ObjectData,'A')
            flag_mask=double(ObjectData.Mask>200);%=0 for masked regions
            AX=ObjectData.AX;%x coordiantes for the scalar field
            AY=ObjectData.AY;%y coordinates for the scalar field
            MaskX=ObjectData.MaskX;%x coordiantes for the mask
            MaskY=ObjectData.MaskY;%y coordiantes for the mask
            if ~isequal(MaskX,AX)||~isequal(MaskY,AY)
                nxy=size(flag_mask);
                sizpx=(ObjectData.MaskX(end)-ObjectData.MaskX(1))/(nxy(2)-1);%size of a mask pixel
                sizpy=(ObjectData.MaskY(1)-ObjectData.MaskY(end))/(nxy(1)-1);
                x_mask=ObjectData.MaskX(1):sizpx:ObjectData.MaskX(end); % pixel x coordinates for image display
                y_mask=ObjectData.MaskY(1):-sizpy:ObjectData.MaskY(end);% pixel x coordinates for image display
                %project on the positions of the scalar
                npxy=size(ObjectData.A);
                dxy(1)=(ObjectData.AY(end)-ObjectData.AY(1))/(npxy(1)-1);%grid mesh in y
                dxy(2)=(ObjectData.AX(end)-ObjectData.AX(1))/(npxy(2)-1);%grid mesh in x
                xi=ObjectData.AX(1):dxy(2):ObjectData.AX(end);
                yi=ObjectData.AY(1):dxy(1):ObjectData.AY(end);
                [XI,YI]=meshgrid(xi,yi);% creates the matrix of regular coordinates
                flag_mask = interp2(x_mask,y_mask,flag_mask,XI,YI);
            end
            AClass=class(ObjectData.A);
            ObjectData.A=flag_mask.*double(ObjectData.A);
            ObjectData.A=feval(AClass,ObjectData.A);
            ind_off=[];
            if isfield(ObjectData,'ListVarName')
                for ilist=1:length(ObjectData.ListVarName)
                    if isequal(ObjectData.ListVarName{ilist},'Mask')||isequal(ObjectData.ListVarName{ilist},'MaskX')||isequal(ObjectData.ListVarName{ilist},'MaskY')
                        ind_off=[ind_off ilist];
                    end
                end
                ObjectData.ListVarName(ind_off)=[];
                VarDimIndex(ind_off)=[];
                ind_off=[];
                for ilist=1:length(ListDimName)
                    if isequal(ListDimName{ilist},'MaskX') || isequal(ListDimName{ilist},'MaskY')
                        ind_off=[ind_off ilist];
                    end
                end
                ListDimName(ind_off)=[];
                DimValue(ind_off)=[];
            end
        end
        if ~isempty(ObjectData)
            PlotType='none'; %default
            if imap==2 && isempty(view_field_handle)
                view_field(ObjectData)
            else
                [PlotType,PlotParamOut]=plot_field(ObjectData,haxes(imap),PlotParam{imap},PosColorbar{imap});
                write_plot_param(plot_handles{imap},PlotParamOut) %update the auto plot parameters
                if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
                    ObjectData.Mesh=Field.Mesh; % gives an estimated mesh size (useful for mouse action on the plot)
                end
            end
            if isequal(PlotType,'none')
                hget_field=findobj(allchild(0),'name','get_field');
                if isempty(hget_field)
                    get_field(filename)% the projected field cannot be automatically plotted: use get_field to specify the variablesdelete(hget_field)
                end
                errormsg='The field defined by get_field cannot be plotted';
                return
            end
        end
    end
    
    %% update the mask
    if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
        update_mask(handles,num_i1,num_i2);
    end
    
    %% prepare the menus of histograms and plot them (histogram of the whole volume in 3D case)
    menu_histo=(UvData.Field.ListVarName)';%list of field variables to be displayed for the menu of histogram display
    ind_skip=[];
    % nb_histo=1;
    Ustring='';
    Vstring='';
    % suppress coordinates from the histogram menu
    for ivar=1:numel(menu_histo)%l loop on field variables:
        if isfield(UvData.Field,'VarAttribute') && numel(UvData.Field.VarAttribute)>=ivar && isfield(UvData.Field.VarAttribute{ivar},'Role')
            Role=UvData.Field.VarAttribute{ivar}.Role;
            switch Role
                case {'coord_x','coord_y','coord_z','dimvar'}
                    ind_skip=[ind_skip ivar];
                case {'vector_x'}
                    Ustring=UvData.Field.ListVarName{ivar};
                    ind_skip=[ind_skip ivar];
                case {'vector_y'}
                    Vstring=UvData.Field.ListVarName{ivar};
                    ind_skip=[ind_skip ivar];
            end
        end
        DimCell=UvData.Field.VarDimName{ivar};
        DimName='';
        if ischar(DimCell)
            DimName=DimCell;
        elseif iscell(DimCell)&& numel(DimCell)==1
            DimName=DimCell{1};
        end
        if strcmp(DimName,menu_histo{ivar})
            ind_skip=[ind_skip ivar];
        end
    end
    menu_histo(ind_skip)=[];% remove skipped items
    if ~isempty(Ustring)
        menu_histo=[{[Ustring ',' Vstring]};menu_histo];% add U, V at the beginning if they exist
    end
    
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    % display menus and plot histograms
    test_v=0;
    if ~isempty(menu_histo)
        set(handles.histo1_menu,'Value',1)
        set(handles.histo1_menu,'String',menu_histo)
        histo1_menu_Callback(handles.histo1_menu, [], handles)% plot first histogram
    end
end

%------------------------------------------------------------------------
function histo1_menu_Callback(hObject, eventdata, handles)
%--------------------------------------------
%plot first histo
%huvmat=get(handles.histo1_menu,'parent');
histo_menu=get(handles.histo1_menu,'String');
histo_value=get(handles.histo1_menu,'Value');
FieldName=histo_menu{histo_value};
% update_histo(handles.histo_u,handles.uvmat,FieldName)
% 
% %------------------------------------------------------------------------
% function histo2_menu_Callback(hObject, eventdata, handles)
% %------------------------------------------------------------------------
% %plot second histo
% %huvmat=get(handles.histo2_menu,'parent');
% histo_menu=get(handles.histo2_menu,'String');
% histo_value=get(handles.histo2_menu,'Value');
% FieldName=histo_menu{histo_value};
% update_histo(handles.histo_v,handles.uvmat,FieldName)
% 
% %------------------------------------------------------------------------
% %read the field .Fieldname stored in UvData and plot its histogram
% function update_histo(haxes,huvmat,FieldName)
%------------------------------------------------------------------------
UvData=get(handles.uvmat,'UserData');
Field=UvData.Field;
r=regexp(FieldName,'(?<var1>.*)(?<sep>,)(?<var2>.*)','names');
FieldName_2='';
if ~isempty(r)
    FieldName=r.var1;
    FieldName_2=r.var2;
end
if ~isfield(UvData.Field,FieldName)
    msgbox_uvmat('ERROR',['no field  ' FieldName ' for histogram'])
    return
end
FieldHisto=Field.(FieldName);
if isfield(Field,'FF') && ~isempty(Field.FF) && isequal(size(Field.FF),size(FieldHisto))
    indsel=find(Field.FF==0);%find values marked as false
    if ~isempty(indsel)
        FieldHisto=FieldHisto(indsel);
        if ~isempty(FieldName_2)
            FieldHisto(:,:,2)=Field.(FieldName_2)(indsel);
        end
    end
end
if isempty(Field)
    msgbox_uvmat('ERROR',['empty field ' FieldName])
else
    nxy=size(FieldHisto);
    Amin=double(min(min(min(FieldHisto))));%min of field value
    Amax=double(max(max(max(FieldHisto))));%max of field value
    if isequal(Amin,Amax)
        cla(handles.histo_u)
    else
        Histo.ListVarName={FieldName,'histo'};
        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
            Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
        else
            if numel(nxy)==2
                Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
            else
                Histo.VarDimName={FieldName,{FieldName,'component'}}; %dimensions for the histogram
            end
        end
        %unit
        units=[]; %default
        for ivar=1:numel(Field.ListVarName)
            if strcmp(Field.ListVarName{ivar},FieldName)
                if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'units')
                    units=Field.VarAttribute{ivar}.units;
                    break
                end
            end
        end
        if ~isempty(units)
            Histo.VarAttribute{1}.units=units;
        end
        eval(['Histo.' FieldName '=linspace(Amin,Amax,50);'])%absissa values for histo
        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
            C=reshape(double(FieldHisto),1,[]);% reshape in a vector
            Histo.histo(:,1)=hist(C, Histo.(FieldName));  %calculate histogram
        else
            for col=1:size(FieldHisto,3)
                B=FieldHisto(:,:,col);
                C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector
                Histo.histo(:,col)=hist(C, Histo.(FieldName));  %calculate histogram
            end
        end
        plot_field(Histo,handles.histo_u);
        hlegend=legend;
        if isempty(FieldName_2)
        set(hlegend,'String',FieldName)
        else
            set(hlegend,'String',{FieldName;FieldName_2})
        end
%         hh=get(handles.histo_u,'children');
%         get(hh(1))
%         get(hh(2))
    end
end

%-------------------------------------------------------------------
% --- translate coordinate to matrix index
%-------------------------------------------------------------------
function [indx,indy]=pos2ind(x0,rangx0,nxy)
indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel  
indy=1+round((nxy(1)-1)*(y12-rangy0(1))/(rangy0(2)-rangy0(1)));% index y of pixel


%-------------------------------------------------------------------
% --- Executes on button press in 'CheckZoom'.
%-------------------------------------------------------------------
function CheckZoom_Callback(hObject, eventdata, handles)

if (get(handles.CheckZoom,'Value') == 1); 
    set(handles.CheckZoom,'BackgroundColor',[1 1 0])
    set(handles.CheckFixLimits,'Value',1)% propose by default fixed limits for the plotting axes
    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0]) 
else
    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
end

%-------------------------------------------------------------------
% --- Executes on button press in 'CheckFixLimits'.
%-------------------------------------------------------------------
function CheckFixLimits_Callback(hObject, eventdata, handles)
test=get(handles.CheckFixLimits,'Value');
if test
    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
else
    set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
    update_plot(handles);
end

%-------------------------------------------------------------------
% --- Executes on button press in CheckFixAspectRatio.
function CheckFixAspectRatio_Callback(hObject, eventdata, handles)
%-------------------------------------------------------------------
if get(handles.CheckFixAspectRatio,'Value')
    set(handles.CheckFixAspectRatio,'BackgroundColor',[1 1 0])
    update_plot(handles);
else
    set(handles.CheckFixAspectRatio,'BackgroundColor',[0.7 0.7 0.7])
    update_plot(handles);
end

%-------------------------------------------------------------------
function num_AspectRatio_Callback(hObject, eventdata, handles)
%-------------------------------------------------------------------
set(handles.CheckFixAspectRatio,'Value',1)% select the fixed aspect ratio button
set(handles.CheckFixAspectRatio,'BackgroundColor',[1 1 0])% mark in yellow
update_plot(handles);
%-------------------------------------------------------------------

%-------------------------------------------------------------------



%-------------------------------------------------------------------
%----Executes on button press in 'record': records the current flags of manual correction.
%-------------------------------------------------------------------
function record_Callback(hObject, eventdata, handles)
% [filebase,num_i1,num_j1,num_i2,num_j2,Ext,NomType,SubDir]=read_input_file(handles);
[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
%filename=read_file_boxes(handles);
[erread,message]=fileattrib(filename);
if ~isempty(message) && ~isequal(message.UserWrite,1)
     msgbox_uvmat('ERROR',['no writting access to ' filename])
     return
end
test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
if ~test_civ2 && ~test_civ1
    msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
end 
if test_civ2
    nbname='nb_vectors2';
   flagname='vec2_FixFlag';
   attrname='fix2';
end
if test_civ1
    nbname='nb_vectors';
   flagname='vec_FixFlag';
   attrname='fix';
end
%write fix flags in the netcdf file
UvData=get(handles.uvmat,'UserData');
hhh=which('netcdf.open');% look for built-in matlab netcdf library
if ~isequal(hhh,'')% case of new builtin Matlab netcdf library
    nc=netcdf.open(filename,'NC_WRITE'); 
    netcdf.reDef(nc);
    netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),attrname,1);
    dimid = netcdf.inqDimID(nc,nbname); 
    try
        varid = netcdf.inqVarID(nc,flagname);% look for already existing fixflag variable
    catch
        varid=netcdf.defVar(nc,flagname,'double',dimid);%create fixflag variable if it does not exist
    end
    netcdf.endDef(nc);
    netcdf.putVar(nc,varid,UvData.axes3.FF);
    netcdf.close(nc);  
else %old netcdf library
    netcdf_toolbox(filename,AxeData,attrname,nbname,flagname)
end

%-------------------------------------------------------------------
%----Correct the netcdf file, using toolbox (old versions of Matlab).
%-------------------------------------------------------------------
function netcdf_toolbox(filename,AxeData,attrname,nbname,flagname)
nc=netcdf(filename,'write'); %open netcdf file
result=redef(nc);
eval(['nc.' attrname '=1;']);
theDim=nc(nbname) ;% get the number of velocity vectors
nb_vectors=size(theDim);
var_FixFlag=ncvar(flagname,nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag
var_FixFlag(1:nb_vectors)=AxeData.FF;% 
fin=close(nc);

%-------------------------------------------------------------------
% --- Executes on button press in SubField
function SubField_Callback(hObject, eventdata, handles)
%-------------------------------------------------------------------
UvData=get(handles.uvmat,'UserData');
if get(handles.SubField,'Value')==0% if the subfield button is desactivated   
    set(handles.RootPath_1,'String','')
    set(handles.RootFile_1,'String','')
    set(handles.SubDir_1,'String','');
    set(handles.FileIndex_1,'String','');
    set(handles.FileExt_1,'String','');
    set(handles.RootPath_1,'Visible','off')
    set(handles.RootFile_1,'Visible','off')
    set(handles.SubDir_1,'Visible','off');
    set(handles.NomType_1,'Visible','off');
    set(handles.abs_time_1,'Visible','off')
    set(handles.FileIndex_1,'Visible','off');
    set(handles.FileExt_1,'Visible','off');
    set(handles.Fields_1,'Value',1);%set to blank state
    set(handles.VelType_1,'Value',1);%set to blank state
    set(handles.num_Opacity,'String','')% desactivate opacity setting
    if ~strcmp(get(handles.VelType,'Visible'),'on')
        set(handles.VelType_1,'Visible','off')
    end
    if isfield(UvData,'XmlData_1')
        UvData=rmfield(UvData,'XmlData_1');
    end 
    set(handles.uvmat,'UserData',UvData);
    run0_Callback(hObject, eventdata, handles); %run
else
    MenuBrowse_1_Callback(hObject, eventdata, handles)
end

%------------------------------------------------------------------------
% --- read the data displayed for the input rootfile windows (new): TODO use read_GUI

function [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles)
%------------------------------------------------------------------------
InputFile=read_GUI(handles.InputFile);
RootPath=InputFile.RootPath;
SubDir=regexprep(InputFile.SubDir,'/|\','');
RootFile=regexprep(InputFile.RootFile,'/|\','');
FileIndices=InputFile.FileIndex;
FileExt=InputFile.FileExt;


%------------------------------------------------------------------------
% ---- read the data displayed for the second input rootfile windows
function [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1,NomType_1]=read_file_boxes_1(handles)
%------------------------------------------------------------------------
RootPath_1=get(handles.RootPath_1,'String'); % read the data from the file1_input window
if isequal(get(handles.RootPath_1,'Visible'),'off') || isequal(RootPath_1,'"')
    RootPath_1=get(handles.RootPath,'String');
end;
SubDir_1=get(handles.SubDir_1,'String');
if isequal(get(handles.SubDir_1,'Visible'),'off')|| isequal(SubDir_1,'"')
    SubDir_1=get(handles.SubDir,'String');
end
SubDir_1=regexprep(SubDir_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
RootFile_1=get(handles.RootFile_1,'String');
if isequal(get(handles.RootFile_1,'Visible'),'off') || isequal(RootFile_1,'"')
    RootFile_1=get(handles.RootFile,'String'); 
end
RootFile_1=regexprep(RootFile_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
FileIndex_1=get(handles.FileIndex_1,'String');
if isequal(get(handles.FileIndex_1,'Visible'),'off')|| isequal(FileIndex_1,'"')
    FileIndex_1=get(handles.FileIndex,'String');
end
FileExt_1=get(handles.FileExt_1,'String');
if isequal(get(handles.FileExt_1,'Visible'),'off') || isequal(FileExt_1,'"')
    FileExt_1=get(handles.FileExt,'String');%read FileExt by default
end
NomType_1=get(handles.NomType_1,'String');
if isequal(get(handles.NomType_1,'Visible'),'off') || isequal(NomType_1,'"')
    NomType_1=get(handles.NomType,'String');%read FileExt by default
end
%------------------------------------------------------------------------
% --- Executes on menu selection Fields
function Fields_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
list_fields=get(handles.Fields,'String');% list menu fields
index_fields=get(handles.Fields,'Value');% selected string index
field= list_fields{index_fields(1)}; % selected string
if isequal(field,'get_field...')
    set(handles.FixVelType,'visible','off')
    set(handles.VelType,'visible','off')
    set(handles.VelType_1,'visible','off')
    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
    filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
    %filename=read_file_boxes(handles);
    hget_field=findobj(allchild(0),'name','get_field');
    if ~isempty(hget_field)
        delete(hget_field)
    end
    hget_field=get_field(filename);
    set(hget_field,'Name','get_field')
    hhget_field=guidata(hget_field);
    set(hhget_field.list_fig,'Value',1)
    set(hhget_field.list_fig,'String',{'uvmat'})
    set(handles.transform_fct,'Value',1)% no transform by default
    set(handles.path_transform,'String','')
    return %no action
end
list_fields=get(handles.Fields_1,'String');% list menu fields
index_fields=get(handles.Fields_1,'Value');% selected string index
field_1= list_fields{index_fields(1)}; % selected string
UvData=get(handles.uvmat,'UserData');

%read the rootfile input display
[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
[tild,tild,tild,i1,i2,j1,j2,tild,NomType]=fileparts_uvmat(['xxx' get(handles.FileIndex,'String') FileExt]);
% NomTypeNew=NomType;%default
if isequal(field,'image')
%     if isequal(NomType,'_1-2_1')||isequal(NomType,'_1_1-2')
%         NomTypeNew='_1_1';
%     elseif isequal(NomType,'#_ab')
%         NomTypeNew='#a';
%     elseif isequal(NomType,'_1-2')
%         NomTypeNew='_1';
%     end
    imagename=fullfile_uvmat(RootPath,SubDir,RootFile,'.png',NomType,i1,[],j1,[]);
    if ~exist(imagename,'file')
        [FileName,PathName] = uigetfile( ...
            {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
            '*.jpg',' jpeg image files'; ...
            '*.png','.png image files'; ...
            '*.tif','.tif image files'; ...
            '*.avi;*.AVI','.avi movie files'; ...
            '*.vol','.volume images (png)'; ...
            '*.*',  'All Files (*.*)'}, ...
            'Pick an image',imagename);   
        imagename=[PathName FileName];
    end
     % display the selected field and related information
    display_file_name(handles,imagename)%display the image
    return
else
    ext=get(handles.FileExt,'String');
    if ~isequal(ext,'.nc') %find the new NomType if the previous display was not already a netcdf file
        [FileName,PathName] = uigetfile( ...
            {'*.nc', ' (*.nc)';
            '*.nc',' netcdf files'; ...
            '*.*',  'All Files (*.*)'}, ...
            'Pick a netcdf file',FileBase);
        filename=[PathName FileName];
        % display the selected field and related information
        display_file_name( handles,filename)
        return
    end
end
indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
set(handles.FileIndex,'String',indices)
% set(handles.NomType,'String',NomType)

%common to Fields_1_Callback
if isequal(field,'image')||isequal(field_1,'image')
    set(handles.TitleNpx,'Visible','on')% visible npx,pxcm... buttons
    set(handles.TitleNpy,'Visible','on')
    set(handles.num_Npx,'Visible','on')
    set(handles.num_Npy,'Visible','on')
else
    set(handles.TitleNpx,'Visible','off')% visible npx,pxcm... buttons
    set(handles.TitleNpy,'Visible','off')
    set(handles.num_Npx,'Visible','off')
    set(handles.num_Npy,'Visible','off')
end
if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
    run0_Callback(hObject, eventdata, handles)
end

%---------------------------------------------------
% --- Executes on menu selection Fields
function Fields_1_Callback(hObject, eventdata, handles)
%-------------------------------------------------
%% read input data
check_new=~get(handles.SubField,'Value'); %check_new=1 if a second field was not previously entered
UvData=get(handles.uvmat,'UserData');
if check_new && isfield(UvData,'XmlData')
    UvData.XmlData{2}=UvData.XmlData{1};
end
if isfield(UvData,'Field_1')
    UvData=rmfield(UvData,'Field_1');% remove the stored second field (a new one needs to be read)
end
UvData.filename_1='';% desactivate the use of a constant second file
list_fields=get(handles.Fields,'String');% list menu fields
field= list_fields{get(handles.Fields,'Value')}; % selected string
list_fields=get(handles.Fields_1,'String');% list menu fields
field_1= list_fields{get(handles.Fields_1,'Value')}; % selected string for the second field
if isempty(field_1)%||(numel(UvData.FileType)>=2 && strcmp(UvData.FileType{2},'image'))
    set(handles.SubField,'Value',0)
    SubField_Callback(hObject, eventdata, handles)
    return
else
    set(handles.SubField,'Value',1)%state that a second field is now entered
end

%% read the rootfile input display
[RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
% set(handles.FileIndex_1,'Visible','on')
% set(handles.FileExt_1,'Visible','on')
switch field_1
    case 'get_field...'
        set_veltype_display(0) % no veltype display
        hget_field=findobj(allchild(0),'name','get_field_1');
        if ~isempty(hget_field)
            delete(hget_field)
        end
        hget_field=get_field(filename_1);
        set(hget_field,'name','get_field_1')
        hhget_field=guidata(hget_field);
        set(hhget_field.list_fig,'Value',1)
        set(hhget_field.list_fig,'String',{'uvmat'})
        set(handles.transform_fct,'Value',1)% no transform by default
        set(handles.path_transform,'String','')
        if check_new
            UvData.FileType{2}=UvData.FileType{1};
            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
%             set(handles.FileExt_1,'String',get(handles.FileExt,'String'))
              set(handles.uvmat,'UserData',UvData)
        end
    case 'image'
        % guess the image name corresponding to the current netcdf name (no unique correspondance)
        imagename=fullfile_uvmat(RootPath_1,'',RootFile_1,'.png',get(handles.NomType,'String'),i1,[],j1);
        if ~exist(imagename,'file') % browse for images if it is not found
            [FileName,PathName] = uigetfile( ...
                {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
                '*.jpg',' jpeg image files'; ...
                '*.png','.png image files'; ...
                '*.tif','.tif image files'; ...
                '*.avi;*.AVI','.avi movie files'; ...
                '*.vol','.volume images (png)'; ...
                '*.*',  'All Files (*.*)'}, ...
                'Pick an image',imagename);
            imagename=[PathName FileName];
        end
        if ~ischar(imagename)% quit if the browser has  been closed
            set(handles.SubField,'Value',0)
        else %valid browser input:  display the selected image
            set(handles.TitleNpx,'Visible','on')% visible npx,pxcm... buttons
            set(handles.TitleNpy,'Visible','on')
            set(handles.num_Npx,'Visible','on')
            set(handles.num_Npy,'Visible','on')
            display_file_name(handles,imagename,2)%display the imag
        end
    otherwise
        if check_new
            UvData.FileType{2}=UvData.FileType{1};
            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
            set(handles.FileExt_1,'String',get(handles.FileExt,'String'))
        end
        if ~isequal(field,'image')
            set(handles.TitleNpx,'Visible','off')% visible npx,pxcm... buttons
            set(handles.TitleNpy,'Visible','off')
            set(handles.num_Npx,'Visible','off')
            set(handles.num_Npy,'Visible','off')
        end
        set(handles.uvmat,'UserData',UvData)
        if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
            run0_Callback(hObject, eventdata, handles)
        end
end

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

%------------------------------------------------------------------------
% --- Executes on button press in FixVelType.
function FixVelType_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
% refresh the current plot if the fixed  veltype is unselected
if ~get(handles.FixVelType,'Value')
    run0_Callback(hObject, eventdata, handles)
end

%------------------------------------------------------------------------
% --- Executes on button press in VelType.
function VelType_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(handles.FixVelType,'Value',1)
run0_Callback(hObject, eventdata, handles)

%------------------------------------------------------------------------
% --- Executes on button press in VelType_1.
function VelType_1_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(handles.FixVelType,'Value',1)% the velocity type is now imposed by the GUI (not automatic)
UvData=get(handles.uvmat,'UserData');
%refresh field with a second filename=first file name
set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
drawnow   
InputFile=read_GUI(handles.InputFile);
[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];

if isempty(InputFile.VelType_1)
        filename_1='';% we plot the current field without the second field
        set(handles.SubField,'Value',0)
        SubField_Callback(hObject, eventdata, handles)
elseif get(handles.SubField,'Value')% if subfield is already 'on'
      [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
     filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
else
     filename_1=filename;% we compare two fields in the same file by default
     UvData.FileType{2}=UvData.FileType{1};
     set(handles.SubField,'Value',1)
end
if isfield(UvData,'Field_1')
    UvData=rmfield(UvData,'Field_1');% removes the stored second field if it exists
end
UvData.filename_1='';% desactivate the use of a constant second file
set(handles.uvmat,'UserData',UvData)
num_i1=stra2num(get(handles.i1,'String'));
num_i2=stra2num(get(handles.i2,'String'));
num_j1=stra2num(get(handles.j1,'String'));
num_j2=stra2num(get(handles.j2,'String'));

errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2);

if ~isempty(errormsg)
    msgbox_uvmat('ERROR',errormsg);
else
    set(handles.i1,'BackgroundColor',[1 1 1])
    set(handles.i2,'BackgroundColor',[1 1 1])
    set(handles.j1,'BackgroundColor',[1 1 1])
    set(handles.j2,'BackgroundColor',[1 1 1])
    set(handles.FileIndex,'BackgroundColor',[1 1 1])
    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
end
set(handles.run0,'BackgroundColor',[1 0 0])

%-----------------------------------------------
% --- reset civ buttons
function reset_vel_type(handles_civ0,handle1)
for ibutton=1:length(handles_civ0)
    set(handles_civ0(ibutton),'BackgroundColor',[0.831 0.816 0.784])
    set(handles_civ0(ibutton),'Value',0)
end
if exist('handle1','var')%handles of selected button
        set(handle1,'BackgroundColor',[1 1 0])  
end

%-------------------------------------------------------
% --- Executes on button press in MENUVOLUME.
%-------------------------------------------------------
function VOLUME_Callback(hObject, eventdata, handles)
%errordlg('command VOL not implemented yet')
if ishandle(handles.UVMAT_title)
    delete(handles.UVMAT_title)
end
UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface 
if isequal(get(handles.VOLUME,'Value'),1)
    set(handles.CheckZoom,'Value',0)
    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
    set(handles.edit_vect,'Value',0)
    edit_vect_Callback(hObject, eventdata, handles)
    set(handles.edit_object,'Value',0)
    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
%     set(handles.cal,'Value',0)
%     set(handles.cal,'BackgroundColor',[0 1 0])
    set(handles.edit_vect,'Value',0)
    edit_vect_Callback(hObject, eventdata, handles)
    %initiate set_object GUI
    data.Name='VOLUME';
    if isfield(UvData,'CoordType')
        data.CoordType=UvData.CoordType;
    end
    if isfield(UvData.Field,'Mesh')&~isempty(UvData.Field.Mesh)
        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
        data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
        data.DX=UvData.Field.Mesh;
        data.DY=UvData.Field.Mesh;
    elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
        np=size(UvData.Field.A);
        meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
        meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
        data.RangeY=max(meshx,meshy);
        data.RangeX=max(meshx,meshy);
        data.DX=max(meshx,meshy);
    end 
    data.ParentButton=handles.VOLUME;
    PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
    [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes,
                                                      % associate the set_object interface handle to the plotting axes
    if isfield(UvData.OpenParam,'SetObjectOrigin')                                                
    pos_uvmat=get(handles.uvmat,'Position');
    pos_set_object(1:2)=UvData.OpenParam.SetObjectOrigin + pos_uvmat(1:2);
    pos_set_object(3:4)=UvData.OpenParam.SetObjectSize .* pos_uvmat(3:4);  
    set(hset_object,'Position',pos_set_object)
    end
    UvData.MouseAction='create_object';
else
    set(handles.VOLUME,'BackgroundColor',[0 1 0])
    UvData.MouseAction='none';
end
set(handles.uvmat,'UserData',UvData)

%-------------------------------------------------------
function edit_vect_Callback(hObject, eventdata, handles)
%-------------------------------------------------------
% 
% UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface 
if isequal(get(handles.edit_vect,'Value'),1)
    test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
    test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
    if ~test_civ2 && ~test_civ1
        msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
    end 
    set(handles.record,'Visible','on')
    set(handles.edit_vect,'BackgroundColor',[1 1 0])
    set(handles.edit_object,'Value',0)
    set(handles.CheckZoom,'Value',0)
    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
%     set(handles.create,'Value',0)
%     set(handles.create,'BackgroundColor',[0 1 0])
    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
    set(gcf,'Pointer','arrow')
%     UvData.MouseAction='edit_vect';
else
    set(handles.record,'Visible','off')
    set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7])
%     UvData.MouseAction='none';
end
% set(handles.uvmat,'UserData',UvData)

%----------------------------------------------
function save_mask_Callback(hObject, eventdata, handles)
%-----------------------------------------------------------------------
UvData=get(handles.uvmat,'UserData');

flag=1;
npx=size(UvData.Field.A,2);
npy=size(UvData.Field.A,1);
xi=0.5:npx-0.5;
yi=0.5:npy-0.5;
[Xi,Yi]=meshgrid(xi,yi);
if isfield(UvData,'Object')
    for iobj=1:length(UvData.Object)
        ObjectData=UvData.Object{iobj};
        if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
            flagobj=1;
            testphys=0; %coordinates in pixels by default
            if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys')
                if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
                    Calib=UvData.XmlData{1}.GeometryCalib;
                    testphys=1;
                end
            end
            if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style') 
                if isequal(ObjectData.Type,'polygon') 
                    X=ObjectData.Coord(:,1);
                    Y=ObjectData.Coord(:,2);
                    if testphys
                        [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
                    end
                    flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside                  
                elseif isequal(ObjectData.Type,'ellipse')
                    if testphys
                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
                    end
                    RangeX=max(ObjectData.RangeX);
                    RangeY=max(ObjectData.RangeY);
                    X2Max=RangeX*RangeX;
                    Y2Max=RangeY*RangeY;
                    distX=(Xi-ObjectData.Coord(1,1));
                    distY=(Yi-ObjectData.Coord(1,2));
                    flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
                elseif isequal(ObjectData.Type,'rectangle')
                    if testphys
                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
                    end
                    distX=abs(Xi-ObjectData.Coord(1,1));
                    distY=abs(Yi-ObjectData.Coord(1,2));
                    flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
                end
                if isequal(ObjectData.ProjMode,'mask_outside')
                    flagobj=~flagobj;
                end
                flag=flag & flagobj;
            end
        end
    end
end
% flag=~flag;
%mask name
RootPath=get(handles.RootPath,'String');
RootFile=get(handles.RootFile,'String');
RootFile=regexprep(RootFile,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
filebase=fullfile(RootPath,RootFile);
list=get(handles.masklevel,'String');
masknumber=num2str(length(list));
maskindex=get(handles.masklevel,'Value');
mask_name=fullfile_uvmat(RootPath,SubDir,[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
%mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
imflag=flipdim(imflag,1);
% imflag=uint8(255*flag);% =0 for flag=0 (vectors=0 when 20<imflag<200)
msgbox_uvmat('CONFIRMATION',[mask_name ' saved'])
imwrite(imflag,mask_name,'BitDepth',8); 

%display the mask
figure;
vec=linspace(0,1,256);%define a linear greyscale colormap
map=[vec' vec' vec'];
colormap(map)

image(imflag);

%-------------------------------------------------------------------
%-------------------------------------------------------------------
%  - FUNCTIONS FOR SETTING PLOTTING PARAMETERS

%------------------------------------------------------------------
%-------------------------------------------------------------
% --- Executes on selection change in transform_fct.
function transform_fct_Callback(hObject, eventdata, handles)
%-------------------------------------------------------------
UvData=get(handles.uvmat,'UserData');
menu=get(handles.transform_fct,'String');
ind_coord=get(handles.transform_fct,'Value');
coord_option=menu{ind_coord};
list_transform=get(handles.transform_fct,'UserData');
ff=functions(list_transform{end});  
if isequal(coord_option,'more...'); 
    coord_fct='';
    prompt = {'Enter the name of the transform function'};
    dlg_title = 'user defined transform';
    num_lines= 1;
    [FileName, PathName] = uigetfile( ...
       {'*.m', ' (*.m)';
        '*.m',  '.m files '; ...
        '*.*', 'All Files (*.*)'}, ...
        'Pick a file', ff.file);
    if isequal(PathName(end),'/')||isequal(PathName(end),'\')
        PathName(end)=[];
    end
    transform_selected =fullfile(PathName,FileName);
    if ~exist(transform_selected,'file')
           return
    end
   [ppp,transform,ext_fct]=fileparts(FileName);% removes extension .m
   if ~isequal(ext_fct,'.m')
        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
        return
   end
   menu=update_menu(handles.transform_fct,transform);%add the selected fct to the menu
   ind_coord=get(handles.transform_fct,'Value');
   addpath(PathName)
   list_transform{ind_coord}=str2func(transform);% create the function handle corresponding to the newly seleced function
   set(handles.transform_fct,'UserData',list_transform)
   rmpath(PathName)
   % save the new menu in the personal file 'uvmat_perso.mat' 
   dir_perso=prefdir;%personal Matalb directory
   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
   if exist(profil_perso,'file')
       nb_builtin=UvData.OpenParam.NbBuiltin;
       for ilist=nb_builtin+1:numel(list_transform)
           ff=functions(list_transform{ilist});
           transform_fct{ilist-nb_builtin}=ff.file;
       end 
        save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
   end   
end

%% check the current path to the selected function
if isa(list_transform{ind_coord},'function_handle')
    func=functions(list_transform{ind_coord});
    set(handles.path_transform,'String',fileparts(func.file)); %show the path to the senlected function
else
    set(handles.path_transform,'String','')
end

set(handles.CheckFixLimits,'Value',0)
set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])

%% delete drawn objects
hother=findobj('Tag','proj_object');%find all the proj objects
for iobj=1:length(hother)
    delete_object(hother(iobj))
end
hother=findobj('Tag','DeformPoint');%find all the proj objects
for iobj=1:length(hother)
    delete_object(hother(iobj))
end
hh=findobj('Tag','calib_points');
if ~isempty(hh)
    delete(hh)
end
hhh=findobj('Tag','calib_marker');
if ~isempty(hhh)
    delete(hhh)
end
if isfield(UvData,'Object')
     UvData.Object=UvData.Object(1);
end 
set(handles.ListObject,'Value',1)
set(handles.ListObject,'String',{'plane'})
set(handles.ListObject_1,'Value',1)
set(handles.ListObject_1,'String',{'plane'})

%delete mask if it is displayed 
% if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
%    UvData=rmfield(UvData,'MaskName'); %will impose mask refresh  
% end
set(handles.uvmat,'UserData',UvData)
run0_Callback(hObject, eventdata, handles)



%------------------------------------------------
%CALLBACKS FOR PLOTTING PARAMETERS
%-------------------------------------------------
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Plot coordinates
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%------------------------------------------------------------------------
function num_MinX_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(handles.CheckFixLimits,'Value',1) %suppress auto mode
set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
update_plot(handles);

%------------------------------------------------------------------------
function num_MaxX_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(handles.CheckFixLimits,'Value',1) %suppress auto mode
set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
update_plot(handles);

%------------------------------------------------------------------------
function num_MinY_Callback(hObject, eventdata, handles)
%------------------------------------------
set(handles.CheckFixLimits,'Value',1) %suppress auto mode
set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
update_plot(handles);

%------------------------------------------------------------------------
function num_MaxY_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(handles.CheckFixLimits,'Value',1) %suppress auto mode
set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
update_plot(handles);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Scalar or image representation
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%------------------------------------------------------------------------
function num_MinA_Callback(hObject, eventdata, handles)
%------------------------------------------
set(handles.CheckFixScalar,'Value',1) %suppress auto mode
set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
MinA=str2double(get(handles.num_MinA,'String'));
MaxA=str2double(get(handles.num_MaxA,'String'));
if MinA>MaxA% switch minA and maxA in case of error
    MinA_old=MinA;
    MinA=MaxA;
    MaxA=MinA_old;
    set(handles.num_MinA,'String',num2str(MinA,5));
    set(handles.num_MaxA,'String',num2str(MaxA,5));
end
update_plot(handles);

%------------------------------------------------------------------------
function num_MaxA_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(handles.CheckFixScalar,'Value',1) %suppress auto mode
set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
MinA=str2double(get(handles.num_MinA,'String'));
MaxA=str2double(get(handles.num_MaxA,'String'));
if MinA>MaxA% switch minA and maxA in case of error
        MinA_old=MinA;
    MinA=MaxA;
    MaxA=MinA_old;
    set(handles.num_MinA,'String',num2str(MinA,5));
    set(handles.num_MaxA,'String',num2str(MaxA,5));
end
update_plot(handles);

%------------------------------------------------------------------------
function CheckFixScalar_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
test=get(handles.CheckFixScalar,'Value');
if test
    set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
else
    set(handles.CheckFixScalar,'BackgroundColor',[0.7 0.7 0.7])
    update_plot(handles);
end

%-------------------------------------------------------------------
function CheckBW_Callback(hObject, eventdata, handles)
%-------------------------------------------------------------------
update_plot(handles);

%-------------------------------------------------------------------
function num_Opacity_Callback(hObject, eventdata, handles)
update_plot(handles);
%-------------------------------------------------------------------

%-------------------------------------------------------------------
function ListContour_Callback(hObject, eventdata, handles)
%-------------------------------------------------------------------
val=get(handles.ListContour,'Value');
if val==2
    set(handles.interval_txt,'Visible','on')
    set(handles.num_IncrA,'Visible','on')
else
    set(handles.interval_txt,'Visible','off')
    set(handles.num_IncrA,'Visible','off')
end
update_plot(handles);

%-------------------------------------------------------------------
function num_IncrA_Callback(hObject, eventdata, handles)
%-------------------------------------------------------------------
update_plot(handles);


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Vector representation
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%-------------------------------------------------------------------
function CheckHideWarning_Callback(hObject, eventdata, handles)
%-------------------------------------------------------------------
update_plot(handles);

%-------------------------------------------------------------------
function CheckHideFalse_Callback(hObject, eventdata, handles)
%-------------------------------------------------------------------
update_plot(handles);

%-------------------------------------------------------------------
function num_VecScale_Callback(hObject, eventdata, handles)
%-------------------------------------------------------------------
set(handles.CheckFixVectors,'Value',1);
set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
update_plot(handles);

%-------------------------------------------------------------------
function CheckFixVectors_Callback(hObject, eventdata, handles)
%-------------------------------------------------------------------
test=get(handles.CheckFixVectors,'Value');
if test
    set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
else
    update_plot(handles);
    %set(handles.num_VecScale,'String',num2str(ScalOut.num_VecScale,3))
    set(handles.CheckFixVectors,'BackgroundColor',[0.7 0.7 0.7])
end

%------------------------------------------------------------------------
% --- Executes on selection change in CheckDecimate4 (nb_vec/4).
function CheckDecimate4_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
update_plot(handles);

%------------------------------------------------------------------------
% --- Executes on selection change in ColorCode menu
function ColorCode_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
% edit the choice for color code
update_color_code_boxes(handles);
update_plot(handles);

%------------------------------------------------------------------------
function update_color_code_boxes(handles)
%------------------------------------------------------------------------
list_code=get(handles.ColorCode,'String');% list menu fields
colcode= list_code{get(handles.ColorCode,'Value')}; % selected field
enable_slider='off';%default
enable_bounds='off';%default
enable_scalar='off';%default
switch colcode
    case {'rgb','bgr'}
        enable_slider='on';
        enable_bounds='on';
        enable_scalar='on';
    case '64 colors'
        enable_bounds='on';
        enable_scalar='on';
end
set(handles.Slider1,'Visible',enable_slider)
set(handles.Slider2,'Visible', enable_slider)
set(handles.num_ColCode1,'Visible',enable_slider)
set(handles.num_ColCode2,'Visible',enable_slider)
set(handles.TitleColCode1,'Visible',enable_slider)
set(handles.TitleColCode2,'Visible',enable_slider)
set(handles.CheckFixVecColor,'Visible',enable_bounds)
set(handles.num_MinVec,'Visible',enable_bounds)
set(handles.num_MaxVec,'Visible',enable_bounds)
set(handles.ColorScalar,'Visible',enable_scalar)
set_vec_col_bar(handles)

%------------------------------------------------------------------
% --- Executes on selection change in ColorScalar: choice of the color code.
function ColorScalar_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------
% edit the choice for color code
list_scalar=get(handles.ColorScalar,'String');% list menu fields
col_scalar= list_scalar{get(handles.ColorScalar,'Value')}; % selected field
if isequal(col_scalar,'ima_cor')
    set(handles.CheckFixVecColor,'Value',1)%fixed scale by default
    ColorCode='rgb';
    set(handles.num_MinVec,'String','0')
    set(handles.num_MaxVec,'String','1')
    set(handles.num_ColCode1,'String','0.333')
    set(handles.num_ColCode2,'String','0.666')
else
    set(handles.CheckFixVecColor,'Value',0)%auto scale between min,max by default
    ColorCode='64 colors';
end
ColorCodeList=get(handles.ColorCode,'String');
ichoice=find(strcmp(ColorCode,ColorCodeList),1);
set(handles.ColorCode,'Value',ichoice)% set color code in the menu

update_color_code_boxes(handles);
%replot the current graph
run0_Callback(hObject, eventdata, handles)

%----------------------------------------------------------------
% -- Executes on slider movement to set the color code
%
function Slider1_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------
slider1=get(handles.Slider1,'Value');
min_val=str2num(get(handles.num_MinVec,'String'));
max_val=str2num(get(handles.num_MaxVec,'String'));
col=min_val+(max_val-min_val)*slider1;
set(handles.num_ColCode1,'String',num2str(col))
if(get(handles.Slider2,'Value') < col)%move also the second slider at the same value if needed
    set(handles.Slider2,'Value',col)
    set(handles.num_ColCode2,'String',num2str(col))
end
set_vec_col_bar(handles)
update_plot(handles);

%----------------------------------------------------------------
% Executes on slider movement to set the color code
%----------------------------------------------------------------
function Slider2_Callback(hObject, eventdata, handles)
slider2=get(handles.Slider2,'Value');
min_val=str2num(get(handles.num_MinVec,'String'));
max_val=str2num(get(handles.num_MaxVec,'String'));
col=min_val+(max_val-min_val)*slider2;
set(handles.num_ColCode2,'String',num2str(col))
if(get(handles.Slider1,'Value') > col)%move also the first slider at the same value if needed
    set(handles.Slider1,'Value',col)
    set(handles.num_ColCode1,'String',num2str(col))
end
set_vec_col_bar(handles)
update_plot(handles);

%----------------------------------------------------------------
% --- Execute on return carriage on the edit box corresponding to slider 1
%----------------------------------------------------------------
function num_ColCode1_Callback(hObject, eventdata, handles) 
set_vec_col_bar(handles)
update_plot(handles);

%----------------------------------------------------------------
% --- Execute on return carriage on the edit box corresponding to slider 2
%----------------------------------------------------------------
function num_ColCode2_Callback(hObject, eventdata, handles)
set_vec_col_bar(handles)
update_plot(handles);
%------------------------------------------------------------------------
%-------------------------------------------------------
% --- Executes on button press in CheckFixVecColor.
%-------------------------------------------------------
function VecColBar_Callback(hObject, eventdata, handles)
set_vec_col_bar(handles)

%------------------------------------------------------------------------
% --- Executes on button press in CheckFixVecColor.
function CheckFixVecColor_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
if ~get(handles.CheckFixVecColor,'Value')
    update_plot(handles);
end

%------------------------------------------------------------------------
% --- Executes on selection change in num_MaxVec.
function num_MinVec_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
max_vec_Callback(hObject, eventdata, handles)

%------------------------------------------------------------------------
% --- Executes on selection change in num_MaxVec.
function num_MaxVec_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(handles.CheckFixVecColor,'Value',1)
CheckFixVecColor_Callback(hObject, eventdata, handles)
min_val=str2num(get(handles.num_MinVec,'String'));
max_val=str2num(get(handles.num_MaxVec,'String'));
slider1=get(handles.Slider1,'Value');
slider2=get(handles.Slider2,'Value');
colcode1=min_val+(max_val-min_val)*slider1;
colcode2=min_val+(max_val-min_val)*slider2;
set(handles.num_ColCode1,'String',num2str(colcode1))
set(handles.num_ColCode2,'String',num2str(colcode2))
update_plot(handles);

%------------------------------------------------------------------------
% --- update the display of color code for vectors (on vecColBar)
function set_vec_col_bar(handles)
%------------------------------------------------------------------------
%get the image of the color display button 'VecColBar' in pixels
set(handles.VecColBar,'Unit','pixel');
pos_vert=get(handles.VecColBar,'Position');
set(handles.VecColBar,'Unit','Normalized');
width=ceil(pos_vert(3));
height=ceil(pos_vert(4));

%get slider indications
list=get(handles.ColorCode,'String');
ichoice=get(handles.ColorCode,'Value');
colcode.ColorCode=list{ichoice};
colcode.MinVec=str2num(get(handles.num_MinVec,'String'));
colcode.MaxVec=str2num(get(handles.num_MaxVec,'String'));
test3color=strcmp(colcode.ColorCode,'rgb') || strcmp(colcode.ColorCode,'bgr');
if test3color
    colcode.ColCode1=str2num(get(handles.num_ColCode1,'String'));
    colcode.ColCode2=str2num(get(handles.num_ColCode2,'String'));
end
vec_C=colcode.MinVec+(colcode.MaxVec-colcode.MinVec)*(0.5:width-0.5)/width;%sample of vec_C values from min to max
[colorlist,col_vec]=set_col_vec(colcode,vec_C);
oneheight=ones(1,height);
A1=colorlist(col_vec,1)*oneheight;
A2=colorlist(col_vec,2)*oneheight;
A3=colorlist(col_vec,3)*oneheight;
A(:,:,1)=A1';
A(:,:,2)=A2';
A(:,:,3)=A3';
set(handles.VecColBar,'Cdata',A)

%-------------------------------------------------------------------
function update_plot(handles)
%-------------------------------------------------------------------
UvData=get(handles.uvmat,'UserData');
AxeData=UvData.axes3;% retrieve the current plotted data
PlotParam=read_GUI(handles.uvmat);
[tild,PlotParamOut]= plot_field(AxeData,handles.axes3,PlotParam);
write_plot_param(handles,PlotParamOut); %update the auto plot parameters

%------------------------------------------------------------------------
%------------------------------------------------------------------------
%   SELECTION AND EDITION OF PROJECTION OBJECTS
%------------------------------------------------------------------------
%------------------------------------------------------------------------

% --- Executes on selection change in ListObject_1.
function ListObject_1_Callback(hObject, eventdata, handles)
list_str=get(handles.ListObject,'String');
UvData=get(handles.uvmat,'UserData');
ObjectData=UvData.Object{get(handles.ListObject_1,'Value')};

%% update the projection plot on uvmat
ProjData= proj_field(UvData.Field,ObjectData);%project the current input field on object ObjectData
plot_field(ProjData,handles.axes3,read_GUI(handles.uvmat));% plot the projected field;
%replot all the objects within the new projected field
for IndexObj=1:numel(list_str)
    IndexObj
        hobject=UvData.Object{IndexObj}.DisplayHandle.uvmat
        if isempty(hobject) || ~ishandle(hobject)
            hobject=handles.axes3
        end
        if isequal(IndexObj,get(handles.ListObject,'Value'))
            objectcolor='m'; %paint in magenta the currently selected object in ListObject
        else
            objectcolor='b';
        end
        UvData.Object{IndexObj}.DisplayHandle.uvmat=plot_object(UvData.Object{IndexObj},ObjectData,hobject,objectcolor);%draw the object in uvmat      
end
set(handles.uvmat,'UserData',UvData)

%% display the object parameters if the GUI set_object is already opened
if ~get(handles.ViewObject,'Value')
    ZBounds=0; % default
    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
    end
    ObjectData.Name=list_str{get(handles.ListObject_1,'Value')};
    set_object(ObjectData,[],ZBounds);
    set(handles.ViewObject,'Value',1)% show that the selected object in ListObject_1 is currently visualised
end

%  desactivate the edit object mode
set(handles.edit_object,'Value',0) 
set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 

%------------------------------------------------------------------------
% --- Executes on selection change in ListObject.
function ListObject_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
list_str=get(handles.ListObject,'String');
IndexObj=get(handles.ListObject,'Value');%present object selection

%% The object  is displayed in set_object if this GUI is already opened
UvData=get(handles.uvmat,'UserData');
ObjectData=UvData.Object{IndexObj};
hset_object=findobj(allchild(0),'tag','set_object');
if ~isempty(hset_object)
    ZBounds=0; % default
    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
    end
    ObjectData.Name=list_str{IndexObj};
    set_object(ObjectData,[],ZBounds);
    set(handles.ViewField,'Value',1)% show that the selected object in ListObject is currently visualised
end

%%  desactivate the edit object mode
set(handles.edit_object,'Value',0) 
set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 

%% update the  plot on view_field if view_field is already openened
hview_field=findobj(allchild(0),'tag','view_field');
if isempty(hview_field)
    hhview_field.axes3=[];
else
    Data=get(hview_field,'UserData');
    hhview_field=guidata(hview_field);
    ProjData= proj_field(UvData.Field,ObjectData);%project the current interface field on ObjectData
    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.axes3,read_GUI(hview_field));%read plotting parameters on the uvmat interfachhview_fiel
    write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
    haxes=findobj(hview_field,'tag','axes3');
    pos=get(hview_field,'Position');  
    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
        pos_table=get(h_TableDisplay,'Position');
        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
        drawnow% needed to change position before the next command
        set(hview_field,'UserData',Data);% restore the previously stored GUI position after GUI resizing
    else
        set(hview_field,'Position',Data.GUISize)% return to the previously stored GUI position and size
    end
end

%% update the color of the graphic object representation: the selected object in magenta, others in blue
update_object_color(handles.axes3,hhview_field.axes3,UvData.Object{IndexObj}.DisplayHandle.uvmat)

%------------------------------------------------------------------------
%--- update the color representation of objects (indicating the selected ones)
function update_object_color(axes_uvmat,axes_view_field,DisplayHandle)
%------------------------------------------------------------------------
if isempty(axes_view_field)% case with no view_field plot
hother=[findobj(axes_uvmat,'Tag','proj_object');findobj(axes_uvmat,'Tag','DeformPoint')];%find all the proj object and deform point representations
else
hother=[findobj(axes_uvmat,'Tag','proj_object') ;findobj(axes_view_field,'Tag','proj_object');... %find all the proj object representations
findobj(axes_uvmat,'Tag','DeformPoint'); findobj(axes_view_field,'Tag','DeformPoint')];%find all the deform point representations
end
for iobj=1:length(hother)
    if isequal(get(hother(iobj),'Type'),'rectangle')||isequal(get(hother(iobj),'Type'),'patch')
        set(hother(iobj),'EdgeColor','b')
        if isequal(get(hother(iobj),'FaceColor'),'m')
            set(hother(iobj),'FaceColor','b')
        end
    elseif isequal(get(hother(iobj),'Type'),'image')
        Acolor=get(hother(iobj),'CData');
        Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2));
        set(hother(iobj),'CData',Acolor);
    else
        set(hother(iobj),'Color','b')
    end
    set(hother(iobj),'Selected','off')
end
if ishandle(DisplayHandle)
    linetype=get(DisplayHandle,'Type');
    if isequal(linetype,'line')
        set(DisplayHandle,'Color','m'); %set the selected object to magenta color
    elseif isequal(linetype,'rectangle')
        set(DisplayHandle,'EdgeColor','m'); %set the selected object to magenta color
    elseif isequal(linetype,'patch')
        set(DisplayHandle,'FaceColor','m'); %set the selected object to magenta color
    end
    SubObjectData=get(DisplayHandle,'UserData');
    if isfield(SubObjectData,'SubObject') & ishandle(SubObjectData.SubObject)
        for iobj=1:length(SubObjectData.SubObject)
            hsub=SubObjectData.SubObject(iobj);
            if isequal(get(hsub,'Type'),'rectangle')
                set(hsub,'EdgeColor','m'); %set the selected object to magenta color
            elseif isequal(get(hsub,'Type'),'image')
                Acolor=get(hsub,'CData');
                Acolor(:,:,1)=Acolor(:,:,3);
                set(hsub,'CData',Acolor);
            else
                set(hsub,'Color','m')
            end
        end
    end
    if isfield(SubObjectData,'DeformPoint') & ishandle(SubObjectData.DeformPoint)
        set(SubObjectData.DeformPoint,'Color','m')
    end
end

%-------------------------------------------------------------------
% --- Executes on selection change in edit_object.
function edit_object_Callback(hObject, eventdata, handles)
%-------------------------------------------------------------------
UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface 
hset_object=findobj(allchild(0),'Tag','set_object');
if get(handles.edit_object,'Value')
    set(handles.edit_object,'BackgroundColor',[1,1,0])  
    %suppress the other options 
    set(handles.CheckZoom,'Value',0)
    CheckZoom_Callback(hObject, eventdata, handles)
    hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
    if ishandle(hgeometry_calib)
        hhgeometry_calib=guidata(hgeometry_calib);
        set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
        set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
    end
    set(handles.ViewObject,'value',1)
    ViewObject_Callback(hObject, eventdata, handles)
%     if isempty(hset_object)% open the GUI set_object with data of the currently selected object
%         ViewObject_Callback(hObject, eventdata, handles)
%         %         hset_object=findobj(allchild(0),'Tag','set_object');
%     else
%         hhset_object=guidata(hset_object);
%         set(hhset_object.PLOT,'enable','on');
%         set(get(hset_object,'children'),'enable','on')
%     end
else % desctivate object edit mode
    set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])  
    if ~isempty(hset_object)% open the 
        hhset_object=guidata(hset_object);
        set(hhset_object.PLOT,'enable','off'); 
        set(get(hset_object,'children'),'enable','inactive')
    end
end


%------------------------------------------------------------------------
% --- Executes on button press in ViewObject.
function ViewObject_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
check_view=get(handles.ViewObject,'Value');

if check_view %activate set_object    
    IndexObj=get(handles.ListObject,'Value');
    list_object=get(handles.ListObject,'String');
    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
    UvData.Object{IndexObj}.Name=list_object{IndexObj};
    if numel(UvData.Object)<IndexObj;% error in UvData
        msgbox_uvmat('ERROR','invalid object list')
        return
    end
    ZBounds=0; % default
    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
    end
%     set(handles.ListObject_1,'Value',IndexObj);%restore ListObject selection after set_object deletion
    data=UvData.Object{IndexObj};
    if ~isfield(data,'Type')% default plane
        data.Type='plane';
    end
    if isfield(UvData,'Field')
        Field=UvData.Field;
        if isfield(UvData.Field,'Mesh')&&~isempty(UvData.Field.Mesh)
            data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
            if strcmp(data.Type,'line')||strcmp(data.Type,'polyline')
                data.RangeY=UvData.Field.Mesh;
            else
                data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
            end
            data.DX=UvData.Field.Mesh;
            data.DY=UvData.Field.Mesh;
        end
        if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
            data.Coord=[0 0 0]; %default
        end
        if isfield(Field,'CoordUnit')
            data.CoordUnit=Field.CoordUnit;
        end
    end
    hset_object=set_object(data,[],ZBounds);
    hhset_object=guidata(hset_object);
    if get(handles.edit_object,'Value')% edit mode
        set(hhset_object.PLOT,'Enable','on')
        set(get(hset_object,'children'),'enable','on')
    else
        set(hhset_object.PLOT,'Enable','off')
        set(get(hset_object,'children'),'enable','inactive')% deactivate the GUI except SAVE
        set(hhset_object.SAVE,'Enable','on')
    end
else
    hset_object=findobj(allchild(0),'tag','set_object');
    if ~isempty(hset_object)
        delete(hset_object)% delete existing version of set_object
    end
end
  

%------------------------------------------------------------------------
% --- Executes on button press in ViewField.
function ViewField_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
check_view=get(handles.ViewField,'Value');

if check_view
    IndexObj=get(handles.ListObject,'Value');
    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
    if numel(UvData.Object)<IndexObj(end);% error in UvData
        msgbox_uvmat('ERROR','invalid object list')
        return
    end
    ZBounds=0; % default
    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
    end
    set(handles.ListObject,'Value',IndexObj);%restore ListObject selection after set_object deletion
    if ~isfield(UvData.Object{IndexObj(1)},'Type')% default plane
        UvData.Object{IndexObj(1)}.Type='plane';
    end
    list_object=get(handles.ListObject,'String');
    UvData.Object{IndexObj(end)}.Name=list_object{IndexObj(end)};
    
    %% show the projection of the selected object on view_field
    ProjData= proj_field(UvData.Field,UvData.Object{IndexObj});%project the current field on ObjectData
    hview_field=findobj(allchild(0),'tag','view_field');
    if isempty(hview_field)
        hview_field=view_field;
    end
    hhview_field=guidata(hview_field);
    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.axes3,read_GUI(hview_field));%read plotting parameters on the GUI view_field);
    write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
    haxes=findobj(hview_field,'tag','axes3');
    pos=get(hview_field,'Position');
    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
        pos_table=get(h_TableDisplay,'Position');
        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
    else
        Data=get(hview_field,'UserData');
        set(hview_field,'Position',Data.GUISize)% restore the size of view_field for plots
    end
else
    hview_field=findobj(allchild(0),'tag','view_field');
    if ~isempty(hview_field)
        delete(hview_field)% delete existing version of set_object
    end
end


%------------------------------------------------------------------------
% --- Executes on button press in delete_object.
function delete_object_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
IndexObj=get(handles.ListObject,'Value');
IndexObj_1=get(handles.ListObject_1,'Value');
if IndexObj>1 && ~isequal(IndexObj,IndexObj_1)
    delete_object(IndexObj)
end

%------------------------------------------------------------------------
%------------------------------------------------------------------------
%  II - TOOLS FROM THE UPPER MENU BAR
%------------------------------------------------------------------------
%------------------------------------------------------------------------

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Export  Menu Callbacks
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%------------------------------------------------------------------------
% --- Executes on button press in Menu/Export/field in workspace.
function MenuExportField_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
global Data_uvmat
Data_uvmat=get(handles.uvmat,'UserData');
evalin('base','global Data_uvmat')%make CurData global in the workspace
display('current field :')
evalin('base','Data_uvmat') %display CurData in the workspace
commandwindow; %brings the Matlab command window to the front

%------------------------------------------------------------------------
% --- Executes on button press in Menu/Export/extract figure.
function MenuExportFigure_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
% huvmat=get(handles.MenuExport,'parent');
hfig=figure;
copyobj(handles.axes3,hfig);
map=colormap(handles.axes3);
colormap(map);%transmit the current colormap to the zoom fig
colorbar

% %------------------------------------------------------
% % --- Executes on button press in Menu/Export/extract figure.
% %------------------------------------------------------
% function MenuExport_plot_Callback(hObject, eventdata, handles)
% huvmat=get(handles.MenuExport_plot,'parent');
% UvData=get(huvmat,'UserData');
% hfig=figure;
% newaxes=copyobj(handles.axes3,hfig);
% map=colormap(handles.axes3);
% colormap(map);%transmit the current colormap to the zoom fig
% colorbar

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

%------------------------------------------------------------------------
% --------------------------------------------------------------------
function MenuExportMovie_Callback(hObject, eventdata, handles)
% --------------------------------------------------------------------
set(handles.MenuExportMovie,'BusyAction','queue')% activate the button
huvmat=get(handles.run0,'parent');
UvData=get(huvmat,'UserData');
%[xx,xx,FileBase]=read_file_boxes(handles);
[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
FileBase=fullfile(RootPath,RootFile);
 %read the current input file name
prompt = {'movie file name';'frames per second';'frame resolution (*[512x384] pixels)';'axis position relative to the frame';'total frame number (starting from the current uvmat display)'};
dlg_title = 'select properties of the output avi movie';
num_lines= 1;
% nbfield_cell=get(handles.last_i,'String');
def     = {[FileBase '_out.avi'];'10';'1';'[0.03 0.05 0.95 0.92]';'10'};
answer = inputdlg(prompt,dlg_title,num_lines,def,'on');
aviname=answer{1};
fps=str2double(answer{2});
% check for existing file with output name aviname
if exist(aviname,'file')
    backup=aviname;
    testexist=2;
    while testexist==2
        backup=[backup '~'];
        testexist=exist(backup,'file');      
    end
    [success,message]=copyfile(aviname,backup);%make backup of the existing file
    if isequal(success,1)
        delete(aviname)%delete existing file 
    else
        msgbox_uvmat('ERROR',message)
        return
    end 
end
%create avi open
aviobj=avifile(aviname,'Compression','None','fps',fps);

%display first view for tests
newfig=figure;
newaxes=copyobj(handles.axes3,newfig);%new plotting axes in the new figure
set(newaxes,'Tag','movieaxes')
nbpix=[512 384]*str2double(answer{3});
set(gcf,'Position',[1 1 nbpix])% resolution XVGA 
set(newaxes,'Position',eval(answer{4}));
map=colormap(handles.axes3);
colormap(map);%transmit the current colormap to the zoom fig
msgbox_uvmat('INPUT_Y-N',{['adjust figure ' num2str(newfig) ' with its matlab edit menu '] ;...
        ['then press OK to get the avi movie as a copy of figure ' num2str(newfig) ' display']});
UvData.plotaxes=newaxes;% the axis in the new figure becomes the current main plotting axes
set(huvmat,'UserData',UvData);
increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
set(handles.STOP,'Visible','on')
set(handles.speed,'Visible','on')
set(handles.speed_txt,'Visible','on')
set(handles.Movie,'BusyAction','queue')

%imin=str2double(get(handles.i1,'String'));
imax=str2double(answer{5});
% if isfield(UvData,'Time')
htitle=get(newaxes,'Title');
xlim=get(newaxes,'XLim');
ylim=get(newaxes,'YLim');
set(htitle,'Position',[xlim(2)+0.07*(xlim(2)-xlim(1)) ylim(2)-0.05*(ylim(2)-ylim(1)) 0])
time_str=get(handles.abs_time,'String');
set(htitle,'String',['t=' time_str])
set(handles.speed,'Value',1)
for i=1:imax
    if get(handles.speed,'Value')~=0 && isequal(get(handles.MenuExportMovie,'BusyAction'),'queue') % enable STOP command
            runpm(hObject,eventdata,handles,increment)% run plus 
            drawnow
            time_str=get(handles.abs_time,'String');
            if ishandle(htitle)
             set(htitle,'String',['t=' time_str])
            end
            mov=getframe(newfig);
            aviobj=addframe(aviobj,mov);
    end
end
aviobj=close(aviobj);
UvData=rmfield(UvData,'plotaxes');
%UvData.Object{1}.plotaxes=handles.axes3;
set(huvmat,'UserData',UvData);
msgbox_uvmat('CONFIRMATION',{['movie ' aviname ' created '];['with ' num2str(imax) ' frames']})


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Projection Objects Menu Callbacks
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% -----------------------------------------------------------------------
function Menupoints_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
data.Type='points';
data.ProjMode='projection';%default
data.ProjModeMenu={};% do not restrict ProjMode menus
create_object(data,handles)

% -----------------------------------------------------------------------
function Menuline_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
data.Type='line';
data.ProjMode='projection';%default
data.ProjModeMenu={};% do not restrict ProjMode menus
create_object(data,handles)

%------------------------------------------------------------------------
function Menupolyline_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
data.Type='polyline';
data.ProjMode='projection';%default
data.ProjModeMenu={};% do not restrict ProjMode menus
create_object(data,handles)

%------------------------------------------------------------------------
function Menupolygon_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
data.Type='polygon';
data.ProjMode='inside';%default
data.ProjModeMenu={};% do not restrict ProjMode menus
create_object(data,handles)

%------------------------------------------------------------------------
function Menurectangle_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
data.Type='rectangle';
data.ProjMode='inside';%default
data.ProjModeMenu={};% do not restrict ProjMode menus
create_object(data,handles)

%------------------------------------------------------------------------
function Menuellipse_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
data.Type='ellipse';
data.ProjMode='inside';%default
data.ProjModeMenu={};% do not restrict ProjMode menus
create_object(data,handles)

%------------------------------------------------------------------------
function MenuMaskObject_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
data.Type='polygon';
data.TypeMenu={'polygon'};
data.ProjMode='mask_inside';%default
data.ProjModeMenu={'mask_inside';'mask_outside'};
create_object(data,handles)

%------------------------------------------------------------------------
function Menuplane_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
data.Type='plane';
data.ProjMode='projection';%default
data.ProjModeMenu={};% do not restrict ProjMode menus
create_object(data,handles)

%------------------------------------------------------------------------
function Menuvolume_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
data.Type='volume';
data.ProjMode='interp';%default
data.ProjModeMenu={};
% set(handles.create,'Visible','on')
% set(handles.create,'Value',1)
% VOLUME_Callback(hObject,eventdata,handles)data.ProjModeMenu={};
create_object(data,handles)

%------------------------------------------------------------------------
% --- generic function used for the creation of a projection object
function create_object(data,handles)
%------------------------------------------------------------------------
% desactivate geometric calibration if opened
hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
if ishandle(hgeometry_calib)
    hhgeometry_calib=guidata(hgeometry_calib);
    set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
    set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
end
set(handles.edit_object,'Value',0); %suppress the object edit mode
set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])  
ListObject=get(handles.ListObject,'String');
if ~strcmp(ListObject{end},'')
    ListObject=[ListObject;{''}]; %append a blank to the list (if nort already done) to indicate the creation of a new object
    set(handles.ListObject,'String',ListObject)
end
IndexObj=length(ListObject);
set(handles.ListObject,'Value',IndexObj)
UvData=get(handles.uvmat,'UserData');
UvData.Object{IndexObj}=[]; %create a new empty object
UvData.Object{IndexObj}.DisplayHandle.uvmat=handles.axes3; % axes for plot_object
UvData.Object{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation
data.Name=data.Type;% default name=type
data.Coord=[0 0]; %default
if isfield(UvData,'Field')
    Field=UvData.Field;
    if isfield(UvData.Field,'Mesh')&&~isempty(UvData.Field.Mesh)
        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
        if strcmp(data.Type,'line')||strcmp(data.Type,'polyline')||strcmp(data.Type,'points')
            data.RangeY=UvData.Field.Mesh;
        else
            data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
        end
        data.DX=UvData.Field.Mesh;
        data.DY=UvData.Field.Mesh;
    end
    if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
         data.Coord=[0 0 0]; %default
    end
    if isfield(Field,'CoordUnit')
        data.CoordUnit=Field.CoordUnit;
    end
end
if ishandle(handles.UVMAT_title)
    delete(handles.UVMAT_title)%delete the initial display of uvmat if no field has been entered
end
hset_object=set_object(data,handles);% call the set_object interface
hhset_object=guidata(hset_object);
hchild=get(hset_object,'children');
set(hchild,'enable','on')
set(handles.uvmat,'UserData',UvData)
set(handles.CheckZoom,'Value',0) %desactivate the zoom for object creation by the mouse
CheckZoom_Callback(handles.uvmat, [], handles)
set(handles.delete_object,'Visible','on')

%------------------------------------------------------------------------
function MenuBrowseObject_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
%get the object file 
[FileName, PathName, filterindex] = uigetfile( ...
       {'*.xml;*.mat', ' (*.xml,*.mat)';
       '*.xml',  '.xml files '; ...
        '*.mat',  '.mat matlab files '}, ...
        'Pick an xml Object file',get(handles.RootPath,'String'));
fileinput=[PathName FileName];%complete file name 
sizf=size(fileinput);
if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end

%read the file
data=xml2struct(fileinput);

[tild,data.Name]=fileparts(FileName);% object name set as file name
ListObject=get(handles.ListObject,'String');
if ~strcmp(ListObject{end},'')
    ListObject=[ListObject;{''}]; %append a blank to the list (if not already done) to indicate the creation of a new object
    set(handles.ListObject,'String',ListObject)
end
UvData=get(handles.uvmat,'UserData');
UvData.Object{IndexObj}=[]; %create a new empty object
UvData.Object{IndexObj}.DisplayHandle.uvmat=[]; %no plot handle before plot_field operation
UvData.Object{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation
set(handles.uvmat,'UserData',UvData)
set(handles.ListObject,'Value',length(ListObject))
hset_object=set_object(data);% call the set_object interface
set(get(hset_object,'children'),'enable','on')% enable edit action on elements on GUI set_object
set(handles.edit_object,'Value',0); %suppress the object edit mode
set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])  
set(handles.delete_object,'Visible','on')


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% MenuEdit Callbacks
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%------------------------------------------------------------------------
function MenuEditObject_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(handles.edit_object,'Value',1)
edit_Callback(hObject, eventdata, handles)

% %------------------------------------------------------------------------
% function enable_transform(handles,state)
% %------------------------------------------------------------------------
% set(handles.transform_fct,'Visible',state)
% set(handles.TRANSFORM_txt,'Visible',state)    
% set(handles.transform_fct,'Visible',state)  
% set(handles.path_transform,'Visible',state)
% set(handles.pxcmx_txt,'Visible',state)
% set(handles.pxcmy_txt,'Visible',state)
% set(handles.pxcm,'Visible',state)
% set(handles.pycm,'Visible',state)

%------------------------------------------------------------------------
function MenuEditVectors_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(handles.edit_vect,'Visible','on')
set(handles.edit_vect,'Value',1)
edit_vect_Callback(hObject, eventdata, handles)

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% MenuTools Callbacks
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%------------------------------------------------------------------------
function MenuCalib_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------

UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface 

%suppress competing options 
set(handles.CheckZoom,'Value',0)
set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
set(handles.ListObject,'Value',1)      
% initiate display of GUI geometry_calib
data=[]; %default
if isfield(UvData,'CoordType')
    data.CoordType=UvData.CoordType;
end
pos=get(handles.uvmat,'Position');
pos(1)=pos(1)+pos(3)-0.311+0.04; %0.311= width of the geometry_calib interface (units relative to the srcreen)
pos(2)=pos(2)-0.02;
[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
set(handles.view_xml,'Backgroundcolor',[1 1 0])%indicate the reading of the current xml file by geometry_calib
if isfield(UvData.OpenParam,'CalOrigin')
    pos_uvmat=get(handles.uvmat,'Position');
    pos_cal(1)=pos_uvmat(1)+UvData.OpenParam.CalOrigin(1)*pos_uvmat(3);
    pos_cal(2)=pos_uvmat(2)+UvData.OpenParam.CalOrigin(2)*pos_uvmat(4);
    pos_cal(3:4)=UvData.OpenParam.CalSize .* pos_uvmat(3:4);
end
geometry_calib(FileName,pos_cal);% call the geometry_calib interface    
set(handles.view_xml,'Backgroundcolor',[1 1 1])%indicate the end of reading of the current xml file by geometry_calib
set(handles.MenuCalib,'checked','on')% indicate that MenuCalib is activated, test used by mouse action

%------------------------------------------------------------------------
function MenuMask_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface 
ListObj=UvData.Object;
select=zeros(1,numel(ListObj));
for iobj=1:numel(ListObj);
    if strcmp(ListObj{iobj}.ProjMode,'mask_inside')||strcmp(ListObj{iobj}.ProjMode,'mask_outside')
        select(iobj)=1;
    end
end
val=find(select);
if isempty(val)
    msgbox_uvmat('ERROR','polygons must be first created by Projection object/mask polygon in the menu bar');
    return
else
%     set(handles.ListObject,'Max',2);%allow multiple selection
    set(handles.ListObject,'Value',val);
    flag=1;
    npx=size(UvData.Field.A,2);
    npy=size(UvData.Field.A,1);
    xi=0.5:npx-0.5;
    yi=0.5:npy-0.5;
    [Xi,Yi]=meshgrid(xi,yi);
    if isfield(UvData,'Object')
        for iobj=1:length(UvData.Object)
            ObjectData=UvData.Object{iobj};
            if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
                flagobj=1;
                testphys=0; %coordinates in pixels by default
                if isfield(ObjectData,'CoordUnit') && ~isequal(ObjectData.CoordUnit,'pixel')
                    if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
                        Calib=UvData.XmlData{1}.GeometryCalib;
                        testphys=1;
                    end
                end
                if isfield(ObjectData,'Coord')&& isfield(ObjectData,'Type')
                    if isequal(ObjectData.Type,'polygon')
                        X=ObjectData.Coord(:,1);
                        Y=ObjectData.Coord(:,2);
                        if testphys
                            [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
                        end
                        flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside
                    elseif isequal(ObjectData.Type,'ellipse')
                        if testphys
                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
                        end
                        RangeX=max(ObjectData.RangeX);
                        RangeY=max(ObjectData.RangeY);
                        X2Max=RangeX*RangeX;
                        Y2Max=RangeY*RangeY;
                        distX=(Xi-ObjectData.Coord(1,1));
                        distY=(Yi-ObjectData.Coord(1,2));
                        flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
                    elseif isequal(ObjectData.Type,'rectangle')
                        if testphys
                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
                        end
                        distX=abs(Xi-ObjectData.Coord(1,1));
                        distY=abs(Yi-ObjectData.Coord(1,2));
                        flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
                    end
                    if isequal(ObjectData.ProjMode,'mask_outside')
                        flagobj=~flagobj;
                    end
                    flag=flag & flagobj;
                end
            end
        end
    end 
    %mask name
    RootPath=get(handles.RootPath,'String');
    RootFile=get(handles.RootFile,'String');
    if ~isempty(RootFile)&&(isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
        RootFile(1)=[];
    end
    filebase=fullfile(RootPath,RootFile);
    list=get(handles.masklevel,'String');
    masknumber=num2str(length(list));
    maskindex=get(handles.masklevel,'Value');
    mask_name=fullfile_uvmat(RootPath,'',[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
    %mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
    imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
    imflag=flipdim(imflag,1);

    %display the mask
    hfigmask=figure;
    set(hfigmask,'Name','mask image')
    vec=linspace(0,1,256);%define a linear greyscale colormap
    map=[vec' vec' vec'];
    colormap(map)
    image(imflag);
    answer=msgbox_uvmat('INPUT_TXT','mask file name:', mask_name);
    if ~strcmp(answer,'Cancel')
        mask_dir=fileparts(answer);
        if ~exist(mask_dir,'dir')
            msgbox_uvmat('ERROR',['directory ' mask_dir ' does not exist'])
            return
        end
        imwrite(imflag,answer,'BitDepth',8);
    end
    set(handles.ListObject,'Value',1)
%     set(handles.ListObject,'Max',1)
end

%------------------------------------------------------------------------
%-- open the GUI set_grid.fig to create grid
function MenuGrid_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
%suppress the other options if grid is chosen
set(handles.edit_vect,'Value',0)
edit_vect_Callback(hObject, eventdata, handles)
set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
set(handles.ListObject,'Value',1)      

%prepare display of the set_grid GUI
[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
CoordList=get(handles.transform_fct,'String');
val=get(handles.transform_fct,'Value');
set_grid(FileName,CoordList{val});% call the set_object interface


%------------------------------------------------------------------------
function MenuRuler_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
set(handles.CheckZoom,'Value',0)
CheckZoom_Callback(handles.uvmat, [], handles)
set(handles.MenuRuler,'checked','on')
UvData=get(handles.uvmat,'UserData');
UvData.MouseAction='ruler';
set(handles.uvmat,'UserData',UvData);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% MenuRun Callbacks
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%------------------------------------------------------------------------
% open the GUI 'series'
function MenuSeries_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
series; %first display of the GUI to fill waiting time
[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
param.FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
if isequal(get(handles.SubField,'Value'),1)
    [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
    FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
    if ~isequal(FileName_1,param.FileName)
        param.FileName_1=FileName_1;
    end
end
param.NomType=get(handles.NomType,'String');
param.NomType_1=get(handles.NomType_1,'String');
param.CheckFixPair=get(handles.CheckFixPair,'Value');
huvmat=get(handles.MenuSeries,'parent');
UvData=get(huvmat,'UserData');
if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'Time')
    param.Time=UvData.XmlData{1}.Time;
end
if isequal(get(handles.scan_i,'Value'),1)
    param.incr_i=str2num(get(handles.increment_scan,'String'));
elseif isequal(get(handles.scan_j,'Value'),1)
    param.incr_j=str2num(get(handles.increment_scan,'String'));
end
param.list_fields=get(handles.Fields,'String');% list menu fields
param.list_fields(1)=[]; %suppress  'image' option 
param.index_fields=get(handles.Fields,'Value');% selected string index
if param.index_fields>1
    param.index_fields=param.index_fields-1;
end
param.list_fields_1=get(handles.Fields_1,'String');% list menu fields
param.list_fields_1(1)=[]; %suppress  'image' option
param.index_fields_1=get(handles.Fields_1,'Value')-1;% selected string index
if param.index_fields_1>1
    param.index_fields_1=param.index_fields_1-1;
end
param.menu_coord_str=get(handles.transform_fct,'String');
param.menu_coord_val=get(handles.transform_fct,'Value');
series(param); %run the series interface

%------------------------------------------------------------------------
% -- open the GUI civ.fig for PIV
function MenuPIV_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
 FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
civ(FileName);% interface de civ(not in the uvmat file)

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