Description of uvmat

0001 %'uvmat': function associated with the GUI 'uvmat.fig' for images and data field visualization
0002 %------------------------------------------------------------------------
0003 % function huvmat=uvmat(input)
0004 %
0005 %OUTPUT
0006 % huvmat=current handles of the GUI uvmat.fig
0007 %
0008 %INPUT:
0009 % input: input file name (if character chain), or input image matrix to
0010 % visualize, or Matlab structure representing  netcdf fields (with fields
0011 % ListVarName....)
0012 %
0013 %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
0014 %  Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org.
0015 %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
0016 %     This open is part of the toolbox UVMAT.
0017 %
0018 %     UVMAT is free software; you can redistribute it and/or modify
0019 %     it under the terms of the GNU General Public License as published by
0020 %     the Free Software Foundation; either version 2 of the License, or
0021 %     (at your option) any later version.
0022 %
0023 %     UVMAT is distributed in the hope that it will be useful,
0024 %     but WITHOUT ANY WARRANTY; without even the implied warranty of
0025 %     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
0026 %     GNU General Public License (open UVMAT/COPYING.txt) for more details.
0027 %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
0028 %
0029 % Information stored on the interface:
0030 %    'Strings' of all edit boxes and menus: get(handles.Tag,'String')
0031 %    'Values' of all menus and toggle buttons: get(handles.Tag,'Value')
0032 %     Matlab structure stored as 'UserData' of the figure uvmat.fig,(can be obtained by right mouse click on the interface).
0033 %          It contains the following fields:
0034 %     - Fixed specifiacation of plotting figures and axes (defined bu uvmat_OpeningFcn)
0035 %          .PosColorbar: [0.8210 0.4710 0.0190 0.4450]; specified position of the colorbar on figures
0036 %     - Information read in the documentation open of a series (activated by RootPath_Callback) :
0037 %          .XmlData, with fields:
0038 %               .Time: matrix of times of the images with index i and j
0039 %               .GeometryCalib: [1x1 struct]
0040 %     - Information defined from the interface:
0041 %           .NewSeries: =1 when the first view of a new field series is displayed, else 0
0042 %           .filename:(char string)
0043 %           .VelType:(char string) type of velocity field selected
0044 %           .VelType_1:(char string)  REMPLACER LE CELL ACTUEL
0045 %           .FieldName: (char string) main field selected('image', 'velocity'...)
0046 %           .FieldName_1:(char string) second field selected('image', 'velocity'...)
0047 %           .CName: (char string)name of the scalar used for vector colors
0048 %           .CoordType: (char string) coordinate transform: e.g. 'phys' or 'px'
0049 %           .MouseAction: store the current effect of mouse button (create or edit objects)
0050 %     - Information on  projection objects
0051 %           .Object: {[1x1 struct]}
0052 %           .CurrentObjectIndex: index of the projection object .Object currently selected for editing
0053 %     -Information on the current field (Field{i})
0054 %            .Txt : text information to display (e.g. error message)
0055 %            .NbDim: number of dimensions (=0 by default)
0056 %            .NbCoord: number of vector components
0057 %            .CoordType: expresses the type of coordinate ('px' for image, 'sig' for instruments, or 'phys')
0058 %            .dt: time interval for the corresponding image pair
0059 %            .Mesh: estimated typical distance between vectors
0060 %            .ZMax:
0061 %            .ZMin:
0062 %            .X, .Y, .Z: set of vector coordinates
0063 %            .U,.V,.W: corresponding set of vector components
0064 %            .F: corresponding set of warning flags
0065 %            .FF: corresponding set of false flags, =0 for good vectors
0066 %            .C: corresponding values of the scalar used for vector color
0067 %             (.X, .Y, .Z,.U,.V,.W,.F,.FF,.C are matlab vectors of the same length,
0068 %                     equal to the number of vectors stored in the input open)
0069 %            .CName: name of the scalar .C
0070 %            .CType: type of the scalar .C, setting how the scalar is obtained (see 'Scalars' below)
0071 %            .A image or scalar
0072 %            .AX: vector of dimension 2 representing the first and last values
0073 %              of the X coordinates for the image or scalar known on a regular grid,
0074 %              or vector of dimension .A for a scaler defined on irregular grid.
0075 %            .AY: same as .AX along the Y direction
0076 %            .AName: name of the scalar, ='image' for an image
0077 
0078 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%   DATA FLOW  (for run0_Callback) %%%%%%%%%%%%%%%%%%%%:
0079 %
0080 %               Main input open   second input open(_1)        second image (pair animation)
0081 % read_ncfield.m         |                 |
0082 % read_image.m           |                 |
0083 %                     Field{1}         Field{2}
0084 %                                                                         |
0085 % coord transform (phys.m) or other user defined  fct acting on Field{i}  |
0086 %                                                                   Field{i}
0087 %                                                                    |
0088 % calc_field.m: calculate scalar or other derived fields (vort, div..).
0089 %
0090 % sub_field.m: combine the input Field{i} in a single set of fields (vector + scalar):
0091 %              Field{i=1->3}.X --> UvData.X                          |
0092 %                                                                    |
0093 %                                                                 UvData
0094 %                                                                    |
0095 % plot histograms of the whole  field
0096 % proj_field.m: project the set of fields on the current projection objects defined by UvData.Object
0097 %                                                                    |                                                                          |
0098 %                                                                ObjectData
0099 %                                                                    |
0100 % plot_field.m: plot the projected fields and store them as user     |
0101 % data of the plotting axes                                          |
0102 %                                                                    |
0103 %                                                                AxeData
0104 %
0105 %%%%%%%%%%%%%%    SCALARS: %%%%%%%%%%%%ùù%%%
0106 % scalars are displayed either as an image or countour plot, either as a color of
0107 % velocity vectors. The scalar values in the first case is represented by
0108 % UvData.Field.A, and by UvData.Field.C in the second case. The corresponding set of X
0109 % and Y coordinates are represented by UvData.Field.AX and UvData.Field.AY, and .X and
0110 % .Y for C (the same as velocity vectors). If A is a nxxny matrix (scalar
0111 % on a regtular grid), then .AX andf.AY contains only two elements, represneting the
0112 % coordinates of the four image corners. The scalar name is represented by
0113 % the strings .AName and/or .CName.
0114 % If the scalar exists in an input open (image or scalar stored under its
0115 % name in a netcdf open), it is directly read at the level of Field{1}or Field{2}.
0116 % Else only its name AName is recorded in Field{i}, and its field is then calculated
0117 %by the fuction calc_scal after the coordinate transform or after projection on an edit
0118      
0119 % Properties attached to plotting figures (standard Matlab properties):
0120 %    'CurrentAxes'= gca or get(gcf,'CurrentAxes');
0121 %    'CurrentPoint'=get(gcf,'CurrentPoint'): figure coordinates of the point over which the mouse is positioned
0122 %    'CurrentCharacter'=get(gcf,'CurrentCharacter'): last character typed  over the figure where the mouse is positioned
0123 %    'WindowButtonMotionFcn': function permanently called by mouse motion over the figure
0124 %    'KeyPressFcn': function called by pressing a key on the key board
0125 %    'WindowButtonDownFcn':  function called by pressing the mouse over the  figure
0126 %    'WindowButtonUpFcn': function called by releasing  the mouse pressure over the  figure
0127 
0128 % Properties attached to plotting axes:
0129 %    'CurrentPoint'=get(gca,'CurrentPoint'); (standard Matlab) same as for the figure, but position in plot coordinates.
0130 %     AxeData:=get(gca,'UserData');
0131 %     AxeData.Drawing  = create: create a new edit
0132 %                       = deform: modify an existing edit by moving its defining create
0133 %                      = off: no current drawing action
0134 %                     = translate: translate an existing edit
0135 %                    = zoom: isolate a subregion for zoom in=1 if an edit is being currently drawn, 0 else (set to 0 by releasing mouse button)
0136 %            .hset_edit=handle of the set_edit interface (if a projection edit is edited);
0137 %            .CurrentOrigin: Origin of a curently drawn edit
0138 %            .CurrentLine: currently drawn menuline (A REVOIR)
0139 %            .CurrentObject: handle of the currently drawn edit
0140 %            .CurrentRectZoom: current rectangle used for zoom
0141 %            .zoomon : zoom state (a revoir)
0142 %            .X, .Y, .Z: array of coordinates defining the position of the vector: ASSOCIER AU PLAN (OBJET) PLUTOT QU'A L'AXE ?
0143 %            .U, .V, .W: array of components of the vector
0144 %            .C:
0145 %            .F:
0146 %            .FF:
0147 %            .A
0148 
0149 % Properties attached to projection objects (create, menuline, menuplane...):
0150 %    'Tag'='proj_edit': for all projection objects
0151 %    ObjectData.Style=...: style of projection edit:
0152 %              .ProjMode
0153 %              .Coord: defines the position of the edit
0154 %              .XMin,YMin....
0155 %              .XMax,YMax....
0156 %              .DX,DY,DZ
0157 %              .Phi, .Theta, .Psi : Euler angles
0158 %              .X,.Y,.U,.V.... : field data projected on the edit
0159 %              .IndexObj: index in the list of UvData.Object
0160            %during plotting
0161 %               .plotaxes: handles of the current axes used to plot the  result of field projection on the object
0162 %               .plothandle: vector of handle(s) of the object graphic represnetation in all the opened plotting axes
0163 % To each projection object #iobj, corresponds an axis
0164 % Object{iobj}.plotaxes and nbobj representation graphs  Object{iobj}.plothandles(:) (where nbobj is the
0165 % nbre of current objects opened in uvmat. Note that Object{iobj}.plothandles(iobj)=[] : an object is not represented in its own projection field;
0166 %-------------------------------------------------------------------
0167 %-------------------------------------------------------------------
0168 %  I - MAIN FUNCTION UVMAT (DO NOT MODIFY)
0169 %-------------------------------------------------------------------
0170 %-------------------------------------------------------------------
0171 function varargout = uvmat(varargin)
0172 
0173 % Begin initialization code - DO NOT EDIT
0174 gui_Singleton = 1;
0175 gui_State = struct('gui_Name',          mfilename, ...
0176                    'gui_Singleton',     gui_Singleton, ...
0177                    'gui_OpeningFcn',    @uvmat_OpeningFcn, ...
0178                    'gui_OutputFcn',     @uvmat_OutputFcn, ...
0179                    'gui_LayoutFcn',     [], ...
0180                    'gui_Callback',      []);
0181 if nargin && ischar(varargin{1})
0182     gui_State.gui_Callback = str2func(varargin{1});
0183 end
0184 
0185 if nargout
0186     varargout{1:nargout} = gui_mainfcn(gui_State, varargin{:});
0187 else
0188     gui_mainfcn(gui_State, varargin{:});
0189 end
0190 % End initialization code - DO NOT EDIT
0191 
0192 %-------------------------------------------------------------------
0193 % --- Executes just before uvmat is made visible.
0194 function uvmat_OpeningFcn(hObject, eventdata, handles, input )
0195 %-------------------------------------------------------------------
0196 %WARNING: avoid the second input parameter, leads to erros
0197 global dircur dir_opening
0198 % Choose default command menuline output for uvmat
0199 handles.output = hObject;
0200 
0201 % %group handles for input file in a structure handles.InputFile
0202 % handlesInputFile={handles.RootPath,handles.SubDir,handles.RootFile,handles.FileIndex,handles.FileExt};
0203 % TagsInputFile={'RootPath','SubDir','RootFile','FileIndex','FileExt'};
0204 % handles.InputFile=cell2struct(handlesInputFile,TagsInputFile,2);
0205 %
0206 % %group handles for the second input file in a structure handles.InputFile_1
0207 % handlesInputFile={handles.RootPath_1,handles.SubDir_1,handles.RootFile_1,handles.FileIndex_1,handles.FileExt_1};
0208 % TagsInputFile={'RootPath','SubDir','RootFile','FileIndex','FileExt'};
0209 % handles.InputFile_1=cell2struct(handlesInputFile,TagsInputFile,2);
0210 
0211 % Update handles structure
0212 guidata(hObject, handles);
0213 
0214 dircur=pwd; %current working directory
0215 dir_opening=dircur;
0216 
0217 % set the position of colorbar and ancillary GUIs:
0218 set(hObject,'Units','Normalized')
0219 movegui(hObject,'center')
0220 UvData.PosColorbar=[0.805 0.022 0.019 0.445];
0221 UvData.SetObjectOrigin=[-0.05 -0.03]; %position for set_object
0222 UvData.SetObjectSize=[0.3 0.7];
0223 UvData.CalOrigin=[0.95 -0.03];%position for geometry_calib (TO IMPROVE)
0224 UvData.CalSize=[0.28 1];
0225 
0226 %functions for the mouse and keyboard
0227 set(handles.histo_u,'NextPlot','replacechildren');
0228 set(handles.histo_v,'NextPlot','replacechildren');
0229 set(hObject,'KeyPressFcn',{'keyboard_callback',handles})%set keyboard action function
0230 set(hObject,'WindowButtonMotionFcn',{'mouse_motion',handles})%set mouse action functio
0231 set(hObject,'WindowButtonDownFcn',{'mouse_down'})%set mouse click action function
0232 set(hObject,'WindowButtonUpFcn',{'mouse_up',handles}) 
0233 %set(hObject,'ResizeFcn',{@resize_uvmat})
0234 
0235 %load the list of previously browsed files in menus Open and Open_1
0236  dir_perso=prefdir;
0237  profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
0238  if exist(profil_perso,'file')
0239       h=load (profil_perso);
0240       if isfield(h,'MenuFile_1')
0241           set(handles.MenuFile_1,'Label',h.MenuFile_1);
0242           set(handles.MenuFile_1_1,'Label',h.MenuFile_1);
0243       end
0244       if isfield(h,'MenuFile_1')
0245           set(handles.MenuFile_2,'Label',h.MenuFile_2);
0246           set(handles.MenuFile_2_1,'Label',h.MenuFile_2);
0247       end
0248       if isfield(h,'MenuFile_1')
0249           set(handles.MenuFile_3,'Label',h.MenuFile_3);
0250           set(handles.MenuFile_3_1,'Label',h.MenuFile_3);
0251       end
0252       if isfield(h,'MenuFile_1')
0253           set(handles.MenuFile_4,'Label',h.MenuFile_4);
0254           set(handles.MenuFile_4_1,'Label',h.MenuFile_4);
0255       end
0256       if isfield(h,'MenuFile_1')
0257           set(handles.MenuFile_5,'Label',h.MenuFile_5);
0258           set(handles.MenuFile_5_1,'Label',h.MenuFile_5);
0259      end
0260  end
0261  
0262 %initiates menu of vector colors
0263 list_menu=calc_field;
0264 %list_menu=[{'ima_cor'};{'black'};{'white'};list_menu(3:end)];
0265 set(handles.col_vec,'String',list_menu)
0266 
0267 %check the path and date of modification of all functions in uvmat
0268 path_to_uvmat=which ('uvmat');% check the path detected for source file uvmat
0269 [errormsg,date_str]=check_functions;%check the path of the functions called by uvmat.m
0270 
0271 %check the path of menu_coord transform
0272 %set(handles.menu_coord,'String',{'';'phys';'px';'more...'})
0273 path_fct{1}='';
0274 path_fct{2}=fileparts(path_to_uvmat);
0275 path_fct{3}=fileparts(path_to_uvmat);
0276 path_fct{4}=fileparts(path_to_uvmat);
0277 set(handles.menu_coord,'UserData',path_fct)
0278 
0279 %case of an input argument for uvmat
0280 testinputfield=0;
0281 inputfile=[];
0282 Field=[];
0283 if exist('input','var')
0284     if ~isempty(errormsg)
0285         warndlg_uvmat(errormsg,'WARNING')
0286     end
0287     if ishandle(handles.UVMAT_title)
0288         delete(handles.UVMAT_title)
0289     end   
0290     if isstruct(input)
0291         if isfield(input,'InputFile')
0292             inputfile=input.InputFile;
0293         end
0294         Field=input;
0295     elseif ischar(input)% file name introduced as input
0296            inputfile=input;
0297     elseif isnumeric(input)
0298         sizinput=size(input);
0299         if sizinput(1)<=1 || sizinput(2)<=1
0300             warndlg_uvmat('bad input for uvmat: file name, structure or numerical matrix accepted','ERROR')
0301             return
0302         end
0303         Field.A=input;
0304         Field.AX=[0.5 size(input,2)-0.5];
0305         Field.AY=[size(input,1)-0.5 0.5];
0306     end
0307     if ~isempty(inputfile)
0308         display_file_name(hObject, eventdata, handles,inputfile)
0309         testinputfield=1;
0310     else
0311         UvData.TestInputFile=0;
0312     end
0313     if ~isempty(Field)
0314         set(handles.Fields,'Value',1)
0315         set(handles.Fields,'String',{'get_field...'})
0316 %         set(handles.Fields,'Value',2)% option 'get_field...'
0317         set(handles.Fields,'UserData',Field)
0318         testinputfield=1;
0319         
0320         % set the colorbar position on the interface:
0321         UvData.PosColorbar=[0.805 0.022 0.019 0.445];
0322     elseif ischar(input)
0323         scan_i_Callback(handles.scan_i, eventdata, handles);        
0324     end
0325 else
0326    if ishandle(handles.UVMAT_title)
0327         set(handles.UVMAT_title,'String',[{'Copyright Joel Sommeria, 2008, Coriolis/ LEGI / CNRS-UJF-INPG';'GNU General Public License'; path_to_uvmat; 'version 2.2.beta';date_str};errormsg]);
0328    end
0329 end
0330 UvData.NewSeries=1;
0331 set(hObject,'UserData',UvData)
0332 if testinputfield
0333     %delete drawn objects
0334     hother=findobj(handles.axes3,'Tag','proj_object');%find all the proj objects
0335     for iobj=1:length(hother)
0336         delete_object(hother(iobj))
0337     end  
0338     if isempty(inputfile)
0339         run0_Callback(hObject, eventdata, handles)
0340         set(handles.MenuTools,'Enable','on')
0341         set(handles.OBJECT_txt,'Visible','on')
0342         set(handles.edit,'Visible','on')
0343         set(handles.list_object,'Visible','on')
0344         set(handles.frame_object,'Visible','on')
0345     else
0346         update_rootinfo(hObject,eventdata,handles);
0347     end
0348 end
0349 set_vec_col_bar(handles)
0350 
0351 %-------------------------------------------------------------------
0352 % --- Outputs from this function are returned to the command menuline.
0353 function varargout = uvmat_OutputFcn(hObject, eventdata, handles)
0354 varargout{1} = handles.output;% the only output argument is the handle to the GUI figure
0355 
0356 %-------------------------------------------------------------------
0357 %-------------------------------------------------------------------
0358 % II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
0359 % automatically sets the global properties when the rootfile name is introduced
0360 % then activate the view-field action if selected
0361 % it is activated either by clicking on the RootPath window or by the
0362 % browser
0363 %------------------------------------------------------------------
0364 %------------------------------------------------------------------
0365 
0366 % --- Executes on the menu Open/Browse...
0367 % search the files, recognize their type according to their name and fill the rootfile input windows
0368 function MenuBrowse_Callback(hObject, eventdata, handles)
0369 oldfile=read_file_boxes(handles);
0370 
0371 if isempty(oldfile)||isequal(oldfile,'') %loads the previously stored file name and set it as default in the file_input box
0372          dir_perso=prefdir;
0373          profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
0374          if exist(profil_perso,'file')
0375               h=load (profil_perso);
0376              if isfield(h,'MenuFile_1')
0377                   oldfile=h.MenuFile_1;
0378              end
0379          end
0380 end
0381 [FileName, PathName] = uigetfile( ...
0382        {'*.xml;*.xls;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;*.cmx;*.fig;*.log;*.dat', ' (*.xml,*.xls,*.civ,*.jpg ,*.png, .tif, *.avi,*.nc,*.cmx ,*.fig,*.log,*.dat)';
0383        '*.xml',  '.xml files '; ...
0384         '*.xls',  '.xls files '; ...
0385         '*.civ',  '.civ files '; ...
0386         '*.jpg',' jpeg image files'; ...
0387         '*.png','.png image files'; ...
0388         '*.tif','.tif image files'; ...
0389         '*.avi;*.AVI','.avi movie files'; ...
0390         '*.nc','.netcdf files'; ...
0391         '*.cdf','.netcdf files'; ...
0392         '*.cmx','.cmx text files';...
0393         '*.cmx2','.cmx2 text files';...
0394         '*.fig','.fig files (matlab fig)';...
0395         '*.log','.log text files ';...
0396         '*.dat','.dat text files ';...
0397         '*.*',  'All Files (*.*)'}, ...
0398         'Pick a file',oldfile);
0399 %global filebase
0400 fileinput=[PathName FileName];%complete file name
0401 testblank=findstr(fileinput,' ');%look for blanks
0402 if ~isempty(testblank)
0403     warndlg_uvmat(['The input file name ' fileinput ' contains blank character : This is not allowed. Please change name'],'ERROR')
0404     return
0405 end
0406 sizf=size(fileinput);
0407 if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
0408 
0409 % display the selected field and related information
0410 display_file_name(hObject, eventdata, handles,fileinput)
0411 
0412 %update list of recent files in the menubar
0413 MenuFile_1=fileinput;
0414 MenuFile_2=get(handles.MenuFile_1,'Label');
0415 MenuFile_3=get(handles.MenuFile_2,'Label');
0416 MenuFile_4=get(handles.MenuFile_3,'Label');
0417 MenuFile_5=get(handles.MenuFile_4,'Label');
0418 set(handles.MenuFile_1,'Label',MenuFile_1)
0419 set(handles.MenuFile_2,'Label',MenuFile_2)
0420 set(handles.MenuFile_3,'Label',MenuFile_3)
0421 set(handles.MenuFile_4,'Label',MenuFile_4)
0422 set(handles.MenuFile_5,'Label',MenuFile_5)
0423 set(handles.MenuFile_1_1,'Label',MenuFile_1)
0424 set(handles.MenuFile_2_1,'Label',MenuFile_2)
0425 set(handles.MenuFile_3_1,'Label',MenuFile_3)
0426 set(handles.MenuFile_4_1,'Label',MenuFile_4)
0427 set(handles.MenuFile_5_1,'Label',MenuFile_5)
0428 dir_perso=prefdir;
0429 profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
0430 if exist(profil_perso,'file')
0431     save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
0432 else
0433     txt=ver;
0434     Release=txt(1).Release;
0435     relnumb=str2double(Release(3:4));
0436     if relnumb >= 14
0437         save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
0438     else
0439         save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
0440     end
0441 end
0442 
0443 % --------------------------------------------------------------------
0444 function MenuFile_1_Callback(hObject, eventdata, handles)
0445 fileinput=get(handles.MenuFile_1,'Label');
0446 display_file_name(hObject, eventdata, handles,fileinput)
0447 
0448 % --------------------------------------------------------------------
0449 function MenuFile_2_Callback(hObject, eventdata, handles)
0450 fileinput=get(handles.MenuFile_2,'Label');
0451 display_file_name(hObject, eventdata, handles,fileinput)
0452 
0453 % --------------------------------------------------------------------
0454 function MenuFile_3_Callback(hObject, eventdata, handles)
0455 fileinput=get(handles.MenuFile_3,'Label');
0456 display_file_name(hObject, eventdata, handles,fileinput)
0457 
0458 % --------------------------------------------------------------------
0459 function MenuFile_4_Callback(hObject, eventdata, handles)
0460 fileinput=get(handles.MenuFile_4,'Label');
0461 display_file_name(hObject, eventdata, handles,fileinput)
0462 
0463 % --------------------------------------------------------------------
0464 function MenuFile_5_Callback(hObject, eventdata, handles)
0465 fileinput=get(handles.MenuFile_5,'Label');
0466 display_file_name(hObject, eventdata, handles,fileinput)
0467 
0468 %-----------------------------------------------------------------
0469 % fills the edit boxes RootPath, RootFile,NomType...from an input file name 'fileinput'
0470 %----------------------------------------------------------------
0471 function display_file_name(hObject, eventdata, handles,fileinput)
0472 [RootPath,RootFile,i1,i2,str_a,str_b,ext,NomType,SubDir]=name2display(fileinput);
0473 form=imformats(ext(2:end));%test valid Matlab image formats
0474 if ~isempty(form)
0475     ext_test='.image';
0476     imainfo=imfinfo(fileinput);  
0477     if length(imainfo) >1 %case of image with multiple frames
0478         i1='1'; % set the frame counter to 1 by default
0479         i2='';
0480         str_a='';
0481         str_b='';
0482         NomType='*'; %indicate a set of indexed frames within a single file
0483         [RootPath,RootFile]=fileparts(fileinput); %include the indices in the root file
0484     end
0485 elseif isequal(lower(ext),'.avi')
0486     ext_test='.image';
0487     i1='1'; % set the frame counter to 1 by default
0488     i2='';
0489     str_a='';
0490     str_b='';
0491     NomType='*'; %indicate a set of indexed frames within a single file
0492     [RootPath,RootFile]=fileparts(fileinput); %include the indices in the root file
0493 else
0494     ext_test=lower(ext);
0495 end
0496 switch ext_test
0497     case {'.civ','.log','.cmx','.cmx2','.txt'}  %display text file
0498         edit(fileinput)  
0499     case '.fig'                           %display matlab figure
0500         hfig=open(fileinput);
0501         set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
0502         set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
0503         set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
0504     case {'.xml','.xls'}                % edit xml or Excel files
0505        editxml(fileinput);
0506     case {'.avi','.image','.vol','.nc','.cdf'}    
0507         set(handles.RootPath,'String',RootPath);
0508         if  isequal(SubDir,'')
0509             rootname=fullfile(RootPath,RootFile);
0510         else
0511             rootname=fullfile(RootPath,SubDir,RootFile);
0512             SubDir=['/' SubDir]; %display the separator
0513         end
0514         set(handles.SubDir,'String',SubDir);
0515         set(handles.RootFile,'String',['/' RootFile]); %display the separator
0516         indices=fileinput(length(rootname)+1:end);
0517         indices(end-length(ext)+1:end)=[]; %remove extension
0518         set(handles.FileIndex,'String',indices);        
0519         set(handles.FileIndex,'UserData',NomType);
0520         set(handles.FileExt,'String',ext);
0521         % fill file index counters
0522         set(handles.i1,'String',i1);
0523       
0524         set(handles.i2,'String',i2);
0525         set(handles.j1,'String',str_a);
0526         set(handles.j2,'String',str_b);
0527         
0528         % synchronise indices of the second  input file if it exists
0529         if get(handles.SubField,'Value')==1% if the subfield button is activated, update the field numbers
0530             [FileName_1,RootPath_1,FileBase_1,FileIndices_1,FileExt_1,SubDir_1]=read_file_boxes_1(handles);
0531             NomType_1=get(handles.FileIndex_1,'UserData');     
0532             [FileName_1,idetect]=name_generator(FileBase_1,stra2num(i1),stra2num(i2),FileExt_1,NomType_1,1,stra2num(str_a),stra2num(str_b),SubDir_1);
0533             if idetect
0534                 FileIndex_1=name_generator('',stra2num(i1),stra2num(i2),'',NomType_1,1,stra2num(str_a),stra2num(str_b),'');
0535                 set(handles.FileIndex_1,'String',FileIndex_1)
0536             else
0537                 set(handles.SubField,'Value',0)
0538                 SubField_Callback(hObject, eventdata, handles)
0539             end
0540         end  
0541 
0542         %enable other menus
0543         set(handles.MenuOpen_1,'Enable','on')
0544         set(handles.MenuFile_1_1,'Enable','on')
0545         set(handles.MenuFile_2_1,'Enable','on')
0546         set(handles.MenuFile_3_1,'Enable','on')
0547         set(handles.MenuFile_4_1,'Enable','on')
0548         set(handles.MenuFile_5_1,'Enable','on')
0549         set(handles.MenuExport,'Enable','on')
0550         set(handles.MenuExportFigure,'Enable','on')
0551         set(handles.MenuExportMovie,'Enable','on')
0552         set(handles.MenuTools,'Enable','on')
0553         set(handles.OBJECT_txt,'Visible','on')
0554         set(handles.edit,'Visible','on')
0555         set(handles.list_object,'Visible','on')
0556         set(handles.frame_object,'Visible','on')
0557          % initiate input file:
0558         update_rootinfo(hObject,eventdata,handles);  
0559     otherwise
0560         warndlg_uvmat(['invalid input file extension' ext],'ERROR')
0561 end
0562 
0563 %-------------------------------------------------------------------
0564 function RootPath_Callback(hObject,eventdata,handles)
0565 update_rootinfo(hObject,eventdata,handles);
0566 
0567 %-------------------------------------------------------------------
0568 %-- called by action in RootFile edit box
0569 %-------------------------------------------------------------------
0570 function SubDir_Callback(hObject, eventdata, handles)
0571 %refresh the menu of input fields
0572 Fields_Callback(hObject, eventdata, handles);
0573 % refresh the current field
0574 run0_Callback(hObject, eventdata, handles); 
0575 
0576 
0577 %-------------------------------------------------------------------
0578 %-- called by action in RootFile edit box
0579 %-------------------------------------------------------------------
0580 function RootFile_Callback(hObject, eventdata, handles)
0581 update_rootinfo(hObject,eventdata,handles)
0582 
0583 %-------------------------------------------------------------------
0584 %-- called by action in FileIndex edit box
0585 %-------------------------------------------------------------------
0586 function FileIndex_Callback(hObject, eventdata, handles)
0587 NomType_str=get(handles.FileIndex,'String') ;
0588 [P,F,str1,str2,str_a,str_b]=name2display(['xx' NomType_str get(handles.FileExt,'String')]);
0589 % display the new index values on the counters
0590 set(handles.i1,'String',str1); 
0591 set(handles.i2,'String',str2);
0592 set(handles.j1,'String',str_a);
0593 set(handles.j2,'String',str_b);
0594 
0595 %-------------------------------------------------------------------
0596 % -- update information about a new field series (indices to scan, timing, calibration from an xml file, then refresh current plots
0597 %-------------------------------------------------------------------
0598 function update_rootinfo(hObject,eventdata,handles)
0599 global dircur  dir_opening
0600 
0601 set(handles.RootPath,'BackgroundColor',[1 1 0])
0602 drawnow
0603 set(handles.Fields,'UserData',[])% reinialize data from uvmat opening
0604 huvmat=get(handles.RootPath,'parent');
0605 UvData=get(huvmat,'UserData');%huvmat=handles of the uvmat interface
0606 UvData.NewSeries=1; %flag for run0: begin a new series
0607 UvData.TestInputFile=1;
0608 set(handles.fix_pair,'Value',0) % desactivate by default the comp_input '-'input window
0609 %FileIndex_Callback(hObject, eventdata, handles)% update field counters
0610 
0611 [FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles);
0612 if ~exist(FileName,'file')
0613    msgbox_uvmat('ERROR',['input file ' FileName ' not found']);
0614     return
0615 end
0616 nbfield=[];%default
0617 nburst=[];%default
0618 
0619 % read timing and total frame number from the current file (movie files) !! may be overrid by xml file
0620 XmlData.Time=[];%default
0621 XmlData.GeometryCalib=[];%default
0622 TimeUnit=[];%default
0623 testima=0; %test for image input
0624 if isequal(lower(FileExt),'.avi') %.avi file
0625     testima=1;
0626     info=aviinfo([FileBase FileIndices FileExt]);
0627     nbfield=info.NumFrames;
0628     nburst=1;
0629     set(handles.Dt_txt,'String',['Dt=' num2str(1000/info.FramesPerSecond) 'ms']);%display the elementary time interval in millisec
0630     XmlData.Time=[0:1/info.FramesPerSecond:(info.NumFrames-1)/info.FramesPerSecond]';
0631     TimeUnit='s';
0632     set(handles.npx,'String',num2str(info.Width));%fills nbre of pixels x box
0633     set(handles.npy,'String',num2str(info.Height));%fills nbre of pixels y box
0634     hhh=which('mmreader');
0635     if ~isequal(hhh,'')&& mmreader.isPlatformSupported()% if the function is found (recent version of matlab)
0636         UvData.MovieObject=mmreader([FileBase FileIndices FileExt]);
0637     end
0638 elseif ~isempty(imformats(FileExt(2:end))) || isequal(FileExt,'.vol')%&& isequal(NomType,'*')% multi-frame image
0639     testima=1;
0640     if ~isequal(SubDir,'')
0641        RootFile=get(handles.RootFile,'String');
0642         imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]);
0643     else
0644         imainfo=imfinfo([FileBase FileIndices FileExt]);
0645     end
0646     if length(imainfo) >1 %case of image with multiple frames
0647         nbfield=length(imainfo);
0648         nburst=1;
0649     end 
0650     if isfield(UvData,'MovieObject')
0651         UvData=rmfield(UvData,'MovieObject');
0652     end
0653 else 
0654     %set(handles.last_i,'String','');%fills last_field box
0655     set(handles.npx,'String','');%fills nbre of pixels x box
0656     set(handles.npy,'String','');%fills nbre of pixels y box
0657     if isfield(UvData,'MovieObject')
0658         UvData=rmfield(UvData,'MovieObject');
0659     end
0660 end
0661 
0662 % read parameters (time, geometric calibration..) from a documentation file (.xml advised)
0663 filexml=[FileBase '.xml'];
0664 fileciv=[FileBase '.civ'];
0665 warntext='';%default warning message
0666 NbSlice=1;%default
0667 
0668 if exist(filexml,'file')
0669     [XmlData,warntext]=imadoc2struct(filexml);
0670     if ~isempty(warntext)
0671         msgbox_uvmat('WARNING',warntext)
0672     end
0673     if isfield(XmlData,'Camera')
0674         if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
0675             TimeUnit=XmlData.Camera.TimeUnit;
0676         end
0677     end
0678     set(handles.view_xml,'Visible','on')
0679     set(handles.view_xml,'String','view .xml')
0680 elseif exist(fileciv,'file')% if .civ file found
0681     [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']);
0682     GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
0683     GeometryCalib.Tx=0;
0684     GeometryCalib.Ty=0;
0685     GeometryCalib.Tz=1;
0686     GeometryCalib.dpx=1;
0687     GeometryCalib.dpy=1;
0688     GeometryCalib.sx=1;
0689     GeometryCalib.Cx=0;
0690     GeometryCalib.Cy=0;
0691     GeometryCalib.f=1;
0692     GeometryCalib.kappa1=0;
0693     GeometryCalib.CoordUnit='cm';
0694     XmlData.GeometryCalib=GeometryCalib;
0695     if error==2, warntext=['no file ' FileBase '.civ'];
0696     elseif error==1, warntext='inconsistent number of fields in the .civ file';
0697     end  
0698     set(handles.npx,'String',num2str(npx));%fills nbre of pixels x box
0699     set(handles.npy,'String',num2str(npy));%fills nbre of pixels y box
0700     set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box
0701     set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box
0702     set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box
0703     set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box
0704     set(handles.view_xml,'Visible','on')
0705     set(handles.view_xml,'String','view .civ')
0706 else
0707     set(handles.view_xml,'Visible','off')
0708 end
0709 
0710 % store last index in handles.lat_i and .last_j
0711 
0712 if ~isempty(XmlData.Time)
0713     nbfield=size(XmlData.Time,1);
0714     nburst=size(XmlData.Time,2);   
0715 end
0716 last_i_cell=get(handles.last_i,'String');
0717 if isempty(nbfield)
0718     last_i_cell{1}='';
0719 else
0720     last_i_cell{1}=num2str(nbfield);
0721 end
0722 set(handles.last_i,'String',last_i_cell)
0723 last_j_cell=get(handles.last_j,'String');
0724 if isempty(nburst)
0725      last_j_cell{1}='';
0726 else
0727      last_j_cell{1}=num2str(nburst);
0728 end
0729 set(handles.last_j,'String',last_j_cell);
0730 
0731 % store geometric calibration in UvData
0732 if isfield(XmlData,'GeometryCalib')
0733 GeometryCalib=XmlData.GeometryCalib;
0734 if isempty(GeometryCalib)
0735     set(handles.pxcm,'String','')
0736     set(handles.pycm,'String','')
0737     set(handles.menu_coord,'Value',1); %  no transform by default
0738 else
0739     if (isfield(GeometryCalib,'R')& ~isequal(GeometryCalib.R(2,1),0) & ~isequal(GeometryCalib.R(1,2),0)) |...
0740         (isfield(GeometryCalib,'kappa1')& ~isequal(GeometryCalib.kappa1,0))
0741         set(handles.pxcm,'String','var')
0742         set(handles.pycm,'String','var')
0743     else
0744         pixcmx=GeometryCalib.f*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx);
0745         pixcmy=GeometryCalib.f*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy);
0746         set(handles.pxcm,'String',num2str(pixcmx))
0747         set(handles.pycm,'String',num2str(pixcmy))
0748     end
0749     set(handles.menu_coord,'Value',2); % phys transform by default
0750     if isfield(GeometryCalib,'SliceCoord')
0751        siz=size(GeometryCalib.SliceCoord);
0752        if siz(1)>1
0753            NbSlice=siz(1);
0754            set(handles.slices,'Visible','on')
0755            set(handles.slices,'Value',1)
0756        end
0757        set(handles.nb_slice,'String',num2str(NbSlice))
0758        slices_Callback(hObject, eventdata, handles)
0759 %        Coord=UvData.XmlData.GeometryCalib.SliceCoord;
0760 %        ZIndex=num_i1-NbSlice*(floor((num_i1-1)/NbSlice));
0761     end
0762 end
0763 end
0764 
0765 %update the data attached to the uvmat interface
0766 set(handles.nb_slice,'String',num2str(NbSlice)) 
0767 if ~isempty(TimeUnit)
0768     set(handles.time_txt,'String',['time (' TimeUnit ')'])
0769 end
0770 %set(handles.DtUnit,'String',['10^(-3)' TimeUnit])
0771 UvData.TimeUnit=TimeUnit;
0772 UvData.XmlData=XmlData;
0773 UvData.NewSeries=1;
0774 set(huvmat,'UserData',UvData)
0775 
0776 %display warning message
0777 if ~isequal(warntext,'')
0778     warndlg_uvmat(warntext,'WARNING');
0779 end
0780 
0781 % set default options in menu 'Fields'
0782 if testima
0783    set(handles.Fields,'Value',1) % set menu to 'image'
0784    set(handles.Fields,'String',{'image';'get_field...';'velocity';'vort';'div';'more...'})
0785 elseif isequal(FileExt,'.nc')|isequal(FileExt,'.cdf')
0786    Data=nc2struct(FileName,[]);
0787    col_vec=get(handles.col_vec,'String');
0788    if isfield(Data,'absolut_time_T0')
0789        set(handles.Fields,'String',{'image';'get_field...';'velocity';'vort';'div';'more...'})
0790        set(handles.Fields,'Value',3) % set menu to 'velocity'
0791        col_vec{1}='ima_cor';
0792    else
0793        set(handles.Fields,'Value',1) % set menu to 'get_field...
0794        set(handles.Fields,'String',{'get_field...'})
0795        col_vec{1}='get_field...';
0796    end
0797    set(handles.col_vec,'String',col_vec)
0798 else
0799     warndlg_uvmat(['invalid input file extension ' FileExt],'ERROR')
0800     return
0801 end  
0802 
0803 %
0804 
0805 % set index navigation options and refresh plots
0806 set(handles.RootPath,'BackgroundColor',[1 1 1])
0807 drawnow
0808 set_scan_options(hObject, eventdata, handles)
0809 
0810 %-------------------------------------------------------------------
0811 %-- set index navigation options for new series input and refresh plot
0812 %-------------------------------------------------------------------
0813 function set_scan_options(hObject, eventdata, handles)
0814 
0815 %  set the corresponding index navigation options (TO CHECK WITH THE SECOND FIELD)
0816 NomType=get(handles.FileIndex,'UserData');
0817 NomType_1=get(handles.FileIndex_1,'UserData');
0818 state_j='off'; %default
0819 scan_option='i';
0820 switch NomType
0821     case {'_i_j','_i_j1-j2','_i1-i2_j','#_ab'},% two navigation indices
0822         state_j='on';
0823         if exist('nbfield','var') && isequal(nbfield,1)
0824             scan_option='j'; 
0825         else
0826             scan_option='i';                
0827         end 
0828 end
0829 if ~isempty(NomType_1)
0830     switch NomType_1
0831         case {'_i_j','_i_j1-j2','_i1-i2_j','#_ab'},% two navigation indices
0832             state_j='on';
0833             if exist('nbfield','var') && isequal(nbfield,1)
0834                 scan_option='j'; 
0835             else
0836                 scan_option='i';                
0837             end 
0838     end
0839 end
0840 if isequal(scan_option,'i')
0841      set(handles.scan_i,'Value',1)
0842      scan_i_Callback(hObject, eventdata, handles); 
0843 else
0844      set(handles.scan_j,'Value',1)
0845      scan_j_Callback(hObject, eventdata, handles); 
0846 end
0847 set(handles.scan_j,'Visible',state_j)
0848 set(handles.j1,'Visible',state_j)
0849 set(handles.j2,'Visible',state_j)
0850 set(handles.last_j,'Visible',state_j);
0851 set(handles.frame_j,'Visible',state_j);
0852 set(handles.j_text,'Visible',state_j);
0853 
0854 % refresh the mask view if the option is selected
0855 % if isequal(get(handles.mask_test,'Value'),1)
0856 %     set_mask(handles,RootPath,FileBase,NomType,str2num(i1),stra2num(j1))
0857 % end
0858     
0859 % view the field  if the viewfield action is selected and no subfield option
0860 run0_Callback(hObject, eventdata, handles); %view field
0861 
0862 %-------------------------------------------------------------------
0863 function MenuBrowse_1_Callback(hObject, eventdata, handles)
0864 %-------------------------------------------------------------------
0865 huvmat=get(handles.run0,'parent');
0866 UvData=get(huvmat,'UserData');
0867 
0868 RootPath=get(handles.RootPath,'String');
0869 [FileName, PathName, filterindex] = uigetfile( ...
0870        {'*.xml;*.xls;*.civ;*.jpg;*.png;*.avi;*.AVI;*.nc;*.cmx;*.fig;*.log;*.dat', ' (*.xml,*.xls,*.civ, *.jpg,*.png, *.avi,*.nc,*.cmx ,*.fig,*.log,*.dat)';
0871        '*.xml',  '.xml files '; ...
0872         '*.xls',  '.xls files '; ...
0873         '*.civ',  '.civ files '; ...
0874         '*.jpg','.jpg image files'; ...
0875         '*.png','.png image files'; ...
0876         '*.avi;*.AVI','.avi movie files'; ...
0877         '*.nc','.netcdf files'; ...
0878         '*.cdf','.netcdf files'; ...
0879         '*.cmx','.cmx text files';...
0880         '*.cmx2','.cmx2 text files';...
0881         '*.fig','.fig files (matlab fig)';...
0882         '*.log','.log text files ';...
0883         '*.dat','.dat text files ';...
0884         '*.*',  'All Files (*.*)'}, ...
0885         'Pick a file',RootPath);
0886 fileinput_1=[PathName FileName];%complete file name
0887 testblank=findstr(fileinput_1,' ');%look for blanks
0888 if ~isempty(testblank)
0889     warndlg_uvmat(['The input file name ' fileinput_1 ' contains blank character : This is not allowed. Please change name'],'ERROR')
0890     return
0891 end
0892 sizf=size(fileinput_1);
0893 if (~ischar(fileinput_1)|~isequal(sizf(1),1)),return;end
0894 
0895 % refresh the current displayed field
0896 display_file_name_1(hObject,eventdata,handles,fileinput_1)
0897 
0898 %update list of recent files in the menubar
0899 MenuFile_1=fileinput_1;
0900 MenuFile_2=get(handles.MenuFile_1,'Label');
0901 MenuFile_3=get(handles.MenuFile_2,'Label');
0902 MenuFile_4=get(handles.MenuFile_3,'Label');
0903 MenuFile_5=get(handles.MenuFile_4,'Label');
0904 set(handles.MenuFile_1,'Label',MenuFile_1)
0905 set(handles.MenuFile_2,'Label',MenuFile_2)
0906 set(handles.MenuFile_3,'Label',MenuFile_3)
0907 set(handles.MenuFile_4,'Label',MenuFile_4)
0908 set(handles.MenuFile_5,'Label',MenuFile_5)
0909 set(handles.MenuFile_1_1,'Label',MenuFile_1)
0910 set(handles.MenuFile_2_1,'Label',MenuFile_2)
0911 set(handles.MenuFile_3_1,'Label',MenuFile_3)
0912 set(handles.MenuFile_4_1,'Label',MenuFile_4)
0913 set(handles.MenuFile_5_1,'Label',MenuFile_5)
0914 dir_perso=prefdir;
0915 profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
0916 if exist(profil_perso,'file')
0917     save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
0918 else
0919     txt=ver;
0920     Release=txt(1).Release;
0921     relnumb=str2num(Release(3:4));
0922     if relnumb >= 14
0923         save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
0924     else
0925         save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
0926     end
0927 end
0928 
0929 % --------------------------------------------------------------------
0930 function MenuFile_1_1_Callback(hObject, eventdata, handles)
0931 fileinput_1=get(handles.MenuFile_1_1,'Label');
0932 display_file_name_1(hObject,eventdata,handles,fileinput_1)
0933 
0934 % --------------------------------------------------------------------
0935 function MenuFile_2_1_Callback(hObject, eventdata, handles)
0936 fileinput_1=get(handles.MenuFile_2_1,'Label');
0937 display_file_name_1(hObject,eventdata,handles,fileinput_1)
0938 
0939 % --------------------------------------------------------------------
0940 function MenuFile_3_1_Callback(hObject, eventdata, handles)
0941 fileinput_1=get(handles.MenuFile_3_1,'Label');
0942 display_file_name_1(hObject,eventdata,handles,fileinput_1)
0943 
0944 % --------------------------------------------------------------------
0945 function MenuFile_4_1_Callback(hObject, eventdata, handles)
0946 fileinput_1=get(handles.MenuFile_4_1,'Label');
0947 display_file_name_1(hObject,eventdata,handles,fileinput_1)
0948 
0949 % --------------------------------------------------------------------
0950 function MenuFile_5_1_Callback(hObject, eventdata, handles)
0951 fileinput_1=get(handles.MenuFile_5_1,'Label');
0952 display_file_name_1(hObject,eventdata,handles,fileinput_1)
0953 
0954 %-----------------------------------------------------------------
0955 % fills the edit boxes RootPath, RootFile,NomType...from an input file name 'fileinput'
0956 %----------------------------------------------------------------
0957 function display_file_name_1(hObject,eventdata,handles,fileinput_1)
0958 
0959 %[path,name,ext]=fileparts(fileinput_1);
0960 [RootPath_1,RootFile_1,field_count,str2,str_a,str_b,FileExt_1,NomType_1,SubDir_1]=name2display(fileinput_1);
0961 nbfield_1=1; %default
0962 ext_test=FileExt_1;%default
0963 form=imformats(FileExt_1(2:end));
0964 if ~isempty(form) % if the extension corresponds to an image format recognized by Matlab
0965     imainfo=imfinfo(fileinput_1);  
0966     nbfield_1=length(imainfo);
0967     ext_test='.image';
0968 elseif isequal(lower(FileExt_1),'.avi')
0969     info=aviinfo(fileinput_1);
0970     nbfield_1=info.NumFrames;
0971     ext_test='.image';
0972 end
0973 
0974 %open directly fig or text files
0975 switch ext_test
0976     case {'.civ','.log','.cmx','.cmx2','.txt'}  %display text file
0977         edit(fileinput)  
0978         return
0979     case '.fig'                           %display matlab figure
0980         hfig=open(fileinput);
0981         set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
0982         set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
0983         set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
0984         return
0985     case {'.xml','.xls'}                % edit xml or Excel files
0986        heditxml=editxml(fileinput);
0987        return
0988     case {'.image','.nc','.cdf'}
0989 %         set(handles.FileIndex,'UserData',NomType_1);
0990     otherwise
0991         warndlg_uvmat(['invalid input file extension ' FileExt_1 ' for uvmat'],'ERROR')
0992         return
0993 end
0994 
0995 % test for image series in a single file and synchronise file indices of the two series
0996 if nbfield_1 >1 %case of image with multiple frames
0997     if nbfield_1 < num_i1
0998         warndlg_uvmat('current frame index beyond the input movie length','ERROR')
0999         return
1000     else
1001         NomType_1='*'; %indicate a set of indexed frames within a single file
1002         filename_new=fileinput_1;
1003     end
1004 else  % cases of data files
1005     RootPath=get(handles.RootPath,'String');
1006     RootFile=get(handles.RootFile,'String');
1007     FileBase=fullfile(RootPath,RootFile);
1008     FileBase_1=fullfile(RootPath_1,RootFile_1);
1009     if isequal(FileBase,FileBase_1)
1010         filename_new=fileinput_1;
1011     else        
1012         num_i1=stra2num(get(handles.i1,'String'));%get the current file indices from counters
1013         num_j1=stra2num(get(handles.j1,'String'));
1014         num_i2=stra2num(get(handles.i2,'String'));
1015         num_j2=stra2num(get(handles.j2,'String'));
1016         [filename_new,idetect]=...
1017            name_generator(FileBase_1,num_i1,num_j1,FileExt_1,NomType_1,1,num_i2,num_j2,SubDir_1);%create name with indices synchronised with the first file
1018         indices=''; %default
1019         if ~idetect
1020             warndlg_uvmat('second input file with indices corresponding to the first one does not exist','ERROR')
1021             return
1022         end 
1023     end
1024 end
1025 set(handles.FileIndex,'UserData',NomType_1);
1026 
1027 % make visible and fill the second raw of edit boxes
1028 set(handles.RootPath_1,'Visible','on')
1029 set(handles.RootFile_1,'Visible','on')
1030 set(handles.SubDir_1,'Visible','on');
1031 set(handles.FileIndex_1,'Visible','on');
1032 set(handles.FileExt_1,'Visible','on');
1033 [FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles);
1034 if isequal(FileBase,FileBase_1)
1035     set(handles.RootPath_1,'String','"')
1036     set(handles.RootFile_1,'String','"');
1037 else
1038     set(handles.RootPath_1,'String',RootPath_1)
1039     set(handles.RootFile_1,'String',['/' RootFile_1]);
1040 end 
1041 if  isequal(SubDir_1,'')
1042      set(handles.SubDir_1,'String','');
1043      FileBaseSub_1=FileBase_1;
1044 else  
1045     set(handles.SubDir_1,'String',['/' SubDir_1]);
1046     FileBaseSub_1=fullfile(FileBase_1,SubDir_1);
1047 end
1048 indices=filename_new(length(FileBaseSub_1)+1:end);
1049 indices(end-length(FileExt_1)+1:end)=[]; %remove extension
1050 set(handles.FileIndex_1,'String',indices)
1051 set(handles.FileIndex_1,'UserData',NomType_1)
1052 set(handles.FileExt_1,'String',FileExt_1);
1053 
1054 % default choice of fields
1055 if isequal(ext_test,'.image')
1056    set(handles.Fields_1,'String',{'';'image';'get_field...';'velocity';'vort';'div';'more...'})
1057    set(handles.Fields_1,'Value',2) % set menu to 'image'
1058 elseif isequal(FileExt_1,'.nc')|isequal(FileExt_1,'.cdf')
1059    Data=nc2struct(fileinput_1,[]);
1060    if isfield(Data,'absolut_time_T0')
1061        set(handles.Fields_1,'String',{'';'image';'get_field...';'velocity';'vort';'div';'more...'})
1062        set(handles.Fields_1,'Value',4) % set menu to 'velocity'
1063    else   
1064        set(handles.Fields_1,'Value',2) % set menu to 'get_field...'
1065        set(handles.Fields_1,'String',{'';'get_field...'});
1066    end
1067 end  
1068 set(handles.SubField,'Visible','on')
1069 set(handles.SubField,'Value',1)
1070 RootPath_1_Callback(hObject,eventdata,handles);  
1071 
1072 
1073 %-----------------------------------------------------
1074 function RootPath_1_Callback(hObject,eventdata,handles)
1075 update_rootinfo_1(hObject,eventdata,handles)
1076 
1077 %-------------------------------------------------------------------
1078 function RootFile_1_Callback(hObject, eventdata, handles)
1079 update_rootinfo_1(hObject,eventdata,handles)
1080 %-------------------------------------------------------------------
1081 
1082 %-------------------------------------------------------------------
1083 function update_rootinfo_1(hObject,eventdata,handles) %A REVOIR
1084 
1085 set(handles.RootPath_1,'BackgroundColor',[1 1 0])% indicate active program by yellow color
1086 drawnow
1087 huvmat=get(handles.RootPath,'parent');
1088 UvData=get(huvmat,'UserData');%huvmat=handles of the uvmat interface
1089 UvData.NewSeries=1; %flag for run0: begin a new series
1090 
1091 [FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes_1(handles);
1092 if ~exist(FileName,'file')
1093     msgbox_uvmat('ERROR',['input file ' FileName ' not found']);
1094 end
1095 nbfield_1=[];%default
1096 nburst_1=[];%default
1097 XmlData.Time=[];
1098 XmlData.GeometryCalib=[];%default
1099 TimeUnit=[];
1100 if isfield(UvData,'TimeUnit')
1101     TimeUnit=UvData.TimeUnit;
1102 end
1103 TimeUnit_1=[];
1104 testima=0; %test for image input
1105 if isequal(lower(FileExt),'.avi') %.avi file
1106     testima=1;
1107     info=aviinfo([FileBase FileIndices FileExt]);
1108     nbfield_1=info.NumFrames;
1109     nburst_1=1;
1110     %set(handles.last_i,'String',num2str(info.NumFrames));%fills last_field box
1111     set(handles.Dt_txt,'String',['Dt=' num2str(1000/info.FramesPerSecond) 'ms']);%display the elementary time interval in millisec
1112 %     set(handles.dt,'UserData',info.FramesPerSecond);
1113     time=[0:1/info.FramesPerSecond:(info.NumFrames-1)/info.FramesPerSecond]';
1114     npx=get(handles.npx,'String');
1115     npy=get(handles.npy,'String');
1116     if isequal(npx,'') || isequal(npy,'')
1117         set(handles.npx,'String',num2str(info.Width));%fills nbre of pixels x box
1118         set(handles.npy,'String',num2str(info.Height));%fills nbre of pixels y box
1119     end
1120 elseif ~isempty(imformats(FileExt(2:end))) %&& isequal(NomType,'*')% multi-frame image
1121     testima=1;
1122     imainfo=imfinfo([FileBase FileIndices FileExt]);  
1123     if length(imainfo) >1 %case of image with multiple frames
1124         nbfield_1=length(imainfo);
1125         nburst_1=1;
1126         %set(handles.last_i,'String',num2str(length(imainfo)));%fills last_field box
1127     end       
1128 else 
1129     %set(handles.last_i,'String','');%fills last_field box
1130     set(handles.npx,'String','');%fills nbre of pixels x box
1131     set(handles.npy,'String','');%fills nbre of pixels y box
1132 end
1133 
1134 % find scaling parameters
1135 filexml=[FileBase '.xml'];
1136 fileciv=[FileBase '.civ'];
1137 warntext='';%default warning text
1138 if exist(filexml,'file')
1139     [XmlData,warntext]=imadoc2struct(filexml);
1140     if ~isempty(warntext)
1141         msgbox_uvmat('WARNING',warntext)
1142     end
1143     if isfield(XmlData,'Camera')
1144 %         if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
1145 %             NbSlice=XmlData.Camera.NbSlice;
1146 %         end
1147         if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
1148             TimeUnit=XmlData.Camera.TimeUnit;
1149         end
1150     end 
1151 elseif exist(fileciv,'file')% if .civ file found
1152     [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']);
1153     GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
1154     GeometryCalib.Tx=0;
1155     GeometryCalib.Ty=0;
1156     GeometryCalib.Tz=1;
1157     GeometryCalib.dpx=1;
1158     GeometryCalib.dpy=1;
1159     GeometryCalib.sx=1;
1160     GeometryCalib.Cx=0;
1161     GeometryCalib.Cy=0;
1162     GeometryCalib.f=1;
1163     GeometryCalib.kappa1=0;
1164     GeometryCalib.CoordUnit='cm';
1165     XmlData.GeometryCalib=GeometryCalib;
1166     if error==2, warntext=['no file ' FileBase '.civ'];
1167     elseif error==1, warntext='inconsistent number of fields in the .civ file';
1168     end
1169     
1170     set(handles.npx,'String',num2str(npx));%fills nbre of pixels x box
1171     set(handles.npy,'String',num2str(npy));%fills nbre of pixels y box
1172     set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box
1173     set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box
1174     set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box
1175     set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box
1176 end   
1177 if ~isempty(TimeUnit_1) && ~isequal(TimeUnit_1,TimeUnit)
1178         warndlg_uvmat('the time units for the second series differs from the first one','WARNING')
1179 end
1180         
1181 % store last index in handles.lat_i and .last_j
1182 if ~isempty(XmlData.Time)
1183     nbfield_1=size(XmlData.Time,1);
1184     nburst_1=size(XmlData.Time,2);   
1185 end
1186 last_i_cell=get(handles.last_i,'String');
1187 if isempty(nbfield_1)
1188     last_i_cell{2}='';
1189 else
1190     last_i_cell{2}=num2str(nbfield_1);
1191 end
1192 set(handles.last_i,'String',last_i_cell)
1193 last_j_cell=get(handles.last_j,'String');
1194 if isempty(nburst_1)
1195      last_j_cell{2}='';
1196 else
1197      last_j_cell{2}=num2str(nburst_1);
1198 end
1199 set(handles.last_j,'String',last_j_cell);
1200 if ~isequal(last_i_cell{1},last_i_cell{2}) || ~isequal(last_j_cell{1},last_j_cell{2})
1201         warndlg_uvmat('the numbers of input file of the second series differs from the first one','WARNING')
1202 end
1203 
1204 % store calibration data
1205 GeometryCalib=XmlData.GeometryCalib;
1206 if isempty(GeometryCalib)
1207     if isfield(UvData, 'GeometryCalib_1')
1208         UvData=rmfield(UvData,'GeometryCalib_1');
1209     end
1210 else
1211     UvData.GeometryCalib_1=GeometryCalib;
1212     if (isfield(GeometryCalib,'R')& ~isequal(GeometryCalib.R(2,1),0) & ~isequal(GeometryCalib.R(1,2),0)) |...
1213         (isfield(GeometryCalib,'kappa1')& ~isequal(GeometryCalib.kappa1,0))
1214         set(handles.pxcm,'String','var')
1215         set(handles.pycm,'String','var')
1216     else
1217         pixcmx=GeometryCalib.f*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx);
1218         pixcmy=GeometryCalib.f*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy);
1219         set(handles.pxcm,'String',num2str(pixcmx))
1220         set(handles.pycm,'String',num2str(pixcmy))
1221     end
1222 end
1223 UvData.XmlData_1=XmlData;
1224 set(huvmat,'UserData',UvData)%update the data attached to the uvmat interface
1225 
1226 if ~isequal(warntext,'')
1227     warndlg_uvmat(warntext,'WARNING')
1228 end
1229 
1230 set(handles.RootPath_1,'BackgroundColor',[1 1 1])% signa the end the input operation
1231 drawnow
1232 
1233 set_scan_options(hObject, eventdata, handles)
1234 
1235 
1236 %---------------------------------------------------
1237 % switch file index scanning options scan_i and scan_j in an exclusive way
1238 function scan_i_Callback(hObject, eventdata, handles)
1239 %---------------------------------------------------
1240 if get(handles.scan_i,'Value')==1
1241     set(handles.scan_i,'BackgroundColor',[1 1 0])
1242     set(handles.scan_j,'Value',0)
1243     set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
1244 else
1245     set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1246     set(handles.scan_j,'Value',1)
1247     set(handles.scan_j,'BackgroundColor',[1 1 0])
1248 end
1249 %-------------------------------------------------------------------
1250 %---------------------------------------------------
1251 % switch file index scanning options scan_i and scan_j in an exclusive way
1252 function scan_j_Callback(hObject, eventdata, handles)
1253 %---------------------------------------------------
1254 %-------------------------------------------------------------------
1255 if get(handles.scan_j,'Value')==1
1256     set(handles.scan_j,'BackgroundColor',[1 1 0])
1257     set(handles.scan_i,'Value',0)
1258     set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1259 else
1260     set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
1261     set(handles.scan_i,'Value',1)
1262     set(handles.scan_i,'BackgroundColor',[1 1 0])
1263 end
1264 
1265 %-------------------------------------------------------------------
1266 function i1_Callback(hObject, eventdata, handles)
1267 %-------------------------------------------------------------------
1268 % [filebase,num1,num_a,num2,num_b,ext,NomType,subdir]=read_input_file(handles);
1269 [FileName,RootPath,filebase,xx,FileExt]=read_file_boxes(handles);
1270 NomType=get(handles.FileIndex,'UserData');
1271 num1=stra2num(get(handles.i1,'String'));
1272 num2=stra2num(get(handles.i2,'String'));
1273 num_a=stra2num(get(handles.j1,'String'));
1274 num_b=stra2num(get(handles.j2,'String'));
1275 indices=name_generator('',num1,num_a,'',NomType,1,num2,num_b,'');
1276 set(handles.FileIndex,'String',indices)
1277 if get(handles.SubField,'Value')==1
1278     NomType_1=get(handles.FileIndex_1,'String');
1279      FileExt_1=get(handles.FileExt_1,'String');
1280     [P,F,str1,str2,str_a,str_b,Ext,NomType_1]=name2display(['xx' NomType_1 FileExt_1]);
1281      indices=name_generator('',num1,num_a,'',NomType_1,1,num2,num_b,'');
1282      set(handles.FileIndex_1,'String',indices)
1283 end
1284 run0_Callback(hObject, eventdata, handles)
1285 
1286 %-------------------------------------------------------------------
1287 function i2_Callback(hObject, eventdata, handles)
1288 i1_Callback(hObject, eventdata, handles)
1289 %-------------------------------------------------------------------
1290 
1291 %-------------------------------------------------------------------
1292 function j1_Callback(hObject, eventdata, handles)
1293 i1_Callback(hObject, eventdata, handles)
1294 %-------------------------------------------------------------------
1295 
1296 %-------------------------------------------------------------------
1297 function j2_Callback(hObject, eventdata, handles)
1298 i1_Callback(hObject, eventdata, handles)
1299 %-------------------------------------------------------------------
1300 
1301 %-------------------------------------------------------------------
1302 function slices_Callback(hObject, eventdata, handles)
1303 %-------------------------------------------------------------------
1304 if get(handles.slices,'Value')==1
1305     set(handles.slices,'BackgroundColor',[1 1 0])
1306     set(handles.nb_slice,'Visible','on')
1307     set(handles.z_text,'Visible','on')
1308     set(handles.z_index,'Visible','on')
1309     nb_slice_Callback(hObject, eventdata, handles)
1310 %      z=mod(num_i1-1,nbslice)+1;
1311 %         set(handles.z_index,'String',num2str(z))
1312 else
1313     set(handles.nb_slice,'Visible','off')
1314     set(handles.slices,'BackgroundColor',[0.7 0.7 0.7])
1315     set(handles.z_text,'Visible','off')
1316     set(handles.z_index,'Visible','off') 
1317     set(handles.masklevel,'Value',1)
1318     set(handles.masklevel,'String',{'1'})
1319 end
1320 
1321 %-------------------------------------------------------------------
1322 function nb_slice_Callback(hObject, eventdata, handles)
1323 %-------------------------------------------------------------------
1324 num_i1=str2num(get(handles.i1,'String'));
1325 nbslice=str2num(get(handles.nb_slice,'String'));
1326 z=mod(num_i1-1,nbslice)+1;
1327 set(handles.z_index,'String',num2str(z))
1328 for ilist=1:nbslice
1329     list_index{ilist,1}=num2str(ilist);
1330 end   
1331 set(handles.masklevel,'String',list_index)
1332 set(handles.masklevel,'Value',z)
1333 
1334 
1335 %-------------------------------------------------------------------
1336 % --- Executes on button press in view_xml.
1337 function view_xml_Callback(hObject, eventdata, handles)
1338 [FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles);
1339 option=get(handles.view_xml,'String');
1340 if isequal(option,'view .xml')
1341     FileXml=[FileBase '.xml'];
1342     heditxml=editxml(FileXml);
1343 end
1344 
1345 %-------------------------------------------------------------------
1346 % --- Executes on button press in mask_test.
1347 function mask_test_Callback(hObject, eventdata, handles)
1348 %-------------------------------------------------------------------
1349 if isequal(get(handles.mask_test,'Value'),1)
1350     [FF,RootPath,FileBase]=read_file_boxes(handles);
1351     num_i1=stra2num(get(handles.i1,'String'));
1352     num_j1=stra2num(get(handles.j1,'String'));
1353     %NomType=get(handles.FileIndex,'UserData');
1354     %[xx,xx,i1,i2,j1,j2,ext,NomType,subdir]=name2display(FileName);
1355     currentdir=pwd;  
1356     cd(RootPath);
1357     maskfiles=dir('*_*mask_*.png');%look for a mask file
1358     cd(currentdir);%come back to the working directory
1359     mdetect=0;
1360     if isempty(maskfiles)
1361          warndlg_uvmat('no mask file detected (format ..._xxmask_ii.png needed), use the menu bar Tools/Make mask','ERROR')
1362          return
1363     end
1364     for ilist=1:length(maskfiles)
1365         maskname=maskfiles(ilist).name;% take the first mask file in the list
1366         [rr,ff,x1,x2,xa,xb,xext,Mask.NomType]=name2display(maskname);
1367         [Path2,Name,ext]=fileparts(maskname);
1368         Namedouble=double(Name);
1369         val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1370         ind_mask=findstr('mask',Name);
1371         i=ind_mask-1;
1372         while val(i)==0 & i>0
1373             i=i-1;
1374         end
1375         nbslice(ilist)=str2num(Name(i+1:ind_mask-1)); % number of different masks (slices)
1376     end
1377     if isequal(min(nbslice),max(nbslice))
1378         nbslice=nbslice(1);
1379     else
1380         warndlg_uvmat('several mask sets coexist in the current image directory','ERROR')
1381          return
1382     end
1383     if ~isequal(nbslice,[]) && Name(i)=='_'
1384         Mask.Base=[FileBase Name(i:ind_mask+3)];
1385         [maskname,mdetect]=name_generator(Mask.Base,num_i1,num_j1,'.png',Mask.NomType);%
1386         if mdetect==1
1387             set(handles.nb_slice,'String',Name(i+1:ind_mask-1));
1388             set(handles.nb_slice,'BackgroundColor',[1 1 0])
1389             set(handles.mask_test,'UserData',Mask);  
1390             set(handles.mask_test,'BackgroundColor',[1 1 0])
1391             if nbslice > 1
1392                 set(handles.slices,'value',1)
1393                 slices_Callback(hObject, eventdata, handles)
1394             end
1395         end
1396     end
1397     if mdetect==0
1398          warndlg_uvmat('no mask file detected (format ..._xxmask_ii.png needed), use the menu bar Tools/Make mask','ERROR')
1399          set(handles.mask_test,'Value',0)
1400          return
1401     end    
1402     update_mask(handles,num_i1,num_j1);
1403 else
1404     MaskData=get(handles.mask_test,'UserData');
1405     if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1406           delete(MaskData.maskhandle)    
1407     end
1408     set(handles.mask_test,'UserData',[])    
1409     huvmat=get(handles.mask_test,'parent');
1410     UvData=get(huvmat,'UserData');
1411     if isfield(UvData,'MaskName')
1412         UvData=rmfield(UvData,'MaskName');
1413         set(huvmat,'UserData',UvData)
1414     end
1415     set(handles.mask_test,'BackgroundColor',[0.7 0.7 0.7])
1416 end
1417 
1418 %-------------------------------------------------------------------
1419 function update_mask(handles,num_i1,num_j1)
1420 %-------------------------------------------------------------------
1421 
1422 MaskData=get(handles.mask_test,'UserData');
1423 if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1424     uistack(MaskData.maskhandle,'top');
1425 end
1426 [MaskName,mdetect]=name_generator(MaskData.Base,num_i1,num_j1,'.png',MaskData.NomType);
1427 huvmat=get(handles.mask_test,'parent');
1428 UvData=get(huvmat,'UserData');
1429 
1430 %update mask image if the mask is new
1431 if ~ (isfield(UvData,'MaskName') && isequal(UvData.MaskName,MaskName)) 
1432     UvData.MaskName=MaskName; %update the recorded name on UvData
1433     set(huvmat,'UserData',UvData);
1434     if mdetect==0
1435         if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1436             delete(MaskData.maskhandle)    
1437         end
1438     else
1439         %read mask image
1440         Mask.AName='image';
1441         Mask.A=imread(MaskName);
1442         npxy=size(Mask.A);
1443         Mask.AX=[0.5 npxy(2)-0.5];
1444         Mask.AY=[npxy(1)-0.5 0.5 ];
1445         Mask.CoordType='px';
1446         
1447         %px to phys or other transform on field
1448         menu_transform=get(handles.menu_coord,'String');
1449         choice_value=get(handles.menu_coord,'Value');
1450         transform=menu_transform{choice_value};%name of the transform fct  given by the menu 'menu_coord'
1451         if  ~isequal(transform,'') && ~isequal(transform,'px')
1452             if isfield(UvData,'XmlData') && isfield(UvData.XmlData,'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
1453                 Calib=UvData.XmlData.GeometryCalib;
1454                 Mask=feval(transform,Mask,UvData.XmlData);
1455             end
1456         end
1457         flagmask=Mask.A < 200;
1458         
1459         %make brown color image
1460         imflag(:,:,1)=0.9*flagmask;
1461         imflag(:,:,2)=0.7*flagmask;
1462         imflag(:,:,3)=zeros(size(flagmask));
1463         
1464         %update mask image
1465         hmask=[]; %default
1466         if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1467             hmask=MaskData.maskhandle;
1468         end
1469         if ~isempty(hmask)
1470             set(hmask,'CData',imflag)    
1471             set(hmask,'AlphaData',flagmask*0.6)
1472             set(hmask,'XData',Mask.AX);
1473             set(hmask,'YData',Mask.AY);
1474 %             uistack(hmask,'top')
1475         else
1476             axes(handles.axes3)
1477             hold on    
1478             MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*flagmask);
1479 %             set(MaskData.maskhandle,'AlphaData',0.6*flagmask)
1480             set(handles.mask_test,'UserData',MaskData)
1481         end
1482     end
1483 end
1484 
1485 
1486 %-------------------------------------------------------------------
1487 function MenuExportFigure_Callback(hObject, eventdata, handles)
1488 %-------------------------------------------------------------------
1489 huvmat=get(handles.MenuExport,'parent');
1490 UvData=get(huvmat,'UserData');
1491 hfig=figure;
1492 newaxes=copyobj(handles.axes3,hfig);
1493 map=colormap(handles.axes3);
1494 colormap(map);%transmit the current colormap to the zoom fig
1495 colorbar
1496 
1497 %-------------------------------------------------------------------
1498 %-------------------------------------------------------------------
1499 % III - MAIN REFRESH FUNCTIONS : 'FRAME PLOT'
1500 %-------------------------------------------------------------------
1501 %-------------------------------------------------------------------
1502 
1503 %Executes on button press in runplus: make one step forward and call
1504 %run0. The step forward is along the fields series 1 or 2 depending on
1505 %the scan_i and scan_j check box (exclusive each other)
1506 %-------------------------------------------------------------------
1507 function runplus_Callback(hObject, eventdata, handles)
1508 increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
1509 runpm(hObject,eventdata,handles,increment)
1510 
1511 %-------------------------------------------------------------------
1512 %Executes on button press in runmin: make one step backward and call
1513 %run0. The step backward is along the fields series 1 or 2 depending on
1514 %the scan_i and scan_j check box (exclusive each other)
1515 %-------------------------------------------------------------------
1516 function runmin_Callback(hObject, eventdata, handles)
1517 increment=-str2num(get(handles.increment_scan,'String')); %get the field increment d
1518 runpm(hObject,eventdata,handles,increment)
1519 
1520 %-------------------------------------------------------------------
1521 %Executes on button press in runmin: make one step backward and call
1522 %run0. The step backward is along the fields series 1 or 2 depending on
1523 %the scan_i and scan_j check box (exclusive each other)
1524 %-------------------------------------------------------------------
1525 function RunMovie_Callback(hObject, eventdata, handles)
1526 %------------------------------------------------------------------
1527 set(handles.RunMovie,'BackgroundColor',[1 1 0])%paint the command button in yellow
1528 drawnow
1529 increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
1530 set(handles.STOP,'Visible','on')
1531 set(handles.speed,'Visible','on')
1532 set(handles.speed_txt,'Visible','on')
1533 set(handles.RunMovie,'BusyAction','queue')
1534 testavi=0;
1535 huvmat=get(handles.RunMovie,'parent');
1536 UvData=get(huvmat,'UserData');
1537 
1538 while get(handles.speed,'Value')~=0 & isequal(get(handles.RunMovie,'BusyAction'),'queue') % enable STOP command
1539         runpm(hObject,eventdata,handles,increment)
1540         pause(1.02-get(handles.speed,'Value'))% wait for next image
1541 end
1542 if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1543     UvData.aviobj=close(UvData.aviobj);
1544    set(huvmat,'UserData',UvData);
1545 end
1546 set(handles.RunMovie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1547 
1548 %-------------------------------------------------------------------
1549 function STOP_Callback(hObject, eventdata, handles)
1550 %-------------------------------------------------------------------
1551 set(handles.run0,'BusyAction','Cancel')
1552 set(handles.RunMovie,'BusyAction','Cancel')
1553 set(handles.MenuExportMovie,'BusyAction','Cancel')
1554 
1555 
1556 %------------------------------------------------------------------
1557 function runpm(hObject,eventdata,handles,increment)
1558 %------------------------------------------------------------------
1559 %read the data on the current input rootfile(s)
1560 
1561 [FileName,RootPath,filebase,FileIndices,FileExt,subdir]=read_file_boxes(handles);
1562 NomType=get(handles.FileIndex,'UserData');
1563 
1564 num1=stra2num(get(handles.i1,'String'));
1565 num2=stra2num(get(handles.i2,'String'));
1566 num_a=stra2num(get(handles.j1,'String'));
1567 num_b=stra2num(get(handles.j2,'String'));
1568 
1569 sub_value= get(handles.SubField,'Value');
1570 if sub_value ==1
1571     [FileName_1,RootPath_1,filebase_1,FileIndices_1,FileExt_1,SubDir_1]=read_file_boxes_1(handles);
1572 end   
1573 
1574 comp_input=get(handles.fix_pair,'Value');
1575 if isequal(NomType,'_i1-i2')|isequal(NomType,'_i1-i2_j')
1576     comp_input=1; %impose a fixed pair interval
1577     set(handles.fix_pair,'Value',1)
1578 end
1579 
1580 %case of scanning along the first direction (rootfile numbers)
1581 if get(handles.scan_i,'Value')==1% case of scanning along field numbers
1582      num1=num1+increment;
1583      num2=num2+increment;
1584     if comp_input==0% find a free pair
1585         [filename,idetect,num_i1_out,num_j1_out,num_i2_out,num_j2_out]=...
1586            name_generator(filebase,num1,num_a,FileExt,NomType,0,num2,num_b,subdir);
1587         if idetect==1
1588             num_a=num_j1_out;
1589             num_b=num_j2_out;
1590         end 
1591     end
1592     if sub_value>=2
1593         num_i1=num_i1+increment;
1594         num_i2=num_i2+increment;
1595     end   
1596 else % case of scanning along the second direction (burst numbers)
1597     lastfield_cell=get(handles.last_j,'String'); % get the last field number
1598     lastfield=str2num(lastfield_cell{1});
1599     num_a=num_a+increment;
1600     num_b=num_b+increment;
1601     if sub_value >=2
1602       num_j1=num_j1+increment;
1603       num_j2=num_j2+increment;
1604     elseif ~isempty(lastfield) && num_a>lastfield
1605         num_a=1;
1606         num1=num1+1;
1607         num2=num2+1;
1608     end
1609 end
1610 
1611 % display the new open numbers
1612 set(handles.i1,'String',num2stra(num1,NomType,1)); 
1613 set(handles.i2,'String',num2stra(num2,NomType,1));
1614 set(handles.j1,'String',num2stra(num_a,NomType,2));
1615 set(handles.j2,'String',num2stra(num_b,NomType,2));
1616 [indices]=name_generator('',num1,num_a,'',NomType,1,num2,num_b,'');
1617 set(handles.FileIndex,'String',indices);
1618 if sub_value ==1
1619     NomType_1=get(handles.FileIndex_1,'UserData');
1620      [indices]=...
1621            name_generator('',num1,num_a,'',NomType_1,1,num2,num_b,'');
1622      set(handles.FileIndex_1,'String',indices);
1623 end
1624 
1625 % refresh plots
1626 run0_Callback(hObject, eventdata, handles); %run
1627 
1628 
1629 %-------------------------------------------------------
1630 % --- Executes on button press in movie_pair.
1631 %-------------------------------------------------------
1632 function movie_pair_Callback(hObject, eventdata, handles)
1633 %initialisation
1634 set(handles.movie_pair,'BackgroundColor',[1 1 0])%paint the command button in yellow
1635 drawnow
1636 list_fields=get(handles.Fields,'String');% list menu fields
1637 index_fields=get(handles.Fields,'Value');% selected string index
1638 FieldName=list_fields{index_fields}; % selected field
1639 huvmat=get(handles.movie_pair,'parent');
1640 if isequal(FieldName,'image')
1641     run0_Callback(hObject, eventdata, handles)%display the first image
1642     UvData=get(huvmat,'UserData');
1643 else
1644     warndlg_uvmat('an image or movie must be first introduced as input','ERROR')
1645     return
1646 end
1647 [ff,rr,filebase,xx,Ext,SubDir]=read_file_boxes(handles);
1648 NomType=get(handles.FileIndex,'UserData');
1649 num_i2=str2num(get(handles.i2,'String'));
1650 num_j2=str2num(get(handles.j2,'String'));
1651 if ~isempty(num_j2) 
1652     num_i1=str2num(get(handles.i1,'String'));
1653     [imaname_1,idetect]=name_generator(filebase,num_i1,num_j2,Ext,NomType);
1654     if idetect==0
1655         warndlg_uvmat(['second input open (-)  ' imaname_1 ' not found'],'ERROR');
1656         return
1657     end
1658     set(handles.i2,'String',''); % indicates that the second index i2 is not used
1659 elseif ~isempty(num_i2)
1660     num_j1=str2num(get(handles.j1,'String'));
1661     [imaname_1,idetect]=name_generator(filebase,num_i2,num_j1,Ext,NomType);
1662     if idetect==0
1663         warndlg_uvmat(['second input open (-)  ' imaname_1 ' not found'],'ERROR');
1664         return
1665     end
1666 else   
1667     warndlg_uvmat('a second image index i2 or j2 is needed to show the pair as a movie','ERROR')
1668     return
1669 end 
1670 
1671 %read the second image
1672 Field.AName='image';
1673 % Field.ListDimName={'AY','AX'}; %A FAIRE
1674 % Field.DimValue=[];
1675 % Field.ListVarName={'A'};
1676 Field.AX=UvData.Field.AX;
1677 Field.AY=UvData.Field.AY;
1678 Field.CoordType='px';
1679 [Field.A,error]=read_image(imaname_1,NomType,num_i2);
1680 
1681 
1682 %px to phys or other transform on field
1683 menu_transform=get(handles.menu_coord,'String');
1684 choice_value=get(handles.menu_coord,'Value');
1685 transform=menu_transform{choice_value};%name of the transform fct  given by the menu 'menu_coord'
1686 if  ~isequal(transform,'') && ~isequal(transform,'px')
1687     if isfield(UvData,'XmlData') && isfield(UvData.XmlData,'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
1688         Field=feval(transform,Field,UvData.XmlData);
1689     end
1690 end
1691 
1692  % make movie until movie speed is set to 0 or STOP is activated
1693 hima=findobj(handles.axes3,'Tag','ima');% %handles.axes3 =main plotting window (A GENERALISER)
1694 set(handles.STOP,'Visible','on')
1695 set(handles.speed,'Visible','on')
1696 set(handles.speed_txt,'Visible','on')
1697 while get(handles.speed,'Value')~=0 & isequal(get(handles.run0,'BusyAction'),'queue'); % enable STOP command
1698     % read and plot the series of images in non erase mode
1699     set(hima,'CData',Field.A); 
1700     pause(1.02-get(handles.speed,'Value'));% wait for next image
1701     set(hima,'CData',UvData.Field.A);
1702     pause(1.02-get(handles.speed,'Value'));% wait for next image
1703 end
1704 set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1705 
1706 %run0_Callback(hObject, eventdata, handles)
1707 
1708 %-------------------------------------------------------
1709 % --- Executes on button press in run0.
1710 %-------------------------------------------------
1711 function run0_Callback(hObject, eventdata, handles)
1712 
1713 %initialisation
1714 set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
1715 drawnow
1716 abstime=[];
1717 abstime_1=[];
1718 dt=[];
1719 CalibCell={};%default
1720 Field={};
1721 huvmat=get(handles.run0,'parent');
1722 UvData=get(huvmat,'UserData');
1723 if isfield(UvData,'Txt')
1724     UvData=rmfield(UvData,'Txt');%erase previous error message
1725 end
1726 set(handles.run0,'BusyAction','queue');
1727 if ishandle(handles.UVMAT_title) %remove title panel on uvmat
1728     delete(handles.UVMAT_title)
1729 end
1730 
1731 % determine the main input file information for action
1732 TestInputFile=1;%default
1733 if isfield(UvData,'TestInputFile')&& isequal(UvData.TestInputFile,0),
1734     TestInputFile=0;
1735 end
1736 num_i1=[];%default
1737 if TestInputFile
1738     [filename,RootPath,filebase,xx,Ext,SubDir]=read_file_boxes(handles);
1739     if ~exist(filename,'file')
1740         msgbox_uvmat('ERROR',['input file ' filename ' does not exist'])
1741         return
1742     end
1743     num_i1=stra2num(get(handles.i1,'String'));
1744     num_i2=stra2num(get(handles.i2,'String'));
1745     num_j1=stra2num(get(handles.j1,'String'));
1746     num_j2=stra2num(get(handles.j2,'String'));
1747     NomType=get(handles.FileIndex,'UserData');
1748     %update the z position index
1749 %     if isequal(get(handles.nb_slice,'String'),'vol.')%case of volume
1750 %         set(handles.z_index,'String',get(handles.j1,'String'));
1751 %     else
1752     nbslice=str2num(get(handles.nb_slice,'String'));
1753     z_index=mod(num_i1-1,nbslice)+1;
1754     if ~isempty(nbslice)
1755         z_index=mod(num_i1-1,nbslice)+1;
1756         set(handles.z_index,'String',num2str(z_index))
1757         % refresh menu for save_mask if relevant
1758         masknumber=get(handles.masklevel,'String');
1759         if length(masknumber)>=z_index
1760             set(handles.masklevel,'Value',z_index)
1761         end
1762     end
1763 %     end
1764     % choose the main field
1765     testima=0;
1766     if isequal(lower(Ext),'.avi')||isequal(lower(Ext),'.vol')
1767        testima=1; 
1768        FieldName='image';
1769     else 
1770        form=imformats(Ext([2:end]));
1771        if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
1772            testima=1;
1773            FieldName='image';
1774        end
1775     end
1776 else
1777     filename=[];
1778     FieldName='get_field...';
1779     testima=0;
1780 end
1781 VelType=[];%default
1782 
1783 if ~testima
1784     list_fields=get(handles.Fields,'String');% list menu fields
1785     index_fields=get(handles.Fields,'Value');% selected string index
1786     FieldName= list_fields{index_fields}; % selected field
1787     if isequal(FieldName,'get_field...')% read the field names on the interface get_field...
1788         VelType=get(handles.Fields,'UserData'); 
1789         Field{1}=get(handles.Fields,'UserData');
1790     else
1791        VelType=setfield(handles);
1792        %enable_transform(handles,'on')% no field transform (possible transform in the GUI get_field)
1793     end
1794 end
1795 
1796 % choose a second field if Subfield option is 'on'
1797 filename_1=[];
1798 VelType_1=[];%default
1799 FieldName_1=[];
1800 scal_color=[];
1801 testvel=0;
1802 testX=0;%default
1803 VelType_1=setfield_1(handles);
1804 sub_value=get(handles.SubField,'Value');
1805 if sub_value==1
1806     filename_1=read_file_boxes_1(handles);
1807     if ~exist(filename_1,'file')
1808         msgbox_uvmat('ERROR',['second file ' filename_1 ' does not exist'])
1809         return
1810     end
1811     NomType_1=get(handles.FileIndex_1,'UserData');
1812     list_fields=get(handles.Fields_1,'String');% list menu fields
1813     index_fields=get(handles.Fields_1,'Value');% selected string index
1814     FieldName_1= list_fields{index_fields}; % selected field
1815     if isequal(VelType_1,'*')% free veltype choice
1816         VelType_1=[];
1817     elseif isequal(VelType_1,'"')% veltype the same as for the first field
1818         if isempty(VelType)
1819             VelType_1=[];
1820         else
1821             VelType_1=VelType;
1822         end
1823     end
1824 end
1825 
1826 % test for keeping the previous stored data if the input files are unchanged
1827 test_keepdata_1=0;%defautl
1828 test_keepdata=0;
1829 if sub_value>=2
1830     if ~isequal(NomType_1,'*')%in cas of a series of files (not avi movie)
1831         if isfield(UvData,'filename_1')& isfield(UvData,'VelType_1') & isfield(UvData,'FieldName_1')
1832             test_keepdata_1= isequal(filename_1,UvData.filename_1)&...
1833                 isequal(VelType_1,UvData.filename_1) & isequal(FieldName_1,UvData.FieldName_1);
1834 
1835         end
1836     end
1837 end
1838 
1839 %read the input field(s)
1840 testima_1=isequal(FieldName_1,'image');
1841 %read images
1842 if  ~isempty(filename) && testima
1843     if isfield(UvData,'MovieObject')
1844         A=read(UvData.MovieObject,num_i1);
1845     else
1846         [A,error]=read_image(filename,NomType,num_i1);
1847         if ~isequal(error,0)
1848             msgbox_uvmat('ERROR',error)
1849             return
1850         end
1851     end 
1852     npxy=size(A);
1853     set(handles.npx,'String',num2str(npxy(2)));% display image size on the interface
1854     set(handles.npy,'String',num2str(npxy(1)));
1855     Rangx=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
1856     Rangy=[npxy(1)-0.5 0.5]; %
1857     npx=str2num(get(handles.npx,'String'));
1858     npy=str2num(get(handles.npy,'String'));
1859     if isfield(UvData.XmlData,'Time')
1860         abs_time=UvData.XmlData.Time;
1861     end
1862     Field{1}.AName='image';
1863     Field{1}.ListVarName={'AY','AX','A'}; %
1864     if size(A,3)==3;%color
1865         Field{1}.VarDimName={'AY','AX',{'AY','AX','rgb'}}; %
1866     else
1867         Field{1}.VarDimName={'AY','AX',{'AY','AX'}}; %
1868     end
1869     Field{1}.AY=Rangy;
1870     Field{1}.AX=Rangx;
1871     Field{1}.A=A;
1872     Field{1}.CoordType='px'; %used for mouse_motion
1873     Field{1}.CoordUnit='pixel'; %used for mouse_motion
1874 end
1875 if ~isfield(UvData,'Txt')& ~isempty(filename_1) & testima_1
1876     [A,error]=read_image(filename_1,NomType_1,num_i1);
1877     if ~isequal(error,0)
1878         msgbox_uvmat('ERROR',error)
1879         return
1880     end
1881     npxy=size(A);
1882     set(handles.npx,'String',num2str(npxy(2)));% display image size on the interface
1883     set(handles.npy,'String',num2str(npxy(1)));
1884     Rangx=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
1885     Rangy=[npxy(1)-0.5 0.5]; %
1886     npx=str2num(get(handles.npx,'String'));
1887     npy=str2num(get(handles.npy,'String'));
1888     if isfield(UvData,'Time')
1889         abs_time=UvData.XmlData.Time;
1890     end
1891     Field{2}.AName='image';
1892     Field{1}.ListVarName={'AY','AX','A'}; %
1893     if size(A,3)==3;%color
1894         Field{1}.VarDimName={'AY','AX',{'AY','AX','rgb'}}; %
1895     else
1896         Field{1}.VarDimName={'AY','AX',{'AY','AX'}}; %
1897     end
1898     Field{2}.AY=Rangy;
1899     Field{2}.AX=Rangx;
1900     Field{2}.A=A;
1901     Field{2}.CoordType='px'; %used for mouse_motion
1902     Field{2}.CoordUnit='px'; %used for move_mou
1903 end
1904 
1905 %read ncfile(s)
1906 CivStage_1=0;%default
1907 VelType_out_1=[];
1908 InputField={FieldName};
1909 InputField_1={FieldName_1};
1910 if ~isfield(UvData,'Txt') && ((~isempty(filename)&~testima) || (~isempty(filename_1)&~testima_1)) ;
1911     %read the velocity field(s) from netcdf rootfile(s)
1912     list_code=get(handles.col_vec,'String');% list menu fields
1913     index_code=get(handles.col_vec,'Value');% selected string index
1914     scal_color= list_code{index_code(1)}; % selected field
1915     if isequal(FieldName,'velocity')&& ~isequal(scal_color,'black') && ~isequal(scal_color,'white')
1916         InputField=[InputField scal_color];
1917         %ScalName=scal_color;
1918 %     else
1919 %         ScalDisplay='image';
1920 %        % ScalName=FieldName;
1921     end
1922     if isequal(FieldName_1,'velocity') && ~isequal(scal_color,'black') && ~isequal(scal_color,'white')
1923 %         ScalDisplay_1='vec_color';
1924         InputField_1=[InputField_1 scal_color];
1925 %         ScalName_1=scal_color;
1926 %     else
1927 %         ScalDisplay_1='image';
1928 %         ScalName_1=FieldName_1;
1929     end
1930     if ~testima  %read the first nc field
1931         if isequal(FieldName,'get_field...')% read the field names on the interface get_field.
1932             test_detect=0;%default
1933             VelType=get(handles.Fields,'UserData');
1934             hget_field=findobj(allchild(0),'Name','get_field');%find the get_field... GUI
1935             if isempty(hget_field)
1936                 hget_field= get_field(filename);%open the get_field GUI
1937             end
1938             test_detect=1;
1939             hhget_field=guidata(hget_field);
1940             set(hhget_field.inputfile,'String',filename)% update the list of input fields in get_field
1941             set(hhget_field.ACTION,'Value',1)% PLOT option selected
1942             set(hhget_field.list_fig,'Value',2)% plotting axes =uvmat selected
1943             [Field{1},errormsg]=read_get_field(hget_field); %read the names of the variables to plot in the get_field GUI
1944             if ~isempty(errormsg)
1945                 msgbox_uvmat('ERROR',['error in uvmat/run0_Callback/read_get_field: ' errormsg])
1946                 return
1947             end
1948 %             [Field{1},var_detect]=nc2struct(filename,SubField.ListVarName); %read the corresponding input data          (included in read_get_field
1949 %             Field{1}.VarAttribute=SubField.VarAttribute;
1950             CivStage=0;
1951             VelType_out=[];
1952             %update the display on get_field
1953            
1954 %             set(hhget_field.variables,'Value',1)
1955 %             Tabchar={''};%default
1956 %             Tabcell=[];
1957 %             if isfield(Field{1},'ListGlobalAttribute')& ~isempty(Field{1}.ListGlobalAttribute)
1958 %                 for iline=1:length(Field{1}.ListGlobalAttribute)
1959 %                     Tabcell{iline,1}=Field{1}.ListGlobalAttribute{iline};
1960 %                     if isfield(Field{1}, Field{1}.ListGlobalAttribute{iline})
1961 %                         eval(['val=Field{1}.' Field{1}.ListGlobalAttribute{iline} ';'])
1962 %                         if ischar(val);
1963 %                             Tabcell{iline,2}=val;
1964 %                         else
1965 %                             Tabcell{iline,2}=num2str(val);
1966 %                         end
1967 %                     end
1968 %                     if isequal(Field{1}.ListGlobalAttribute{iline},'Time')
1969 %                         abstime=Field{1}.Time;
1970 %                     end
1971 %                 end
1972 %                 if ~isempty(Tabcell)
1973 %                     Tabchar=cell2tab(Tabcell,'=');
1974 %                     Tabchar=[{''};Tabchar];
1975 %                 end
1976 %             end
1977             %set(hhget_field.attributes,'String',Tabchar);%update list of global attributes in get_field
1978         else
1979             %[nxx,UvData.NbDim,cxx,CivStage,abstime,Field{1},VelType_out]...
1980             %    =read_ncfield(filename,VelType,ScalDisplay,ScalName);%
1981             [Field{1},VelType_out]=read_civxdata(filename,InputField,VelType);
1982             if isfield(Field{1},'Txt')
1983                 msgbox_uvmat('ERROR',Field{1}.Txt)
1984                 return
1985             end
1986             CivStage=Field{1}.CivStage;
1987             UvData.NbDim=Field{1}.nb_dim;
1988         end
1989     end
1990     if ~isempty(filename_1) && ~testima_1 %read the second file
1991         if isequal(FieldName_1,'get_field...')% read the field names on the interface get_field.
1992             test_detect=0;%default
1993             hget_field=findobj(allchild(0),'Name','get_field_1');%find the get_field... GUI
1994              if isempty(hget_field)
1995                  hget_field= get_field(filename_1);%open the get_field GUI
1996                  set(hget_field,'name','get_field_1')
1997 %                 enable_transform(handles,'off')% no field transform (possible transform in the GUI get_field)
1998              end
1999             test_detect=1;
2000             hhget_field=guidata(hget_field);%handles of GUI elements in get_field
2001             SubField=get_field('read_var_names',hObject,eventdata,hhget_field); %read the names of the variables to plot in the get_field GUI
2002             [Field{2},var_detect]=nc2struct(filename_1,SubField.ListVarName); %read the corresponding input data
2003             Field{2}.VarAttribute=SubField.VarAttribute;
2004             if isequal(get(hhget_field.menu_coord,'Visible'),'on')
2005                 list_transform=get(hhget_field.menu_coord,'String');
2006                 val_list=get(hhget_field.menu_coord,'Value');
2007                 transf=list_transform{val_list};
2008                 if ~isempty(transf)
2009                     Field{2}=feval(transf,Field{2});
2010                 end
2011             end
2012 %             CivStage_1=0;
2013 %              VelType_out_1=[];
2014             %update the display on get_field
2015             set(hhget_field.inputfile,'String',filename_1)
2016             set(hhget_field.variables,'Value',1)
2017             Tabchar={''};%default
2018             Tabcell=[];
2019             if isfield(Field{2},'ListGlobalAttribute')& ~isempty(Field{2}.ListGlobalAttribute)
2020                 for iline=1:length(Field{2}.ListGlobalAttribute)
2021                     Tabcell{iline,1}=Field{2}.ListGlobalAttribute{iline};
2022                     if isfield(Field{2}, Field{2}.ListGlobalAttribute{iline})
2023                         eval(['val=Field{2}.' Field{2}.ListGlobalAttribute{iline} ';'])
2024                         if ischar(val);
2025                             Tabcell{iline,2}=val;
2026                         else
2027                             Tabcell{iline,2}=num2str(val);
2028                         end
2029                     end
2030                 end
2031                 if ~isempty(Tabcell)
2032                     Tabchar=cell2tab(Tabcell,'=');
2033                     Tabchar=[{''};Tabchar];
2034                 end
2035             end
2036             set(hhget_field.attributes,'String',Tabchar);%update list of global attributes in get_field
2037         else
2038             %[nxx,UvData.NbDim,cxx,CivStage_1,abstime_1,Field{2},VelType_out_1]...
2039            %     =read_ncfield(filename_1,VelType_1,ScalDisplay_1,ScalName_1);%TODO:  REPLACE BY read_civxdata
2040             [Field{2},VelType_out_1]=read_civxdata(filename_1,[],VelType_1);
2041             CivStage_1=Field{2}.CivStage;
2042         end
2043         if testima
2044             VelType_out=VelType_out_1;
2045         end
2046     end
2047 end
2048 
2049 %update the display buttons for the first velocity type (first menuline)
2050 veltype_handles=[handles.civ1 handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2];
2051 if testima
2052     %reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
2053     reset_vel_type(veltype_handles)
2054 elseif isempty(VelType)
2055     set_veltype_display(veltype_handles,CivStage)%update the display of available velocity types for the first field
2056     if isempty(VelType_out)
2057         %reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
2058         reset_vel_type(veltype_handles)
2059     else
2060         handle1=eval(['handles.' VelType_out]);
2061         %reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2],handle1)
2062         reset_vel_type(veltype_handles,handle1)
2063     end
2064 end
2065 
2066 %update the display buttons for the second velocity type (second menuline)
2067 veltype_handles_1=[handles.civ1_1 handles.interp1_1 handles.filter1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1];
2068 if testima_1
2069     reset_vel_type(veltype_handles_1)
2070 elseif isempty(VelType_1)
2071     set_veltype_display(veltype_handles_1,CivStage_1)%update the display of available velocity types for the first field
2072     if isempty(VelType_out_1)
2073         reset_vel_type(veltype_handles_1)
2074     else
2075         handle1=eval(['handles.' VelType_out_1 '_1']);
2076         reset_vel_type(veltype_handles_1,handle1)
2077     end
2078 end
2079 
2080 %introduce w as background image by default for a new series (only for nbdim=2)
2081 if ~isfield(UvData,'NewSeries')
2082     UvData.NewSeries=1;
2083 end
2084 %put W as background image by default if NbDim=2:
2085 if ~isfield(UvData,'NbDim')|isempty(UvData.NbDim)|~isequal(UvData.NbDim,3)
2086     if UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W);
2087         set(handles.SubField,'Value',1);
2088         menu=update_menu(handles.Fields_1,'w');%update the menu for the background scalar nd set the choice to 'w'
2089         set(handles.RootPath_1,'String','"')
2090         set(handles.RootFile_1,'String','"')
2091         set(handles.SubDir_1,'String','"');
2092         [indices]=name_generator('',num_i1,num_j1,'',NomType,1,num_i2,num_j2,'');
2093         set(handles.FileIndex_1,'String',indices)
2094         set(handles.FileExt_1,'String','"');
2095         set(handles.Fields_1,'Visible','on');
2096         set(handles.Fields_1,'Visible','on');
2097         set(handles.RootPath_1,'Visible','on')
2098         set(handles.RootFile_1,'Visible','on')
2099         set(handles.SubDir_1,'Visible','on');
2100         set(handles.FileIndex_1,'Visible','on');
2101         set(handles.FileExt_1,'Visible','on');
2102         set(handles.Fields_1,'Visible','on');
2103         Field{1}.AName='w';
2104         testscal=1;
2105     end
2106 end           
2107 
2108 %multislice case
2109 if TestInputFile &&(~isfield(UvData,'NbDim') || isequal(UvData.NbDim,2))&&...%2D case
2110       isfield(UvData,'XmlData') && isfield(UvData.XmlData,'GeometryCalib')&& isfield(UvData.XmlData.GeometryCalib,'SliceCoord')
2111 %     nbfield2=str2num(get(handles.last_j,'String'));
2112        siz=size(UvData.XmlData.GeometryCalib.SliceCoord);
2113        if siz(1)>1
2114            NbSlice=siz(1);
2115            set(handles.slices,'Visible','on')
2116            set(handles.slices,'Value',1)
2117        else
2118            NbSlice=1;
2119        end
2120        set(handles.nb_slice,'String',num2str(NbSlice))
2121        slices_Callback(hObject, eventdata, handles)
2122        Coord=UvData.XmlData.GeometryCalib.SliceCoord;
2123        ZIndex=num_i1-NbSlice*(floor((num_i1-1)/NbSlice));
2124        Field{1}.Z=ZIndex;
2125 end
2126 
2127 %store the current open names, fields and vel types in uvmat interface
2128 UvData.filename=filename;
2129 UvData.filename_1=filename_1;
2130 UvData.VelType=VelType;
2131 UvData.VelType_1=VelType_1;
2132 UvData.FieldName=FieldName;
2133 UvData.FieldName_1=FieldName_1;
2134 if ~isempty(scal_color)
2135     UvData.CName=scal_color;
2136 end
2137 
2138 %coordinate transform or user fct
2139 XmlData=[];%default
2140 if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority
2141     XmlData=UvData.XmlData;
2142 end
2143 XmlData_1=[];%default
2144 if isfield(UvData,'XmlData_1')
2145    XmlData_1=UvData.XmlData_1;
2146 end
2147 menu_transform=get(handles.menu_coord,'String');
2148 choice_value=get(handles.menu_coord,'Value');
2149 transform=menu_transform{choice_value};%name of the transform fct  given by the menu 'menu_coord'
2150 
2151 % z index
2152 if TestInputFile
2153     Field{1}.ZIndex=mod(num_i1-1,nbslice)+1;
2154 end
2155 %px to phys or other transform on field
2156 if  ~isequal(transform,'') 
2157     if length(Field)>=2
2158         Field{2}.ZIndex=mod(num_i1-1,nbslice)+1;
2159         [Field{1},Field{2}]=feval(transform,Field{1},XmlData,Field{2},XmlData_1);
2160         if isempty(Field{2})
2161             Field(2)=[];
2162         end
2163     else
2164         Field{1}=feval(transform,Field{1},XmlData);
2165     end
2166 end 
2167 
2168 %calculate scalar
2169 if ~testima && ~isequal(FieldName,'get_field...')%
2170     Field{1}=calc_field(InputField,Field{1});
2171 end
2172 if length(Field)==2 && ~testima_1 && ~isequal(FieldName,'get_field...')
2173     Field{2}=calc_field(InpuField_1,Field{2});
2174 end
2175 
2176 % combine the two input fields (e.g. substract velocity fields)
2177 if length(Field)==2
2178     if ~(isequal(get(handles.movie_pair,'Value'),1) & isequal(FieldName,'image') & isequal(FieldName_1,'image')) %combine fields if not viewing image pairs
2179         UvData.Field=sub_field(UvData,Field); %TO UPDATE FOR MORE GENERAL INPUT
2180     end
2181 else
2182    UvData.Field=Field{1};
2183 end
2184 UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback)
2185 % test 3D , default projection menuplane and typical mesh (needed to menuopen set_object)
2186 test_x=0;
2187 test_z=0;% test for unstructured z coordinate
2188 UvData.ZMax=0;
2189 UvData.ZMin=0;%default
2190 UvData.Mesh=1; %default
2191 [UvData.Field,errormsg]=check_field_structure(UvData.Field);
2192 if ~isempty(errormsg)
2193     msgbox_uvmat('ERROR',['error in uvmat/run0_Callback/check_field_structure: ' errormsg])
2194     return
2195 end
2196 [CellVarIndex,NbDim,VarType]=find_field_indices(UvData.Field);
2197 [NbDim,imax]=max(NbDim);
2198 if isempty(imax)
2199    DimVarIndex=0;    
2200     coord_x=[];
2201 else
2202     VarIndex=CellVarIndex{imax};
2203     coord_x=VarType{imax}.coord_x;
2204     
2205    % DimVarIndex=DimVarIndex(UvData.Field.VarDimIndex{VarIndex(1)});
2206 end
2207 if isfield(UvData,'NbDim') & ~isempty(UvData.NbDim)
2208     NbDim=UvData.NbDim;
2209 else  
2210     UvData.NbDim=NbDim;
2211 end
2212 if ~isempty(CellVarIndex) & ~isempty(VarType{imax}.coord_x)  & ~isempty(VarType{imax}.coord_y)    %unstructured coordinate z
2213     XName=UvData.Field.ListVarName{VarType{imax}.coord_x};
2214     YName=UvData.Field.ListVarName{VarType{imax}.coord_y};
2215     test_x=1;
2216 elseif isfield(UvData.Field,'X')&isfield(UvData.Field,'Y')
2217     XName='X';
2218     YName='Y';
2219     test_x=1;
2220 end
2221 if test_x
2222     eval(['UvData.XMax=max(UvData.Field.' XName ');'])
2223     eval(['UvData.XMin=min(UvData.Field.' XName ');'])
2224     eval(['UvData.YMax=max(UvData.Field.' YName ');'])
2225     eval(['UvData.YMin=min(UvData.Field.' YName ');'])
2226     eval(['nbvec=length(UvData.Field.' XName ');'])
2227     if NbDim==3%
2228         if ~isempty(CellVarIndex) & ~isempty(VarType{imax}.coord_z)%unstructured coordinate z
2229             ZName=UvData.ListVarName{VarType{imax}.coord_z};
2230             eval(['UvData.ZMax=max(UvData.Field.' ZName ');'])
2231             eval(['UvData.ZMin=min(UvData.Field.' ZName ');'])
2232             test_z=1;   
2233         elseif isfield(UvData,'Z')% usual civ data
2234             UvData.ZMax=max(UvData.Z);
2235             UvData.ZMin=min(UvData.Z);
2236             test_z=1;
2237         end
2238     end
2239     if isequal(UvData.ZMin,UvData.ZMax)%no z dependency
2240         NbDim=2;
2241         test_z=0;
2242     end    
2243     if test_z
2244          UvData.Mesh=((UvData.XMax-UvData.XMin)*(UvData.YMax-UvData.YMin)*(UvData.ZMax-UvData.ZMin))/nbvec;% volume per vector
2245          UvData.Mesh=(UvData.Mesh)^(1/3);
2246     else
2247         UvData.Mesh=sqrt((UvData.XMax-UvData.XMin)*(UvData.YMax-UvData.YMin)/nbvec);%2D
2248     end
2249 end
2250 %case of structured coordinates
2251 if isfield(UvData.Field,'AX') & isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')
2252     UvData.XMax=max(UvData.Field.AX);
2253     UvData.XMin=min(UvData.Field.AX);
2254     UvData.YMax=max(UvData.Field.AY);
2255     UvData.YMin=min(UvData.Field.AY);
2256     np_A=size(UvData.Field.A);
2257     UvData.Mesh=sqrt((UvData.XMax-UvData.XMin)*(UvData.YMax-UvData.YMin)/((np_A(1)-1) * (np_A(2)-1))) ; 
2258 end
2259 if  isempty(coord_x)&~isempty(CellVarIndex)
2260     VarIndex=CellVarIndex{imax}; % list of variable indices
2261     DimIndex=UvData.Field.VarDimIndex{VarIndex(1)}; %list of dim indices for the variable
2262     if NbDim==3
2263         nbpoints=UvData.Field.DimValue(DimIndex(1));
2264         %Zvar=DimVarIndex(DimIndex(1));
2265          %Zvar=DimVarIndex(1);
2266          Zvar=VarType{imax}.coord_3;
2267         if Zvar~=0 % z is a dimension variable
2268             ZName=UvData.Field.ListVarName{Zvar};
2269             eval(['UvData.ZMax=max(UvData.Field.' ZName ');'])
2270             eval(['UvData.ZMin=min(UvData.Field.' ZName ');'])
2271         else
2272             testcoord_z=0;
2273             if length(UvData.Field.VarAttribute)>=VarIndex(1)
2274                 if isfield(UvData.Field.VarAttribute{VarIndex(1)},'Coord_1')%regular grid
2275                     Coord_z=UvData.Field.VarAttribute{VarIndex(1)}.Coord_1;
2276                     UvData.ZMax=max(Coord_z);
2277                     UvData.ZMin=min(Coord_z);
2278                     testcoord_z=1;
2279                 end
2280             end
2281             if ~testcoord_z
2282                   UvData.ZMin=1;
2283                   UvData.ZMax=UvData.Field.DimValue(DimIndex(1));
2284             end
2285         end
2286         UvData.Mesh=(UvData.ZMax-UvData.ZMin)/(nbpoints-1); 
2287     elseif NbDim==2
2288         nbpoints_y=UvData.Field.DimValue(DimIndex(1));       
2289         %Yvar=DimVarIndex(1);
2290         Yvar=VarType{imax}.coord_y;
2291         if Yvar~=0  % x is a dimension variable
2292             YName=UvData.Field.ListVarName{Yvar};
2293             eval(['UvData.YMax=max(UvData.Field.' YName ');'])
2294             eval(['UvData.YMin=min(UvData.Field.' YName ');'])
2295         else
2296             testcoord_y=0;
2297 %             if length(UvData.Field.VarAttribute)>=VarIndex(1)
2298 %                 if isfield(UvData.Field.VarAttribute{VarIndex(1)},'Coord_1') %regular grid
2299 %                     Coord_y=UvData.Field.VarAttribute{VarIndex(1)}.Coord_1;
2300 %                     UvData.YMax=max(Coord_y);
2301 %                     UvData.YMin=min(Coord_y);
2302 %                     testcoord_y=1;
2303 %                 end
2304 %             end
2305             if ~testcoord_y
2306                   UvData.YMin=1;
2307                   UvData.YMax=UvData.Field.DimValue(DimIndex(1));
2308             end
2309         end
2310         DY=(UvData.YMax-UvData.YMin)/(nbpoints_y-1);
2311         nbpoints_x=UvData.Field.DimValue(DimIndex(2));
2312         %Xvar=DimVarIndex(2);
2313         Xvar=VarType{imax}.coord_x;
2314         if Xvar~=0  % x is a dimension variable
2315             XName=UvData.Field.ListVarName{Xvar};
2316             eval(['UvData.XMax=max(UvData.Field.' XName ');'])
2317             eval(['UvData.XMin=min(UvData.Field.' XName ');'])
2318         else
2319             testcoord_x=0;
2320 %             if length(UvData.Field.VarAttribute)>=VarIndex(1)
2321 %                 if isfield(UvData.Field.VarAttribute{VarIndex(1)},'Coord_2') %regular grid
2322 %                     Coord_x=UvData.Field.VarAttribute{VarIndex(1)}.Coord_2;
2323 %                     UvData.XMax=max(Coord_x);
2324 %                     UvData.XMin=min(Coord_x);
2325 %                     testcoord_x=1;
2326 %                 end
2327 %             end
2328             if ~testcoord_x
2329                   UvData.XMin=1;
2330                   UvData.XMax=UvData.Field.DimValue(DimIndex(2));
2331             end
2332         end
2333         DX=(UvData.XMax-UvData.XMin)/(nbpoints_x-1);
2334         UvData.Mesh= sqrt(DX*DY); 
2335     end
2336 end
2337 
2338 %create a default projection menuplane
2339 UvData.Object{1}.Style='plane';%main plotting plane
2340 UvData.Object{1}.ProjMode='projection';%main plotting plane
2341 if ~isfield(UvData.Object{1},'plotaxes')
2342     UvData.Object{1}.plotaxes=handles.axes3;%default plotting axis
2343     set(handles.list_object,'String',{'1-PLANE';'...'});
2344     set(handles.list_object,'Value',1);
2345 end
2346 
2347 %3D case (menuvolume)
2348 if NbDim==3
2349     UvData.Object{1}.NbDim=UvData.NbDim;%test for 3D objects
2350     UvData.Object{1}.RangeZ=UvData.Mesh;%main plotting plane
2351     UvData.Object{1}.Coord(1,3)=(UvData.ZMin+UvData.ZMax)/2;%section at a middle plane chosen
2352     UvData.Object{1}.Phi=0;
2353     UvData.Object{1}.Theta=0;
2354     UvData.Object{1}.Psi=0;
2355     UvData.Object{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR
2356     PlotHandles=get_plot_handles(handles);
2357     ZBounds(1)=UvData.ZMin; %minimum for the Z slider
2358     ZBounds(2)=UvData.ZMax;%maximum for the Z slider
2359     set_object(UvData.Object{1},PlotHandles,ZBounds);
2360     set(handles.list_object,'Value',1);
2361 %multilevel case (single menuplane in a 3D space)
2362 elseif isfield(UvData,'Z')
2363     if isfield(UvData,'CoordType')& isequal(UvData.CoordType,'phys') & isfield(UvData,'XmlData')
2364         XmlData=UvData.XmlData;
2365         if isfield(XmlData,'PlanePos')
2366              UvData.Object{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:);
2367         end
2368         if isfield(XmlData,'PlaneAngle')
2369             siz=size(XmlData.PlaneAngle);
2370             indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning)
2371             UvData.Object{1}.Phi=XmlData.PlaneAngle(indangle,1);
2372             UvData.Object{1}.Theta=XmlData.PlaneAngle(indangle,2);
2373             UvData.Object{1}.Psi=XmlData.PlaneAngle(indangle,3);
2374         end
2375     elseif isfield(UvData,'ZIndex')
2376         UvData.Object{1}.ZObject=UvData.ZIndex;
2377     end
2378 end
2379 
2380 %Plot the projections on all existing  projection objects
2381 keeplim=get(handles.FixedLimits,'Value');
2382 %reset the min and max of scalar if only the mask is displayed
2383 if isfield(UvData,'Mask')&~isfield(UvData,'A')
2384     set(handles.MinA,'String','0')
2385     set(handles.MaxA,'String','255')
2386 end
2387 
2388 Object=UvData.Object;
2389 for iobj=1:length(Object)
2390     if ~isempty(Object{iobj})%& isfield(Object{iobj},'plotaxes')& ishandle(Object{iobj}.plotaxes)
2391         %Projeter les champs sur l'objet:*
2392         ObjectData=proj_field(UvData.Field,Object{iobj},iobj);
2393    
2394         %use of mask
2395         if isfield(ObjectData,'NbDim')&isequal(ObjectData.NbDim,2)
2396             if isfield(ObjectData,'Mask') & isfield(ObjectData,'A')
2397                 %if isfield(ProjData,'A') %case of an existing scalar field or image: put the image to 'NaN' behind the mask
2398                  flag_mask=double(ObjectData.Mask>200);%=0 for masked regions
2399                  AX=ObjectData.AX;
2400                  AY=ObjectData.AY;
2401                  MaskX=ObjectData.MaskX;
2402                  MaskY=ObjectData.MaskY;
2403                  if ~isequal(MaskX,AX)|~isequal(MaskY,AY)
2404                      nxy=size(flag_mask);
2405                      sizpx=(ObjectData.MaskX(end)-ObjectData.MaskX(1))/(nxy(2)-1);%size of a mask pixel
2406                      sizpy=(ObjectData.MaskY(1)-ObjectData.MaskY(end))/(nxy(1)-1);
2407                      x_mask=[ObjectData.MaskX(1):sizpx:ObjectData.MaskX(end)]; % pixel x coordinates for image display
2408                      y_mask=[ObjectData.MaskY(1):-sizpy:ObjectData.MaskY(end)];% pixel x coordinates for image display
2409                      %project on the positions of the scalar
2410                      npxy=size(ObjectData.A);
2411                      dxy(1)=(ObjectData.AY(end)-ObjectData.AY(1))/(npxy(1)-1);%grid mesh in y
2412                      dxy(2)=(ObjectData.AX(end)-ObjectData.AX(1))/(npxy(2)-1);%grid mesh in x
2413                      xi=[ObjectData.AX(1):dxy(2):ObjectData.AX(end)];
2414                      yi=[ObjectData.AY(1):dxy(1):ObjectData.AY(end)];      
2415                      [XI,YI]=meshgrid(xi,yi);% creates the matrix of regular coordinates
2416                     flag_mask = interp2(x_mask,y_mask,flag_mask,XI,YI);
2417                  end
2418                  AClass=class(ObjectData.A);
2419                  ObjectData.A=flag_mask.*double(ObjectData.A);
2420                  ObjectData.A=feval(AClass,ObjectData.A);
2421                  ind_off=[];
2422                  if isfield(ObjectData,'ListVarName')
2423                       for ilist=1:length(ObjectData.ListVarName)
2424                            if isequal(ObjectData.ListVarName{ilist},'Mask')|isequal(ObjectData.ListVarName{ilist},'MaskX')|isequal(ObjectData.ListVarName{ilist},'MaskY')
2425                                ind_off=[ind_off ilist];
2426                            end
2427                       end
2428                       ObjectData.ListVarName(ind_off)=[];
2429                       ObjectData.VarDimIndex(ind_off)=[];
2430                       ind_off=[];        
2431                       for ilist=1:length(ObjectData.ListDimName)       
2432                            if isequal(ObjectData.ListDimName{ilist},'MaskX')|isequal(ObjectData.ListDimName{ilist},'MaskY')
2433                                ind_off=[ind_off ilist];
2434                            end
2435                       end
2436                       ObjectData.ListDimName(ind_off)=[];
2437                       ObjectData.DimValue(ind_off)=[];
2438                  end
2439             end  
2440         end
2441         if ~isempty(ObjectData)
2442             haxes=[];%default
2443             if isfield(Object{iobj},'plotaxes')
2444                 haxes=Object{iobj}.plotaxes;%axes used for representing the projection on the object
2445             end
2446             PosColorbar=[];%default: no colorbar
2447             if ishandle(haxes) & isequal(get(haxes,'Tag'),'axes3')& isfield(UvData,'PosColorbar')
2448                 PosColorbar=UvData.PosColorbar;%prescribe the colorbar position on the uvmat interface
2449             else
2450                 PosColorbar='*';%default position
2451             end
2452             PlotParam=read_plot_param(handles);%read plotting parameters on the uvmat interface
2453             [PlotType,ScalOut,UvData.Object{iobj}.plotaxes]=plot_field(ObjectData,haxes,PlotParam,keeplim,PosColorbar);
2454             if isequal(PlotType,'none')
2455                 hget_field=findobj(allchild(0),'name','get_field');
2456                 if isempty(hget_field)
2457                     get_field([],ObjectData)% the projected field cannot be automatically plotted: use get_field to specify the variablesdelete(hget_field)
2458                 else
2459                     msgbox_uvmat('ERROR','The field defined by get_field cannot be plotted')
2460                 end 
2461             end  
2462             UvData.Object{iobj}.PlotParam=ScalOut; %record the plotting parameters
2463         end
2464         
2465     end
2466 end
2467 
2468 %display the updated plotting parameters for the base menuplane
2469 write_plot_param(handles,UvData.Object{1}.PlotParam);% update the display of the plotting parameters
2470 set(huvmat,'UserData',UvData)
2471 
2472 %update the mask
2473 if isequal(get(handles.mask_test,'Value'),1)%if the mask option is on
2474    update_mask(handles,num_i1,num_i2);
2475 end
2476 
2477 %prepare the menus of histograms (for the whole menuvolume in 3D case)
2478 menu_histo=(UvData.Field.ListVarName)';
2479 ind_bad=[];
2480 nb_histo=1;
2481 for ivar=1:numel(menu_histo)
2482     if isfield(UvData.Field,'VarAttribute') && numel(UvData.Field.VarAttribute)>=ivar && isfield(UvData.Field.VarAttribute{ivar},'Role')
2483         Role=UvData.Field.VarAttribute{ivar}.Role;
2484         switch Role
2485             case {'coord_x','coord_y','coord_z','dimvar'}
2486                 ind_bad=[ind_bad ivar];
2487             case {'vector_y'}
2488                 nb_histo=nb_histo+1;
2489         end
2490     end
2491     DimCell=UvData.Field.VarDimName{ivar};
2492     DimName='';
2493     if ischar(DimCell)
2494         DimName=DimCell;
2495     elseif iscell(DimCell)&& numel(DimCell)==1
2496         DimName=DimCell{1};
2497     end
2498     if strcmp(DimName,menu_histo{ivar})
2499         ind_bad=[ind_bad ivar];
2500     end
2501 end
2502 menu_histo(ind_bad)=[];
2503 test_v=0;
2504 if ~isempty(menu_histo)
2505     set(handles.histo1_menu,'Value',1)
2506     set(handles.histo1_menu,'String',menu_histo)
2507     histo1_menu_Callback(hObject, eventdata, handles)
2508     if nb_histo > 1
2509         test_v=1;
2510         set(handles.histo2_menu,'Visible','on')
2511         set(handles.histo_v,'Visible','on')
2512         set(handles.histo2_menu,'String',menu_histo)
2513         set(handles.histo2_menu,'Value',2)
2514         histo2_menu_Callback(hObject, eventdata, handles)
2515     end
2516 end
2517 if ~test_v
2518     set(handles.histo2_menu,'Visible','off')
2519     set(handles.histo_v,'Visible','off')
2520     cla(handles.histo_v)
2521     set(handles.histo2_menu,'Value',1)
2522 end
2523 
2524 %display time
2525 testimedoc=0;
2526 if isfield(UvData,'XmlData') && isfield(UvData.XmlData,'Time')
2527     if isempty(num_i2)
2528         num_i2=num_i1;
2529     end
2530     if isempty(num_j1)
2531         num_j1=1;
2532     end
2533     if isempty(num_j2)
2534         num_j2=num_j1;
2535     end
2536     siz=size(UvData.XmlData.Time);
2537     if siz(1)>=max(num_i1,num_i2) & siz(2)>=max(num_j1,num_j2)
2538         abstime=(UvData.XmlData.Time(num_i1,num_j1)+UvData.XmlData.Time(num_i2,num_j2))/2;%overset the time read from files
2539         dt=(UvData.XmlData.Time(num_i2,num_j2)-UvData.XmlData.Time(num_i1,num_j1));
2540         testimedoc=1;
2541     end
2542 end
2543 if isfield(UvData,'XmlData_1') && isfield(UvData.XmlData_1,'Time')
2544     [P,F,str1,str2,str_a,str_b,E,NomType]=name2display(['xx' get(handles.FileIndex_1,'String') get(handles.FileExt_1,'String')]);
2545     num_i2=str2num(str2);
2546     if isempty(num_i2)
2547         num_i2=num_i1;
2548     end
2549     num_j1=str2num(str_a);
2550     if isempty(num_j1)
2551         num_j1=1;
2552     end
2553     num_j2=str2num(str_b);
2554     if isempty(num_j2)
2555         num_j2=num_j1;
2556     end
2557     num_i1=str2num(str1);
2558     siz=size(UvData.XmlData_1.Time);
2559     if siz(1)>=max(num_i1,num_i2) & siz(2)>=max(num_j1,num_j2)
2560         abstime_1=(UvData.XmlData_1.Time(num_i1,num_j1)+UvData.XmlData_1.Time(num_i2,num_j2))/2;%overset the time read from files
2561     end
2562 end
2563 set(handles.abs_time,'String',num2str(abstime,4))
2564 set(handles.abs_time_1,'String',num2str(abstime_1,4))
2565 if testimedoc && isfield(UvData,'dt')
2566     dt=UvData.dt;
2567 end 
2568 if isequal(dt,0)
2569     set(handles.Dt_txt,'String','')
2570 else
2571     if ~(isfield(UvData,'TimeUnit') && ~isempty(UvData.TimeUnit))
2572         set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  10^(-3)'] )
2573     else
2574         set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  m' UvData.TimeUnit] )
2575     end
2576 end
2577 set(handles.run0,'BackgroundColor',[1 0 0])
2578 
2579 
2580 
2581 %-------------------------------------------------------------------
2582 % --- translate coordinate to matrix index
2583 %-------------------------------------------------------------------
2584 function [indx,indy]=pos2ind(x0,rangx0,nxy)
2585 indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel
2586 indy=1+round((nxy(1)-1)*(y12-rangy0(1))/(rangy0(2)-rangy0(1)));% index y of pixel
2587 
2588 %-------------------------------------------------------------------
2589 % --- Executes on button press in 'FixedLimits'.
2590 %-------------------------------------------------------------------
2591 function FixedLimits_Callback(hObject, eventdata, handles)
2592 test=get(handles.FixedLimits,'Value');
2593 if test
2594     set(handles.FixedLimits,'BackgroundColor',[1 1 0])
2595 else
2596     set(handles.FixedLimits,'BackgroundColor',[0.7 0.7 0.7])
2597 end
2598 
2599 %-------------------------------------------------------------------
2600 % --- Executes on button press in auto_xy.
2601 function auto_xy_Callback(hObject, eventdata, handles)
2602 test=get(handles.auto_xy,'Value');
2603 if test
2604     set(handles.auto_xy,'BackgroundColor',[1 1 0])
2605     cla(handles.axes3)
2606     update_plot(handles)
2607 else
2608     set(handles.auto_xy,'BackgroundColor',[0.7 0.7 0.7])
2609     update_plot(handles)
2610 %     axis(handles.axes3,'image')
2611 end
2612 
2613 
2614 %-------------------------------------------------------------------
2615 
2616 %-------------------------------------------------------------------
2617 % --- Executes on button press in 'zoom'.
2618 %-------------------------------------------------------------------
2619 function zoom_Callback(hObject, eventdata, handles)
2620 huvmat=get(handles.zoom,'parent');%general input
2621 UvData=get(huvmat,'UserData');
2622 if (get(handles.zoom,'Value') == 1); 
2623     set(handles.zoom,'BackgroundColor',[1 1 0])
2624     set(handles.FixedLimits,'Value',1)% propose by default fixed limits for the plotting axes
2625     set(handles.FixedLimits,'BackgroundColor',[1 1 0])
2626     %UvData.ZoomOn=1;   %test for mouse action
2627 else
2628     set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
2629     %UvData.ZoomOn=0;  %test for mouse action
2630 end
2631 set(huvmat,'UserData',UvData);
2632 
2633 %-------------------------------------------------------------------
2634 %----Executes on button press in 'record': records the current flags of manual correction.
2635 %-------------------------------------------------------------------
2636 function record_Callback(hObject, eventdata, handles)
2637 % [filebase,num_i1,num_j1,num_i2,num_j2,Ext,NomType,SubDir]=read_input_file(handles);
2638 filename=read_file_boxes(handles);
2639 AxeData=get(gca,'UserData');
2640 [erread,message]=fileattrib(filename);
2641 if ~isempty(message) & ~isequal(message.UserWrite,1)
2642      msgbox_uvmat('ERROR',['no writting access to ' filename])
2643      return
2644 end
2645 nc=netcdf(filename,'write'); %open netcdf file
2646 result=redef(nc);
2647 if isempty(result), warndlg_uvmat('##Bad redef operation.','ERROR'),end
2648 test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
2649 if ~test_civ2
2650     test_civ1=isequal(get(handles.civ1,'BackgroundColor'),[1 1 0]);
2651 end 
2652 if test_civ2 % for civ2
2653    
2654     theDim=nc('nb_vectors2') ;% get the number of velocity vectors
2655     nb_vectors2=size(theDim);
2656     var_FixFlag=ncvar('vec2_FixFlag',nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag
2657     var_FixFlag(1:nb_vectors2)=AxeData.FF;%
2658 elseif test_civ1 % for civ1
2659     
2660     theDim=nc('nb_vectors') ;% get the number of velocity vectors
2661     nb_vectors=size(theDim);
2662      var_FixFlag=ncvar('vec_FixFlag',nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag
2663     var_FixFlag(1:nb_vectors)=AxeData.FF;%
2664 else
2665     msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
2666 end 
2667 fin=close(nc);
2668 
2669 
2670 
2671 %-------------------------------------------------------------------
2672 %determines the fields to read from the interface
2673 %------------------------------------------------------------------
2674 function [VelType,civ]=setfield(handles)
2675 
2676 VelType=[]; %default
2677 if (get(handles.civ1,'Value') == 1);
2678 %     if isequal(get(handles.civ1,'String'),'civ1')
2679         VelType='civ1';
2680 %     else
2681 %         huvmat=get(handles.civ1,'parent');%general input
2682 %         UvData=get(huvmat,'UserData');
2683 %         if isfield (UvData,'VelType')
2684 %             VelType=UvData.VelType;
2685 %         end
2686 %     end
2687 % interp1
2688 elseif (get(handles.interp1,'Value') == 1);
2689     VelType='interp1';
2690 % filter1
2691 elseif (get(handles.filter1,'Value') == 1); 
2692     VelType='filter1';  
2693 % CIV2
2694 elseif (get(handles.civ2,'Value') == 1);
2695     VelType='civ2';
2696 % interp2
2697 elseif (get(handles.interp2,'Value') == 1); 
2698     VelType='interp2';
2699 % filter2
2700 elseif (get(handles.filter2,'Value') == 1);  
2701     VelType='filter2'; 
2702 end 
2703 
2704 if isequal(get(handles.filter2,'Visible'),'on');
2705     civ=6;
2706 % interp1
2707 elseif isequal(get(handles.interp2,'Visible'),'on');
2708     civ=5;
2709 % filter1
2710 elseif isequal(get(handles.civ2,'Visible'),'on'); 
2711     civ=4;  
2712 % CIV2
2713 elseif isequal(get(handles.filter1,'Visible'),'on');
2714    civ=3;
2715 % interp2
2716 elseif isequal(get(handles.interp1,'Visible'),'on'); 
2717     civ=2;
2718 % filter2
2719 elseif isequal(get(handles.civ1,'Visible'),'on');  
2720     civ=1; 
2721 else
2722     civ=0;
2723 end 
2724 
2725 %-------------------------------------------------------------------
2726 %determines the veltype of the second field to read from the iinterface
2727 %------------------------------------------------------------------
2728 function VelType=setfield_1(handles)
2729 
2730 VelType=[]; %default
2731 if (get(handles.civ1_1,'Value') == 1);
2732     VelType='civ1';
2733 % interp1
2734 elseif (get(handles.interp1_1,'Value') == 1);
2735     VelType='interp1';
2736 % filter1
2737 elseif (get(handles.filter1_1,'Value') == 1); 
2738     VelType='filter1';  
2739 % CIV2
2740 elseif (get(handles.civ2_1,'Value') == 1);
2741     VelType='civ2';
2742 % interp2
2743 elseif (get(handles.interp2_1,'Value') == 1); 
2744     VelType='interp2';
2745 % filter2
2746 elseif (get(handles.filter2_1,'Value') == 1);  
2747     VelType='filter2'; 
2748 end 
2749 
2750 
2751 %---------------------------------------------------
2752 % --- Executes on button press in SubField
2753 function SubField_Callback(hObject, eventdata, handles)
2754 huvmat=get(handles.run0,'parent');
2755 UvData=get(huvmat,'UserData');
2756 if get(handles.SubField,'Value')==0% if the subfield button is desactivated
2757     set(handles.RootPath_1,'String','')
2758     set(handles.RootFile_1,'String','')
2759     set(handles.SubDir_1,'String','');
2760     set(handles.FileIndex_1,'String','');
2761     set(handles.FileExt_1,'String','');
2762     set(handles.RootPath_1,'Visible','off')
2763     set(handles.RootFile_1,'Visible','off')
2764     set(handles.SubDir_1,'Visible','off');
2765     set(handles.FileIndex_1,'Visible','off');
2766     set(handles.FileExt_1,'Visible','off');
2767     set(handles.Fields_1,'Value',1);%set to blank state
2768     set_veltype_display([handles.civ1_1 handles.interp1_1 handles.filter1_1 ...
2769             handles.civ2_1 handles.interp2_1 handles.filter2_1],0)
2770 
2771 %     if isfield(UvData,'Time_1')
2772 %         UvData=rmfield(UvData,'Time_1');
2773 %     end
2774     if isfield(UvData,'XmlData_1')
2775         UvData=rmfield(UvData,'XmlData_1');
2776     end 
2777     set(huvmat,'UserData',UvData);
2778     run0_Callback(hObject, eventdata, handles); %run
2779 end
2780 
2781 % %----------------------------------------------
2782 % %read the data displayed for the input rootfile windows (new)
2783 % %-------------------------------------------------
2784 function [FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles)
2785 RootPath=get(handles.RootPath,'String');
2786 FileName=RootPath; %default
2787 SubDir=get(handles.SubDir,'String');
2788 if ~isempty(SubDir) && ~isequal(SubDir,'')
2789     if (isequal(SubDir(1),'/')|| isequal(SubDir(1),'\'))
2790         SubDir(1)=[]; %suppress possible / or \ separator
2791     end
2792     FileName=fullfile(RootPath,SubDir);
2793 end
2794 RootFile=get(handles.RootFile,'String');
2795 if ~isempty(RootFile) && ~isequal(RootFile,'')
2796     if (isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
2797         RootFile(1)=[]; %suppress possible / or \ separator
2798     end
2799     FileName=fullfile(FileName,RootFile);
2800 end
2801 FileBase=fullfile(RootPath,RootFile);
2802 FileIndices=get(handles.FileIndex,'String');
2803 FileExt=get(handles.FileExt,'String');
2804 FileName=[FileName FileIndices FileExt];
2805 
2806 %----------------------------------------------
2807 %read the data displayed for the second input rootfile windows
2808 %-------------------------------------------------
2809 function [FileName_1,RootPath_1,FileBase_1,FileIndices_1,FileExt_1,SubDir_1]=read_file_boxes_1(handles)
2810 RootPath_1=get(handles.RootPath_1,'String'); % read the data from the file1_input window
2811 if isequal(RootPath_1,'"'),RootPath_1=get(handles.RootPath,'String'); end;
2812 FileName_1=RootPath_1; %default
2813 SubDir_1=get(handles.SubDir_1,'String');
2814 if isequal(SubDir_1,'"')
2815     SubDir_1=get(handles.SubDir,'String');
2816 end
2817 if ~isempty(SubDir_1) && ~isequal(SubDir_1,'')
2818     if (isequal(SubDir_1(1),'/')|| isequal(SubDir_1(1),'\'))
2819         SubDir_1(1)=[]; %suppress possible / or \ separator
2820     end
2821     FileName_1=fullfile(RootPath_1,SubDir_1);
2822 end
2823 RootFile_1=get(handles.RootFile_1,'String');
2824 if isequal(RootFile_1,'"'),RootFile_1=get(handles.RootFile,'String'); end;
2825 if ~isempty(RootFile_1) && ~isequal(RootFile_1,'')
2826     if ~(isequal(RootFile_1(1),'/')|isequal(RootFile_1(1),'\'))
2827         RootFile_1(1)=[];%suppress possible / or \ separator
2828     end
2829     FileName_1=fullfile(FileName_1,RootFile_1);
2830 end
2831 FileBase_1=fullfile(RootPath_1,RootFile_1);
2832 FileIndices_1=get(handles.FileIndex_1,'String');
2833 FileExt_1=get(handles.FileExt_1,'String');
2834 if isequal(FileExt_1,'"'),FileExt_1=get(handles.FileExt,'String'); end;
2835 FileName_1=[FileName_1 FileIndices_1 FileExt_1];
2836 
2837 %---------------------------------------------------
2838 % --- Executes on menu selection Fields
2839 function Fields_Callback(hObject, eventdata, handles)
2840 %-------------------------------------------------
2841 huvmat=get(handles.Fields,'parent');
2842 list_fields=get(handles.Fields,'String');% list menu fields
2843 index_fields=get(handles.Fields,'Value');% selected string index
2844 field= list_fields{index_fields(1)}; % selected string
2845 if isequal(field,'get_field...')
2846      veltype_handles=[handles.civ1 handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2];
2847      set_veltype_display(veltype_handles,0) % unvisible civ buttons
2848      filename=read_file_boxes(handles);
2849      hget_field=findobj(allchild(0),'name','get_field');
2850      if ~isempty(hget_field)
2851          delete(hget_field)
2852      end
2853      get_field(filename)
2854     return %no action
2855 end
2856 list_fields=get(handles.Fields_1,'String');% list menu fields
2857 index_fields=get(handles.Fields_1,'Value');% selected string index
2858 field_1= list_fields{index_fields(1)}; % selected string
2859 UvData=get(huvmat,'UserData');
2860 
2861 %read the rootfile input display
2862 FileExt=get(handles.FileExt,'String');
2863 [P,F,str1,str2,str_a,str_b,E,NomType]=name2display(['xxx' get(handles.FileIndex,'String') FileExt]);
2864 NomTypeNew=NomType;%default
2865 if isequal(field,'image') 
2866     % transform netc type to the corresponding image type
2867     if isequal(NomType,'_i1-i2_j')||isequal(NomType,'_i_j1-j2')|| isequal(NomType,'#_ab')|| isequal(NomType,'_i1-i2')
2868         UvData.SubDir=get(handles.SubDir,'String'); %preserve the subdir in memory
2869         if ~isempty(UvData.SubDir) && (isequal(UvData.SubDir(1),'/')|isequal(UvData.SubDir(1),'/'))
2870             UvData.SubDir(1)=[];
2871         end
2872         set(handles.SubDir,'String','')
2873         set(handles.FileExt,'String','.png');
2874         if isequal(NomType,'_i1-i2_j')|isequal(NomType,'_i_j1-j2')
2875             NomTypeNew='_i_j';
2876         elseif isequal(NomType,'#_ab')
2877             NomTypeNew='#a';
2878         elseif isequal(NomType,'_i1-i2')
2879             NomTypeNew='_i';
2880         end  
2881     end
2882     veltype_handles=[handles.civ1 handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2];
2883     set_veltype_display(veltype_handles,0) % unvisible civ buttons
2884 else
2885     ext=get(handles.FileExt,'String');
2886     if ~isequal(ext,'.nc') %find the new NomType if the previous display was not already a netcdf file
2887          MenuBrowse_Callback(hObject, eventdata, handles)
2888     end
2889     if isequal(field,'vort') || isequal(field,'div') || isequal(field,'strain')
2890         set(handles.civ1,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey
2891         set(handles.civ2,'BackgroundColor',[0.702 0.702 0.702])
2892         set(handles.interp1,'BackgroundColor',[0.702 0.702 0.702])
2893         set(handles.interp2,'BackgroundColor',[0.702 0.702 0.702])
2894     elseif isequal(field,'more...'); 
2895         set(handles.civ1,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey
2896         set(handles.civ2,'BackgroundColor',[0.702 0.702 0.702])
2897         str=calc_field;%get the list of available scalars by the function calc_scal
2898         [ind_answer,v] = listdlg('PromptString','Select a file:',...
2899                 'SelectionMode','single',...
2900                 'ListString',str);
2901        % edit the choice in the field and action menu
2902         scalar=cell2mat(str(ind_answer));
2903         menu=update_menu(handles.Fields,scalar);
2904         menu=[{''};menu];
2905         set(handles.Fields_1,'String',menu);% store the selected scalar type
2906     end
2907 end
2908 indices=name_generator('',str2num(str1),str2num(str_a),'',NomTypeNew,1,str2num(str2),str2num(str_b),'');
2909 set(handles.FileIndex,'String',indices)
2910 set(handles.FileIndex,'UserData',NomTypeNew)
2911 %common to Fields_1_Callback
2912 if isequal(field,'image')|isequal(field_1,'image')
2913     set(handles.npx_title,'Visible','on')% visible npx,pxcm... buttons
2914     set(handles.npy_title,'Visible','on')
2915     set(handles.npx,'Visible','on')
2916     set(handles.npy,'Visible','on')
2917     set(handles.fix_pair,'Value',0)
2918 else
2919     set(handles.npx_title,'Visible','off')% visible npx,pxcm... buttons
2920     set(handles.npy_title,'Visible','off')
2921     set(handles.npx,'Visible','off')
2922     set(handles.npy,'Visible','off')
2923     set(handles.fix_pair,'Value',1)
2924 end
2925 if isequal(field,'velocity')|isequal(field_1,'velocity');
2926     state_vect='on';
2927 else
2928     state_vect='off';
2929 end 
2930 if ~isequal(field,'velocity')|(~isequal(field_1,'velocity'));
2931     state_scal='on';
2932 else
2933     state_scal='off';
2934 end 
2935 setfield(handles);% update the field structure ('civ1'....)
2936 
2937 if ~isfield(UvData,'NewSeries')|isequal(UvData.NewSeries,0)
2938     run0_Callback(hObject, eventdata, handles)
2939 end
2940 
2941 %---------------------------------------------------
2942 % --- Executes on menu selection Fields
2943 function Fields_1_Callback(hObject, eventdata, handles)
2944 %-------------------------------------------------
2945 huvmat=get(handles.Fields_1,'parent');
2946 list_fields=get(handles.Fields,'String');% list menu fields
2947 index_fields=get(handles.Fields,'Value');% selected string index
2948 field= list_fields{index_fields(1)}; % selected string
2949 list_fields=get(handles.Fields_1,'String');% list menu fields
2950 index_fields=get(handles.Fields_1,'Value');% selected string index
2951 field_1= list_fields{index_fields(1)}; % selected string for the second field
2952 if isequal(field_1,'') %remove second field if 'blank' field is selected
2953     set(handles.SubField,'Value',0)
2954     SubField_Callback(hObject, eventdata, handles)
2955     return
2956 end
2957 UvData=get(huvmat,'UserData');
2958 
2959 %read the rootfile input display
2960 FileExt_prev=get(handles.FileExt_1,'String');
2961 if isempty(FileExt_prev)|isequal(FileExt_prev,'')
2962     FileExt_1=get(handles.FileExt,'String');
2963 else
2964     FileExt_1=FileExt_prev;
2965 end
2966 NomType_1=get(handles.FileIndex_1,'UserData');
2967 if isempty(NomType_1)|isequal(NomType_1,'')
2968     NomType_1=get(handles.FileIndex,'UserData');
2969 end
2970 NomTypeNew=NomType_1;%default
2971 
2972 set(handles.SubField,'Value',1)%introduce second field
2973 if isfield(UvData,'XmlData')
2974     UvData.XmlData_1=UvData.XmlData;
2975 end
2976 set(handles.FileIndex_1,'Visible','on')
2977 set(handles.FileExt_1,'Visible','on')
2978 RootPath_1=get(handles.RootPath_1,'String');
2979 RootFile_1=get(handles.RootFile_1,'String');
2980 if isempty(RootPath_1)|isequal(RootPath_1,'')
2981     set(handles.RootPath_1,'String','"')
2982 end
2983 if isempty(RootFile_1) | isequal(RootFile_1,'')
2984     set(handles.RootFile_1,'String','"')
2985 end
2986 if ~isempty(RootFile_1)&(isequal(RootFile_1(1),'/')|isequal(RootFile_1(1),'\'))
2987     RootFile_1(1)=[];
2988 end
2989 
2990 if isequal(field_1,'get_field...')
2991      veltype_handles=[handles.civ1 handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2];
2992      set_veltype_display(veltype_handles,0) % unvisible civ buttons
2993      filename=read_file_boxes_1(handles);
2994      hget_field=findobj(allchild(0),'name','get_field_1');
2995      if ~isempty(hget_field)
2996          delete(hget_field)
2997      end
2998      hget_field=get_field(filename);
2999      set(hget_field,'name','get_field_1')
3000     return %no action
3001 end
3002 if isequal(field_1,'image') 
3003     % transform netc type to the corresponding image type
3004     set(handles.FileExt_1,'String','.png');
3005     if isequal(NomType_1,'_i1-i2_j')|isequal(NomType_1,'_i_j1-j2')| isequal(NomType_1,'#_ab')| isequal(NomType_1,'_i1-i2')
3006         UvData.SubDir_1=get(handles.SubDir_1,'String'); %preserve the subdir in memory
3007         set(handles.SubDir_1,'String','')
3008 %         set(handles.FileExt_1,'String','.png');
3009         if isequal(NomType_1,'_i1-i2_j')|isequal(NomType_1,'_i_j1-j2')
3010             NomTypeNew='_i_j';
3011         elseif isequal(NomType_1,'#_ab')
3012             NomTypeNew='#a';
3013         elseif isequal(NomType_1,'_i1-i2')
3014             NomTypeNew='_i';
3015         end  
3016     end
3017     veltype_handles=[handles.civ1_1 handles.interp1_1 handles.filter1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1];
3018     set_veltype_display(veltype_handles,0) % unvisible civ buttons
3019 else
3020     set(handles.SubDir_1,'Visible','on')
3021     if ~isequal(FileExt_prev,'.nc') %find the new NomType if the previous display was not already a netcdf file
3022         veltype_handles=[handles.civ1_1 handles.interp1_1 handles.filter1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1];
3023         set_veltype_display(veltype_handles,6); % make all civ buttons visible
3024         RootPath_1=get(handles.RootPath_1,'String');
3025         RootFile_1=get(handles.RootFile_1,'String');
3026         if isempty(RootPath_1)|isequal(RootPath_1,'')
3027             set(handles.RootPath_1,'String','"')
3028         end
3029         if isempty(RootFile_1) | isequal(RootFile_1,'')
3030             set(handles.RootFile_1,'String','"')
3031         end
3032         if ~isempty(RootFile_1)&(isequal(RootFile_1(1),'/')|isequal(RootFile_1(1),'\'))
3033             RootFile_1(1)=[];
3034         end
3035         filebase_1=fullfile(RootPath_1,RootFile_1);
3036         SubDir_1=get(handles.SubDir,'String');
3037         if isempty(SubDir_1)|isequal(SubDir_1,'')
3038             if isfield(UvData,'SubDir_1')
3039                 SubDir_1=UvData.SubDir_1;%retrieve previous subdir
3040             else
3041                 SubDir_1='?';
3042             end
3043         end
3044         if isequal(NomType_1,'#_ab')|isequal(NomType_1,'_i1-i2_j')|isequal(NomType_1,'_i_j1-j2')|isequal(NomType_1,'_i1-i2')
3045             NomTypeNew=NomType_1;
3046         elseif isequal(NomType_1,'#a')
3047              [filename,idetect,n1,na,n2,nb,SubDir_1]=name_generator(filebase_1, str2num(str1),str2num(str_a),'.nc','#_ab',0,[],[],SubDir_1);
3048              NomTypeNew='#_ab';
3049         elseif isequal(NomType_1,'_i_j')
3050              [filename,idetect,n1,na,n2,nb,SubDir_1]=name_generator(filebase_1,str2num(str1),str2num(str_a),'.nc','_i1-i2_j',0,str2num(str1),[],SubDir_1);
3051             if idetect==1
3052                 NomTypeNew='_i1-i2_j';
3053             else
3054                 NomTypeNew='_i_j1-j2';
3055             end
3056         else %for instance avi files or any ima_num series
3057             [filename,idetect,n1,na,n2,nb,SubDir_1]=name_generator(filebase_1,str2num(str1),str2num(str_a),'.nc','_i1-i2',0,str2num(str1),[],SubDir_1);
3058             NomTypeNew='_i1-i2';
3059         end            
3060         [Path,Name]=fileparts(filebase_1);
3061         set(handles.FileExt_1,'String','.nc');
3062         if ~isempty(SubDir_1) & ~isequal(SubDir_1,'''')& ~isequal(SubDir_1,'"')
3063             SubDir_1=['/' SubDir_1];
3064         end
3065         set(handles.SubDir_1,'String',SubDir_1);
3066     end
3067     if isequal(field,'vort') | isequal(field,'div') | isequal(field,'strain')
3068         set(handles.civ1_1,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey
3069         set(handles.civ2_1,'BackgroundColor',[0.702 0.702 0.702])
3070         set(handles.interp1_1,'BackgroundColor',[0.702 0.702 0.702])
3071         set(handles.interp2_1,'BackgroundColor',[0.702 0.702 0.702])
3072     elseif isequal(field_1,'more...'); %add new item to the menu
3073         set(handles.civ1_1,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey
3074         set(handles.civ2_1,'BackgroundColor',[0.702 0.702 0.702])
3075         str=calc_field;%get the list of available scalars by the function calc_scal
3076         [ind_answer,v] = listdlg('PromptString','Select a file:',...
3077                 'SelectionMode','single',...
3078                 'ListString',str);
3079        % edit the choice in the field and action menu
3080         scalar=cell2mat(str(ind_answer));
3081         menu=update_menu(handles.Fields_1,scalar);
3082         set(handles.Fields_1,'String',menu);% store the selected scalar type
3083     end
3084 end
3085 str1=get(handles.i1,'String');
3086 str2=get(handles.i2,'String');
3087 str_a=get(handles.j1,'String');
3088 str_b=get(handles.j2,'String');
3089 indices=name_generator('',str2num(str1),stra2num(str_a),'',NomTypeNew,1,str2num(str2),stra2num(str_b),'');
3090 set(handles.FileIndex_1,'String',indices)
3091 set(handles.FileIndex_1,'UserData',NomTypeNew)
3092 
3093 %common to Fields_Callback
3094 if isequal(field,'image')|isequal(field_1,'image')
3095     set(handles.npx_title,'Visible','on')% visible npx,pxcm... buttons
3096     set(handles.npy_title,'Visible','on')
3097     set(handles.npx,'Visible','on')
3098     set(handles.npy,'Visible','on')
3099     set(handles.fix_pair,'Value',0)
3100 else
3101     set(handles.npx_title,'Visible','off')% visible npx,pxcm... buttons
3102     set(handles.npy_title,'Visible','off')
3103     set(handles.npx,'Visible','off')
3104     set(handles.npy,'Visible','off')
3105     set(handles.fix_pair,'Value',1)
3106 end
3107 if isequal(field,'velocity')|isequal(field_1,'velocity');
3108     state_vect='on';
3109 else
3110     state_vect='off';
3111 end 
3112 if ~isequal(field,'velocity')|(~isequal(field_1,'velocity')&~isequal(field_1,''));
3113     state_scal='on';
3114 else
3115     state_scal='off';
3116 end 
3117 set(huvmat,'UserData',UvData)
3118 setfield(handles);% update the field structure ('civ1'....)
3119 if ~isfield(UvData,'NewSeries')|isequal(UvData.NewSeries,0)
3120     run0_Callback(hObject, eventdata, handles)
3121 end
3122 
3123 
3124 %-----------------------------------
3125 %set the visibility of relevant velocity type menus:
3126 %-----------------------------------
3127 %Civ=0; all states 'off'
3128 %Civ=6; all states 'on'
3129 function set_veltype_display(handles,Civ)
3130 if isequal(Civ,0)
3131     imax=0;
3132 %    set(handles(1),'Visible','on')  % unvisible civ buttons
3133 % else
3134 %    set(handles(1),'String','civ1')
3135 % end
3136 elseif isequal(Civ,1)
3137    imax=1;
3138 elseif isequal(Civ,2) | isequal(Civ,3) 
3139     imax=3;
3140 elseif isequal(Civ,4) | isequal(Civ,5)
3141     imax=4;
3142 elseif isequal(Civ,6) 
3143     imax=6;
3144 end
3145 for ibutton=1:imax;
3146     set(handles(ibutton),'Visible','on')  % unvisible civ buttons
3147 end
3148 % for ibutton=max(imax+1,2):6;
3149 for ibutton=imax+1:6;
3150     set(handles(ibutton),'Visible','off')  % unvisible civ buttons
3151     set(handles(ibutton),'Value',0)%unactivate unvisible buttons
3152 end
3153 
3154 %-------------------------------------------------------------------
3155 % --- Executes on button press in civ1.
3156 function civ1_Callback(hObject, eventdata, handles)
3157 %-------------------------------------------------------------------
3158 if get(handles.civ1,'Value')==1
3159     reset_vel_type([handles.interp1 handles.civ2 handles.filter1 handles.interp1 handles.interp2 handles.filter2],handles.civ1)
3160 else
3161     reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3162 end
3163 run0_Callback(hObject, eventdata, handles)
3164 
3165 %-------------------------------------------------------------------
3166 % --- Executes on button press in interp1.
3167 function interp1_Callback(hObject, eventdata, handles)
3168 %-------------------------------------------------------------------
3169 if get(handles.interp1,'Value')==1
3170     reset_vel_type([handles.civ1 handles.civ2 handles.filter1 handles.interp2 handles.filter2],handles.interp1)
3171 else
3172      reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3173 end
3174 run0_Callback(hObject, eventdata, handles)
3175 
3176 %-------------------------------------------------------------------
3177 % --- Executes on button press in filter1.
3178 function filter1_Callback(hObject, eventdata, handles)
3179 %-------------------------------------------------------------------
3180 if get(handles.filter1,'Value')==1
3181     reset_vel_type([handles.civ1 handles.civ2 handles.interp1 handles.interp2 handles.filter2],handles.filter1)
3182 else
3183      reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3184 end
3185 run0_Callback(hObject, eventdata, handles)
3186 
3187 %-------------------------------------------------------------------
3188 % --- Executes on button press in civ2.
3189 function civ2_Callback(hObject, eventdata, handles)
3190 %-------------------------------------------------------------------
3191 if get(handles.civ2,'Value')==1
3192     reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.interp2 handles.filter2],handles.civ2)
3193 else
3194      reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3195 end
3196 run0_Callback(hObject, eventdata, handles)
3197 
3198 %-----------------------------------------
3199 % --- Executes on button press in interp2.
3200 %-------------------------------------------
3201 function interp2_Callback(hObject, eventdata, handles)
3202 if get(handles.interp2,'Value')==1
3203     reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.filter2],handles.interp2)
3204 else
3205      reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3206 end
3207 run0_Callback(hObject, eventdata, handles)
3208 %---------------------------------------------
3209 % --- Executes on button press in filter2.
3210 %-------------------------------------------
3211 function filter2_Callback(hObject, eventdata, handles)
3212 if get(handles.filter2,'Value')==1
3213     reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2],handles.filter2)
3214 else
3215      reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3216 end
3217 run0_Callback(hObject, eventdata, handles)
3218 
3219 %---------------------------------------------
3220 function civ1_1_Callback(hObject, eventdata, handles)
3221 %---------------------------------------------
3222 if get(handles.civ1_1,'Value')==1
3223     reset_vel_type([handles.interp1_1 handles.civ2_1 handles.filter1_1 handles.interp1_1 handles.interp2_1 handles.filter2_1],handles.civ1_1)
3224 else
3225      reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3226 end
3227 run0_Callback(hObject, eventdata, handles)
3228 
3229 %--------------------------------------------
3230 function interp1_1_Callback(hObject, eventdata, handles)
3231 %--------------------------------------------
3232 if get(handles.interp1_1,'Value')==1
3233     reset_vel_type([handles.civ1_1 handles.civ2_1 handles.filter1_1 handles.interp2_1 handles.filter2_1],handles.interp1_1)
3234 else
3235     reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3236 end
3237 run0_Callback(hObject, eventdata, handles)
3238 
3239 %--------------------------------------------
3240 function filter1_1_Callback(hObject, eventdata, handles)
3241 %--------------------------------------------
3242 if get(handles.filter1_1,'Value')==1
3243     reset_vel_type([handles.interp1_1 handles.civ2_1 handles.interp1_1 handles.interp2_1 handles.filter2_1],handles.filter1_1)
3244 else
3245     reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3246 end
3247 run0_Callback(hObject, eventdata, handles)
3248 
3249 %--------------------------------------------
3250 function civ2_1_Callback(hObject, eventdata, handles)
3251 %--------------------------------------------
3252 if get(handles.civ2_1,'Value')==1
3253     reset_vel_type([handles.civ1_1 handles.interp1_1  handles.filter1_1 handles.interp2_1 handles.filter2_1],handles.civ2_1)
3254 else
3255     reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3256 end
3257 run0_Callback(hObject, eventdata, handles)
3258 
3259 %--------------------------------------------
3260 function interp2_1_Callback(hObject, eventdata, handles)
3261 %--------------------------------------------
3262 if get(handles.interp2_1,'Value')==1
3263     reset_vel_type([handles.civ1_1 handles.civ2_1 handles.filter1_1 handles.interp1_1 handles.filter2_1],handles.interp2_1)
3264 else
3265     reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3266 end
3267 run0_Callback(hObject, eventdata, handles)
3268 
3269 %--------------------------------------------
3270 function filter2_1_Callback(hObject, eventdata, handles)
3271 %--------------------------------------------
3272 if get(handles.filter2_1,'Value')==1
3273     reset_vel_type([handles.civ1_1 handles.interp1_1 handles.civ2_1 handles.filter1_1 handles.interp1_1 handles.interp2_1],handles.filter2_1)
3274 else
3275     reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3276 end
3277 run0_Callback(hObject, eventdata, handles)
3278 
3279 %-----------------------------------------------
3280 % --- reset civ buttons
3281 function reset_vel_type(handles_civ0,handle1)
3282 for ibutton=1:length(handles_civ0)
3283     set(handles_civ0(ibutton),'BackgroundColor',[0.831 0.816 0.784])
3284     set(handles_civ0(ibutton),'Value',0)
3285 end
3286 if exist('handle1','var')%handles of selected button
3287     set(handle1,'BackgroundColor',[1 1 0])  
3288 end
3289 
3290 %------------------------------------------------
3291 function create_Callback(hObject,eventdata,handles)
3292 %------------------------------------------------
3293 if ishandle(handles.UVMAT_title)
3294     delete(handles.UVMAT_title)
3295 end
3296 huvmat=get(handles.create,'parent');
3297 UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface (handles huvmat)
3298 if isequal(get(handles.create,'Value'),1)
3299     set(handles.zoom,'Value',0)
3300     zoom_Callback(hObject, eventdata, handles)
3301      set(handles.create,'BackgroundColor',[1 1 0]) %visualise in yellow
3302     set(handles.edit_vect,'Value',0)  
3303     edit_vect_Callback(hObject, eventdata, handles)
3304     set(handles.edit,'Value',0)
3305     set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
3306     list_object=get(handles.list_object,'String');
3307     if ~isempty(list_object)
3308         set(handles.list_object,'Value',length(list_object))
3309     end
3310     MouseAction='create_object';
3311     hset_object=findobj(allchild(0),'Name','set_object');
3312     uistack(hset_object,'top')
3313 else
3314     set(handles.create,'BackgroundColor',[0 1 0])
3315     set(handles.edit,'Value',1)
3316     set(handles.edit,'BackgroundColor',[1 1 0])
3317     MouseAction='none';
3318 end
3319 
3320 UvData.MouseAction=MouseAction;
3321 set(huvmat,'UserData',UvData);
3322 
3323 %------------------------------------------------
3324 function POINTS_Callback(hObject,eventdata,handles)
3325 %------------------------------------------------
3326 if ishandle(handles.UVMAT_title)
3327     delete(handles.UVMAT_title)
3328 end
3329 huvmat=get(handles.create,'parent');
3330 UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface (handles huvmat)
3331 if isequal(get(handles.create,'Value'),1)
3332     set(handles.zoom,'Value',0)
3333     zoom_Callback(hObject, eventdata, handles)
3334     set(handles.edit_vect,'Value',0)  
3335     edit_vect_Callback(hObject, eventdata, handles)
3336     set(handles.edit,'Value',0)
3337     set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
3338     %set(handles.grid,'Value',0)
3339     %set(handles.grid,'BackgroundColor',[0 1 0])
3340     % initiate set_object GUI
3341      data.TITLE='POINTS';
3342     if isfield(UvData,'CoordType')
3343         data.CoordType=UvData.CoordType;
3344     end
3345     if isfield(UvData,'Mesh')&~isempty(UvData.Mesh)
3346         data.RangeY=UvData.Mesh;
3347     elseif isfield(UvData,'AX')&isfield(UvData,'AY')& isfield(UvData,'A')%only image
3348         np=size(UvData.Field.A);
3349         meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
3350         meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
3351         data.RangeY=max(meshx,meshy);
3352         data.DX=max(meshx,meshy);
3353     end
3354     data.Coord=[0 0 0]; %default
3355     data.ParentButton=handles.create;
3356     PlotHandles=get_plot_handles(handles);%get the handles of the graphic objects setting the plotting parameters
3357     [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface
3358     if isfield(UvData,'SetObjectOrigin')
3359     pos_uvmat=get(huvmat,'Position');
3360     pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2);
3361     pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4);
3362     set(hset_object,'Position',pos_set_object)
3363     end
3364     %set(hset_object,'Position',[pos_uvmat(1) pos_uvmat(2)-0.05*pos_uvmat(4) 0.2*pos_uvmat(3)  0.5*pos_uvmat(4)]);
3365     list_object=get(handles.list_object,'String');
3366     if ~isempty(list_object)
3367         set(handles.list_object,'Value',length(list_object))
3368     end
3369     MouseAction='create_object';
3370     %UvData.ZoomOn=0;
3371 else
3372     set(handles.create,'BackgroundColor',[0 1 0])
3373     set(handles.edit,'Value',1)
3374     set(handles.edit,'BackgroundColor',[1 1 0])
3375     MouseAction='none';
3376 end
3377 
3378 UvData.MouseAction=MouseAction;
3379 set(huvmat,'UserData',UvData);
3380 
3381 %-----------------------------------------------------------
3382 function LINE_Callback(hObject, eventdata, handles)
3383 %-------------------------------------------------
3384 if ishandle(handles.UVMAT_title)
3385     delete(handles.UVMAT_title)
3386 end
3387 huvmat=get(handles.create,'parent');
3388 UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface
3389 % if (get(handles.LINE,'Value')==1)
3390     %suppress the other options if MENULINE is chosen
3391     set(handles.zoom,'Value',0)
3392     zoom_Callback(hObject, eventdata, handles)
3393 %     set(handles.create,'Value',0)
3394 %     set(handles.create,'BackgroundColor',[0 1 0])
3395 %     set(handles.LINE,'Value',1)
3396 %     set(handles.LINE,'BackgroundColor',[1 1 0])
3397 %     set(handles.PATCH,'Value',0)
3398 %     set(handles.PATCH,'BackgroundColor',[0 1 0])
3399 %     set(handles.PLANE,'Value',0)
3400 %     set(handles.PLANE,'BackgroundColor',[0 1 0])%put activated buttons to yellow
3401 %     set(handles.VOLUME,'Value',0)
3402 %     set(handles.VOLUME,'BackgroundColor',[0 1 0])
3403     %et(handles.makemask,'Value',0)
3404     %makemask_Callback(hObject, eventdata, handles)
3405     set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7])
3406     set(handles.edit_vect,'Value',0)
3407     edit_vect_Callback(hObject, eventdata, handles)
3408     set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
3409     set(handles.edit,'Value',0)
3410     set(handles.list_object,'Value',1);
3411     edit_vect_Callback(hObject, eventdata, handles)
3412     set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
3413     set(handles.cal,'Value',0)
3414     set(handles.cal,'BackgroundColor',[0 1 0])
3415    % set(handles.grid,'Value',0)
3416    % set(handles.grid,'BackgroundColor',[0 1 0])
3417 %  initiate the set_object GUI
3418     data.TITLE='LINE';
3419     if isfield(UvData,'CoordType')
3420         data.CoordType=UvData.CoordType;
3421     end
3422     if isfield(UvData,'Mesh')&~isempty(UvData.Mesh)
3423         data.RangeX=UvData.Mesh;
3424         data.RangeY=UvData.Mesh;
3425 %         data.YMax=UvData.Mesh;
3426 %         data.XMax=UvData.Mesh;
3427         data.DX=UvData.Mesh;
3428         data.DY=UvData.Mesh;
3429     elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3430         np=size(UvData.Field.A);
3431         meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
3432         meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
3433         data.RangeY=max(meshx,meshy);
3434         data.RangeX=max(meshx,meshy);
3435 %         data.YMax=max(meshx,meshy);
3436 %         data.XMax=max(meshx,meshy);
3437         data.DX=max(meshx,meshy);
3438     end 
3439     if isfield(data,'DX')
3440         data.Coord=[[0 0 0];[data.DX 0 0]]; %default
3441     else
3442         data.Coord=[[0 0 0];[1 0 0]]; %default
3443     end
3444     data.ParentButton=handles.create;
3445     PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
3446     [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes,
3447                                                       % associate the set_edit interface handle to the plotting axes
3448     pos_uvmat=get(huvmat,'Position');
3449     if isfield(UvData,'SetObjectOrigin')
3450         pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2);
3451         pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4);  
3452         set(hset_object,'Position',pos_set_object)
3453     end
3454     list_object=get(handles.list_object,'String');
3455     if ~isempty(list_object)
3456         set(handles.list_object,'Value',length(list_object))
3457     end
3458      MouseAction='create_object';
3459 % else
3460 %     set(handles.LINE,'BackgroundColor',[0 1 0])
3461 %      MouseAction='none';
3462 % end
3463 
3464 UvData.MouseAction=MouseAction;
3465 set(huvmat,'UserData',UvData)
3466 
3467 %-----------------------------------------------------------
3468 function PATCH_Callback(hObject, eventdata, handles)
3469 %-----------------------------------------------------------
3470 if ishandle(handles.UVMAT_title)
3471     delete(handles.UVMAT_title)
3472 end
3473 huvmat=get(handles.create,'parent');
3474 UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface
3475 % if isequal(get(handles.PATCH,'Value'),1)
3476     set(handles.zoom,'Value',0)
3477     set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
3478 %     set(handles.create,'Value',0)%suppress the other options if LINE is chosen
3479 %     set(handles.create,'BackgroundColor',[0 1 0])
3480 %     set(handles.LINE,'Value',0)
3481 %     set(handles.LINE,'BackgroundColor',[0 1 0])
3482 %     set(handles.PATCH,'Value',1)
3483 %     set(handles.PATCH,'BackgroundColor',[1 1 0])
3484 %     set(handles.PLANE,'Value',0)
3485 %     set(handles.PLANE,'BackgroundColor',[0 1 0])%put activated buttons to yellow
3486 %     set(handles.VOLUME,'Value',0)
3487 %     set(handles.VOLUME,'BackgroundColor',[0 1 0])
3488     %set(handles.makemask,'Value',0)
3489     %makemask_Callback(hObject, eventdata, handles)
3490     set(handles.edit_vect,'Value',0)
3491     edit_vect_Callback(hObject, eventdata, handles)
3492     set(handles.edit,'Value',0)
3493     set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
3494     set(handles.edit_vect,'Value',0)  
3495     edit_vect_Callback(hObject, eventdata, handles)
3496     set(handles.cal,'Value',0)
3497     set(handles.cal,'BackgroundColor',[0 1 0])
3498     %set(handles.grid,'Value',0)
3499     %set(handles.grid,'BackgroundColor',[0 1 0])
3500     %initiate set_object GUI
3501     data.TITLE='PATCH';
3502     if isfield(UvData,'CoordType')
3503         data.CoordType=UvData.CoordType;
3504     end
3505     if isfield(UvData,'Mesh')&~isempty(UvData.Mesh)
3506         data.YMax=UvData.Mesh;
3507     elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3508         np=size(UvData.Field.A);
3509         meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/(np(2)-1);
3510         meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/(np(1)-1);
3511         data.YMax=max(meshx,meshy);
3512         data.DX=max(meshx,meshy);
3513     end
3514     data.Coord=[0 0 0]; %default
3515     data.ParentButton=handles.create;
3516     PlotHandles=get_plot_handles(handles);%get the handles of the graphic objects setting the plotting parameters
3517     [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface
3518     pos_uvmat=get(huvmat,'Position');
3519     if isfield(UvData,'SetObjectOrigin')
3520         pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2);
3521         pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4); 
3522         set(hset_object,'Position',pos_set_object)
3523     end
3524     list_object=get(handles.list_object,'String');
3525     if ~isempty(list_object)
3526         set(handles.list_object,'Value',length(list_object))
3527     end
3528     UvData.MouseAction='create_object';
3529     set(huvmat,'UserData',UvData);
3530 %-------------------------------------------------------
3531 function PLANE_Callback(hObject, eventdata, handles)
3532 %-------------------------------------------------------
3533 if ishandle(handles.UVMAT_title)
3534     delete(handles.UVMAT_title)
3535 end
3536 huvmat=get(handles.create,'parent');
3537 UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface
3538 set(handles.zoom,'Value',0)
3539 set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
3540 set(handles.edit_vect,'Value',0)
3541 edit_vect_Callback(hObject, eventdata, handles)
3542 set(handles.edit,'Value',0)
3543 set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
3544 set(handles.cal,'Value',0)
3545 set(handles.cal,'BackgroundColor',[0 1 0])
3546 %set(handles.grid,'Value',0)
3547 %set(handles.grid,'BackgroundColor',[0 1 0])
3548 %initiate set_object GUI
3549 data.TITLE='PLANE';
3550 if isfield(UvData,'CoordType')
3551     data.CoordType=UvData.CoordType;
3552 end
3553 %Si 3D data.nbdim=3;
3554 %Si 2D
3555 if isfield(UvData,'Mesh')&~isempty(UvData.Mesh)
3556     data.ZMax=UvData.Mesh;
3557     data.DX=UvData.Mesh;
3558     data.DY=UvData.Mesh;
3559 elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3560     np=size(UvData.Field.A);
3561     meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/(np(2)-1);
3562     meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/(np(1)-1);
3563     data.DX=max(meshx,meshy);
3564 end
3565 if isfield(UvData,'DX')
3566     data.DX=UvData.DX;
3567 end
3568 if isfield(UvData,'DY')
3569     data.DY=UvData.DY;
3570 elseif isfield(UvData,'Mesh')
3571     data.DY=UvData.Mesh;
3572 end
3573 if isfield(UvData.Field,'X')& isfield(UvData.Field,'Y')
3574     data.Coord=[0 0 0];
3575     data.Style='plane';
3576     data.Phi=0;
3577     data.IndexObj=1; %act on the first reference plane by default
3578     haxes= handles.axes3;%GENERALISER
3579     plot_object(data,[],haxes,'m'); %plot the axes of the default plane
3580 end
3581 data.ParentButton=handles.create;
3582 PlotHandles=get_plot_handles(handles);%get the handles of the graphic objects setting the plotting parameters
3583 ZBounds=0; % default
3584 if isfield(UvData,'ZMin') && isfield(UvData,'ZMax')
3585     ZBounds(1)=UvData.ZMin; %minimum for the Z slider
3586     ZBounds(2)=UvData.ZMax;%maximum for the Z slider
3587 end
3588 [hset_object,UvData.sethandles]=set_object(data,PlotHandles,ZBounds);% call the set_object interface with action on haxes,
3589 if isfield(UvData,'SetObjectOrigin')
3590 pos_uvmat=get(huvmat,'Position');
3591 pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2);
3592 pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4);  
3593 set(hset_object,'Position',pos_set_object)
3594 end
3595 list_object=get(handles.list_object,'String');
3596 nbobject=length(list_object);
3597 set(handles.list_object,'Value',nbobject)
3598 UvData.MouseAction='create_object';
3599 set(huvmat,'UserData',UvData)
3600 
3601 %-------------------------------------------------------
3602 % --- Executes on button press in MENUVOLUME.
3603 %-------------------------------------------------------
3604 function VOLUME_Callback(hObject, eventdata, handles)
3605 %errordlg('command VOL not implemented yet')
3606 if ishandle(handles.UVMAT_title)
3607     delete(handles.UVMAT_title)
3608 end
3609 huvmat=get(handles.create,'parent');
3610 UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface
3611 if isequal(get(handles.VOLUME,'Value'),1)
3612     set(handles.zoom,'Value',0)
3613     set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
3614     set(handles.edit_vect,'Value',0)
3615     edit_vect_Callback(hObject, eventdata, handles)
3616     set(handles.edit,'Value',0)
3617     set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
3618     set(handles.cal,'Value',0)
3619     set(handles.cal,'BackgroundColor',[0 1 0])
3620     set(handles.edit_vect,'Value',0)
3621     edit_vect_Callback(hObject, eventdata, handles)
3622     %initiate set_object GUI
3623     data.TITLE='VOLUME';
3624     if isfield(UvData,'CoordType')
3625         data.CoordType=UvData.CoordType;
3626     end
3627     if isfield(UvData,'Mesh')&~isempty(UvData.Mesh)
3628         data.RangeY=UvData.Mesh;
3629         data.RangeX=UvData.Mesh;
3630         data.DX=UvData.Mesh;
3631         data.DY=UvData.Mesh;
3632     elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3633         np=size(UvData.Field.A);
3634         meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
3635         meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
3636         data.RangeY=max(meshx,meshy);
3637         data.RangeX=max(meshx,meshy);
3638         data.DX=max(meshx,meshy);
3639     end 
3640     data.ParentButton=handles.VOLUME;
3641     PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
3642     [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes,
3643                                                       % associate the set_edit interface handle to the plotting axes
3644     if isfield(UvData,'SetObjectOrigin')                                                
3645     pos_uvmat=get(huvmat,'Position');
3646     pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2);
3647     pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4);  
3648     set(hset_object,'Position',pos_set_object)
3649     end
3650     UvData.MouseAction='create_object';
3651 else
3652     set(handles.VOLUME,'BackgroundColor',[0 1 0])
3653     UvData.MouseAction='none';
3654 end
3655 set(huvmat,'UserData',UvData)
3656 
3657 %-------------------------------------------------------
3658 function edit_vect_Callback(hObject, eventdata, handles)
3659 %-------------------------------------------------------
3660 huvmat=get(handles.edit_vect,'parent');
3661 UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface
3662 if isequal(get(handles.edit_vect,'Value'),1)
3663     set(handles.record,'Visible','on')
3664     set(handles.edit_vect,'BackgroundColor',[1 1 0])
3665     set(handles.edit,'Value',0)
3666     set(handles.create,'Value',0)
3667     set(handles.create,'BackgroundColor',[0 1 0])
3668     set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
3669     set(gcf,'Pointer','arrow')
3670     UvData.MouseAction='edit_vect';
3671 else
3672     set(handles.record,'Visible','off')
3673     set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7])
3674     UvData.MouseAction='none';
3675 end
3676 set(huvmat,'UserData',UvData)
3677 
3678 %----------------------------------------------
3679 function save_mask_Callback(hObject, eventdata, handles)
3680 %-----------------------------------------------------------------------
3681 huvmat=get(handles.save_mask,'parent');
3682 UvData=get(huvmat,'UserData');
3683 
3684 hpatch=findobj(huvmat,'Type','patch');
3685 flag=1;
3686 npx=size(UvData.Field.A,2);
3687 npy=size(UvData.Field.A,1);
3688 xi=[0.5:npx-0.5];
3689 yi=[0.5:npy-0.5];
3690 [Xi,Yi]=meshgrid(xi,yi);
3691 if isfield(UvData,'Object')
3692     for iobj=1:length(UvData.Object)
3693         ObjectData=UvData.Object{iobj};
3694         if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
3695             flagobj=1;
3696             testphys=0; %coordinates in pixels by default
3697             if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys')
3698                 if isfield(UvData,'XmlData')&& isfield(UvData.XmlData,'GeometryCalib')
3699                     Calib=UvData.XmlData.GeometryCalib;
3700                     testphys=1;
3701                 end
3702             end
3703             if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style') 
3704                 if isequal(ObjectData.Style,'polygon') 
3705                     X=ObjectData.Coord(:,1);
3706                     Y=ObjectData.Coord(:,2);
3707                     if testphys
3708                         [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
3709                     end
3710                     flagobj=~inpolygon(Xi,Yi,X,Y);%=0 inside the polygon, 1 outside
3711                 elseif isequal(ObjectData.Style,'ellipse')
3712                     if testphys
3713                         %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3714                     end
3715                     RangeX=max(ObjectData.RangeX);
3716                     RangeY=max(ObjectData.RangeY);
3717                     X2Max=RangeX*RangeX;
3718                     Y2Max=RangeY*RangeY;
3719                     distX=(Xi-ObjectData.Coord(1,1));
3720                     distY=(Yi-ObjectData.Coord(1,2));
3721                     flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
3722                 elseif isequal(ObjectData.Style,'rectangle')
3723                     if testphys
3724                         %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3725                     end
3726                     distX=abs(Xi-ObjectData.Coord(1,1));
3727                     distY=abs(Yi-ObjectData.Coord(1,2));
3728                     flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
3729                 end
3730                 if isequal(ObjectData.ProjMode,'mask_outside')
3731                     flagobj=~flagobj;
3732                 end
3733                 flag=flag & flagobj;
3734             end
3735         end
3736     end
3737 end
3738 % flag=~flag;
3739 %mask name
3740 RootPath=get(handles.RootPath,'String');
3741 RootFile=get(handles.RootFile,'String');
3742 if ~isempty(RootFile)&(isequal(RootFile(1),'/')| isequal(RootFile(1),'\'))
3743         RootFile(1)=[];
3744 end
3745 filebase=fullfile(RootPath,RootFile);
3746 list=get(handles.masklevel,'String');
3747 masknumber=num2str(length(list));
3748 maskindex=get(handles.masklevel,'Value');
3749 mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
3750 imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
3751 imflag=flipdim(imflag,1);
3752 % imflag=uint8(255*flag);% =0 for flag=0 (vectors=0 when 20<imflag<200)
3753 warndlg_uvmat([mask_name ' saved'],'CONFIRMATION')
3754 imwrite(imflag,mask_name,'BitDepth',8); 
3755 
3756 %display the mask
3757 %update_mask(handles,num_i1,num_j1)
3758 figure;
3759 vec=linspace(0,1,256);%define a linear greyscale colormap
3760 map=[vec' vec' vec'];
3761 colormap(map)
3762 
3763 image(imflag);
3764 
3765 %-------------------------------------------------------------------
3766 %-------------------------------------------------------------------
3767 %  - FUNCTIONS FOR SETTING PLOTTING PARAMETERS
3768 
3769 %------------------------------------------------------------------
3770 
3771 
3772 
3773 %------------------------------------------------------------------
3774 % --- Executes on selection change in col_vec: choice of the color code.
3775 %
3776 function col_vec_Callback(hObject, eventdata, handles)
3777 %------------------------------------------------------------------
3778 % edit the choice for color code
3779 list_code=get(handles.col_vec,'String');% list menu fields
3780 index_code=get(handles.col_vec,'Value');% selected string index
3781 col_code= list_code{index_code(1)}; % selected field
3782 if isequal(col_code,'black') | isequal(col_code,'white')
3783    set(handles.slider1,'Visible','off')
3784    set(handles.slider2,'Visible','off')
3785    set(handles.colcode1,'Visible','off')
3786    set(handles.colcode2,'Visible','off')
3787    set(handles.AutoVecColor,'Visible','off')
3788    set_vec_col_bar(handles)
3789 else
3790    set(handles.slider1,'Visible','on')
3791    set(handles.slider2,'Visible','on') 
3792    set(handles.colcode1,'Visible','on')
3793    set(handles.colcode2,'Visible','on')
3794    set(handles.AutoVecColor,'Visible','on')  
3795    if isequal(col_code,'ima_cor')
3796        set(handles.AutoVecColor,'Value',0)%fixed scale by default
3797        set(handles.vec_col_bar,'Value',0)% 3 colors r,g,b by default
3798        set(handles.slider1,'Min',0);
3799        set(handles.slider1,'Max',1);
3800        set(handles.slider2,'Min',0);
3801        set(handles.slider2,'Max',1);
3802  %      set(handles.min_title_vec,'String','0')
3803        set(handles.max_vec,'String','1')
3804        set(handles.colcode1,'String','0.333')
3805        colcode1_Callback(hObject, eventdata, handles)
3806        set(handles.colcode2,'String','0.666')
3807        colcode2_Callback(hObject, eventdata, handles)
3808    else
3809        set(handles.AutoVecColor,'Value',1)%auto scale between min,max by default
3810        set(handles.vec_col_bar,'Value',1)% colormap 'jet' by default
3811        minval=get(handles.slider1,'Min');
3812        maxval=get(handles.slider1,'Max');
3813        set(handles.slider1,'Value',minval)
3814        set(handles.slider2,'Value',maxval)
3815        set_vec_col_bar(handles)
3816    end
3817 %    slider_update(handles)
3818 end
3819 %replot the current graph
3820 run0_Callback(hObject, eventdata, handles)
3821 
3822 
3823 %----------------------------------------------------------------
3824 % -- Executes on slider movement to set the color code
3825 %
3826 function slider1_Callback(hObject, eventdata, handles)
3827 %------------------------------------------------------------------
3828 slider1=get(handles.slider1,'Value');
3829 min_val=str2num(get(handles.min_vec,'String'));
3830 max_val=str2num(get(handles.max_vec,'String'));
3831 col=min_val+(max_val-min_val)*slider1;
3832 set(handles.colcode1,'String',num2str(col))
3833 if(get(handles.slider2,'Value') < col)%move also the second slider at the same value if needed
3834     set(handles.slider2,'Value',col)
3835     set(handles.colcode2,'String',num2str(col))
3836 end
3837 colcode1_Callback(hObject, eventdata, handles)
3838 
3839 %----------------------------------------------------------------
3840 % Executes on slider movement to set the color code
3841 %----------------------------------------------------------------
3842 function slider2_Callback(hObject, eventdata, handles)
3843 slider2=get(handles.slider2,'Value');
3844 min_val=str2num(get(handles.min_vec,'String'));
3845 max_val=str2num(get(handles.max_vec,'String'));
3846 col=min_val+(max_val-min_val)*slider2;
3847 set(handles.colcode2,'String',num2str(col))
3848 if(get(handles.slider1,'Value') > col)%move also the first slider at the same value if needed
3849     set(handles.slider1,'Value',col)
3850     set(handles.colcode1,'String',num2str(col))
3851 end
3852 colcode2_Callback(hObject, eventdata, handles)
3853 
3854 %----------------------------------------------------------------
3855 %execute on return carriage on the edit box corresponding to slider 1
3856 %----------------------------------------------------------------
3857 function colcode1_Callback(hObject, eventdata, handles)
3858 % col=str2num(get(handles.colcode1,'String'));
3859 % set(handles.slider1,'Value',col)
3860 set_vec_col_bar(handles)
3861 update_plot(handles)
3862 
3863 %----------------------------------------------------------------
3864 %execute on return carriage on the edit box corresponding to slider 2
3865 %----------------------------------------------------------------
3866 function colcode2_Callback(hObject, eventdata, handles)
3867 % col=str2num(get(handles.colcode2,'String'));
3868 % set(handles.slider2,'Value',col)
3869 % slider2_Callback(hObject, eventdata, handles)
3870 set_vec_col_bar(handles)
3871 update_plot(handles)
3872 %------------------------------------------------------------
3873 %update the slider values after displaying vectors
3874 %--------------------------------------------------------
3875 % function slider_update(handles,auto,minC,colcode1,colcode2,maxC)
3876 % set(handles.slider1,'Min',minC)
3877 % set(handles.slider1,'Max',maxC)
3878 % set(handles.slider2,'Min',minC)
3879 % set(handles.slider2,'Max',maxC)
3880 % set(handles.min_title_vec,'String',num2str(minC))
3881 % set(handles.max_vec,'String',num2str(maxC))
3882 % if auto
3883 %         set(handles.colcode1,'String',num2str(colcode1,3))%update display
3884 %         set(handles.colcode2,'String',num2str(colcode2,3))
3885 % end
3886 % set(handles.slider1,'Value',colcode1)%update slider with constant display
3887 % set(handles.slider2,'Value',colcode2)
3888 % set_vec_col_bar(handles)
3889 
3890 
3891 %-------------------------------------------------------
3892 % --- Executes on button press in AutoVecColor.
3893 %-------------------------------------------------------
3894 function vec_col_bar_Callback(hObject, eventdata, handles)
3895 set_vec_col_bar(handles)
3896 
3897 % %--------------------------------------------
3898 % %update the display of color code for vectors
3899 % %--------------------------------------------
3900 % function set_vec_col_bar(handles)
3901 % %get the image of the color display button 'vec_col_bar' in pixels
3902 % uni=get(handles.vec_col_bar,'Unit');
3903 % set(handles.vec_col_bar,'Unit','pixel')
3904 % pos_vert=get(handles.vec_col_bar,'Position');
3905 % set(handles.vec_col_bar,'Unit','Normalized')
3906 % width=ceil(pos_vert(3));
3907 % height=ceil(pos_vert(4));
3908 % %get slider indications
3909 % colcode.min=get(handles.slider1,'Min');
3910 % colcode.max=get(handles.slider1,'Max');
3911 % colcode.colcode1=get(handles.slider1,'Value');
3912 % colcode.colcode2=get(handles.slider2,'Value');
3913 % colcode.option=get(handles.vec_col_bar,'Value');
3914 % colcode.auto=1;
3915 % list_code=get(handles.col_vec,'String');% list menu fields
3916 % index_code=get(handles.col_vec,'Value');% selected string index
3917 % colcode.CName= list_code{index_code(1)}; % selected field used for vector color
3918 % vec_C=colcode.min+(colcode.max-colcode.min)*[0.5:width-0.5]/width;%sample of vec_C values from min to max
3919 % [colorlist,col_vec]=set_col_vec(colcode,vec_C);
3920 % oneheight=ones(1,height);
3921 % A1=colorlist(col_vec,1)*oneheight;
3922 % A2=colorlist(col_vec,2)*oneheight;
3923 % A3=colorlist(col_vec,3)*oneheight;
3924 % A(:,:,1)=A1';
3925 % A(:,:,2)=A2';
3926 % A(:,:,3)=A3';
3927 % set(handles.vec_col_bar,'Cdata',A)
3928 
3929 %--------------------------------------------------------
3930 % --- Executes on button press in cal.
3931 function cal_Callback(hObject, eventdata, handles)
3932 
3933 huvmat=get(handles.cal,'parent');%handles of the uvmat interface
3934 UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface
3935 %reinitialize the edit interface associated with uvmat
3936 value=get(handles.cal,'Value'); 
3937 if value
3938         set(handles.cal,'BackgroundColor',[1 1 0])
3939         %suppress the other options if MENULINE is chosen
3940         set(handles.zoom,'Value',0)
3941         set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
3942         set(handles.create,'Value',0)
3943         set(handles.create,'BackgroundColor',[0 1 0])
3944         set(handles.create,'enable','off')      
3945         set(handles.edit_vect,'Value',0)
3946         set(handles.edit_vect,'enable','off')
3947         edit_vect_Callback(hObject, eventdata, handles)
3948         set(handles.edit,'Value',0)
3949         set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
3950         set(handles.edit,'enable','off')
3951         set(handles.list_object,'Value',1)      
3952         % initiate display of GUI geometry_calib
3953         data=[]; %default
3954         if isfield(UvData,'CoordType')
3955             data.CoordType=UvData.CoordType;
3956         end
3957         %data.ParentButton=handles.cal; % transmit the handles of the calling button to the GUI geometry_calib
3958         pos=get(huvmat,'Position');
3959         pos(1)=pos(1)+pos(3)-0.311+0.04; %0.311= width of the geometry_calib interface (units relative to the srcreen)
3960         pos(2)=pos(2)-0.02;
3961         [FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles);
3962 %         [filebase,num_i1,num_j1,num_i2,num_j2,Ext,NomType,SubDir]=read_input_file(handles);
3963 %         [inputfile,idetect]=name_generator(filebase,num_i1,num_j1,Ext,NomType,1,num_i2,num_j2,SubDir);
3964         [UvData.hset_object,UvData.sethandles]=geometry_calib(handles,pos,FileName);% call the set_object interface
3965         pos_uvmat=get(huvmat,'Position');
3966         %pos_cal(1:2)=UvData.CalOrigin + pos_uvmat(1:2);
3967         if isfield(UvData,'CalOrigin')
3968             pos_cal(1)=pos_uvmat(1)+UvData.CalOrigin(1)*pos_uvmat(3);
3969             pos_cal(2)=pos_uvmat(2)+UvData.CalOrigin(2)*pos_uvmat(4);
3970             pos_cal(3:4)=UvData.CalSize .* pos_uvmat(3:4);
3971             set(UvData.hset_object,'Position',pos_cal)
3972         end
3973         UvData.MouseAction='calib';
3974 else
3975      UvData.MouseAction='none';     
3976      hgeometry_calib=findobj(allchild(0),'Name','geometry_calib');
3977      if ~isempty(hgeometry_calib)
3978          answer=questdlg('close the GUI geometry-calib?');
3979          if isequal(answer,'Yes')
3980              delete(hgeometry_calib)
3981              set(handles.cal,'BackgroundColor',[0 1 0])
3982          else
3983              set(handles.cal,'Value',1)% keep the calibration function active
3984          end
3985      end
3986      set(handles.edit_vect,'enable','on')
3987      set(handles.edit,'enable','on')
3988      set(handles.create,'enable','on')
3989 %      set(handles.LINE,'enable','on')
3990 %      set(handles.PATCH,'enable','on')
3991 %      set(handles.PLANE,'enable','on')
3992 %      set(handles.VOLUME,'enable','on')
3993      %set(handles.makemask,'enable','on')
3994      hh=findobj(handles.axes3,'Tag','calib_points');
3995      if ~isempty(hh)
3996          delete(hh)
3997      end
3998      hhh=findobj(handles.axes3,'Tag','calib_marker');
3999      if ~isempty(hhh)
4000          delete(hhh)
4001      end    
4002 end
4003 set(huvmat,'UserData',UvData);
4004 
4005 %-------------------------------------------------------------
4006 % --- Executes on selection change in menu_coord.
4007 function menu_coord_Callback(hObject, eventdata, handles)
4008 %-------------------------------------------------------------
4009 huvmat=get(handles.menu_coord,'parent');
4010 menu=get(handles.menu_coord,'String');
4011 ind_coord=get(handles.menu_coord,'Value');
4012 coord_option=menu{ind_coord};
4013 list_path=get(handles.menu_coord,'UserData');
4014     
4015 if isequal(coord_option,'more...'); 
4016     coord_fct='';
4017     dir_perso=prefdir;
4018     profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
4019     if exist(profil_perso,'file')
4020           h=load (profil_perso);
4021          if isfield(h,'coord_fct')
4022                 coord_fct=h.coord_fct;
4023          end
4024     end
4025     prompt = {'Enter the name of the transform function'};
4026     dlg_title = 'user defined transform';
4027     num_lines= 1;
4028     [FileName, PathName, filterindex] = uigetfile( ...
4029        {'*.m', ' (*.m)';
4030         '*.m',  '.m files '; ...
4031         '*.*', 'All Files (*.*)'}, ...
4032         'Pick a file', coord_fct);
4033     if isequal(PathName(end),'/')||isequal(PathName(end),'\')
4034         PathName(end)=[];
4035     end
4036     coord_fct=fullfile(PathName,FileName);
4037     if ~exist(coord_fct,'file')
4038            msgbox_uvmat('ERROR',['image procesing fct ' coord_fct ' not found'])
4039     else
4040        transform=FileName(1:end-2);%
4041        menu=update_menu(handles.menu_coord,transform);%add the selected fct to the menu
4042        ind_coord=get(handles.menu_coord,'Value');
4043        list_path{ind_coord}=PathName;
4044        set(handles.menu_coord,'UserData',list_path)
4045        if exist(profil_perso,'file')
4046             save (profil_perso,'coord_fct','-append'); %store the root name for future opening of uvmat
4047         end
4048     end   
4049 end
4050 
4051 %check the current path to the selected function
4052 PathName=list_path{ind_coord};
4053 CurrentPath=fileparts(which(coord_option));
4054 if ~isequal(PathName,CurrentPath)
4055     addpath(PathName) 
4056     errormsg=check_functions;
4057     msgbox_uvmat('WARNING',[['path ' PathName ' added to the current Matlab pathes'];errormsg])
4058 end
4059 set(handles.path_transform,'String',fullfile(PathName,' ')); %show the path to the senlected function
4060 set(handles.FixedLimits,'Value',0)
4061 set(handles.FixedLimits,'BackgroundColor',[0.7 0.7 0.7])
4062 
4063 UvData=get(huvmat,'UserData');
4064 
4065 %delete drawn objects
4066 hother=findobj('Tag','proj_object');%find all the proj objects
4067 for iobj=1:length(hother)
4068     delete_object(hother(iobj))
4069 end
4070 hother=findobj('Tag','DeformPoint');%find all the proj objects
4071 for iobj=1:length(hother)
4072     delete_object(hother(iobj))
4073 end
4074 hh=findobj('Tag','calib_points');
4075 if ~isempty(hh)
4076     delete(hh)
4077 end
4078 hhh=findobj('Tag','calib_marker');
4079 if ~isempty(hhh)
4080     delete(hhh)
4081 end
4082 if isfield(UvData,'Object')
4083     nbobject=length(UvData.Object);
4084     UvData.Object([2:nbobject])=[];
4085 end 
4086 
4087 %delete mask if it is displayed
4088 if isequal(get(handles.mask_test,'Value'),1)%if the mask option is on
4089    UvData=rmfield(UvData,'MaskName'); %will impose mask refresh
4090 end
4091 set(huvmat,'UserData',UvData)
4092 run0_Callback(hObject, eventdata, handles)
4093 
4094 %--------------------------------------------
4095 function histo1_menu_Callback(hObject, eventdata, handles)
4096 %--------------------------------------------
4097 %plot first histo
4098 huvmat=get(handles.histo1_menu,'parent');
4099 histo_menu=get(handles.histo1_menu,'String');
4100 histo_value=get(handles.histo1_menu,'Value');
4101 FieldName=histo_menu{histo_value};
4102 UvData=get(huvmat,'UserData');
4103 update_histo(handles.histo_u,huvmat,FieldName)
4104 
4105 %----------------------------------------------
4106 function histo2_menu_Callback(hObject, eventdata, handles)
4107 %----------------------------------------------
4108 %plot second histo
4109 huvmat=get(handles.histo2_menu,'parent');
4110 histo_menu=get(handles.histo2_menu,'String');
4111 histo_value=get(handles.histo2_menu,'Value');
4112 FieldName=histo_menu{histo_value};
4113 UvData=get(huvmat,'UserData');
4114 update_histo(handles.histo_v,huvmat,FieldName)
4115 
4116 
4117 %--------------------------------------------
4118 %read the field .Fieldname stored in UvData and plot its histogram
4119 function update_histo(haxes,huvmat,FieldName)
4120 UvData=get(huvmat,'UserData');
4121 
4122 if ~isfield(UvData.Field,FieldName)
4123     msgbox_uvmat('ERROR',['no field  ' FieldName ' for histogram'])
4124     return
4125 end
4126 Field=UvData.Field;
4127 FieldHisto=eval(['Field.' FieldName]);
4128 if isfield(Field,'FF') & ~isempty(Field.FF) & isequal(size(Field.FF),size(FieldHisto))
4129     indsel=find(Field.FF==0);%find values marked as false
4130     if ~isempty(indsel)
4131         FieldHisto=FieldHisto(indsel);
4132     end
4133 end
4134 if isempty(Field)
4135     msgbox_uvmat('ERROR',['empty field ' FieldName])
4136 else
4137     nxy=size(FieldHisto);
4138     Amin=double(min(min(min(FieldHisto))));%min of image
4139     Amax=double(max(max(max(FieldHisto))));%max of image
4140     if isequal(Amin,Amax)
4141        Histo.Txt=['uniform field =' num2str(Amin)];
4142     else
4143     Histo.ListVarName={FieldName,'histo'};
4144     if numel(nxy)==2
4145         Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
4146     else %color images
4147         Histo.VarDimName={FieldName,{FieldName,'rgb'}}; %dimensions for the histogram
4148     end
4149     %unit
4150     units=[]; %default
4151     for ivar=1:numel(Field.ListVarName)    
4152         if strcmp(Field.ListVarName{ivar},FieldName)
4153             if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'units')
4154                 units=Field.VarAttribute{ivar}.units;
4155                 break
4156             end
4157         end
4158     end
4159     if ~isempty(units)
4160         Histo.VarAttribute{1}.units=units;
4161     end
4162     eval(['Histo.' FieldName '=linspace(Amin,Amax,50);'])%absissa values for histo
4163     for col=1:size(FieldHisto,3)
4164         B=FieldHisto(:,:,col);
4165         C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector
4166        eval(['Histo.histo(:,col)=hist(C, Histo.' FieldName ');']);  %calculate histogram
4167     end
4168     set(haxes,'XLimMode','auto')%reset auto mode (after zoom effect)
4169     set(haxes,'YLimMode','auto')
4170     plot_field(Histo,haxes);
4171     end
4172 end
4173 
4174 
4175 
4176 %------------------------------------------------
4177 %CALLBACKS FOR PLOTTING PARAMETERS
4178 %-------------------------------------------------
4179 
4180 %-----------------------------------------------------------------
4181 function MinA_Callback(hObject, eventdata, handles)
4182 %------------------------------------------
4183 set(handles.AutoScal,'Value',1) %suppress auto mode
4184 set(handles.AutoScal,'BackgroundColor',[1 1 0])
4185 update_plot(handles)
4186 
4187 %-----------------------------------------------------------------
4188 function MaxA_Callback(hObject, eventdata, handles)
4189 %--------------------------------------------
4190 set(handles.AutoScal,'Value',1) %suppress auto mode
4191 set(handles.AutoScal,'BackgroundColor',[1 1 0])
4192 update_plot(handles)
4193 
4194 %-----------------------------------------------
4195 function AutoScal_Callback(hObject, eventdata, handles)
4196 %--------------------------------------------
4197 test=get(handles.AutoScal,'Value');
4198 if test
4199     set(handles.AutoScal,'BackgroundColor',[1 1 0])
4200 else
4201     set(handles.AutoScal,'BackgroundColor',[0.7 0.7 0.7])
4202     update_plot(handles);
4203 %     set(handles.MinA,'String',num2str(ScalOut.MinA,3))
4204 %     set(handles.MaxA,'String',num2str(ScalOut.MaxA,3))
4205 end
4206 
4207 %-------------------------------------------------------------------
4208 function BW_Callback(hObject, eventdata, handles)
4209 %-------------------------------------------------------------------
4210 update_plot(handles)
4211 
4212 %-------------------------------------------------------------------
4213 function Contours_Callback(hObject, eventdata, handles)
4214 %-------------------------------------------------------------------
4215 val=get(handles.Contours,'Value');
4216 if val==2
4217     set(handles.interval_txt,'Visible','on')
4218     set(handles.IncrA,'Visible','on')
4219 else
4220     set(handles.interval_txt,'Visible','off')
4221     set(handles.IncrA,'Visible','off')
4222 end
4223 update_plot(handles)
4224 
4225 %-------------------------------------------------------------------
4226 function IncrA_Callback(hObject, eventdata, handles)
4227 %-------------------------------------------------------------------
4228 update_plot(handles)
4229 
4230 %-------------------------------------------------------------------
4231 function HideWarning_Callback(hObject, eventdata, handles)
4232 %-------------------------------------------------------------------
4233 update_plot(handles)
4234 
4235 %-------------------------------------------------------------------
4236 function HideFalse_Callback(hObject, eventdata, handles)
4237 %-------------------------------------------------------------------
4238 update_plot(handles)
4239 
4240 %-------------------------------------------------------------------
4241 function VecScale_Callback(hObject, eventdata, handles)
4242 %-------------------------------------------------------------------
4243 set(handles.AutoVec,'Value',1);
4244 set(handles.AutoVec,'BackgroundColor',[1 1 0])
4245 update_plot(handles)
4246 
4247 %-------------------------------------------------------------------
4248 function AutoVec_Callback(hObject, eventdata, handles)
4249 %-------------------------------------------------------------------
4250 test=get(handles.AutoVec,'Value');
4251 if test
4252     set(handles.AutoVec,'BackgroundColor',[1 1 0])
4253 else
4254     update_plot(handles);
4255     %set(handles.VecScale,'String',num2str(ScalOut.VecScale,3))
4256     set(handles.AutoVec,'BackgroundColor',[0.7 0.7 0.7])
4257 end
4258 
4259 %-------------------------------------------------------
4260 % --- Executes on selection change in decimate4 (nb_vec/4).
4261 %-------------------------------------------------------
4262 function decimate4_Callback(hObject, eventdata, handles)
4263 update_plot(handles)
4264 
4265 
4266 %-------------------------------------------------------
4267 % --- Executes on selection change in color_code menu
4268 %-------------------------------------------------------
4269 function color_code_Callback(hObject, eventdata, handles)
4270 set_vec_col_bar(handles)
4271 update_plot(handles);
4272 
4273 %-------------------------------------------------------
4274 % --- Executes on button press in AutoVecColor.
4275 %-------------------------------------------------------
4276 function AutoVecColor_Callback(hObject, eventdata, handles)
4277 test=get(handles.AutoVecColor,'Value');
4278 if test
4279     set(handles.AutoVecColor,'BackgroundColor',[1 1 0])
4280 else
4281     update_plot(handles);
4282     %set(handles.VecScale,'String',num2str(ScalOut.VecScale,3))
4283     set(handles.AutoVecColor,'BackgroundColor',[0.7 0.7 0.7])
4284 end
4285 %set_vec_col_bar(handles)
4286 
4287 %-------------------------------------------------------
4288 % --- Executes on selection change in max_vec.
4289 %-------------------------------------------------------
4290 function min_vec_Callback(hObject, eventdata, handles)
4291 max_vec_Callback(hObject, eventdata, handles)
4292 
4293 % --- Executes on selection change in max_vec.
4294 function max_vec_Callback(hObject, eventdata, handles)
4295 set(handles.AutoVecColor,'Value',1)
4296 AutoVecColor_Callback(hObject, eventdata, handles)
4297 min_val=str2num(get(handles.min_vec,'String'));
4298 max_val=str2num(get(handles.max_vec,'String'));
4299 slider1=get(handles.slider1,'Value');
4300 slider2=get(handles.slider2,'Value');
4301 colcode1=min_val+(max_val-min_val)*slider1;
4302 colcode2=min_val+(max_val-min_val)*slider2;
4303 set(handles.colcode1,'String',num2str(colcode1))
4304 set(handles.colcode2,'String',num2str(colcode2))
4305 update_plot(handles);
4306 
4307 %-------------------------------------------------------------------
4308 %update the display of color code for vectors
4309 function set_vec_col_bar(handles)
4310 %-------------------------------------------------------------------
4311 %get the image of the color display button 'vec_col_bar' in pixels
4312 set(handles.vec_col_bar,'Unit','pixel');
4313 pos_vert=get(handles.vec_col_bar,'Position');
4314 set(handles.vec_col_bar,'Unit','Normalized');
4315 width=ceil(pos_vert(3));
4316 height=ceil(pos_vert(4));
4317 
4318 %get slider indications
4319 list=get(handles.color_code,'String');
4320 ichoice=get(handles.color_code,'Value');
4321 colcode.ColorCode=list{ichoice};
4322 colcode.MinC=str2num(get(handles.min_vec,'String'));
4323 colcode.MaxC=str2num(get(handles.max_vec,'String'));
4324 test3color=strcmp(colcode.ColorCode,'rgb') || strcmp(colcode.ColorCode,'bgr');
4325 if test3color
4326 %     set(handles.colcode1,'Visible','on')
4327 %     set(handles.colcode2,'Visible','on')
4328 %     set(handles.slider1,'Visible','on')
4329 %     set(handles.slider2,'Visible','on')
4330     colcode.colcode1=str2num(get(handles.colcode1,'String'));
4331     colcode.colcode2=str2num(get(handles.colcode2,'String'));
4332 else
4333 %     set(handles.colcode1,'Visible','off')
4334 %     set(handles.colcode2,'Visible','off')
4335 %     set(handles.slider1,'Visible','off')
4336 %     set(handles.slider2,'Visible','off')
4337 %     colcode.colcode1=colcode.min;
4338 %     colcode.colcode2=colcode.max;
4339 end
4340 % colcode.option=get(handles.vec_col_bar,'Value');
4341 colcode.FixedCbounds=0;
4342 % list_code=get(handles.col_vec,'String');% list menu fields
4343 % index_code=get(handles.col_vec,'Value');% selected string index
4344 % colcode.CName= list_code{index_code(1)}; % selected field used for vector color
4345 colcode.FixedCbounds=1;
4346 vec_C=colcode.MinC+(colcode.MaxC-colcode.MinC)*[0.5:width-0.5]/width;%sample of vec_C values from min to max
4347 [colorlist,col_vec]=set_col_vec(colcode,vec_C);
4348 oneheight=ones(1,height);
4349 A1=colorlist(col_vec,1)*oneheight;
4350 A2=colorlist(col_vec,2)*oneheight;
4351 A3=colorlist(col_vec,3)*oneheight;
4352 A(:,:,1)=A1';
4353 A(:,:,2)=A2';
4354 A(:,:,3)=A3';
4355 set(handles.vec_col_bar,'Cdata',A)
4356 
4357 
4358 %-------------------------------------------------------------------
4359 function [PlotType,ScalOut]=update_plot(handles)
4360 %-------------------------------------------------------------------
4361 haxes= handles.axes3;
4362 AxeData=get(haxes,'UserData');
4363 PlotParam=read_plot_param(handles);
4364 [PlotType,PlotParamOut]= plot_field(AxeData,haxes,PlotParam,1);
4365 write_plot_param(handles,PlotParamOut); %update the auto plot parameters
4366 
4367 %-------------------------------------------------------------------
4368 % --- Executes on button press in grid.
4369 function grid_Callback(hObject, eventdata, handles)
4370 %-------------------------------------------------------------------
4371 huvmat=get(handles.create,'parent');
4372 UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface
4373 % if isequal(get(handles.grid,'Value'),1)
4374    % set(handles.grid,'BackgroundColor',[1 1 0])
4375     %suppress the other options if grid is chosen
4376     set(handles.create,'Value',0)
4377     set(handles.create,'BackgroundColor',[0 1 0])
4378 %     set(handles.LINE,'Value',0)
4379 %     set(handles.LINE,'BackgroundColor',[0 1 0])
4380 %     set(handles.PATCH,'Value',0)
4381 %     set(handles.PATCH,'BackgroundColor',[0 1 0])
4382 %     set(handles.PLANE,'Value',0)
4383 %     set(handles.PLANE,'BackgroundColor',[0 1 0])%put activated buttons to yellow
4384 %     set(handles.VOLUME,'Value',0)
4385 %     set(handles.VOLUME,'BackgroundColor',[0 1 0])
4386     %set(handles.makemask,'Value',0)
4387     %makemask_Callback(hObject, eventdata, handles)
4388     set(handles.edit_vect,'Value',0)
4389     edit_vect_Callback(hObject, eventdata, handles)
4390     set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
4391     set(handles.edit_vect,'Value',0)  
4392     edit_vect_Callback(hObject, eventdata, handles)
4393     set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
4394     set(handles.list_object,'Value',1)      
4395     set(handles.cal,'Value',0)
4396     set(handles.cal,'BackgroundColor',[0 1 0])   
4397    % set(handles.grid,'BackgroundColor',[1 1 0])
4398     %prepare display of the set_grid GUI
4399     data.fixedtitle=1;
4400     [FileName]=read_file_boxes(handles);
4401     %[filebase,num_i1,num_j1,num_i2,num_j2,Ext,NomType,SubDir]=read_input_file(handles);
4402     %[inputfile,idetect]=name_generator(filebase,num_i1,num_j1,Ext,NomType,1,num_i2,num_j2,SubDir);
4403     [hset_object,UvData.sethandles]=set_grid(FileName);% call the set_object interface
4404     set(huvmat,'UserData',UvData);
4405 % else
4406 %     set(handles.grid,'BackgroundColor',[1 0 1])
4407 % end
4408 
4409 %-------------------------------------------------------------------
4410 % --- Executes on selection change in edit.
4411 function edit_Callback(hObject, eventdata, handles)
4412 %-------------------------------------------------------------------
4413 huvmat=get(handles.list_object,'parent');
4414 UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface
4415 test=get(handles.edit,'Value');
4416 if test
4417     UvData.MouseAction='edit_object';
4418     set(handles.edit,'BackgroundColor',[1,1,0])  
4419     %suppress the other options
4420     set(handles.zoom,'Value',0)
4421     zoom_Callback(hObject, eventdata, handles)
4422     set(handles.create,'Value',0)
4423     set(handles.create,'BackgroundColor',[0 1 0])
4424 %     set(handles.LINE,'Value',0)
4425 %     set(handles.LINE,'BackgroundColor',[0 1 0])
4426 %     set(handles.PATCH,'Value',0)
4427 %     set(handles.PATCH,'BackgroundColor',[0 1 0])
4428 %     set(handles.PLANE,'Value',0)
4429 %     set(handles.PLANE,'BackgroundColor',[0 1 0])%put activated buttons to yellow
4430 %     set(handles.VOLUME,'Value',0)
4431 %     set(handles.VOLUME,'BackgroundColor',[0 1 0])
4432     set(handles.edit_vect,'Value',0)
4433     edit_vect_Callback(hObject, eventdata, handles)  
4434     set(handles.cal,'Value',0)
4435     set(handles.cal,'BackgroundColor',[0 1 0])   
4436     %set(handles.grid,'Value',0)
4437     %set(handles.grid,'BackgroundColor',[0 1 0])
4438     list_object_Callback(hObject, eventdata, handles)
4439 else 
4440     UvData.MouseAction='none';
4441     set(handles.edit,'BackgroundColor',[0.7,0.7,0.7])   
4442 end
4443 set(huvmat,'UserData',UvData);
4444 
4445 %--------------------------------------------------------
4446 % --- Executes on selection change in list_object.
4447 %--------------------------------------------------------
4448 function list_object_Callback(hObject, eventdata, handles)
4449 huvmat=get(handles.list_object,'parent');
4450 UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface
4451 list_str=get(handles.list_object,'String');
4452 IndexObj=get(handles.list_object,'Value');
4453 
4454 if ~(length(UvData.Object)>=IndexObj);
4455     return
4456 end
4457 ObjectData=UvData.Object{IndexObj};
4458 ObjectData.desable_open=1; % desable the OPEN option in the set_object GUI (editing mode)
4459 if isequal(get(handles.edit,'Value'),0)
4460     ObjectData.desable_plot=1; % desable the PLOT option in the set_object GUI (editing mode
4461 end
4462 PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
4463 ZBounds=0; % default
4464     if isfield(UvData,'ZMin') && isfield(UvData,'ZMax')
4465         ZBounds(1)=UvData.ZMin; %minimum for the Z slider
4466         ZBounds(2)=UvData.ZMax;%maximum for the Z slider
4467     end
4468 AxeData.hset_object=set_object(ObjectData,PlotHandles,ZBounds);% call the set_object interface,
4469 pos_uvmat=get(huvmat,'Position');
4470 if isfield(UvData,'SetObjectOrigin')
4471 pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2);
4472 pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4);
4473 set(AxeData.hset_object,'Position',pos_set_object)
4474 end
4475 hother=findobj('Tag','proj_object');%find all the proj objects
4476 for iobj=1:length(hother)
4477     if isequal(get(hother(iobj),'Type'),'rectangle')|isequal(get(hother(iobj),'Type'),'patch')
4478         set(hother(iobj),'EdgeColor','b')
4479         if isequal(get(hother(iobj),'FaceColor'),'m')
4480             set(hother(iobj),'FaceColor','b')
4481         end
4482     elseif isequal(get(hother(iobj),'Type'),'image')
4483            Acolor=get(hother(iobj),'CData');
4484            Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2));
4485            set(hother(iobj),'CData',Acolor);
4486     else
4487          set(hother(iobj),'Color','b')
4488     end
4489     set(hother(iobj),'Selected','off')
4490 end
4491 hother=findobj('Tag','DeformPoint');
4492 set(hother,'Color','b');
4493 set(hother,'Selected','off')    
4494 if isfield(ObjectData,'HandlesDisplay')
4495     for iview=1:length(ObjectData.HandlesDisplay)
4496         if ishandle(ObjectData.HandlesDisplay(iview))
4497             uistack(ObjectData.HandlesDisplay(iview),'top')
4498             linetype=get(ObjectData.HandlesDisplay(iview),'Type');
4499             if isequal(linetype,'line')
4500                 set(ObjectData.HandlesDisplay(iview),'Color','m'); %set the selected object to magenta color
4501             elseif isequal(linetype,'rectangle')
4502                 set(ObjectData.HandlesDisplay(iview),'EdgeColor','m'); %set the selected object to magenta color
4503             elseif isequal(linetype,'patch')
4504                 set(ObjectData.HandlesDisplay(iview),'FaceColor','m'); %set the selected object to magenta color
4505             end 
4506             SubObjectData=get(ObjectData.HandlesDisplay(iview),'UserData');
4507             if isfield(SubObjectData,'SubObject')& ishandle(SubObjectData.SubObject)
4508                 uistack(SubObjectData.SubObject,'top')
4509                 for iobj=1:length(SubObjectData.SubObject)
4510                     hsub=SubObjectData.SubObject(iobj);
4511                     if isequal(get(hsub,'Type'),'rectangle')
4512                         set(hsub,'EdgeColor','m'); %set the selected object to magenta color
4513                     elseif isequal(get(hsub,'Type'),'image')
4514                        Acolor=get(hsub,'CData');
4515                        Acolor(:,:,1)=Acolor(:,:,3);
4516                        set(hsub,'CData',Acolor);
4517                     else
4518                         set(hsub,'Color','m')
4519                     end
4520                 end
4521             end
4522             if isfield(SubObjectData,'DeformPoint')& ishandle(SubObjectData.DeformPoint)
4523                 set(SubObjectData.DeformPoint,'Color','m')
4524             end
4525         end
4526     end
4527 end
4528 
4529 %------------------------------------------------------
4530 % --- Executes on button press in Menu/Export/field in workspace.
4531 %------------------------------------------------------
4532 function MenuExportField_Callback(hObject, eventdata, handles)
4533 
4534 global CurData
4535 huvmat=get(handles.RootPath,'parent');
4536 CurData=get(huvmat,'UserData');
4537 evalin('base','global CurData')%make CurData global in the workspace
4538 display(['UserData of uvmat :'])
4539 evalin('base','CurData') %display CurData in the workspace
4540 commandwindow;
4541 
4542 %------------------------------------------------------
4543 % --- Executes on button press in Menu/Export/extract figure.
4544 %------------------------------------------------------
4545 function MenuExport_plot_Callback(hObject, eventdata, handles)
4546 huvmat=get(handles.MenuExport_plot,'parent');
4547 UvData=get(huvmat,'UserData');
4548 hfig=figure;
4549 newaxes=copyobj(handles.axes3,hfig);
4550 map=colormap(handles.axes3);
4551 colormap(map);%transmit the current colormap to the zoom fig
4552 colorbar
4553 
4554 
4555 % --------------------------------------------------------------------
4556 function Insert_Callback(hObject, eventdata, handles)
4557 
4558 
4559 % --------------------------------------------------------------------
4560 function MenuRun_Callback(hObject, eventdata, handles)
4561 
4562 
4563 % --------------------------------------------------------------------
4564 function MenuHelp_Callback(hObject, eventdata, handles)
4565 % --------------------------------------------------------------------
4566 path_to_uvmat=which ('uvmat');% check the path of uvmat
4567 pathelp=fileparts(path_to_uvmat);
4568 helpfile=fullfile(pathelp,'UVMAT_DOC','uvmat_doc.html');
4569 if isempty(dir(helpfile)), errordlg('Please put the help file uvmat_doc.html in the directory UVMAT/UVMAT_DOC')
4570 else
4571     web(helpfile);
4572 end
4573 
4574 % --------------------------------------------------------------------
4575 function MenuOpen_Callback(hObject, eventdata, handles)
4576 
4577 % --------------------------------------------------------------------
4578 % --- Executes on selection change in sub_menu.
4579 %---------------------------------------------------------------------
4580 function MenuOpen_1_Callback(hObject, eventdata, handles)
4581 
4582 % --------------------------------------------------------------------
4583 function MenuExport_Callback(hObject, eventdata, handles)
4584 
4585 
4586 % --------------------------------------------------------------------
4587 function MenuExportMovie_Callback(hObject, eventdata, handles)
4588 
4589 set(handles.MenuExportMovie,'BusyAction','queue')% activate the button
4590 huvmat=get(handles.run0,'parent');
4591 UvData=get(huvmat,'UserData');
4592 [xx,xx,FileBase]=read_file_boxes(handles);
4593  %read the current input file name
4594 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)'};
4595 dlg_title = 'select properties of the output avi movie';
4596 num_lines= 1;
4597 nbfield_cell=get(handles.last_i,'String');
4598 def     = {[FileBase '_out.avi'];'10';'1';'[0.03 0.05 0.95 0.92]';'10'};
4599 answer = inputdlg(prompt,dlg_title,num_lines,def,'on');
4600 aviname=answer{1};
4601 fps=str2num(answer{2});
4602 % check for existing file with output name aviname
4603 if exist(aviname,'file')
4604     backup=aviname;
4605     testexist=2;
4606     while testexist==2
4607         backup=[backup '~'];
4608         testexist=exist(backup,'file');      
4609     end
4610     [success,message]=copyfile(aviname,backup);%make backup of the existing file
4611     if isequal(success,1)
4612         delete(aviname)%delete existing file
4613     else
4614         msgbox_uvmat('ERROR',message)
4615         return
4616     end 
4617 end
4618 %create avi open
4619 aviobj=avifile(aviname,'Compression','None','fps',fps);
4620 
4621 %display first view for tests
4622 newfig=figure;
4623 newaxes=copyobj(handles.axes3,newfig);%new plotting axes in the new figure
4624 set(newaxes,'Tag','movieaxes')
4625 nbpix=[512 384]*str2num(answer{3});
4626 set(gcf,'Position',[1 1 nbpix])% resolution XVGA
4627 set(newaxes,'Position',eval(answer{4}));
4628 map=colormap(handles.axes3);
4629 colormap(map);%transmit the current colormap to the zoom fig
4630 msgbox_uvmat('INPUT_Y-N',{['adjust figure ' num2str(newfig) ' with its matlab edit menu '] ;...
4631         ['then press OK to get the avi movie as a copy of figure ' num2str(newfig) ' display']});
4632 UvData.Object{1}.plotaxes=newaxes;% the axis in the new figure becomes the current main plotting axes
4633 set(huvmat,'UserData',UvData);
4634 increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
4635 set(handles.STOP,'Visible','on')
4636 set(handles.speed,'Visible','on')
4637 set(handles.speed_txt,'Visible','on')
4638 set(handles.RunMovie,'BusyAction','queue')
4639 
4640 imin=str2num(get(handles.i1,'String'));
4641 imax=str2num(answer{5});
4642 % if isfield(UvData,'Time')
4643 htitle=get(newaxes,'Title');
4644 xlim=get(newaxes,'XLim');
4645 ylim=get(newaxes,'YLim');
4646 set(htitle,'Position',[xlim(2)+0.07*(xlim(2)-xlim(1)) ylim(2)-0.05*(ylim(2)-ylim(1)) 0])
4647 time_str=get(handles.abs_time,'String');
4648 set(htitle,'String',['t=' time_str])
4649 set(handles.speed,'Value',1)
4650 for i=1:imax
4651     if get(handles.speed,'Value')~=0 & isequal(get(handles.MenuExportMovie,'BusyAction'),'queue') % enable STOP command
4652             runpm(hObject,eventdata,handles,increment)
4653             drawnow
4654             time_str=get(handles.abs_time,'String');
4655             if ishandle(htitle)
4656              set(htitle,'String',['t=' time_str])
4657             end
4658             mov=getframe(newfig);
4659             aviobj=addframe(aviobj,mov);
4660     end
4661 end
4662 aviobj=close(aviobj);
4663 UvData.Object{1}.plotaxes=handles.axes3;
4664 set(huvmat,'UserData',UvData);
4665 msgbox_uvmat('CONFIRMATION',{['movie ' aviname ' created '];['with ' num2str(imax) ' frames']})
4666 
4667 % --------------------------------------------------------------------
4668 function MenuPoints_Callback(hObject, eventdata, handles)
4669 set(handles.create,'Visible','on')
4670 set(handles.create,'Value',1)
4671 POINTS_Callback(hObject,eventdata,handles)
4672 
4673 % --------------------------------------------------------------------
4674 function MenuLine_Callback(hObject, eventdata, handles)
4675 set(handles.create,'Visible','on')
4676 set(handles.create,'Value',1)
4677 LINE_Callback(hObject,eventdata,handles)
4678 
4679 % ------------------------------------------------------------------
4680 function MenuPatch_Callback(hObject, eventdata, handles)
4681 set(handles.create,'Visible','on')
4682 set(handles.create,'Value',1)
4683 PATCH_Callback(hObject,eventdata,handles)
4684 
4685 % ------------------------------------------------------------------
4686 function MenuPlane_Callback(hObject, eventdata, handles)
4687 set(handles.create,'Visible','on')
4688 set(handles.create,'Value',1)
4689 PLANE_Callback(hObject,eventdata,handles)
4690 
4691 % ------------------------------------------------------------------
4692 function MenuVolume_Callback(hObject, eventdata, handles)
4693 set(handles.create,'Visible','on')
4694 set(handles.create,'Value',1)
4695 VOLUME_Callback(hObject,eventdata,handles)
4696 
4697 % ------------------------------------------------------------------
4698 function MenuCalib_Callback(hObject, eventdata, handles)
4699 set(handles.TOOLS_txt,'Visible','on')
4700 set(handles.frame_tools,'Visible','on')
4701 set(handles.cal,'Visible','on')
4702 set(handles.cal,'Value',1)
4703 cal_Callback(hObject,eventdata,handles)
4704 
4705 % ------------------------------------------------------------------
4706 function MenuMask_Callback(hObject, eventdata, handles)
4707 set(handles.TOOLS_txt,'Visible','on')
4708 set(handles.frame_tools,'Visible','on')
4709 set(handles.create,'Visible','on')
4710 set(handles.create,'Value',1)
4711 set(handles.create,'BackgroundColor',[1 1 0]) %visualise in yellow
4712 set(handles.save_mask,'Visible','on')
4713 set(handles.masklevel,'Visible','on')
4714 if isequal(get(handles.z_index,'Visible'),'on')
4715     nb_slice=str2num(get(handles.nb_slice,'String'));
4716     for ilist=1:nb_slice
4717         list_index{ilist,1}=num2str(ilist);
4718     end   
4719     set(handles.masklevel,'String',list_index)
4720     val=str2num(get(handles.z_index,'String'));
4721     if val<=nb_slice
4722         set(handles.masklevel,'Value',val)
4723     end
4724 else
4725     set(handles.masklevel,'String',{'1'})
4726     set(handles.masklevel,'Value',1)
4727 end
4728 if ishandle(handles.UVMAT_title)
4729     delete(handles.UVMAT_title)
4730 end
4731 huvmat=get(handles.create,'parent');
4732 UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface
4733 set(handles.zoom,'Value',0)
4734 set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
4735 set(handles.edit_vect,'Value',0)
4736 edit_vect_Callback(hObject, eventdata, handles)
4737 set(handles.edit,'Value',0)
4738 set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
4739 set(handles.edit_vect,'Value',0)  
4740 edit_vect_Callback(hObject, eventdata, handles)
4741 set(handles.cal,'Value',0)
4742 set(handles.cal,'BackgroundColor',[0 1 0])
4743 
4744 %initiate the GUI set_object
4745 data.TITLE='MASK';
4746 if isfield(UvData,'CoordType')
4747     data.CoordType=UvData.CoordType;
4748 end
4749 if isfield(UvData,'Mesh')&&~isempty(UvData.Mesh)
4750     data.YMax=UvData.Mesh;
4751 elseif isfield(UvData.Field,'AX')&&isfield(UvData.Field,'AY')&& isfield(UvData.Field,'A')%only image
4752     np=size(UvData.Field.A);
4753     meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/(np(2)-1);
4754     meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/(np(1)-1);
4755     data.YMax=max(meshx,meshy);
4756     data.DX=max(meshx,meshy);
4757 end
4758 data.Coord=[0 0 0]; %default
4759 PlotHandles=get_plot_handles(handles);%get the handles of the graphic objects setting the plotting parameters
4760 [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface
4761 pos_uvmat=get(huvmat,'Position');
4762 if isfield(UvData,'SetObjectOrigin')
4763     pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2);
4764     pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4); 
4765     set(hset_object,'Position',pos_set_object)
4766 end
4767 list_object=get(handles.list_object,'String');
4768 if ~isempty(list_object)
4769     set(handles.list_object,'Value',length(list_object))
4770 end
4771 UvData.MouseAction='create_object';
4772 set(huvmat,'UserData',UvData);
4773 
4774 % ------------------------------------------------------------------
4775 %-- open the GUI set_grid.fig to create grid
4776 function MenuGrid_Callback(hObject, eventdata, handles)
4777 set(handles.TOOLS_txt,'Visible','on')
4778 set(handles.frame_tools,'Visible','on')
4779 grid_Callback(hObject,eventdata,handles)
4780 
4781 %----------------------------------------------------------------
4782 % open the GUI 'series'
4783 %----------------------------------------------------------------
4784 function MenuSeries_Callback(hObject, eventdata, handles)
4785 
4786 [param.FileName]=read_file_boxes(handles);
4787 if isequal(get(handles.SubField,'Value'),1)
4788     FileName_1=read_file_boxes_1(handles);%
4789     if ~isequal(FileName_1,param.FileName)
4790         param.FileName_1=FileName_1;
4791     end
4792 end
4793 param.NomType=get(handles.FileIndex,'UserData');
4794 param.NomType_1=get(handles.FileIndex_1,'UserData');
4795 param.comp_input=get(handles.fix_pair,'Value');
4796 huvmat=get(handles.MenuSeries,'parent');
4797 UvData=get(huvmat,'UserData');
4798 if isfield(UvData,'Time')
4799     param.Time=UvData.XmlData.Time;
4800 end
4801 if isequal(get(handles.scan_i,'Value'),1)
4802     param.incr_i=str2num(get(handles.increment_scan,'String'));
4803 elseif isequal(get(handles.scan_j,'Value'),1)
4804     param.incr_j=str2num(get(handles.increment_scan,'String'));
4805 end
4806 param.list_fields=get(handles.Fields,'String');% list menu fields
4807 param.list_fields(1)=[]; %suppress  'image' option
4808 param.index_fields=get(handles.Fields,'Value');% selected string index
4809 if param.index_fields>1
4810     param.index_fields=param.index_fields-1;
4811 end
4812 param.list_fields_1=get(handles.Fields_1,'String');% list menu fields
4813 param.list_fields_1(1)=[]; %suppress  'image' option
4814 param.index_fields_1=get(handles.Fields_1,'Value')-1;% selected string index
4815 if param.index_fields_1>1
4816     param.index_fields_1=param.index_fields_1-1;
4817 end
4818 param.civ1=get(handles.civ1,'Value');
4819 param.civ2=get(handles.civ2,'Value');
4820 param.interp1=get(handles.interp1,'Value');
4821 param.interp2=get(handles.interp2,'Value');
4822 param.filter1=get(handles.filter1,'Value');
4823 param.filter2=get(handles.filter2,'Value');
4824 param.menu_coord_str=get(handles.menu_coord,'String');
4825 param.menu_coord_val=get(handles.menu_coord,'Value');
4826 
4827 series(param); %run the series interface
4828 
4829 % ------------------------------------------------------------------
4830 % -- open the GUI civ.fig for civx (PIV)
4831 % ------------------------------------------------------------------
4832 function MenuPIV_Callback(hObject, eventdata, handles)
4833  
4834 [FileName,RootPath,filebase,FileIndices,ext,SubDir]=read_file_boxes(handles);
4835 [P,F,str1,str2,str_a,str_b]=name2display(FileName);
4836 num1=stra2num(str1);
4837 num2=stra2num(str2);
4838 num_a=stra2num(str_a);
4839 num_b=stra2num(str_b);
4840 NomType=get(handles.FileIndex,'UserData');
4841 ind_opening=1; % default (images): will advice civ1 option by default in the civ interface
4842 if isequal(ext,'.nc') ||  isequal(ext,'.cdf')% netcdf files
4843     ind_opening=2;% propose 'fix' as the default option
4844 % +read the current netcdf rootfile
4845     Data=nc2struct(FileName,[]);
4846     if isfield(Data,'fix') & isequal(Data.fix,1)
4847         ind_opening=3;
4848     end
4849     if isfield(Data,'patch') & isequal(Data.patch,1)
4850         ind_opening=4;
4851     end
4852     if isfield(Data,'civ2') & isequal(Data.civ2,1)
4853         ind_opening=5;
4854     end
4855     if isfield(Data,'fix2') & isequal(Data.fix2,1)
4856         ind_opening=6;
4857     end
4858 end      
4859 varargin{1}=filebase;
4860 varargin{2}=NomType;
4861 varargin{3}=num1;
4862 varargin{4}=num2;
4863 varargin{5}=num_a;
4864 varargin{6}=num_b;
4865 varargin{7}=SubDir;
4866 varargin{8}=ind_opening;% A REVOIR +TRANSMETTRE IMADOC INFO
4867 varargin{11}=ext;
4868 civ(varargin);% interface de civ(not in the uvmat file)
4869 
4870 % ------------------------------------------------------------------
4871 function MenuTools_Callback(hObject, eventdata, handles)
4872 
4873 % ------------------------------------------------------------------
4874 function MenuEdit_Callback(hObject, eventdata, handles)
4875 
4876 %--------------------------------------------------------------------------
4877 function enable_transform(handles,state)
4878 set(handles.menu_coord,'Visible',state)
4879 set(handles.TRANSFORM_txt,'Visible',state)    
4880 set(handles.menu_coord,'Visible',state)  
4881 set(handles.path_transform,'Visible',state)
4882 set(handles.pxcmx_txt,'Visible',state)
4883 set(handles.pxcmy_txt,'Visible',state)
4884 set(handles.pxcm,'Visible',state)
4885 set(handles.pycm,'Visible',state)
4886 
4887 % --------------------------------------------------------------------
4888 function MenuEditVectors_Callback(hObject, eventdata, handles)
4889 set(handles.edit_vect,'Visible','on')
4890 set(handles.edit_vect,'Value',1)
4891 edit_vect_Callback(hObject, eventdata, handles)
4892 
4893 
4894 
4895
uvmat

PURPOSE

SYNOPSIS

DESCRIPTION

CROSS-REFERENCE INFORMATION

SUBFUNCTIONS

SOURCE CODE
