source: trunk/src/uvmat.m @ 615

Last change on this file since 615 was 615, checked in by sommeria, 11 years ago

a few bugs repaired

File size: 226.6 KB
Line 
1%'uvmat': function associated with the GUI 'uvmat.fig' for images and data field visualization
2%------------------------------------------------------------------------
3% function huvmat=uvmat(input)
4%
5%OUTPUT
6% huvmat=current handles of the GUI uvmat.fig
7%%
8%
9%INPUT:
10% input: input file name (if character chain), or input image matrix to
11% visualize, or Matlab structure representing  netcdf fieldname (with fieldname
12% ListVarName....)
13%
14%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
15%  Copyright Joel Sommeria,  2008, LEGI / CNRS-UJF-INPG, joel.sommeria@legi.grenoble-inp.fr.
16%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17%     This open is part of the toolbox UVMAT.
18%
19%     UVMAT is free software; you can redistribute it and/or modify
20%     it under the terms of the GNU General Public License as published by
21%     the Free Software Foundation; either version 2 of the License, or
22%     (at your option) any later version.
23%
24%     UVMAT is distributed in the hope that it will be useful,
25%     but WITHOUT ANY WARRANTY; without even the implied warranty of
26%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
27%     GNU General Public License (open UVMAT/COPYING.txt) for more details.
28%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
29%
30% Information stored on the interface:(use 'Export/field in workspace' in
31% the menu bar of uvmat to retrieve it)
32%          .OpenParam: structure containing parameters defined when uvmat is opened
33%                       .PosColorbar: position (1x4 vector)of the colorbar (relative to the fig uvmat)
34%                       .PosGeometryCalib: size of set_object
35%                       .NbBuiltin: nbre of functions always displayed in TransformName menu
36%          .Object: cell array of structures representing the current projection objects, as produced by 'set_object.m'={[]} by default
37%          .NewSeries: =0/1 flag telling whether a new field series has been opened
38%          .FileName_1: name of the current second field (used to detect a  constant field during file scanning)
39%          .FileType: current file type, as defined by the fct  get_file_type.m)
40%          .i1_series,.i2_series,.j1_series,.j1_series: series of i1,i2,j1,j2 indices detected in the input dir,set by  the fct find_file_series
41%          .MovieObject: current movie object
42%          .TimeUnit: unit for time
43%          .XmlData: cell array of 1 or 2 structures representing the xml files associated with the input fieldname (containing timing  and geometry calibration)
44%          .Field: cell array of 1 or 2 structures representing the current  input field(s)
45%          .PlotAxes: field structure representing the current field plotted  on the main axes  (used for mouse operations)
46%          .HistoAxes: idem for histogram axes
47
48% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%   DATA FLOW  (for run0_Callback) %%%%%%%%%%%%%%%%%%%%:
49%
50%
51% 1) Input filenames are determined by MenuBrowse (first field), MenuBrowse_1
52% (second field), or by the stored file name .FileName_1, or as an input of uvmat.
53% 2) These functions call 'uvmat/display_file_name.m' which detects the file series, and fills the file index boxes
54% 3) Then 'uvmat/update_rootinfo.m' Updates information about a new field series (indices to scan, timing, calibration from an xml file)
55% 4) Then fieldname are opened and visualised by the main sub-function 'uvmat/refresh_field.m'
56% The function first reads the name of the input file(s) (one or two) from the edit boxes  of the GUI
57% It then reads the input file(s) with the function read_field.m and perform the following list of operations:
58%
59%    %%%%%%%%  structure of uvmat/refresh_field.m %%%%%%%%
60%
61%           Main input open       second input open_1       
62%                    |                   | 
63%             read_field.m            read_field.m
64%                    |                   |
65%                 Field{1}            Field{2}               
66%                    |                   |                                 
67%                    --->transform fct<---             transform (e.g. phys.m) and combine input fieldname 
68%                            |                                   
69%                        (tps_coeff_field.m)               calculate tps coefficients (for filter projection or spatial derivatives).
70%                            |
71%                       UvData.Field-------------->histogram
72%               _____________|____________
73%              |                          |                   
74%        proj_field.m               proj_field.m       project the field on the projection objects (use set_field_list.m)           
75%              |                          |
76%         UvData.PlotAxes          ViewData.PlotAxes (on view_field)
77%              |                          |
78%       plot_field.m (uvmat)       plot_field.m (view_field)      plot the projected fieldname
79%
80%
81%%%%%%%%%%%%%%    SCALARS: %%%%%%%%%%%%??%%%
82% scalars are displayed either as an image or countour plot, either as a color of
83% velocity vectors. The scalar values in the first case is represented by
84% UvData.Field.A, and by UvData.Field.C in the second case. The corresponding set of X
85% and Y coordinates are represented by UvData.Field.AX and UvData.Field.AY, and .X and
86% .Y for C (the same as velocity vectors). If A is a nxxny matrix (scalar
87% on a regtular grid), then .AX andf.AY contains only two elements, represneting the
88% coordinates of the four image corners. The scalar name is represented by
89% the strings .AName and/or .CName.
90% If the scalar exists in an input open (image or scalar stored under its
91% name in a netcdf open), it is directly read at the level of Field{1}or Field{2}.
92% Else only its name AName is recorded in Field{i}, and its field is then calculated
93%by the fuction calc_scal after the coordinate transform or after projection on an edit_object
94     
95% Properties attached to plotting figures (standard Matlab properties):
96%    'CurrentAxes'= gca or get(gcf,'CurrentAxes');
97%    'CurrentPoint'=get(gcf,'CurrentPoint'): figure coordinates of the point over which the mouse is positioned
98%    'CurrentCharacter'=get(gcf,'CurrentCharacter'): last character typed  over the figure where the mouse is positioned
99%    'WindowButtonMotionFcn': function permanently called by mouse motion over the figure
100%    'KeyPressFcn': function called by pressing a key on the key board
101%    'WindowButtonDownFcn':  function called by pressing the mouse over the  figure
102%    'WindowButtonUpFcn': function called by releasing  the mouse pressure over the  figure
103
104% Properties attached to plotting axes:
105%    'CurrentPoint'=get(gca,'CurrentPoint'); (standard Matlab) same as for the figure, but position in plot coordinates.
106%     AxeData:=get(gca,'UserData');
107%     AxeData.Drawing  = create: create a new object
108%                       = deform: modify an existing object by moving its defining create
109%                      = off: no current drawing action
110%                     = translate: translate an existing object
111%                    = calibration: move a calibration point
112%                    = CheckZoom: isolate a subregion for CheckZoom in=1 if an object is being currently drawn, 0 else (set to 0 by releasing mouse button)
113%            .CurrentOrigin: Origin of a curently drawn edit_object
114%            .CurrentLine: currently drawn menuline (A REVOIR)
115%            .CurrentObject: handle of the currently drawn edit_object
116%            .CurrentRectZoom: current rectangle used for CheckZoom
117
118% Properties attached to projection objects (create, menuline, menuplane...):
119%    'Tag'='proj_object': for all projection objects
120%    ObjectData.Type=...: style of projection object:
121%              .ProjMode
122%              .Coord: defines the position of the object
123%              .XMin,YMin....
124%              .XMax,YMax....
125%              .DX,DY,DZ
126%              .Phi, .Theta, .Psi : Euler angles
127%              .X,.Y,.U,.V.... : field data projected on the object
128%              .IndexObj: index in the list of UvData.Object
129           %during plotting
130%               .plotaxes: handles of the current axes used to plot the  result of field projection on the object
131%               .plothandle: vector of handle(s) of the object graphic represnetation in all the opened plotting axes
132% To each projection object #iobj, corresponds an axis
133% Object{iobj}.plotaxes and nbobj representation graphs  Object{iobj}.plothandles(:) (where nbobj is the
134% nbre of current objects opened in uvmat. Note that Object{iobj}.plothandles(iobj)=[] : an object is not represented in its own projection field;
135
136%------------------------------------------------------------------------
137%------------------------------------------------------------------------
138%  I - MAIN FUNCTION uvmat
139%------------------------------------------------------------------------
140%------------------------------------------------------------------------
141function varargout = uvmat(varargin)
142
143% Begin initialization code - DO NOT EDIT
144gui_Singleton = 1;
145gui_State = struct('gui_Name',          mfilename, ...
146                   'gui_Singleton',     gui_Singleton, ...
147                   'gui_OpeningFcn',    @uvmat_OpeningFcn, ...
148                   'gui_OutputFcn',     @uvmat_OutputFcn, ...
149                   'gui_LayoutFcn',     [], ...
150                   'gui_Callback',      []);
151if nargin && ischar(varargin{1})&& ~isempty(regexp(varargin{1},'_Callback','once'))
152    gui_State.gui_Callback = str2func(varargin{1});
153end
154
155if nargout
156    varargout{1:nargout} = gui_mainfcn(gui_State, varargin{:});
157else
158    gui_mainfcn(gui_State, varargin{:});
159end
160% End initialization code - DO NOT EDIT
161
162%------------------------------------------------------------------------
163% --- Executes just before the GUI uvmat is made visible.
164function uvmat_OpeningFcn(hObject, eventdata, handles, input )
165%------------------------------------------------------------------------
166
167%% Choose default command menuline output for uvmat (standard GUI)
168handles.output = hObject;
169
170%% Update handles structure (standard GUI)
171guidata(hObject, handles);
172
173%% add the path to uvmat (useful if uvmat has been opened in the working directory and a working directory change occured)
174path_uvmat=fileparts(which('uvmat'));
175
176%% set the position of the GUI, colorbar and ancillary GUIs:
177set(hObject,'Units','pixels')%
178set(0,'Units','pixels');
179ScreenSize=get(0,'ScreenSize');%size of the current screen
180Width=1050;
181Height=700;
182%adjust to screen size (reduced by a min margin)
183RescaleFactor=min((ScreenSize(3)-80)/Width,(ScreenSize(4)-80)/Height);
184if RescaleFactor>1
185    RescaleFactor=RescaleFactor/2+1/2; %reduce the rescale factor to provide an increased margin for a big screen
186end
187Width=Width*RescaleFactor;
188Height=Height*RescaleFactor;
189LeftX=80*RescaleFactor;%position of the left fig side, in pixels (put to the left side, with some margin)
190LowY=round(ScreenSize(4)/2-Height/2); % put at the middle height on the screen
191set(hObject,'Position',[LeftX LowY Width Height])
192
193%set(hObject,'Units','Normalized')
194
195%UvData.OpenParam.PosColorbar=[0.8450    0.0900    0.0190    0.3600];
196UvData.OpenParam.PosColorbar=[0.805 0.022 0.019 0.445];
197%UvData.OpenParam.PosSetObject=[-0.05 -0.03 0.3 0.7]; %position for set_object
198UvData.OpenParam.PosGeometryCalib=[0.95 -0.03 0.28 1 ];%position for geometry_calib (TO IMPROVE)
199% UvData.OpenParam.CalSize=[0.28 1];
200% UvData.PlotAxes=[];%initiate the record of plotted field
201% UvData.axes2=[];
202% UvData.axes1=[];
203AxeData.LimEditBox=1; %initialise AxeData
204set(handles.PlotAxes,'UserData',AxeData)
205
206%% set functions for the mouse and keyboard
207set(hObject,'KeyPressFcn',{'keyboard_callback',handles})%set keyboard action function
208set(hObject,'WindowButtonMotionFcn',{'mouse_motion',handles})%set mouse action functio
209set(hObject,'WindowButtonDownFcn',{'mouse_down'})%set mouse click action function
210set(hObject,'WindowButtonUpFcn',{'mouse_up',handles})
211set(hObject,'DeleteFcn',{@closefcn})%
212
213%% initialisation
214set(handles.FieldName,'Value',1)
215set(handles.FieldName,'string',{''})
216UvData.Object={[]};
217
218%% TRANSFORM menu: builtin fcts
219transform_menu={'';'sub_field';'phys';'phys_polar'};
220UvData.OpenParam.NbBuiltin=numel(transform_menu); %number of functions
221transform_path=fullfile(path_uvmat,'transform_field');
222path_list=cell(UvData.OpenParam.NbBuiltin,1);
223path_list{1}='';
224for ilist=2:UvData.OpenParam.NbBuiltin
225path_list{ilist}=transform_path; % set transform_path to the path_list
226end
227
228%% load the list of previously browsed files in menus Open, Open_1 and TransformName
229 dir_perso=prefdir; % path to the directory .matlab containing the personal data of the current user
230 profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmat_perso.mat' in .matlab
231 if exist(profil_perso,'file')
232     h=load (profil_perso);
233     if isfield(h,'MenuFile')% load the menu of previously opened files
234         for ifile=1:min(length(h.MenuFile),5)
235             set(handles.(['MenuFile_' num2str(ifile)]),'Label',h.MenuFile{ifile});
236             set(handles.(['MenuFile_' num2str(ifile) '_1']),'Label',h.MenuFile{ifile});
237         end
238     end
239     if isfield(h,'RootPath')
240         set(handles.RootPath,'UserData',h.RootPath); %store the previous campaign in the UserData of RootPath
241     end
242     if isfield(h,'transform_fct') && iscell(h.transform_fct) % load the menu of transform fct set by user
243         for ilist=1:length(h.transform_fct);
244             if exist(h.transform_fct{ilist},'file')
245                 [path,file]=fileparts(h.transform_fct{ilist});
246                 transform_menu=[transform_menu; {file}];
247                 path_list=[path_list; {path}];
248             end
249         end
250     end
251 end
252transform_menu=[transform_menu;{'more...'}];%append the option more.. to the menu
253set(handles.TransformName,'String',transform_menu)% display the menu of transform fcts
254set(handles.TransformName,'UserData',path_list)% store the corresponding list of path in UserData of uicontrol transform_fct
255set(handles.TransformPath,'String','')
256set(handles.TransformPath,'UserData',[])
257
258%% case of an input argument for uvmat
259testinputfield=0;
260inputfile=[];
261Field=[];
262if exist('input','var')
263    if ishandle(handles.UVMAT_title)
264        delete(handles.UVMAT_title)
265    end   
266    if isstruct(input)
267        if isfield(input,'InputFile')
268            inputfile=input.InputFile;
269        end
270        if isfield(input,'TimeIndex')
271            set(handles.i1,num2str(input.TimeIndex))
272        end
273        if isfield(input,'FieldsString')
274            UvData.FieldsString=input.FieldsString;
275        end
276    elseif ischar(input)% file name introduced as input
277           inputfile=input;
278    elseif isnumeric(input)%simple matrix introduced as input
279        sizinput=size(input);
280        if sizinput(1)<=1 || sizinput(2)<=1
281            msgbox_uvmat('ERROR','bad input for uvmat: file name, structure or numerical matrix accepted')
282            return
283        end
284        UvData.Field.ListVarName={'A','coord_y','coord_x'};
285        UvData.Field.VarDimName={{'coord_y','coord_x'},'cord_y','coord_x'};
286        UvData.Field.A=input;
287        UvData.Field.coord_x=[0.5 size(input,2)-0.5];
288        UvData.Field.coord_y=[size(input,1)-0.5 0.5];
289        testinputfield=1;
290    end
291else
292    %% check the path and date of modification of all functions in uvmat
293    path_to_uvmat=which ('uvmat');% check the path detected for source file uvmat
294    [infomsg,date_str,svn_info]=check_files;%check the path of the functions called by uvmat.m   
295    date_str=['last modification: ' date_str];
296    if ishandle(handles.UVMAT_title)
297        set(handles.UVMAT_title,'String',...
298            [{'Copyright  LEGI UMR 5519 /CNRS-UJF-Grenoble INP, 2010'};...
299            {'GNU General Public License'};...
300            {path_to_uvmat};...
301            {date_str};...
302            infomsg]);
303    end
304end
305set(handles.uvmat,'UserData',UvData)
306if ~isempty(inputfile)
307    %%%%% display the input field %%%%%%%
308    display_file_name(handles,inputfile)
309    %%%%%%%
310end
311
312set_vec_col_bar(handles) %update the display of color code for vectors
313
314%------------------------------------------------------------------------
315% --- Outputs from this function are returned to the command menuline.
316function varargout = uvmat_OutputFcn(hObject, eventdata, handles)
317varargout{1} = handles.output;% the only output argument is the handle to the GUI figure
318
319%------------------------------------------------------------------------
320% --- executed when closing uvmat: delete or desactivate the associated figures if exist
321function closefcn(gcbo,eventdata)
322%------------------------------------------------------------------------
323hh=findobj(allchild(0),'tag','view_field');
324if ~isempty(hh)
325    delete(hh)
326end
327hh=findobj(allchild(0),'tag','geometry_calib');
328if ~isempty(hh)
329    delete(hh)
330end
331hh=findobj(allchild(0),'tag','set_object');
332if ~isempty(hh)
333    hhh=findobj(hh,'tag','PLOT');
334    set(hhh,'enable','off')
335end
336
337%------------------------------------------------------------------------
338%------------------------------------------------------------------------
339%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
340% automatically sets the global properties when the rootfile name is introduced
341% then activate the view-field action if selected
342% it is activated either by clicking on the RootPath window or by the
343% browser
344%------------------------------------------------------------------------
345%------------------------------------------------------------------------
346% --- Executes on the menu Open/Browse...
347% search the files, recognize their type according to their name and fill the rootfile input windows
348function MenuBrowse_Callback(hObject, eventdata, handles)
349[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
350oldfile=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
351if isempty(oldfile) %loads the previously stored file name and set it as default in the file_input box
352    oldfile=get(handles.RootPath,'UserData');
353end
354fileinput=uigetfile_uvmat('select an input file:',oldfile);
355
356%% display the selected field and related information
357if ~isempty(fileinput)
358    display_file_name(handles,fileinput)
359end
360
361% -----------------------------------------------------------------------
362% --- Executes on the menu Open/Browse campaign...
363% search the file inside a campaign, using the GUI view_data
364function MenuBrowseCampaign_Callback(hObject, eventdata, handles)
365% -----------------------------------------------------------------------
366RootPath=get(handles.RootPath,'String');
367if isempty(RootPath)
368    RootPath=get(handles.RootPath,'UserData');%use Rootpath recored from the personal file at uvmat opening
369end
370CampaignPath=fileparts(fileparts(RootPath));
371DirFull = uigetdir(CampaignPath,'Select a Campaign dir, then press OK');
372if ~ischar(DirFull)|| ~exist(DirFull,'dir')
373    return
374end
375OutPut=browse_data(DirFull);% open the GUI browse_data to get select a campaign dir, experiment and device
376if ~isfield(OutPut,'Campaign')
377    return
378end
379DirName=fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.Device{1});
380hdir=dir(DirName); %list files and dirs
381for ilist=1:numel(hdir)
382    if ~isequal(hdir(ilist).isdir,1)%look for files, not dir
383        FileName=hdir(ilist).name;
384        FileType=get_file_type(fullfile(DirName,FileName));
385        switch FileType
386            case {'image','multimage','civx','civdata','netcdf'}
387            break
388        end
389    end
390end
391
392%% display the selected field and related information
393display_file_name( handles,fullfile(DirName,FileName))
394
395% -----------------------------------------------------------------------
396% --- Open again the file whose name has been recorded in MenuFile_1
397function MenuFile_1_Callback(hObject, eventdata, handles)
398%------------------------------------------------------------------------
399fileinput=get(handles.MenuFile_1,'Label');
400display_file_name( handles,fileinput)
401
402% -----------------------------------------------------------------------
403% --- Open again the file whose name has been recorded in MenuFile_2
404function MenuFile_2_Callback(hObject, eventdata, handles)
405%------------------------------------------------------------------------
406fileinput=get(handles.MenuFile_2,'Label');
407display_file_name(handles,fileinput)
408
409% -----------------------------------------------------------------------
410% --- Open again the file whose name has been recorded in MenuFile_3
411function MenuFile_3_Callback(hObject, eventdata, handles)
412%------------------------------------------------------------------------
413fileinput=get(handles.MenuFile_3,'Label');
414display_file_name(handles,fileinput)
415
416% -----------------------------------------------------------------------
417% --- Open again the file whose name has been recorded in MenuFile_4
418function MenuFile_4_Callback(hObject, eventdata, handles)
419%------------------------------------------------------------------------
420fileinput=get(handles.MenuFile_4,'Label');
421display_file_name(handles,fileinput)
422
423% -----------------------------------------------------------------------
424% --- Open again the file whose name has been recorded in MenuFile_5
425function MenuFile_5_Callback(hObject, eventdata, handles)
426%------------------------------------------------------------------------
427fileinput=get(handles.MenuFile_5,'Label');
428display_file_name(handles,fileinput)
429
430%------------------------------------------------------------------------
431% --- Executes on the menu Open/Browse_1 for the second input field,
432%     search the files, recognize their type according to their name and fill the rootfile input windows
433function MenuBrowse_1_Callback(hObject, eventdata, handles)
434%------------------------------------------------------------------------
435RootPath=get(handles.RootPath,'String');
436SubDir=get(handles.SubDir,'String');
437fileinput_1=uigetfile_uvmat('select a second input file:',fullfile(RootPath,SubDir));
438if ~isempty(fileinput_1)
439    % [FileName, PathName] = uigetfile({'*.*','All Files(*.*)'},'Pick a file',RootPath);
440    % if ~ischar(FileName),return,end %abandon if the browser is cancelled
441    % fileinput_1=[PathName FileName];%complete file name
442   
443    % refresh the current displayed field
444    set(handles.SubField,'Value',1)
445    display_file_name(handles,fileinput_1,2)
446   
447    %update list of recent files in the menubar
448    MenuFile_1=fileinput_1;
449    MenuFile_2=get(handles.MenuFile_1,'Label');
450    MenuFile_3=get(handles.MenuFile_2,'Label');
451    MenuFile_4=get(handles.MenuFile_3,'Label');
452    MenuFile_5=get(handles.MenuFile_4,'Label');
453    set(handles.MenuFile_1,'Label',MenuFile_1)
454    set(handles.MenuFile_2,'Label',MenuFile_2)
455    set(handles.MenuFile_3,'Label',MenuFile_3)
456    set(handles.MenuFile_4,'Label',MenuFile_4)
457    set(handles.MenuFile_5,'Label',MenuFile_5)
458    set(handles.MenuFile_1_1,'Label',MenuFile_1)
459    set(handles.MenuFile_2_1,'Label',MenuFile_2)
460    set(handles.MenuFile_3_1,'Label',MenuFile_3)
461    set(handles.MenuFile_4_1,'Label',MenuFile_4)
462    set(handles.MenuFile_5_1,'Label',MenuFile_5)
463end
464
465% --------------------------------------------------------------------
466function MenuBrowseCampaign_1_Callback(hObject, eventdata, handles)
467% -----------------------------------------------------------------------
468CampaignPath=fileparts(fileparts(get(handles.RootPath,'String')));
469DirFull = uigetdir(CampaignPath,'Select a Campaign dir, then press OK');
470if ~ischar(DirFull)|| ~exist(DirFull,'dir')
471    return
472end
473OutPut=browse_data(DirFull);% open the GUI browse_data to get select a campaign dir, experiment and device
474if ~isfield(OutPut,'Campaign')
475    return
476end
477DirName=fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.Device{1});
478hdir=dir(DirName); %list files and dirs
479for ilist=1:numel(hdir)
480    if ~isequal(hdir(ilist).isdir,1)%look for files, not dir
481        FileName=hdir(ilist).name;
482        FileType=get_file_type(fullfile(DirName,FileName));
483        switch FileType
484            case {'image','multimage','civx','civdata','netcdf'}
485            break
486        end
487    end
488end
489
490%% display the selected field and related information
491set(handles.SubField,'Value',1)
492display_file_name( handles,fullfile(DirName,FileName),2)
493
494% -----------------------------------------------------------------------
495% --- Open again as second field the file whose name has been recorded in MenuFile_1
496function MenuFile_1_1_Callback(hObject, eventdata, handles)
497% -----------------------------------------------------------------------
498fileinput_1=get(handles.MenuFile_1_1,'Label');
499set(handles.SubField,'Value',1)
500display_file_name(handles,fileinput_1,2)
501
502% -----------------------------------------------------------------------
503% --- Open again as second field the file whose name has been recorded in MenuFile_2
504function MenuFile_2_1_Callback(hObject, eventdata, handles)
505% -----------------------------------------------------------------------
506fileinput_1=get(handles.MenuFile_2_1,'Label');
507set(handles.SubField,'Value',1)
508display_file_name(handles,fileinput_1,2)
509
510% -----------------------------------------------------------------------
511% --- Open again as second field the file whose name has been recorded in MenuFile_3
512function MenuFile_3_1_Callback(hObject, eventdata, handles)
513% -----------------------------------------------------------------------
514fileinput_1=get(handles.MenuFile_3_1,'Label');
515set(handles.SubField,'Value',1)
516display_file_name(handles,fileinput_1,2)
517
518% -----------------------------------------------------------------------
519% --- Open again as second field the file whose name has been recorded in MenuFile_4
520function MenuFile_4_1_Callback(hObject, eventdata, handles)
521% -----------------------------------------------------------------------
522fileinput_1=get(handles.MenuFile_4_1,'Label');
523set(handles.SubField,'Value',1)
524display_file_name(handles,fileinput_1,2)
525
526% -----------------------------------------------------------------------
527% --- Open again as second field the file whose name has been recorded in MenuFile_5
528function MenuFile_5_1_Callback(hObject, eventdata, handles)
529% -----------------------------------------------------------------------
530fileinput_1=get(handles.MenuFile_5_1,'Label');
531set(handles.SubField,'Value',1)
532display_file_name(handles,fileinput_1,2)
533
534%------------------------------------------------------------------------
535% --- Called by action in RootPath edit box
536function RootPath_Callback(hObject,eventdata,handles)
537%------------------------------------------------------------------------
538% read the current input file name:
539[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
540if ~exist(fullfile(RootPath,SubDir),'dir')
541    msgbox_uvmat('ERROR',['directory ' fullfile(RootPath,SubDir) ' does not exist'])
542    return
543end
544% detect the file type, get the movie object if relevant, and look for the corresponding file series:
545[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,FileInfo,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
546% initiate the input file series and refresh the current field view:
547update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,1);
548
549%-----------------------------------------------------------------------
550% --- Called by action in RootPath_1 edit box
551function RootPath_1_Callback(hObject,eventdata,handles)
552% -----------------------------------------------------------------------
553% update_rootinfo_1(hObject,eventdata,handles)
554[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
555if ~exist(fullfile(RootPath,SubDir),'dir')
556    msgbox_uvmat('ERROR',['directory ' fullfile(RootPath,SubDir) ' does not exist'])
557    return
558end
559% detect the file type, get the movie object if relevant, and look for the corresponding file series:
560[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
561% initiate the input file series and refresh the current field view:
562update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,2);
563
564%------------------------------------------------------------------------
565% --- Called by action in RootFile edit box
566function SubDir_Callback(hObject, eventdata, handles)
567%------------------------------------------------------------------------
568%refresh the menu of input fieldname
569Fields_Callback(hObject, eventdata, handles);
570% refresh the current field view
571run0_Callback(hObject, eventdata, handles);
572
573%------------------------------------------------------------------------
574% --- Called by action in RootFile edit box
575function RootFile_Callback(hObject, eventdata, handles)
576%------------------------------------------------------------------------
577RootPath_Callback(hObject,eventdata,handles)
578
579%-----------------------------------------------------------------------
580% --- Called by action in RootFile_1 edit box
581function RootFile_1_Callback(hObject, eventdata, handles)
582% -----------------------------------------------------------------------
583RootPath_1_Callback(hObject,eventdata,handles)
584
585%------------------------------------------------------------------------
586% --- Called by action in FileIndex edit box
587function FileIndex_Callback(hObject, eventdata, handles)
588%------------------------------------------------------------------------
589[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
590set(handles.i1,'String',num2str(i1));
591set(handles.i2,'String',num2str(i2));
592set(handles.j1,'String',num2str(j1));
593set(handles.j2,'String',num2str(j2));
594
595% refresh the current field view
596run0_Callback(hObject, eventdata, handles)
597
598%------------------------------------------------------------------------
599% --- Called by action in FileIndex_1 edit box
600function FileIndex_1_Callback(hObject, eventdata, handles)
601%------------------------------------------------------------------------
602run0_Callback(hObject, eventdata, handles)
603
604%------------------------------------------------------------------------
605% --- Called by action in NomType edit box
606function NomType_Callback(hObject, eventdata, handles)
607%------------------------------------------------------------------------
608i1=str2num(get(handles.i1,'String'));
609i2=str2num(get(handles.i2,'String'));
610j1=str2num(get(handles.j1,'String'));
611j2=str2num(get(handles.j2,'String'));
612FileIndex=fullfile_uvmat('','','','',get(handles.NomType,'String'),i1,i2,j1,j2);
613set(handles.FileIndex,'String',FileIndex)
614% refresh the current settings and refresh the field view
615RootPath_Callback(hObject,eventdata,handles)
616
617%------------------------------------------------------------------------
618% --- Called by action in NomType edit box
619function NomType_1_Callback(hObject, eventdata, handles)
620%------------------------------------------------------------------------
621i1=str2num(get(handles.i1,'String'));
622i2=str2num(get(handles.i2,'String'));
623j1=str2num(get(handles.j1,'String'));
624j2=str2num(get(handles.j2,'String'));
625FileIndex=fullfile_uvmat('','','','',get(handles.NomType_1,'String'),i1,i2,j1,j2);
626set(handles.FileIndex_1,'String',FileIndex)
627% refresh the current settings and refresh the field view
628RootPath_1_Callback(hObject,eventdata,handles)
629
630%------------------------------------------------------------------------
631% --- Fills the edit boxes RootPath, RootFile,NomType...from an input file name 'fileinput'
632function display_file_name(handles,fileinput,index)
633%------------------------------------------------------------------------
634%% look for the input file existence
635if ~exist(fileinput,'file')
636    msgbox_uvmat('ERROR',['input file ' fileinput  ' does not exist'])
637    return
638end
639
640%% set the mouse pointer to 'watch'
641set(handles.uvmat,'Pointer','watch')
642set(handles.RootPath,'BackgroundColor',[1 1 0])
643drawnow
644
645%% define the relevant handles for the first field series (index=1) or the second file series (index=2)
646if ~exist('index','var')
647    index=1;
648end
649if index==1
650    handles_RootPath=handles.RootPath;
651    handles_SubDir=handles.SubDir;
652    handles_RootFile=handles.RootFile;
653    handles_FileIndex=handles.FileIndex;
654    handles_NomType=handles.NomType;
655    handles_FileExt=handles.FileExt;
656elseif index==2
657    handles_RootPath=handles.RootPath_1;
658    handles_SubDir=handles.SubDir_1;
659    handles_RootFile=handles.RootFile_1;
660    handles_FileIndex=handles.FileIndex_1;
661    handles_NomType=handles.NomType_1;
662    handles_FileExt=handles.FileExt_1;
663    set(handles.RootPath_1,'Visible','on')
664    set(handles.RootFile_1,'Visible','on')
665    set(handles.SubDir_1,'Visible','on');
666    set(handles.FileIndex_1,'Visible','on');
667    set(handles.FileExt_1,'Visible','on');
668    set(handles.NomType_1,'Visible','on');
669end
670
671%% detect root name, nomenclature and indices in the input file name:
672[FilePath,FileName,FileExt]=fileparts(fileinput);
673% detect the file type, get the movie object if relevant, and look for the corresponding file series:
674% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
675[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,FileInfo,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
676
677%% open the file or fill the GUI uvmat according to the detected file type
678switch FileType
679    case ''
680        msgbox_uvmat('ERROR','invalid input file type')
681    case 'txt'
682        edit(fileinput)
683    case 'figure'                           %display matlab figure
684        hfig=open(fileinput);
685        set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
686        set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
687        set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
688    case 'xml'                % edit xml files
689        t=xmltree(fileinput);
690        % the xml file marks a project or project link, open datatree_browser
691        if strcmp(get(t,1,'name'),'Project')&& exist(regexprep(fileinput,'.xml$',''),'dir')
692            datatree_browser(fileinput)
693        else % other xml file, open the xml editor
694            editxml(fileinput);
695        end
696    case 'xls'% Excel file opended by editxml
697        editxml(fileinput);
698    otherwise
699        set(handles_RootPath,'String',RootPath);
700        rootname=fullfile(RootPath,SubDir,RootFile);
701        set(handles_SubDir,'String',['/' SubDir]);
702        set(handles_RootFile,'String',['/' RootFile]); %display the separator
703        indices=fileinput(length(rootname)+1:end);
704        indices(end-length(FileExt)+1:end)=[]; %remove extension
705        set(handles_FileIndex,'String',indices);
706        set(handles_NomType,'String',NomType);
707        set(handles_FileExt,'String',FileExt);
708        if index==1
709            % fill file index counters if the first file series is opened
710            set(handles.i1,'String',num2str(i1));
711            set(handles.i2,'String',num2str(i2));
712            set(handles.j1,'String',num2stra(j1,NomType));
713            set(handles.j2,'String',num2stra(j2,NomType));
714        else %read the current field index to synchronise with the first series
715            i1_s=str2num(get(handles.i1,'String'));
716            i2_0=str2num(get(handles.i2,'String'));
717            if ~isempty(i2_0)
718                i2_s=i2_0;
719            else
720               i2_s=i2;
721            end
722            j1_0=stra2num(get(handles.j1,'String'));
723            if ~isempty(j1_0)
724                j1_s=j1_0;
725            else
726                j1_s=j1;
727            end
728            j2_0=stra2num(get(handles.j2,'String'));
729            if ~isempty(j2_0)
730                j2_s=j2_0;
731            else
732                j2_s=j2;
733            end
734        end
735       
736        % synchronise indices of the second  input file if it exists
737        if get(handles.SubField,'Value')==1% if the subfield button is activated, update the field numbers
738            Input=read_GUI(handles.InputFile);
739            if ~isfield(Input,'RootPath_1')||strcmp(Input.RootPath_1,'"')
740                Input.RootPath_1=Input.RootPath;
741            end
742            if ~isfield(Input,'SubDir_1')||strcmp(Input.SubDir_1,'"')
743                Input.SubDir_1=Input.SubDir;
744            end
745            if ~isfield(Input,'RootFile_1')||strcmp(Input.RootFile_1,'"')
746                Input.RootFile_1=Input.RootFile;
747            end
748            if ~isfield(Input,'FileExt_1')||strcmp(Input.FileExt_1,'"')
749                Input.FileExt_1=Input.FileExt;
750            end
751            if ~isfield(Input,'NomType_1')||strcmp(Input.NomType_1,'"')
752                Input.NomType_1=Input.NomType;
753            end
754            %updtate the indices of the second field series to correspond to the newly opened one
755            FileName_1=fullfile_uvmat(Input.RootPath_1,Input.SubDir_1,Input.RootFile_1,Input.FileExt_1,Input.NomType_1,i1_s,i2_s,j1_s,j2_s);
756            if exist(FileName_1,'file')
757                FileIndex_1=fullfile_uvmat('','','','',Input.NomType_1,i1_s,i2_s,j1_s,j2_s);
758            else
759                FileIndex_1=fullfile_uvmat('','','','',Input.NomType_1,i1,i2,j1,j2);
760                msgbox_uvmat('WARNING','unable to synchronise the indices of the two series')
761            end
762            set(handles.FileIndex_1,'String',FileIndex_1)
763        end
764       
765        %enable other menus
766        set(handles.MenuOpen_1,'Enable','on')
767        set(handles.MenuFile_1_1,'Enable','on')
768        set(handles.MenuFile_2_1,'Enable','on')
769        set(handles.MenuFile_3_1,'Enable','on')
770        set(handles.MenuFile_4_1,'Enable','on')
771        set(handles.MenuFile_5_1,'Enable','on')
772        set(handles.MenuExport,'Enable','on')
773        set(handles.MenuExportFigure,'Enable','on')
774        set(handles.MenuExportMovie,'Enable','on')
775        set(handles.MenuTools,'Enable','on')
776
777        % initiate input file series and refresh the current field view:     
778        update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,index);
779
780end
781
782%% update list of recent files in the menubar and save it for future opening
783MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
784    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
785str_find=strcmp(fileinput,MenuFile);
786if isempty(find(str_find,1))
787    MenuFile=[{fileinput};MenuFile];%insert the current file if not already in the list
788end
789for ifile=1:min(length(MenuFile),5)
790    set(handles.(['MenuFile_' num2str(ifile)]),'Label',MenuFile{ifile});
791    set(handles.(['MenuFile_' num2str(ifile) '_1']),'Label',MenuFile{ifile});
792end
793dir_perso=prefdir;
794profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
795if exist(profil_perso,'file')
796    save (profil_perso,'MenuFile','RootPath','-append'); %store the file names for future opening of uvmat
797else
798    save (profil_perso,'MenuFile','RootPath','-V6'); %store the file names for future opening of uvmat
799end
800
801%% set back the mouse pointer to arrow
802set(handles.uvmat,'Pointer','arrow')
803
804
805%------------------------------------------------------------------------
806% --- Update information about a new field series (indices to scan, timing,
807%     calibration from an xml file, then refresh current plots
808
809function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,VideoObject,index)
810%------------------------------------------------------------------------
811%% define the relevant handles depending on the index (1=first file series, 2= second file series)
812if ~exist('index','var')
813    index=1;
814end
815if index==1
816    handles_RootPath=handles.RootPath;
817    handles_Fields=handles.FieldName;
818elseif index==2
819    handles_RootPath=handles.RootPath_1;
820    handles_Fields=handles.FieldName_1;
821end
822
823set(handles_RootPath,'BackgroundColor',[1 1 0])
824drawnow
825set(handles.FieldName,'UserData',[])% reinialize data from uvmat opening
826UvData=get(handles.uvmat,'UserData');%huvmat=handles of the uvmat interface
827UvData.NewSeries=1; %flag for run0: begin a new series
828UvData.FileName_1='';% name of the current second field (used to detect a  constant field during file scanning)
829UvData.FileType{index}=FileType;
830UvData.i1_series{index}=i1_series;
831UvData.i2_series{index}=i2_series;
832UvData.j1_series{index}=j1_series;
833UvData.j2_series{index}=j2_series;
834set(handles.FixVelType,'Value',0); %desactivate fixed veltype
835if index==1
836    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
837else
838    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
839end
840FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
841FileBase=fullfile(RootPath,RootFile);
842if ~exist(FileName,'file')
843   msgbox_uvmat('ERROR',['input file ' FileName ' not found']);
844    return
845end
846
847%% read timing and total frame number from the current file (movie files) !! may be overrid by xml file
848XmlData.Time=[];%default
849XmlData.GeometryCalib=[];%default
850TimeUnit='';%default
851Time=[];
852imainfo=[];
853ColorType='falsecolor'; %default
854UvData.MovieObject{index}=VideoObject;
855if ~isempty(VideoObject)
856    imainfo=get(VideoObject);
857    TimeUnit='s';
858    if isempty(j1_series); %frame index along i
859        Time=zeros(imainfo.NumberOfFrames+1,2);
860        Time(:,2)=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)';
861    else
862        Time=[0;ones(size(i1_series,3)-1,1)]*(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate);
863    end
864    set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FrameRate) 'ms']);%display the elementary time interval in millisec
865    ColorType='truecolor';
866elseif ~isempty(FileExt(2:end))&&(~isempty(imformats(FileExt(2:end))) || isequal(FileExt,'.vol'))%&& isequal(NomType,'*')% multi-frame image
867%     testima=1;
868    if ~isequal(SubDir,'')
869        imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]);
870    else
871        imainfo=imfinfo([FileBase FileIndices FileExt]);
872    end
873    ColorType=imainfo.ColorType;%='truecolor' for color images
874end
875if isfield(imainfo,'Width') && isfield(imainfo,'Height')
876    if length(imainfo)>1
877        set(handles.num_Npx,'String',num2str(imainfo(1).Width));%fills nbre of pixels x box
878        set(handles.num_Npy,'String',num2str(imainfo(1).Height));%fills nbre of pixels x box
879    else
880        set(handles.num_Npx,'String',num2str(imainfo.Width));%fills nbre of pixels x box
881        set(handles.num_Npy,'String',num2str(imainfo.Height));%fills nbre of pixels x box
882    end
883else
884    set(handles.num_Npx,'String','');%fills nbre of pixels x box
885    set(handles.num_Npy,'String','');%fills nbre of pixels x box
886end
887set(handles.CheckBW,'Value',strcmp(ColorType,'grayscale'))% select handles.CheckBW if grayscale image
888
889%% read parameters (time, geometric calibration..) from a documentation file (.xml advised)
890XmlFileName=find_imadoc(RootPath,SubDir,RootFile,FileExt);
891[tild,tild,DocExt]=fileparts(XmlFileName);
892warntext='';%default warning message
893NbSlice=1;%default
894ImaDoc_str='';
895set(handles.RootPath,'BackgroundColor',[1 1 1])
896if ~isempty(XmlFileName)
897    set(handles.view_xml,'Visible','on')
898    set(handles.view_xml,'BackgroundColor',[1 1 0])% paint  to yellow color to indicate reading of the xml file
899    set(handles.view_xml,'String','view .xml')
900    drawnow
901    [XmlDataRead,warntext]=imadoc2struct(XmlFileName);
902    if ~isempty(warntext)
903        msgbox_uvmat('WARNING',warntext)
904    end
905    if ~isempty(XmlDataRead)
906        ImaDoc_str=['view ' DocExt];   
907        XmlData=XmlDataRead;
908        if isfield(XmlData,'TimeUnit')
909            if isfield(XmlData,'TimeUnit')&& ~isempty(XmlData.TimeUnit)
910                TimeUnit=XmlData.TimeUnit;
911            end
912        end
913        set(handles.view_xml,'BackgroundColor',[1 1 1])% paint black to white
914        drawnow
915        if isfield(XmlData, 'GeometryCalib') && ~isempty(XmlData.GeometryCalib)
916            if isfield(XmlData.GeometryCalib,'VolumeScan') && isequal(XmlData.GeometryCalib.VolumeScan,'y')
917                set (handles.slices,'String','volume')
918            end
919            hgeometry_calib=findobj('tag','geometry_calib');
920            if ~isempty(hgeometry_calib)
921                GUserData=get(hgeometry_calib,'UserData');
922                if ~(isfield(GUserData,'XmlInputFile') && strcmp(GUserData.XmlInputFile,XmlFileName))
923                    answer=msgbox_uvmat('INPUT_Y-N','replace the display of geometry_calib with the new input data?');
924                    if strcmp(answer,'Yes')
925                        geometry_calib(XmlFileName);%diplay the new calibration points and parameters in geometry_calib
926                    end
927                end
928            end
929        end
930    end
931end
932if ~(isfield(XmlData,'Time')&& ~isempty(XmlData.Time))
933    XmlData.Time=Time; %time set by video
934end
935if isempty(ImaDoc_str)
936    set(handles.view_xml,'Visible','off')
937else
938    set(handles.view_xml,'String',ImaDoc_str)
939end
940
941%% store last index in handles.lat_i and .last_j
942nbfield=max(max(max(i2_series)));
943if isempty(nbfield)
944    nbfield=max(max(max(i1_series)));
945end
946nbfield_j=max(max(max(j2_series)));
947if isempty(nbfield_j)
948    nbfield_j=max(max(max(j1_series)));
949end
950if ~isempty(XmlData.Time)
951    %transform .Time to a column vector if it is a line vector the nomenclature uses a single index
952    if isequal(size(XmlData.Time,1),1)
953        %NomType=get(handles.NomType,'String');
954        XmlData.Time=(XmlData.Time)';
955    end
956end
957last_i_cell=get(handles.last_i,'String');
958if isempty(nbfield)
959    last_i_cell{index}='';
960else
961    last_i_cell{index}=num2str(nbfield);
962end
963set(handles.last_i,'String',last_i_cell)
964last_j_cell=get(handles.last_j,'String');
965if isempty(nbfield_j)
966     last_j_cell{index}='';
967else
968     last_j_cell{index}=num2str(nbfield_j);
969end
970set(handles.last_j,'String',last_j_cell);
971
972%% store geometric calibration in UvData
973if isfield(XmlData,'GeometryCalib')
974    GeometryCalib=XmlData.GeometryCalib;
975    if isempty(GeometryCalib)
976        set(handles.pxcm,'String','')
977        set(handles.pycm,'String','')
978        set(handles.TransformName,'Value',1); %  no transform by default
979    else
980        if (isfield(GeometryCalib,'R')&& ~isequal(GeometryCalib.R(2,1),0) && ~isequal(GeometryCalib.R(1,2),0)) ||...
981            (isfield(GeometryCalib,'kappa1')&& ~isequal(GeometryCalib.kappa1,0))
982            set(handles.pxcm,'String','var')
983            set(handles.pycm,'String','var')
984        elseif isfield(GeometryCalib,'fx_fy')
985            pixcmx=GeometryCalib.fx_fy(1);%*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx);
986            pixcmy=GeometryCalib.fx_fy(2);%*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy);
987            set(handles.pxcm,'String',num2str(pixcmx))
988            set(handles.pycm,'String',num2str(pixcmy))
989        end
990        if ~get(handles.CheckFixLimits,'Value')
991            set(handles.TransformName,'Value',3); % phys transform by default if fixedLimits is off
992        end
993        if isfield(GeometryCalib,'SliceCoord')           
994           siz=size(GeometryCalib.SliceCoord);
995           if siz(1)>1
996               NbSlice=siz(1);
997               set(handles.slices,'Visible','on')
998               set(handles.slices,'Value',1)
999           end
1000           if isfield(GeometryCalib,'VolumeScan') && isequal(GeometryCalib.VolumeScan,'y')
1001               set(handles.num_NbSlice,'Visible','off')
1002           else
1003               set(handles.num_NbSlice,'Visible','on')
1004               set(handles.num_NbSlice,'String',num2str(NbSlice))
1005           end
1006           slices_Callback([],[], handles)
1007        end           
1008    end
1009end
1010
1011%% update the data attached to the uvmat interface
1012if ~isempty(TimeUnit)
1013    set(handles.time_txt,'String',['time (' TimeUnit ')'])
1014end
1015UvData.TimeUnit=TimeUnit;
1016UvData.XmlData{index}=XmlData;
1017UvData.NewSeries=1;
1018% UvData.MovieObject=MovieObject;
1019
1020%display warning message
1021if ~isequal(warntext,'')
1022    msgbox_uvmat('WARNING',warntext);
1023end
1024
1025%% set default options in menu 'FieldName'
1026switch FileType
1027    case {'civx','civdata'}
1028%         [FieldList,ColorList]=calc_field;
1029        [FieldList,ColorList]=set_field_list('U','V','C');
1030        set(handles_Fields,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data
1031        set(handles_Fields,'Value',2) % set menu to 'velocity
1032        if index==1
1033            set(handles.FieldName_1,'Value',1);
1034            set(handles.FieldName_1,'String',[{''};{'image'};FieldList;{'get_field...'}]);%standard menu for civx data reproduced for the second field
1035        end
1036        set(handles.ColorScalar,'Value',1)
1037        set(handles.ColorScalar,'String',ColorList)
1038        set(handles.Vectors,'Visible','on')
1039        set(handles.Coord_x,'Value',1);
1040        set(handles.Coord_x,'String',{'X'});
1041        set(handles.Coord_y,'Value',1);
1042        set(handles.Coord_y,'String',{'Y'});
1043    case 'netcdf'
1044        set(handles_Fields,'Value',1)
1045        set(handles_Fields,'String',{'get_field...'})
1046        FieldName_Callback([],[], handles)
1047%         hget_field=get_field(FileName);
1048%         hhget_field=guidata(hget_field);
1049%         get_field('RUN_Callback',hhget_field.RUN,[],hhget_field);
1050    otherwise
1051        set(handles_Fields,'Value',1) % set menu to 'image'
1052        set(handles_Fields,'String',{'image'})
1053        set(handles.Coord_x,'Value',1);
1054        set(handles.Coord_x,'String',{'AX'});
1055        set(handles.Coord_y,'Value',1);
1056        set(handles.Coord_y,'String',{'AY'});
1057end
1058set(handles.uvmat,'UserData',UvData)
1059
1060%% set index navigation options and refresh plots
1061scan_option='i';%default
1062state_j='off'; %default
1063if index==2
1064    if get(handles.scan_j,'Value')
1065        scan_option='j'; %keep the scan option for the second file series
1066    end
1067    if strcmp(get(handles.j1,'Visible'),'on')
1068        state_j='on';
1069    end
1070end
1071[ref_j,ref_i]=find(squeeze(i1_series(1,:,:)));
1072if ~isempty(j1_series)
1073        state_j='on';
1074        if index==1
1075            if isequal(ref_i,ref_i(1)*ones(size(ref_j)))% if ref_i is always equal to its first value
1076                scan_option='j'; %scan j indext               
1077            end
1078        end
1079end
1080if isequal(scan_option,'i')
1081    diff_ref_i=diff(ref_i,1);
1082    if isempty(diff_ref_i)
1083        diff_ref_i=1;
1084    end
1085    if isequal (diff_ref_i,diff_ref_i(1)*ones(size(diff_ref_i)))
1086        set(handles.num_IndexIncrement,'String',num2str(diff_ref_i(1)))
1087    end
1088     set(handles.scan_i,'Value',1)
1089     scan_i_Callback([],[], handles);
1090else
1091    diff_ref_j=diff(ref_j);
1092    if isempty(diff_ref_j)
1093        diff_ref_j=1;
1094    end
1095    if isequal (diff_ref_j,diff_ref_j(1)*ones(size(diff_ref_j)))
1096        set(handles.num_IndexIncrement,'String',num2str(diff_ref_j(1)))
1097    end
1098     set(handles.scan_j,'Value',1)
1099     scan_j_Callback([],[], handles);
1100end
1101set(handles.scan_j,'Visible',state_j)
1102set(handles.j1,'Visible',state_j)
1103set(handles.j2,'Visible',state_j)
1104set(handles.last_j,'Visible',state_j);
1105set(handles.frame_j,'Visible',state_j);
1106set(handles.j_text,'Visible',state_j);
1107if ~isempty(i2_series)||~isempty(j2_series)
1108    set(handles.CheckFixPair,'Visible','on')
1109elseif index==1
1110    set(handles.CheckFixPair,'Visible','off')
1111end
1112
1113%% apply the effect of the transform fct and view the field 
1114transform=get(handles.TransformPath,'UserData');
1115if index==2 && (~isa(transform,'function_handle')||nargin(transform)<3)
1116    set(handles.TransformName,'value',2); % set transform to sub_field if the current fct doe not accept two input fields
1117end
1118TransformName_Callback([],[],handles)
1119mask_test=get(handles.CheckMask,'value');
1120if mask_test
1121    MaskData=get(handles.CheckMask,'UserData');
1122    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1123          delete(MaskData.maskhandle)    %delete old mask
1124    end
1125    CheckMask_Callback([],[],handles)
1126end
1127
1128%------------------------------------------------------------------------
1129% --- switch file index scanning options scan_i and scan_j in an exclusive way
1130function scan_i_Callback(hObject, eventdata, handles)
1131%------------------------------------------------------------------------
1132if get(handles.scan_i,'Value')==1
1133%     set(handles.scan_i,'BackgroundColor',[1 1 0])
1134    set(handles.scan_j,'Value',0)
1135else
1136%     set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1137    set(handles.scan_j,'Value',1)
1138end
1139scan_j_Callback(hObject, eventdata, handles)
1140
1141%------------------------------------------------------------------------
1142% --- switch file index scanning options scan_i and scan_j in an exclusive way
1143function scan_j_Callback(hObject, eventdata, handles)
1144%------------------------------------------------------------------------
1145if get(handles.scan_j,'Value')==1
1146%     set(handles.scan_j,'BackgroundColor',[1 1 0])
1147    set(handles.scan_i,'Value',0)
1148%     set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1149%     NomType=get(handles.NomType,'String');
1150%     switch NomType
1151%     case {'_1_1-2','#_ab','%3dab'},% pair with j index
1152%         set(handles.CheckFixPair,'Visible','on')% option fixed pair on/off made visible (choice of avaible pair with buttons + and - if ='off')
1153%     otherwise
1154%         set(handles.CheckFixPair,'Visible','off')
1155%     end
1156else
1157%     set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
1158    set(handles.scan_i,'Value',1)
1159%     set(handles.scan_i,'BackgroundColor',[1 1 0])
1160    set(handles.CheckFixPair,'Visible','off')
1161end
1162
1163%------------------------------------------------------------------------
1164function i1_Callback(hObject, eventdata, handles)
1165%------------------------------------------------------------------------
1166update_ij(handles,1)
1167
1168%------------------------------------------------------------------------
1169function i2_Callback(hObject, eventdata, handles)
1170%------------------------------------------------------------------------
1171update_ij(handles,2)
1172
1173%------------------------------------------------------------------------
1174function j1_Callback(hObject, eventdata, handles)
1175%------------------------------------------------------------------------
1176update_ij(handles,3)
1177
1178%------------------------------------------------------------------------
1179function j2_Callback(hObject, eventdata, handles)
1180%------------------------------------------------------------------------
1181update_ij(handles,4)
1182
1183%------------------------------------------------------------------------
1184%--- update the index display after action on edit boxes i1, i2, j1 or j2
1185function update_ij(handles,index_rank)
1186NomType=get(handles.NomType,'String');
1187indices=get(handles.FileIndex,'String');
1188[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(indices);% the indices for the second series taken from FileIndex
1189switch index_rank
1190    case 1
1191        indices=fullfile_uvmat('','','','',NomType,stra2num(get(handles.i1,'String')),i2,j1,j2);
1192        set(handles.i1,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation
1193    case 2
1194        indices=fullfile_uvmat('','','','',NomType,i1,stra2num(get(handles.i2,'String')),j1,j2);
1195        set(handles.i2,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation
1196    case 3
1197        indices=fullfile_uvmat('','','','',NomType,i1,i2,stra2num(get(handles.j1,'String')),j2);
1198        set(handles.j1,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation
1199    case 4
1200        indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,stra2num(get(handles.j2,'String')));
1201        set(handles.j2,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation
1202end
1203set(handles.FileIndex,'String',indices)
1204set(handles.FileIndex,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation
1205% update the second index if relevant
1206if strcmp(get(handles.FileIndex_1,'Visible'),'on')
1207    NomType_1=get(handles.NomType_1,'String');
1208    indices_1=get(handles.FileIndex_1,'String');
1209    [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(indices_1);% the indices for the second series taken from FileIndex_1
1210    switch index_rank
1211        case 1
1212            indices_1=fullfile_uvmat('','','','',NomType_1,stra2num(get(handles.i1,'String')),i2_1,j1_1,j2_1);
1213        case 2
1214            indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,stra2num(get(handles.i2,'String')),j1_1,j2_1);
1215        case 3
1216            indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,i2_1,stra2num(get(handles.j1,'String')),j2_1);
1217        case 4
1218            indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,i2_1,j1_1,stra2num(get(handles.j2,'String')));
1219    end
1220    set(handles.FileIndex_1,'String',indices_1)
1221    set(handles.FileIndex_1,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation
1222end
1223   
1224%------------------------------------------------------------------------
1225
1226%------------------------------------------------------------------------
1227function slices_Callback(hObject, eventdata, handles)
1228%------------------------------------------------------------------------
1229if strcmp(get(handles.slices,'String'),'slices')
1230    if get(handles.slices,'Value')==1
1231        set(handles.num_NbSlice,'Visible','on')
1232        set(handles.z_text,'Visible','on')
1233        set(handles.z_index,'Visible','on')
1234        num_NbSlice_Callback(hObject, eventdata, handles)
1235    else
1236        set(handles.num_NbSlice,'Visible','off')
1237        set(handles.z_text,'Visible','off')
1238        set(handles.z_index,'Visible','off')
1239        set(handles.masklevel,'Value',1)
1240        set(handles.masklevel,'String',{'1'})
1241    end
1242end
1243
1244%------------------------------------------------------------------------
1245function num_NbSlice_Callback(hObject, eventdata, handles)
1246%------------------------------------------------------------------------
1247mode=get(handles.slices,'String');
1248nb_slice_str=get(handles.num_NbSlice,'String');
1249if strcmp(mode,'volume')
1250    z=stra2num(get(handles.j1,'String'));
1251else
1252    num=str2double(get(handles.i1,'String'));
1253    nbslice=str2double(get(handles.num_NbSlice,'String'));
1254    z=mod(num-1,nbslice)+1;
1255end
1256set(handles.z_index,'String',num2str(z))
1257for ilist=1:nbslice
1258    list_index{ilist,1}=num2str(ilist);
1259end   
1260set(handles.masklevel,'String',list_index)
1261set(handles.masklevel,'Value',z)
1262
1263%------------------------------------------------------------------------
1264% --- Executes on button press in view_xml.
1265function view_xml_Callback(hObject, eventdata, handles)
1266%------------------------------------------------------------------------
1267%[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles);
1268 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1269FileBase=fullfile(RootPath,RootFile);
1270option=get(handles.view_xml,'String');
1271if isequal(option,'view .xml')
1272    FileXml=fullfile(RootPath,[SubDir '.xml']);
1273    if ~exist(FileXml,'file')% case of civ files , removes the extension for subdir
1274        FileXml=fullfile(RootPath,[regexprep(SubDir,'\..+$','') '.xml']);
1275    end
1276    heditxml=editxml(FileXml);
1277end
1278
1279%------------------------------------------------------------------------
1280% --- Executes on button press in CheckMask.
1281function CheckMask_Callback(hObject, eventdata, handles)
1282%------------------------------------------------------------------------
1283%case of view mask selection
1284if isequal(get(handles.CheckMask,'Value'),1)
1285     [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1286     FileBase=fullfile(RootPath,RootFile);
1287    num_i1=stra2num(get(handles.i1,'String'));
1288    num_j1=stra2num(get(handles.j1,'String'));
1289    currentdir=pwd; 
1290    cd(RootPath);
1291    maskfiles=dir('*_*mask_*.png');%look for a mask file
1292    cd(currentdir);%come back to the working directory
1293    mdetect=0;
1294    if ~isempty(maskfiles)
1295        for ilist=1:length(maskfiles)
1296            maskname=maskfiles(ilist).name;% take the first mask file in the list
1297            [tild,tild,tild,tild,tild,tild,tild,MaskExt,Mask_NomType{ilist}]=fileparts_uvmat(maskname);
1298             [tild,Name]=fileparts(maskname);
1299            Namedouble=double(Name);
1300            val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1301            ind_mask=findstr('mask',Name);
1302            i=ind_mask-1;
1303            while val(i)==0 && i>0
1304                i=i-1;
1305            end
1306            nbmask_str=str2num(Name(i+1:ind_mask-1));
1307            if ~isempty(nbmask_str)
1308                nbslice(ilist)=nbmask_str; % number of different masks (slices)
1309            end
1310        end
1311        if isequal(min(nbslice),max(nbslice))
1312            nbslice=nbslice(1);
1313        else
1314            msgbox_uvmat('ERROR','several inconsistent mask sets coexist in the current image directory')
1315            return
1316        end
1317        if ~isempty(nbslice) && Name(i)=='_'
1318            Mask.Base=[FileBase Name(i:ind_mask+3)];
1319            Mask.NbSlice=nbslice;
1320            num_i1=mod(num_i1-1,nbslice)+1;
1321            Mask.NomType=regexprep(Mask_NomType{1},'0','');%remove '0' in nom type for masks
1322            [RootPath,RootFile]=fileparts(Mask.Base);
1323            maskname=fullfile_uvmat(RootPath,'',RootFile,'.png',Mask.NomType,num_i1,[],num_j1);
1324            %maskname=name_generator(Mask.Base,num_i1,num_j1,'.png',Mask.NomType);%
1325            mdetect=exist(maskname,'file');
1326            if mdetect
1327                set(handles.num_NbSlice,'String',Name(i+1:ind_mask-1));
1328                 set(handles.num_NbSlice,'BackgroundColor',[1 1 0])
1329                set(handles.CheckMask,'UserData',Mask);
1330                set(handles.CheckMask,'BackgroundColor',[1 1 0])
1331                if nbslice > 1
1332                    set(handles.slices,'value',1)
1333                    slices_Callback(hObject, eventdata, handles)
1334                end
1335            end
1336        end
1337    end
1338    errormsg=[];%default
1339    if mdetect==0
1340        [FileName, PathName, filterindex] = uigetfile( ...
1341            {'*.png', ' (*.png)';
1342            '*.png',  '.png files '; ...
1343            '*.*', 'All Files (*.*)'}, ...
1344            'Pick a mask file *.png',FileBase);
1345        if ~ischar(FileName),return,end %abandon if the browser is cancelled
1346        maskname=fullfile(PathName,FileName);
1347        [RootDir,SubDir,RootFile,tild,tild,tild,tild,tild,Mask.NomType]=fileparts_uvmat(maskname);
1348        Mask.Base=fullfile(RootDir,SubDir,RootFile);
1349        Mask.NbSlice=1;
1350        set(handles.CheckMask,'UserData',Mask);
1351        set(handles.CheckMask,'BackgroundColor',[1 1 0])
1352    end
1353    if isempty(errormsg)
1354        errormsg=update_mask(handles,num_i1,num_j1);
1355    end
1356    if ~isempty(errormsg)
1357            set(handles.CheckMask,'Value',0)
1358            set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1359     end
1360else % desactivate mask display
1361    MaskData=get(handles.CheckMask,'UserData');
1362    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1363          delete(MaskData.maskhandle)   
1364    end
1365    set(handles.CheckMask,'UserData',[])   
1366    UvData=get(handles.uvmat,'UserData');
1367    if isfield(UvData,'MaskName')
1368        UvData=rmfield(UvData,'MaskName');
1369        set(handles.uvmat,'UserData',UvData)
1370    end
1371    set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1372end
1373
1374%------------------------------------------------------------------------
1375function errormsg=update_mask(handles,num_i1,num_j1)
1376%------------------------------------------------------------------------
1377errormsg=[];%default
1378MaskData=get(handles.CheckMask,'UserData');
1379if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1380    uistack(MaskData.maskhandle,'top');
1381end
1382num_i1_mask=mod(num_i1-1,MaskData.NbSlice)+1;
1383[RootPath,RootFile]=fileparts(MaskData.Base);
1384MaskName=fullfile_uvmat(RootPath,'',RootFile,'.png',MaskData.NomType,num_i1_mask,[],num_j1);
1385UvData=get(handles.uvmat,'UserData');
1386%update mask image if the mask is new
1387if ~ (isfield(UvData,'MaskName') && isequal(UvData.MaskName,MaskName))
1388    UvData.MaskName=MaskName; %update the recorded name on UvData
1389    set(handles.uvmat,'UserData',UvData);
1390    if ~exist(MaskName,'file')
1391        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1392            delete(MaskData.maskhandle)   
1393        end
1394    else
1395        %read mask image
1396        [Mask,tild,errormsg] = read_field(MaskName,'image');
1397%         Mask.AName='image';
1398%         Mask.A=imread(MaskName);
1399        if ~isempty(errormsg)
1400            return
1401        end
1402        npxy=size(Mask.A);
1403        if length(npxy)>2
1404            errormsg=[MaskName ' is not a grey scale image'];
1405            return
1406        elseif ~isa(Mask.A,'uint8')
1407            errormsg=[MaskName ' is not a 8 bit grey level image'];
1408            return
1409        end
1410%         Mask.AX=[0.5 npxy(2)-0.5];
1411%         Mask.AY=[npxy(1)-0.5 0.5 ];
1412%         Mask.CoordUnit='pixel';
1413        if isequal(get(handles.slices,'Value'),1)
1414           NbSlice=str2num(get(handles.num_NbSlice,'String'));
1415           num_i1=str2num(get(handles.i1,'String'));
1416           Mask.ZIndex=mod(num_i1-1,NbSlice)+1;
1417        end
1418        %px to phys or other transform on field
1419         menu_transform=get(handles.TransformName,'String');
1420        choice_value=get(handles.TransformName,'Value');
1421        transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1422        transform=get(handles.TransformPath,'UserData');
1423        if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
1424            if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
1425                Calib=UvData.XmlData{1}.GeometryCalib;
1426                Mask=transform(Mask,UvData.XmlData{1});
1427            end
1428        end
1429        flagmask=Mask.A < 200;
1430       
1431        %make brown color image
1432        imflag(:,:,1)=0.9*flagmask;
1433        imflag(:,:,2)=0.7*flagmask;
1434        imflag(:,:,3)=zeros(size(flagmask));
1435       
1436        %update mask image
1437        hmask=[]; %default
1438        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1439            hmask=MaskData.maskhandle;
1440        end
1441        if ~isempty(hmask)
1442            set(hmask,'CData',imflag)   
1443            set(hmask,'AlphaData',flagmask*0.6)
1444            set(hmask,'XData',Mask.AX);
1445            set(hmask,'YData',Mask.AY);
1446%             uistack(hmask,'top')
1447        else
1448            axes(handles.PlotAxes)
1449            hold on   
1450            MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*ones(size(flagmask)));
1451            set(handles.CheckMask,'UserData',MaskData)
1452        end
1453    end
1454end
1455
1456%------------------------------------------------------------------------
1457%------------------------------------------------------------------------
1458% III - MAIN REFRESH FUNCTIONS : 'FRAME PLOT'
1459%------------------------------------------------------------------------
1460
1461%------------------------------------------------------------------------
1462% --- Executes on button press in runplus: make one step forward and call
1463% --- run0. The step forward is along the fieldname series 1 or 2 depending on
1464% --- the scan_i and scan_j check box (exclusive each other)
1465function runplus_Callback(hObject, eventdata, handles)
1466%------------------------------------------------------------------------
1467set(handles.runplus,'BackgroundColor',[1 1 0])%paint the command button in yellow
1468drawnow
1469%TODO: introduce the option: increment ='*' to move to the next available view
1470increment=str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d
1471% if isnan(increment)
1472%     set(handles.num_IndexIncrement,'String','1')%default value
1473%     increment=1;
1474% end
1475errormsg=runpm(hObject,eventdata,handles,increment);
1476if ~isempty(errormsg)
1477    msgbox_uvmat('ERROR',errormsg);
1478end
1479set(handles.runplus,'BackgroundColor',[1 0 0])%paint the command button back to red
1480
1481%------------------------------------------------------------------------
1482% --- Executes on button press in runmin: make one step backward and call
1483% --- run0. The step backward is along the fieldname series 1 or 2 depending on
1484% --- the scan_i and scan_j check box (exclusive each other)
1485function runmin_Callback(hObject, eventdata, handles)
1486%------------------------------------------------------------------------
1487set(handles.runmin,'BackgroundColor',[1 1 0])%paint the command button in yellow
1488drawnow
1489increment=-str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d
1490% if isnan(increment)
1491%     set(handles.num_IndexIncrement,'String','1')%default value
1492%     increment=1;
1493% end
1494errormsg=runpm(hObject,eventdata,handles,increment);
1495if ~isempty(errormsg)
1496    msgbox_uvmat('ERROR',errormsg);
1497end
1498set(handles.runmin,'BackgroundColor',[1 0 0])%paint the command button back to red
1499
1500%------------------------------------------------------------------------
1501% -- Executes on button press in Movie: make a series of +> steps
1502function Movie_Callback(hObject, eventdata, handles)
1503%------------------------------------------------------------------------
1504set(handles.Movie,'BackgroundColor',[1 1 0])%paint the command button in yellow
1505drawnow
1506increment=str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d
1507% if isnan(increment)
1508%     set(handles.num_IndexIncrement,'String','1')%default value
1509%     increment=1;
1510% end
1511set(handles.STOP,'Visible','on')
1512set(handles.speed,'Visible','on')
1513set(handles.speed_txt,'Visible','on')
1514set(handles.Movie,'BusyAction','queue')
1515UvData=get(handles.uvmat,'UserData');
1516
1517while get(handles.Movie,'Value')==1 && get(handles.speed,'Value')~=0 && isequal(get(handles.Movie,'BusyAction'),'queue') % enable STOP command
1518        errormsg=runpm(hObject,eventdata,handles,increment);
1519        if ~isempty(errormsg)
1520            set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1521            return
1522        end
1523        pause(1.02-get(handles.speed,'Value'))% wait for next image
1524end
1525if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1526    UvData.aviobj=close(UvData.aviobj);
1527   set(handles.uvmat,'UserData',UvData);
1528end
1529set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1530
1531%------------------------------------------------------------------------
1532% -- Executes on button press in Movie: make a series of <- steps
1533function MovieBackward_Callback(hObject, eventdata, handles)
1534%------------------------------------------------------------------------
1535set(handles.MovieBackward,'BackgroundColor',[1 1 0])%paint the command button in yellow
1536drawnow
1537increment=-str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d
1538set(handles.STOP,'Visible','on')
1539set(handles.speed,'Visible','on')
1540set(handles.speed_txt,'Visible','on')
1541set(handles.MovieBackward,'BusyAction','queue')
1542UvData=get(handles.uvmat,'UserData');
1543
1544while get(handles.MovieBackward,'Value')==1 && get(handles.speed,'Value')~=0 && isequal(get(handles.MovieBackward,'BusyAction'),'queue') % enable STOP command
1545        errormsg=runpm(hObject,eventdata,handles,increment);
1546        if ~isempty(errormsg)
1547            set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1548            return
1549        end
1550        pause(1.02-get(handles.speed,'Value'))% wait for next image
1551end
1552if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1553    UvData.aviobj=close(UvData.aviobj);
1554   set(handles.uvmat,'UserData',UvData);
1555end
1556set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1557
1558%------------------------------------------------------------------------
1559function STOP_Callback(hObject, eventdata, handles)
1560%------------------------------------------------------------------------
1561set(handles.movie_pair,'BusyAction','Cancel')
1562set(handles.movie_pair,'value',0)
1563set(handles.Movie,'BusyAction','Cancel')
1564set(handles.MovieBackward,'BusyAction','Cancel')
1565set(handles.MenuExportMovie,'BusyAction','Cancel')
1566set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1567set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1568set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1569
1570%------------------------------------------------------------------------
1571% --- function activated by runplus and run minus
1572function errormsg=runpm(hObject,eventdata,handles,increment)
1573%------------------------------------------------------------------------
1574errormsg='';%default
1575%% check for movie pair status
1576movie_status=get(handles.movie_pair,'Value');
1577if isequal(movie_status,1)
1578    STOP_Callback(hObject, eventdata, handles)%interrupt movie pair if active
1579end
1580
1581%% read the current input file name(s) and field indices
1582InputFile=read_GUI(handles.InputFile);
1583InputFile.RootFile=regexprep(InputFile.RootFile,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1584InputFile.SubDir=regexprep(InputFile.SubDir,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1585FileExt=InputFile.FileExt;
1586NomType=get(handles.NomType,'String');
1587i1=str2num(get(handles.i1,'String'));%read the field indices (for movie, it is not given by the file name)
1588i2=[];%default
1589if strcmp(get(handles.i2,'Visible'),'on')
1590    i2=str2num(get(handles.i2,'String'));
1591end
1592j1=[];
1593if strcmp(get(handles.j1,'Visible'),'on')
1594    j1=stra2num(get(handles.j1,'String'));
1595end
1596j2=j1;
1597if strcmp(get(handles.j2,'Visible'),'on')
1598    j2=stra2num(get(handles.j2,'String'));
1599end
1600sub_value= get(handles.SubField,'Value');
1601if sub_value % a second input file has been entered
1602     [InputFile.RootPath_1,InputFile.SubDir_1,InputFile.RootFile_1,InputFile.FileIndex_1,InputFile.FileExt_1,InputFile.NomType_1]=read_file_boxes_1(handles);   
1603    [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(InputFile.FileIndex_1);% the indices for the second series taken from FileIndex_1
1604else
1605    filename_1=[];
1606end   
1607
1608%% increment (or decrement) the field indices and update the input filename(s)
1609if isempty(increment)
1610    set(handles.CheckFixPair,'Value',0)
1611end
1612CheckFixPair=get(handles.CheckFixPair,'Value')||(isempty(i2)&&isempty(j2));
1613
1614% the pair i1-i2 or j1-j2 is imposed (check box CheckFixPair selected)
1615        i1_1=i1;
1616        i2_1=i2;
1617        j1_1=j1;
1618        j2_1=j2;
1619if CheckFixPair
1620    if get(handles.scan_i,'Value')==1% case of scanning along index i
1621        i1=i1+increment;
1622        i2=i2+increment;
1623        if sub_value
1624            i1_1=i1_1+increment;
1625            i2_1=i2_1+increment;
1626        end
1627       
1628    else % case of scanning along index j (burst numbers)
1629        j1=j1+increment;
1630        j2=j2+increment;
1631        if sub_value
1632            j1_1=j1_1+increment;
1633            j2_1=j2_1+increment;
1634        end
1635    end
1636   
1637% the pair i1-i2 or j1-j2 is free (check box CheckFixPair not selected): the list of existing indices recorded in UvData is used
1638else
1639    UvData=get(handles.uvmat,'UserData');
1640    ref_i=i1;
1641    if ~isempty(i2)
1642        ref_i=floor((i1+i2)/2);% current reference index i
1643    end
1644    ref_j=1;
1645    if ~isempty(j1)
1646        ref_j=j1;
1647        if ~isempty(j2)
1648            ref_j=floor((j1+j2)/2);% current reference index j
1649        end
1650    end
1651    if ~isempty(increment)
1652        if get(handles.scan_i,'Value')==1% case of scanning along index i
1653            ref_i=ref_i+increment;% increment the current reference index i
1654        else % case of scanning along index j (burst numbers)
1655            ref_j=ref_j+increment;% increment the current reference index j if scan_j option is used
1656        end
1657    else % free increment
1658        runaction=get(gcbo,'tag');
1659        if strcmp(runaction,'runplus')||strcmp(runaction,'Movie')% if runplus or movie is activated
1660            step=1;
1661        else
1662            step=-1;
1663        end
1664        if get(handles.scan_i,'Value')==1% case of scanning along index i
1665            ref_i=ref_i+step;
1666            while ref_i>=0  && size(UvData.i1_series{1},3)>=ref_i+1 && UvData.i1_series{1}(1,ref_j+1,ref_i+1)==0
1667                ref_i=ref_i+step;
1668            end
1669        else % case of scanning along index j (burst numbers)
1670            ref_j=ref_j+step;
1671            while ref_j>=0  && size(UvData.i1_series{1},2)>=ref_j+1 && UvData.i1_series{1}(1,ref_j+1,ref_i+1)==0
1672                ref_j=ref_j+step;
1673            end
1674        end
1675    end
1676    if ref_i<0
1677        errormsg='minimum i index reached';
1678    elseif ref_j<0
1679        errormsg='minimum j index reached';
1680    elseif ref_i+1>size(UvData.i1_series{1},3)
1681        errormsg='maximum i index reached (reload the input file to update the index bound)';
1682    elseif ref_j+1>size(UvData.i1_series{1},2)
1683        errormsg='maximum j index reached (reload the input file to update the index bound)';
1684    end
1685    if ~isempty(errormsg),return,end
1686    siz=size(UvData.i1_series{1});
1687    ref_indices=ref_i*siz(1)*siz(2)+ref_j*siz(1)+1:ref_i*siz(1)*siz(2)+(ref_j+1)*siz(1);
1688    i1_subseries=UvData.i1_series{1}(ref_indices);
1689    ref_indices=ref_indices(i1_subseries>0);
1690    if isempty(ref_indices)% case of pairs (free index i)
1691        ref_indices=ref_i*siz(1)*siz(2)+1:(ref_i+1)*siz(1)*siz(2);
1692        i1_subseries=UvData.i1_series{1}(ref_indices);
1693        ref_indices=ref_indices(i1_subseries>0);
1694    end
1695    if isempty(ref_indices),errormsg='no next frame: set num_IndexIncrement =''*'' to reach the next existing file';return
1696    end
1697    i1=UvData.i1_series{1}(ref_indices(end));
1698    if ~isempty(UvData.i2_series{1})
1699        i2=UvData.i2_series{1}(ref_indices(end));
1700    end
1701    if ~isempty(UvData.j1_series{1})
1702        j1=UvData.j1_series{1}(ref_indices(end));
1703    end
1704    if ~isempty(UvData.j2_series{1})
1705        j2=UvData.j2_series{1}(ref_indices(end));
1706    end
1707   
1708    % case of a second file series
1709    if sub_value
1710        ref_i_1=i1_1;
1711        if ~isempty(i2_1)
1712            ref_i_1=floor((i1_1+i2_1)/2);% current reference index i
1713        end
1714        ref_j_1=1;
1715        if ~isempty(j1_1)
1716            ref_j_1=j1_1;
1717            if ~isempty(j2_1)
1718                ref_j_1=floor((j1_1+j2_1)/2);% current reference index j
1719            end
1720        end
1721        if ~isempty(increment)
1722            if get(handles.scan_i,'Value')==1% case of scanning along index i
1723                ref_i_1=ref_i_1+increment;% increment the current reference index i
1724            else % case of scanning along index j (burst numbers)
1725                ref_j_1=ref_j_1+increment;% increment the current reference index j if scan_j option is used
1726            end
1727        else % free increment, synchronise the ref indices with the first series
1728            ref_i_1=ref_i;
1729            ref_j_1=ref_j;
1730        end
1731        if numel(UvData.i1_series)==1
1732            UvData.i1_series{2}=UvData.i1_series{1};
1733            UvData.j1_series{2}=UvData.j1_series{1};
1734            UvData.i2_series{2}=UvData.i2_series{1};
1735            UvData.j2_series{2}=UvData.j2_series{1};
1736        end
1737        if ref_i_1<0
1738            errormsg='minimum i index reached';
1739        elseif ref_j_1<0
1740            errormsg='minimum j index reached';
1741        elseif ref_i_1+1>size(UvData.i1_series{2},3)
1742            errormsg='maximum i index reached for the second series (reload the input file to update the index bound)';
1743        elseif ref_j_1+1>size(UvData.i1_series{2},2)
1744            errormsg='maximum j index reached for the second series(reload the input file to update the index bound)';
1745        end
1746        if ~isempty(errormsg),return,end
1747        siz=size(UvData.i1_series{2});
1748        ref_indices=ref_i_1*siz(1)*siz(2)+ref_j_1*siz(1)+1:ref_i_1*siz(1)*siz(2)+(ref_j_1+1)*siz(1);
1749        i1_subseries=UvData.i1_series{2}(ref_indices);
1750        ref_indices=ref_indices(i1_subseries>0);
1751        if isempty(ref_indices)% case of pairs (free index i)
1752            ref_indices=ref_i_1*siz(1)*siz(2)+1:(ref_i_1+1)*siz(1)*siz(2);
1753            i1_subseries=UvData.i1_series{2}(ref_indices);
1754            ref_indices=ref_indices(i1_subseries>0);
1755        end
1756        i1_1=UvData.i1_series{2}(ref_indices(end));
1757        if ~isempty(UvData.i2_series{2})
1758            i2_1=UvData.i2_series{2}(ref_indices(end));
1759        end
1760        if ~isempty(UvData.j1_series{2})
1761            j1_1=UvData.j1_series{2}(ref_indices(end));
1762        end
1763        if ~isempty(UvData.j2_series{2})
1764            j2_1=UvData.j2_series{1}(ref_indices(end));
1765        end   
1766    else% the second series (if needed) is the same file as the first
1767        i1_1=i1;
1768        i2_1=i2;
1769        j1_1=j1;
1770        j2_1=j2;
1771    end
1772end
1773filename=fullfile_uvmat(InputFile.RootPath,InputFile.SubDir,InputFile.RootFile,FileExt,NomType,i1,i2,j1,j2);
1774if sub_value
1775    filename_1=fullfile_uvmat(InputFile.RootPath_1,InputFile.SubDir_1,InputFile.RootFile_1,InputFile.FileExt_1,InputFile.NomType_1,i1_1,i2_1,j1_1,j2_1);
1776end
1777
1778%% refresh plots
1779errormsg=refresh_field(handles,filename,filename_1,i1,i2,j1,j2,i1_1,i2_1,j1_1,j2_1);
1780
1781%% update the index counters if the index move is successfull
1782if isempty(errormsg)
1783    set(handles.i1,'String',num2stra(i1,NomType,1));
1784    if isequal(i2,i1)
1785        set(handles.i2,'String','');
1786    else
1787        set(handles.i2,'String',num2stra(i2,NomType,1));
1788    end
1789    set(handles.j1,'String',num2stra(j1,NomType,2));
1790    if isequal(j2,j1)
1791        set(handles.j2,'String','');
1792    else
1793        set(handles.j2,'String',num2stra(j2,NomType,2));
1794    end
1795    indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1796    set(handles.FileIndex,'String',indices);
1797    if ~isempty(filename_1)
1798        indices_1=fullfile_uvmat('','','','',InputFile.NomType_1,i1_1,i2_1,j1_1,j2_1);
1799        set(handles.FileIndex_1,'String',indices_1);
1800    end
1801    if isequal(movie_status,1)
1802        set(handles.movie_pair,'Value',1)
1803        movie_pair_Callback(hObject, eventdata, handles); %reactivate moviepair if it was activated
1804    end
1805end
1806
1807%------------------------------------------------------------------------
1808% --- Executes on button press in movie_pair: create an alternating movie with two view
1809function movie_pair_Callback(hObject, eventdata, handles)
1810%------------------------------------------------------------------------
1811%% stop movie action if the movie_pair button is off
1812if ~get(handles.movie_pair,'value')
1813    set(handles.movie_pair,'BusyAction','Cancel')%stop movie pair if button is 'off'
1814    set(handles.i2,'String','')
1815    set(handles.j2,'String','')
1816    return
1817else
1818    set(handles.movie_pair,'BusyAction','queue')
1819end
1820
1821%% initialisation
1822set(handles.movie_pair,'BackgroundColor',[1 1 0])%paint the command button in yellow
1823drawnow
1824list_fields=get(handles.FieldName,'String');% list menu fields
1825index_fields=get(handles.FieldName,'Value');% selected string index
1826FieldName=list_fields{index_fields}; % selected field
1827UvData=get(handles.uvmat,'UserData');
1828if isequal(FieldName,'image')
1829    index=1;
1830    [RootPath,SubDir,RootFile,FileIndices,Ext]=read_file_boxes(handles);
1831    NomType=get(handles.NomType,'String');
1832else
1833    list_fields=get(handles.FieldName_1,'String');% list menu fields
1834    index_fields=get(handles.FieldName_1,'Value');% selected string index
1835    FieldName=list_fields{index_fields}; % selected field
1836    if isequal(FieldName,'image')
1837        index=2;
1838        [RootPath,tild,RootFile,FileIndex_1,Ext,NomType]=read_file_boxes_1(handles);
1839    else
1840        msgbox_uvmat('ERROR','an image or movie must be first introduced as input')
1841        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1842        set(handles.movie_pair,'Value',0)
1843        return
1844    end
1845end
1846num_i1=str2num(get(handles.i1,'String'));
1847num_j1=stra2num(get(handles.j1,'String'));
1848num_i2=str2num(get(handles.i2,'String'));
1849num_j2=stra2num(get(handles.j2,'String'));
1850imaname_1='';
1851if isempty(num_j2)
1852    if isempty(num_i2)
1853        if strcmp(get(handles.j2,'Visible'),'on') %if the j box is visible
1854            imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,Ext,NomType,num_i1,[],num_j1+1);
1855        end
1856        if exist(imaname_1,'file')
1857            num_j2=num_j1+1;% look by default for the next j index as the second file
1858            set(handles.j2,'String',num2stra(num_j2,NomType));
1859        else
1860            imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,Ext,NomType,num_i1+1,[],num_j1);
1861            if exist(imaname_1,'file')
1862                num_i2=num_i1+1;
1863                set(handles.i2,'String',num2str(num_i2));
1864            else
1865                msgbox_uvmat('ERROR', 'a second image index i2 or j2 is needed to show the pair as a movie')
1866                set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1867                set(handles.movie_pair,'Value',0)
1868                return
1869            end
1870        end
1871    else
1872        num_j2=num_j1;%repeat the index i1 by default
1873    end
1874end
1875if isempty(num_i2)
1876    num_i2=num_i1;%repeat the index i1 by default
1877end
1878imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,Ext,NomType,num_i2,[],num_j2);
1879if strcmp(NomType,'*')
1880    num_frame=num_i2;
1881else
1882    num_frame=num_j2;
1883end
1884if ~exist(imaname_1,'file')
1885      msgbox_uvmat('ERROR',['second input open (-)  ' imaname_1 ' not found']);
1886      set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1887       set(handles.movie_pair,'Value',0)
1888      return
1889end
1890
1891%% get the first image
1892%Field.AName='image';
1893if index==1
1894    Field_a=UvData.Field;% movie on the second field
1895else
1896    Field_a=UvData.Field_1;% movie on the first field
1897end
1898
1899%% read the second image
1900MovieObject=[];
1901if numel(UvData.MovieObject)>=index
1902    MovieObject=UvData.MovieObject{index};
1903end
1904[Field_b,ParamOut,errormsg] = read_field(imaname_1,UvData.FileType{index},MovieObject,num_frame);
1905% Field_b.AX=Field_a.AX;
1906% Field_b.AY=Field_a.AY;
1907% % z index
1908% nbslice=str2double(get(handles.num_NbSlice,'String'));
1909% if ~isempty(nbslice)
1910%     Field_b.ZIndex=mod(num_i2-1,nbslice)+1;
1911% end
1912% Field_b.CoordUnit='pixel';
1913%
1914% %% determine the input file type
1915% if (test_1 && isfield(UvData,'MovieObject')&& numel(UvData.MovieObject>=2))||(~test_1 && ~isempty(UvData.MovieObject{1}))
1916%     FileType='movie';
1917% elseif isequal(lower(Ext),'.avi')
1918%     FileType='avi';
1919% elseif isequal(lower(Ext),'.vol')
1920%     FileType='vol';
1921% else
1922%    form=imformats(Ext(2:end));
1923%    if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
1924%        if isequal(NomType,'*');
1925%            FileType='multimage';
1926%        else
1927%            FileType='image';
1928%        end
1929%    end
1930% end
1931% switch FileType
1932%         case 'movie'
1933%             if test_1
1934%                 Field_b.A=read(UvData.MovieObject{2},num_i2);
1935%             else
1936%                 Field_b.A=read(UvData.MovieObject{1},num_i2);
1937%             end
1938%         case 'avi'
1939%             mov=aviread(imaname_1,num_i2);
1940%             Field_b.A=frame2im(mov(1));
1941%         case 'vol'
1942%             Field_b.A=imread(imaname_1);
1943%         case 'multimage'
1944%             Field_b.A=imread(imaname_1,num_i2);
1945%         case 'image'
1946%             Field_b.A=imread(imaname_1);
1947% end
1948% if get(handles.slices,'Value')
1949%     Field.ZIndex=str2double(get(handles.z_index,'String'));
1950% end
1951
1952%px to phys or other transform on field
1953transform=get(handles.TransformPath,'UserData');
1954if  ~isempty(transform)
1955    if isfield(UvData,'XmlData') && numel(UvData.XmlData)>=index %use geometry calib recorded from the ImaDoc xml file as first priority
1956        if index==2
1957        Field_a=transform(Field_a,UvData.XmlData{index});%the first field has been stored without transform
1958        end
1959        Field_b=transform(Field_b,UvData.XmlData{index});
1960    end
1961end
1962
1963 % make movie until movie speed is set to 0 or STOP is activated
1964hima=findobj(handles.PlotAxes,'Tag','ima');% %handles.PlotAxes =main plotting window (A GENERALISER)
1965set(handles.STOP,'Visible','on')
1966set(handles.speed,'Visible','on')
1967set(handles.speed_txt,'Visible','on')
1968while get(handles.speed,'Value')~=0 && isequal(get(handles.movie_pair,'BusyAction'),'queue')%isequal(get(handles.run0,'BusyAction'),'queue'); % enable STOP command
1969    % read and plot the series of images in non erase mode
1970    set(hima,'CData',Field_b.A);
1971    pause(1.02-get(handles.speed,'Value'));% wait for next image
1972    set(hima,'CData',Field_a.A);
1973    pause(1.02-get(handles.speed,'Value'));% wait for next image
1974end
1975set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1976 set(handles.movie_pair,'Value',0)
1977
1978%------------------------------------------------------------------------
1979% --- Executes on button press in run0.
1980function run0_Callback(hObject, eventdata, handles)
1981%------------------------------------------------------------------------
1982set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
1983drawnow
1984[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
1985filename=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
1986filename_1='';%default
1987FileIndex_1='';
1988if get(handles.SubField,'Value')
1989    [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
1990    filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
1991end
1992num_i1=stra2num(get(handles.i1,'String'));
1993num_i2=stra2num(get(handles.i2,'String'));
1994num_j1=stra2num(get(handles.j1,'String'));
1995num_j2=stra2num(get(handles.j2,'String'));
1996[tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(FileIndex_1);% get the indices of the second series from the string FileIndex_1
1997if isempty(j1_1)% case of movies, the index is not given by file index
1998    j1_1=num_j1;
1999end
2000
2001errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1);
2002
2003if ~isempty(errormsg)
2004      msgbox_uvmat('ERROR',errormsg);
2005else
2006    set(handles.i1,'BackgroundColor',[1 1 1])
2007    set(handles.i2,'BackgroundColor',[1 1 1])
2008    set(handles.j1,'BackgroundColor',[1 1 1])
2009    set(handles.j2,'BackgroundColor',[1 1 1])
2010    set(handles.FileIndex,'BackgroundColor',[1 1 1])
2011    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
2012end   
2013set(handles.run0,'BackgroundColor',[1 0 0])
2014
2015
2016%------------------------------------------------------------------------
2017% --- read the input files and refresh all the plots, including projection.
2018% OUTPUT:
2019%  errormsg: error message char string  =[] by default
2020% INPUT:
2021% filename: first input file (=[] in the absence of input file)
2022% filename_1: second input file (=[] in the asbsenc of secodn input file)
2023% num_i1,num_i2,num_j1,num_j2; frame indices
2024% Field: structure describing an optional input field (then replace the input file)
2025
2026function errormsg=refresh_field(handles,FileName,FileName_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1)
2027%------------------------------------------------------------------------
2028
2029%% initialisation
2030if ~exist('Field','var')
2031    Field={};
2032end
2033UvData=get(handles.uvmat,'UserData');
2034if ishandle(handles.UVMAT_title) %remove title panel on uvmat
2035    delete(handles.UVMAT_title)
2036end
2037
2038%% determine the main input file information for action
2039if ~exist(FileName,'file')
2040    errormsg=['input file ' FileName ' does not exist'];
2041    return
2042end
2043NomType=get(handles.NomType,'String');
2044NomType_1='';
2045if strcmp(get(handles.NomType_1,'Visible'),'on')
2046    NomType_1=get(handles.NomType_1,'String');
2047end
2048%update the z position index
2049mode_slice=get(handles.slices,'String');
2050if strcmp(mode_slice,'volume')
2051    z_index=num_j1;
2052    set(handles.z_index,'String',num2str(z_index))
2053else
2054    nbslice=str2num(get(handles.num_NbSlice,'String'));
2055    z_index=mod(num_i1-1,nbslice)+1;
2056    set(handles.z_index,'String',num2str(z_index))
2057end
2058% refresh menu for save_mask if relevant
2059masknumber=get(handles.masklevel,'String');
2060if length(masknumber)>=z_index
2061    set(handles.masklevel,'Value',z_index)
2062end
2063
2064%% test for need of tps
2065check_proj_tps=0;
2066if  (strcmp(UvData.FileType{1},'civdata')||strcmp(UvData.FileType{1},'civx'))
2067    for iobj=1:numel(UvData.Object)
2068        if isfield(UvData.Object{iobj},'ProjMode')&& strcmp(UvData.Object{iobj}.ProjMode,'interp_tps')
2069            check_proj_tps=1;
2070            break
2071        end
2072    end
2073end
2074
2075%% read the first input field
2076ParamIn.ColorVar='';%default variable name for vector color
2077frame_index=1;%default
2078FieldName='';%default
2079VelType='';%default
2080switch UvData.FileType{1}
2081    case {'civx','civdata','netcdf'};
2082        list_fields=get(handles.FieldName,'String');% list menu fields
2083        FieldName= list_fields{get(handles.FieldName,'Value')}; % selected field
2084        % if get_field... is selected, the GUI get_field will be used to enter fields
2085        if ~strcmp(FieldName,'get_field...')
2086            if get(handles.FixVelType,'Value')
2087                VelTypeList=get(handles.VelType,'String');
2088                VelType=VelTypeList{get(handles.VelType,'Value')};
2089            end
2090        end
2091        % case of input vector field, get the scalar used for vector color
2092        if ~isempty(regexp(FieldName,'^vec('))
2093            list_code=get(handles.ColorCode,'String');% list menu fields
2094            index_code=get(handles.ColorCode,'Value');% selected string index
2095            if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2096                list_code=get(handles.ColorScalar,'String');% list menu fields
2097                index_code=get(handles.ColorScalar,'Value');% selected string index
2098                ParamIn.ColorVar= list_code{index_code}; % selected field
2099            end
2100        end
2101    case {'video','mmreader'}
2102        ParamIn=UvData.MovieObject{1};     
2103        if ~strcmp(NomType,'*')
2104            frame_index=num_j1;%frame index for movies or multimage
2105        else
2106            frame_index=num_i1;
2107        end
2108    case 'multimage'
2109        if ~strcmp(NomType,'*')
2110            frame_index=num_j1;%frame index for movies or multimage
2111        else
2112            frame_index=num_i1;
2113        end
2114    case 'vol' %TODO: update
2115        if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2116            ParamIn.Npy=UvData.XmlData.Npy;
2117            ParamIn.Npx=UvData.XmlData.Npx;
2118        else           
2119            errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2120            return
2121        end
2122end
2123if isstruct (ParamIn)
2124    ParamIn.FieldName=FieldName;
2125    ParamIn.VelType=VelType;
2126    XNameMenu=get(handles.Coord_x,'String');
2127    if ~isempty(XNameMenu)
2128        ParamIn.Coord_x=XNameMenu(get(handles.Coord_x,'Value'));
2129    end
2130    YNameMenu=get(handles.Coord_y,'String');
2131    if ~isempty(YNameMenu)
2132        ParamIn.Coord_y=YNameMenu(get(handles.Coord_y,'Value'));
2133    end
2134end
2135check_tps = 0;         
2136if strcmp(UvData.FileType{1},'civdata')&&~strcmp(ParamIn.FieldName,'velocity')&&~strcmp(ParamIn.FieldName,'get_field...')
2137       check_tps=1;%tps needed to get the requested field
2138end
2139[Field{1},ParamOut,errormsg] = read_field(FileName,UvData.FileType{1},ParamIn,frame_index);
2140if ~isempty(errormsg)
2141    errormsg=['uvmat / refresh_field / read_field( ' FileName ') / ' errormsg];
2142    return
2143end 
2144if isfield(ParamOut,'Npx')&& isfield(ParamOut,'Npy')
2145    set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2146    set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2147end
2148if isfield(ParamOut,'TimeIndex')% case of time obtained from get_field
2149    set(handles.i1,'String',num2str(ParamOut.TimeIndex))
2150end
2151if isfield(ParamOut,'TimeValue')
2152    Field{1}.Time=ParamOut.TimeValue;% case of time obtained from get_field
2153end
2154Field{1}.ZIndex=z_index; %used for multiplane 3D calibration
2155
2156
2157%% choose and read a second field FileName_1 if defined
2158VelType_1=[];%default
2159FieldName_1=[];
2160ParamIn_1=[];
2161ParamOut_1=[];
2162frame_index_1=1;
2163if ~isempty(FileName_1)
2164    if ~exist(FileName_1,'file')
2165        errormsg=['second file ' FileName_1 ' does not exist'];
2166        return
2167    end
2168   % Name=FileName_1;
2169    switch UvData.FileType{2}
2170        case {'civx','civdata','netcdf'};
2171            list_fields=get(handles.FieldName_1,'String');% list menu fields
2172            if ischar(list_fields),list_fields={list_fields};end
2173            FieldName_1= list_fields{get(handles.FieldName_1,'Value')}; % selected field
2174            if ~strcmp(FieldName,'get_field...')
2175                if get(handles.FixVelType,'Value')
2176                    VelTypeList=get(handles.VelType_1,'String');
2177                    VelType_1=VelTypeList{get(handles.VelType_1,'Value')};% read the velocity type.
2178                end
2179            end
2180            if strcmp(FieldName_1,'velocity')&& strcmp(get(handles.ColorCode,'Visible'),'on')
2181                list_code=get(handles.ColorCode,'String');% list menu fields
2182                index_code=get(handles.ColorCode,'Value');% selected string index
2183                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2184                    list_code=get(handles.ColorScalar,'String');% list menu fields
2185                    index_code=get(handles.ColorScalar,'Value');% selected string index
2186                    ParamIn_1.ColorVar= list_code{index_code}; % selected field for vector color display                 
2187                end
2188            end
2189        case {'video','mmreader'}
2190            ParamIn_1=UvData.MovieObject{2};
2191                        if ~strcmp(NomType_1,'*')
2192                frame_index_1=j1_1;%frame index for movies or multimage
2193            else
2194                frame_index_1=i1_1;
2195            end 
2196         case 'multimage'
2197            if strcmp(NomType_1,'*')%frame index for movies or multimage
2198                frame_index_1=i1_1;
2199            else
2200                frame_index_1=j1_1;
2201            end   
2202        case 'vol' %TODO: update
2203            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2204                ParamIn_1.Npy=UvData.XmlData.Npy;
2205                ParamIn_1.Npx=UvData.XmlData.Npx;
2206            else
2207                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2208                return
2209            end
2210    end
2211    if isequal(get(handles.NomType_1,'Visible'),'on')
2212    NomType_1=get(handles.NomType_1,'String');
2213    else
2214        NomType_1=get(handles.NomType,'String');
2215    end
2216    test_keepdata_1=0;% test for keeping the previous stored data if the input files are unchanged
2217    if ~isequal(NomType_1,'*')&& isfield(UvData,'FileName_1')
2218           test_keepdata_1= strcmp(FileName_1,UvData.FileName_1) ;
2219    end
2220    if test_keepdata_1
2221        Field{2}=UvData.Field_1;% keep the stored field
2222        ParamOut_1=UvData.ParamOut_1;
2223    else
2224        if isempty(ParamIn_1) || isstruct(ParamIn_1)
2225        ParamIn_1.FieldName=FieldName_1;
2226        ParamIn_1.VelType=VelType_1;
2227        ParamIn_1.GUIName='get_field_1';
2228        end 
2229        [Field{2},ParamOut_1,errormsg] = read_field(FileName_1,UvData.FileType{2},ParamIn_1,frame_index_1);
2230        if ~isempty(errormsg)
2231            errormsg=['error in reading ' FieldName_1 ' in ' FileName_1 ': ' errormsg];
2232            return
2233        end
2234        if isstruct(ParamOut_1)&&~strcmp(ParamOut_1.FieldName,'get_field...')&& (strcmp(UvData.FileType{2},'civdata')||strcmp(UvData.FileType{2},'civx'))...
2235                &&~strcmp(ParamOut_1.FieldName,'velocity') && ~strcmp(ParamOut_1.FieldName,'get_field...')
2236            if ~check_proj_tps
2237             %   Field{2}=calc_field([{ParamOut_1.FieldName} {ParamOut_1.ColorVar}],Field{2});
2238            end
2239        end
2240    end
2241    Field{2}.ZIndex=z_index;%used for multi-plane 3D calibration
2242end
2243
2244%% update uvmat interface
2245if isfield(ParamOut,'Npx')
2246    set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2247    set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2248elseif isfield(ParamOut_1,'Npx')
2249    set(handles.num_Npx,'String',num2str(ParamOut_1.Npx));% display image size on the interface
2250    set(handles.num_Npy,'String',num2str(ParamOut_1.Npy));
2251end
2252
2253%% update the display menu for the first velocity type (first menuline)
2254test_veltype=0;
2255% if ~isequal(FileType,'netcdf')|| isequal(FieldName,'get_field...')
2256if (strcmp(UvData.FileType{1},'civx')||strcmp(UvData.FileType{1},'civdata'))&& ~strcmp(FieldName,'get_field...')
2257    test_veltype=1;
2258    set(handles.VelType,'Visible','on')
2259    set(handles.VelType_1,'Visible','on')
2260    set(handles.FixVelType,'Visible','on')
2261    menu=set_veltype_display(ParamOut.CivStage,UvData.FileType{1});
2262    index_menu=strcmp(ParamOut.VelType,menu);%look for VelType in  the menu
2263    index_val=find(index_menu,1);
2264    if isempty(index_val)
2265        index_val=1;
2266    end
2267    set(handles.VelType,'Value',index_val)
2268    if ~get(handles.SubField,'value')
2269        set(handles.VelType,'String',menu)
2270        set(handles.VelType_1,'Value',1)
2271        set(handles.VelType_1,'String',[{''};menu])
2272    end
2273else
2274    set(handles.VelType,'Visible','off')
2275end
2276% display the FieldName menu from the input file and pick the selected one:
2277% if isstruct(ParamOut)
2278%     field_index=strcmp(ParamOut.FieldName,ParamOut.FieldList);
2279%     set(handles.FieldName,'String',ParamOut.FieldList); %update the field menu
2280%     set(handles.FieldName,'Value',find(field_index,1))
2281% end
2282
2283%% update the display menu for the second velocity type (second menuline)
2284test_veltype_1=0;
2285if isempty(FileName_1)
2286    %     set(handles.FieldName_1,'Value',1); %update the field menu
2287    %     if isstruct(ParamOut)
2288    %     set(handles.FieldName_1,'String',[{''};ParamOut.FieldList]); %update the field menu
2289    %     end
2290elseif ~test_keepdata_1
2291    if (~strcmp(UvData.FileType{2},'netcdf')&&~strcmp(UvData.FileType{2},'civdata')&&~strcmp(UvData.FileType{2},'civx'))|| isequal(FieldName_1,'get_field...')
2292        set(handles.VelType_1,'Visible','off')
2293    else
2294        test_veltype_1=1;
2295        set(handles.VelType_1,'Visible','on')
2296        menu=set_veltype_display(ParamOut_1.CivStage,UvData.FileType{2});
2297        index_menu=strcmp(ParamOut_1.VelType,menu);
2298        set(handles.VelType_1,'Value',1+find(index_menu,1))
2299        set(handles.VelType_1,'String',[{''};menu])
2300    end
2301    % update the second field menu: the same quantity
2302    if isstruct(ParamOut_1)
2303%        set(handles.FieldName_1,'String',[{''};ParamOut_1.FieldList]); %update the field menu
2304        % display the FieldName menu from the input file and pick the selected one:
2305        FieldList=get(handles.FieldName_1,'String');
2306        field_index=strcmp(ParamOut_1.FieldName,FieldList);
2307        if ~isempty(field_index)
2308            set(handles.FieldName_1,'Value',find(field_index,1))
2309        end
2310    end
2311end
2312if test_veltype||test_veltype_1
2313    set(handles.FixVelType,'Visible','on')
2314else
2315    set(handles.FixVelType,'Visible','off')
2316end
2317
2318% field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
2319% set(handles.FieldName,'String',ParamOut.FieldList); %update the field menu
2320% set(handles.FieldName,'Value',find(field_index,1))
2321   
2322%% introduce w as background image by default for a new series (only for nbdim=2)
2323if ~isfield(UvData,'NewSeries')
2324    UvData.NewSeries=1;
2325end
2326%put W as background image by default if NbDim=2:
2327if  UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W) && ~isequal(Field{1}.NbDim,3);
2328        set(handles.SubField,'Value',1);
2329        set(handles.RootPath_1,'String','"')
2330        set(handles.RootFile_1,'String','"')
2331        set(handles.SubDir_1,'String','"');
2332         indices=fullfile_uvmat('','','','',NomType,num_i1,num_i2,num_j1,num_j2);
2333        set(handles.FileIndex_1,'String',indices)
2334        set(handles.FileExt_1,'String','"');
2335        set(handles.FieldName_1,'Visible','on');
2336        set(handles.FieldName_1,'Visible','on');
2337        set(handles.RootPath_1,'Visible','on')
2338        set(handles.RootFile_1,'Visible','on')
2339        set(handles.SubDir_1,'Visible','on');
2340        set(handles.FileIndex_1,'Visible','on');
2341        set(handles.FileExt_1,'Visible','on');
2342        set(handles.FieldName_1,'Visible','on');
2343        Field{1}.AName='w';
2344end           
2345
2346%% display time
2347abstime=[];%default inputs
2348abstime_1=[];
2349dt=[];
2350TimeUnit='';
2351% time from xml file or video movie
2352if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'Time')
2353    if isempty(num_i2)||isnan(num_i2)
2354        num_i2=num_i1;
2355    end
2356    if isempty(num_j1)||isnan(num_j1)
2357        num_j1=1;
2358    end
2359    if isempty(num_j2)||isnan(num_j2)
2360        num_j2=num_j1;
2361    end
2362    siz=size(UvData.XmlData{1}.Time);
2363    if ~isempty(num_i1)&& ~isempty(num_i2) && num_i1>=0 &&siz(1)>=max(num_i1+1,num_i2+1) && siz(2)>=max(num_j1+1,num_j2+1)
2364        abstime=(UvData.XmlData{1}.Time(num_i1+1,num_j1+1)+UvData.XmlData{1}.Time(num_i2+1,num_j2+1))/2;%overset the time read from files
2365        dt=(UvData.XmlData{1}.Time(num_i2+1,num_j2+1)-UvData.XmlData{1}.Time(num_i1+1,num_j1+1));
2366        Field{1}.Dt=dt;
2367        if isfield(UvData.XmlData{1},'TimeUnit')
2368            TimeUnit=UvData.XmlData{1}.TimeUnit;
2369        end
2370    end
2371    if numel(UvData.XmlData)==2
2372        if isempty(i2_1)
2373            i2_1=num_i1;
2374        end
2375        if isempty(j1_1)
2376            j1_1=1;
2377        end
2378        if isempty(j2_1)
2379            j2_1=j1_1;
2380        end
2381        siz=size(UvData.XmlData{2}.Time);
2382        if ~isempty(i1_1) && siz(1)>=max(i1_1+1,i2_1+1) && siz(2)>=max(j1_1+1,j2_1+1)
2383            abstime_1=(UvData.XmlData{2}.Time(i1_1+1,j1_1+1)+UvData.XmlData{2}.Time(i2_1+1,j2_1+1))/2;%overset the time read from files
2384            Field{2}.Dt=(UvData.XmlData{2}.Time(i2_1+1,j2_1+1)-UvData.XmlData{2}.Time(i1_1+1,j1_1+1));
2385        end
2386    end
2387end
2388% if isfield(Field{1},'Time')
2389%     abstime=Field{1}.Time;%time read from the netcdf input file
2390% end
2391% if numel(Field)==2 && isfield(Field{2},'Time')
2392%     abstime_1=Field{2}.Time;%time read from the netcdf input file
2393% end
2394
2395% look for timing in the input file if not defined in a xml file or movie
2396if isempty(abstime)
2397if isfield(Field{1},'Dt')
2398    dt=Field{1}.Dt;%dt read from the netcdf input file
2399    if isfield(Field{1},'TimeUnit')
2400       TimeUnit=Field{1}.TimeUnit;
2401    end
2402elseif numel(Field)==2 && isfield(Field{2},'Dt')%dt obtained from the second field if not defined in the first
2403    dt=Field{2}.Dt;%dt read from the netcdf input file
2404    if isfield(Field{2},'TimeUnit')
2405       TimeUnit=Field{2}.TimeUnit;
2406    end
2407end
2408end
2409% if ~isequal(numel(abstime),1)
2410%     abstime=[];
2411% end
2412% if ~isequal(numel(abstime_1),1)
2413%       abstime_1=[];
2414% end 
2415set(handles.abs_time,'String',num2str(abstime,5))
2416set(handles.abs_time_1,'String',num2str(abstime_1,5))
2417if isempty(dt)||isequal(dt,0)
2418    set(handles.Dt_txt,'String','')
2419else
2420    if  isempty(TimeUnit)
2421        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  10^(-3)'] )
2422    else
2423        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  m' TimeUnit] )
2424    end
2425end
2426
2427
2428%% store the current open names, fieldname and vel types in uvmat interface
2429UvData.FileName_1=FileName_1;
2430UvData.ParamOut_1=ParamOut_1;
2431if numel(Field)==2
2432UvData.Field_1=Field{2}; %store the second field for possible use at next RUN
2433end
2434
2435%% apply coordinate transform or other user fct
2436transform=get(handles.TransformPath,'UserData');
2437if isempty(transform)
2438    UvData.Field=Field{1};
2439else
2440    XmlData=[];%default
2441    XmlData_1=[];%default
2442    if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority
2443        XmlData=UvData.XmlData{1};
2444        if numel(UvData.XmlData)==2
2445            XmlData_1=UvData.XmlData{2};
2446        end
2447    end
2448    transform=get(handles.TransformPath,'UserData');
2449    switch nargin(transform)
2450        case 4
2451            if length(Field)==2
2452                UvData.Field=transform(Field{1},XmlData,Field{2},XmlData_1);
2453            else
2454                UvData.Field=transform(Field{1},XmlData);
2455            end
2456        case 3
2457            if length(Field)==2
2458                UvData.Field=transform(Field{1},XmlData,Field{2});
2459            else
2460                UvData.Field=transform(Field{1},XmlData);
2461            end
2462        case 2
2463            UvData.Field=transform(Field{1},XmlData);
2464        case 1
2465            UvData.Field=transform(Field{1});
2466    end
2467end
2468
2469%% calculate tps coefficients if needed
2470UvData.Field=tps_coeff_field(UvData.Field,check_proj_tps);
2471
2472%% analyse input field
2473%test_x=0;
2474%test_z=0;% test for unstructured z coordinate
2475%[errormsg,ListDimName,DimValue,VarDimIndex]=check_field_structure(UvData.Field);% check the input field structure
2476% if ~isempty(errormsg)
2477%     errormsg=['error in uvmat/refresh_field/check_field_structure: ' errormsg];% display error
2478%     return
2479% end
2480[CellInfo,NbDimArray,errormsg]=find_field_cells(UvData.Field);% analyse  the input field structure
2481if ~isempty(errormsg)
2482    errormsg=['uvmat /refresh_field / find_field_cells / ' errormsg];% display error
2483    return
2484end
2485
2486NbDim=max(NbDimArray);% spatial dimension of the input field
2487imax=find(NbDimArray==NbDim);% indices of field cells to consider
2488if isfield(UvData.Field,'NbDim')
2489    NbDim=double(UvData.Field.NbDim);% deal with plane fields containing z coordinates
2490end
2491
2492%UvData.Field=get_bounds(UvData.Field);
2493
2494%% get bounds and mesh (needed  to propose default options for projection objects)
2495if NbDim>1
2496    CoordMax=zeros(numel(imax),NbDim);
2497    CoordMin=zeros(numel(imax),NbDim);
2498    Mesh=zeros(1,numel(imax));
2499    for ind=1:numel(imax)
2500        if strcmp(CellInfo{imax(ind)}.CoordType,'tps')
2501            CoordName=UvData.Field.ListVarName{CellInfo{imax(ind)}.CoordIndex};% X,Y coordinates in a single variable
2502            CoordMax(ind,NbDim)=max(max(UvData.Field.(CoordName)(1:end-3,1,:),[],1),[],3);% max of x component (2D case)
2503            CoordMax(ind,NbDim-1)=max(max(UvData.Field.(CoordName)(1:end-3,2,:),[],1),[],3);% max of y component (2D case)
2504            CoordMin(ind,NbDim)=min(min(UvData.Field.(CoordName)(1:end-3,1,:),[],1),[],3);
2505            CoordMin(ind,NbDim-1)=min(min(UvData.Field.(CoordName)(1:end-3,2,:),[],1),[],3);% min of y component (2D case)
2506        else
2507            XName=UvData.Field.ListVarName{CellInfo{imax(ind)}.CoordIndex(end)};
2508            YName=UvData.Field.ListVarName{CellInfo{imax(ind)}.CoordIndex(end-1)};
2509            CoordMax(ind,NbDim)=max(max(UvData.Field.(XName)));
2510            CoordMin(ind,NbDim)=min(min(UvData.Field.(XName)));
2511            CoordMax(ind,NbDim-1)=max(max(UvData.Field.(YName)));
2512            CoordMin(ind,NbDim-1)=min(min(UvData.Field.(YName)));
2513            %         test_x=1;%test for unstructured coordinates
2514            if NbDim==3
2515                ZName=UvData.Field.ListVarName{CellInfo{imax(ind)}.CoordIndex(1)};
2516                CoordMax(imax(ind),1)=max(max(UvData.Field.(ZName)));
2517                CoordMin(ind,1)=min(min(UvData.Field.(ZName)));
2518            end
2519        end
2520        switch CellInfo{imax(ind)}.CoordType
2521           
2522            case {'scattered','tps'} %unstructured coordinates
2523                NbPoints=CellInfo{imax(ind)}.CoordSize;% total nbre of points
2524                Mesh(ind)=(prod(CoordMax(ind,:)-CoordMin(ind,:))/NbPoints)^(1/NbDim); %(volume or area per point)^(1/NbDim)
2525            case 'grid'%structured coordinate
2526                NbPoints=CellInfo{imax(ind)}.CoordSize;% nbre of points in each direction
2527                Mesh(ind)=min((CoordMax(ind,:)-CoordMin(ind,:))./(NbPoints-1));               
2528        end
2529    end
2530    UvData.Field.CoordMesh=min(Mesh);
2531    UvData.Field.XMax=max(CoordMax(ind,end));
2532    UvData.Field.XMin=min(CoordMin(ind,end));
2533    UvData.Field.YMax=max(CoordMax(ind,end-1));
2534    UvData.Field.YMin=max(CoordMin(ind,end-1));
2535    if NbDim==3
2536        UvData.Field.ZMax=max(CoordMax(ind,1));
2537        UvData.Field.ZMin=max(CoordMin(ind,1));
2538    end
2539    % adjust the mesh to a value 1, 2 , 5 *10^n
2540    ord=10^(floor(log10(UvData.Field.CoordMesh)));%order of magnitude
2541    if UvData.Field.CoordMesh/ord>=5
2542        UvData.Field.CoordMesh=5*ord;
2543    elseif UvData.Field.CoordMesh/ord>=2
2544        UvData.Field.CoordMesh=2*ord;
2545    else
2546        UvData.Field.CoordMesh=ord;
2547    end
2548    % default projection plane
2549    if isempty(UvData.Object{1})
2550        UvData.Object{1}.Type='plane';%main plotting plane
2551        UvData.Object{1}.ProjMode='projection';%main plotting plane
2552        UvData.Object{1}.DisplayHandle.uvmat=[]; %plane not visible in uvmat
2553        UvData.Object{1}.DisplayHandle.view_field=[]; %plane not visible in uvmat
2554    end
2555    %% 3D case (menuvolume)
2556    if NbDim==3% && UvData.NewSeries
2557        test_set_object=1;
2558        hset_object=findobj(allchild(0),'tag','set_object');% look for the set_object GUI
2559        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
2560        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
2561        if ~isempty(hset_object) %if set_object is detected
2562            delete(hset_object);% delete the GUI set_object if it does not fit
2563        end
2564        if test_set_object% reinitiate the GUI set_object
2565            delete_object(1);% delete the current projection object in the list UvData.Object, delete its graphic representations and update the list displayed in handles.ListObject and 2
2566            UvData.Object{1}.NbDim=NbDim;%test for 3D objects
2567            UvData.Object{1}.RangeZ=UvData.Field.CoordMesh;%main plotting plane
2568            UvData.Object{1}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen
2569            UvData.Object{1}.Angle=[0 0 0];
2570            UvData.Object{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR
2571            UvData.Object{1}.Name='1-PLANE';
2572            UvData.Object{1}.enable_plot=1;
2573            set_object(UvData.Object{1},handles,ZBounds);
2574            set(handles.ListObject,'Value',1);
2575            set(handles.ListObject,'String',{'1-PLANE'});
2576            set(handles.edit_object,'Value',1)% put the plane in edit mode to enable the z cursor
2577            edit_object_Callback([],[], handles)
2578        end
2579        %multilevel case (single menuplane in a 3D space)
2580    elseif isfield(UvData,'Z')
2581        if isfield(UvData,'CoordType')&& isequal(UvData.CoordType,'phys') && isfield(UvData,'XmlData')
2582            XmlData=UvData.XmlData{1};
2583            if isfield(XmlData,'PlanePos')
2584                UvData.Object{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:);
2585            end
2586            if isfield(XmlData,'PlaneAngle')
2587                siz=size(XmlData.PlaneAngle);
2588                indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning)
2589                UvData.Object{1}.PlaneAngle=XmlData.PlaneAngle(indangle,:);
2590            end
2591        elseif isfield(UvData,'ZIndex')
2592            UvData.Object{1}.ZObject=UvData.ZIndex;
2593        end
2594    end
2595end
2596
2597testnewseries=UvData.NewSeries;
2598UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback)
2599set(handles.uvmat,'UserData',UvData)
2600
2601%% reset the min and max of scalar if only the mask is displayed(TODO: check the need)
2602% if isfield(UvData,'Mask')&& ~isfield(UvData,'A')
2603%     set(handles.num_MinA,'String','0')
2604%     set(handles.num_MaxA,'String','255')
2605% end
2606
2607%% usual 1D (x,y) plots
2608if NbDim<=1
2609    set(handles.Objects,'Visible','off')
2610    set(handles.ListObject_1_title,'Visible','off')
2611    set(handles.ListObject_1,'Visible','off')
2612    [PlotType,PlotParamOut]=plot_field(UvData.Field,handles.PlotAxes,read_GUI(handles.uvmat));
2613    errormsg=fill_GUI(PlotParamOut,handles.uvmat);
2614    for list={'Scalar','Vectors'}
2615        if ~isfield(PlotParamOut,list{1})
2616            set(handles.(list{1}),'Visible','off')
2617        end
2618    end
2619    %write_plot_param(handles,PlotParamOut) %update the auto plot parameters
2620   
2621%% 2D or 3D fieldname are generally projected
2622else
2623    set(handles.Objects,'Visible','on')
2624    set(handles.ListObject_1_title,'Visible','on')
2625    set(handles.ListObject_1,'Visible','on')
2626   
2627    %% Plot the projections on the selected  projection objects
2628    % main projection object (uvmat display)
2629    list_object=get(handles.ListObject_1,'String');
2630    if isequal(list_object,{''})||isequal(list_object,' ')%refresh list of objects if the menu is empty
2631        set(handles.ListObject,'Value',1)
2632        set(handles.ListObject,'String',{'plane'})
2633        UvData.Object{1}.Type='plane';%main plotting plane
2634        UvData.Object{1}.ProjMode='projection';%main plotting plane
2635        UvData.Object{1}.DisplayHandle.uvmat=[]; %plane not visible in uvmat
2636        UvData.Object{1}.DisplayHandle.view_field=[]; %plane not visible in uvmat
2637        set(handles.ListObject_1,'Value',1)
2638        set(handles.ListObject_1,'String',{'plane'})
2639    end
2640    IndexObj(1)=get(handles.ListObject_1,'Value');%selected projection object for main view
2641    if IndexObj(1)> numel(UvData.Object)
2642        IndexObj(1)=1;%select the first object if the selected one does not exist
2643        set(handles.ListObject_1,'Value',1)
2644    end
2645    IndexObj(2)=get(handles.ListObject,'Value');%selected projection object for main view
2646    if isequal(IndexObj(2),IndexObj(1))
2647        IndexObj(2)=[];
2648    end
2649    plot_handles{1}=handles;
2650    if isfield(UvData,'plotaxes')%case of movies
2651        haxes(1)=UvData.plotaxes;
2652    else
2653        haxes(1)=handles.PlotAxes;
2654    end
2655    PlotParam{1}=read_GUI(handles.uvmat);
2656    %default settings if vectors not visible
2657    if ~isfield(PlotParam{1},'Vectors')
2658        PlotParam{1}.Vectors.MaxVec=1;
2659        PlotParam{1}.Vectors.MinVec=0;
2660        PlotParam{1}.Vectors.CheckFixVecColor=1;
2661        PlotParam{1}.Vectors.ColCode1=0.33;
2662        PlotParam{1}.Vectors.ColCode2=0.66;
2663        PlotParam{1}.Vectors.ColorScalar={''};
2664        PlotParam{1}.Vectors.ColorCode= {'rgb'};
2665    end
2666    PosColorbar{1}=UvData.OpenParam.PosColorbar;%prescribe the colorbar position on the uvmat interface
2667   
2668    %% second projection object (view_field display)
2669    if length( IndexObj)>=2
2670        view_field_handle=findobj(allchild(0),'tag','view_field');%handles of the view_field GUI
2671        if ~isempty(view_field_handle)
2672            plot_handles{2}=guidata(view_field_handle);
2673            haxes(2)=plot_handles{2}.PlotAxes;
2674            PlotParam{2}=read_GUI(view_field_handle);
2675           % PlotParam{2}=read_GUI(handles.uvmat);%read plotting parameters on the uvmat interface
2676            PosColorbar{2}='*'; %TODO: deal with colorbar position on view_field
2677        end
2678    end
2679   
2680    %% loop on the projection objects: one or two
2681   
2682    for imap=1:numel(IndexObj)
2683        iobj=IndexObj(imap);
2684        if numel(UvData.Object)<iobj
2685            break
2686        end
2687        [ObjectData,errormsg]=proj_field(UvData.Field,UvData.Object{iobj});% project field on the object
2688        if ~isempty(errormsg)
2689            return
2690        end
2691        if testnewseries
2692            PlotParam{imap}.Scalar.CheckBW=[]; %B/W option depends on the input field (image or scalar)
2693            if isfield(ObjectData,'CoordUnit')
2694                PlotParam{imap}.Coordinates.CheckFixAspectRatio=1;% set x and y scaling equal if CoordUnit is defined (common unit for x and y)
2695                PlotParam{imap}.Coordinates.AspectRatio=1; %set aspect ratio to 1
2696            end
2697        end
2698        %use of mask (TODO: check)
2699        if isfield(ObjectData,'NbDim') && isequal(ObjectData.NbDim,2) && isfield(ObjectData,'Mask') && isfield(ObjectData,'A')
2700            flag_mask=double(ObjectData.Mask>200);%=0 for masked regions
2701            AX=ObjectData.AX;%x coordiantes for the scalar field
2702            AY=ObjectData.AY;%y coordinates for the scalar field
2703            MaskX=ObjectData.MaskX;%x coordiantes for the mask
2704            MaskY=ObjectData.MaskY;%y coordiantes for the mask
2705            if ~isequal(MaskX,AX)||~isequal(MaskY,AY)
2706                nxy=size(flag_mask);
2707                sizpx=(ObjectData.MaskX(end)-ObjectData.MaskX(1))/(nxy(2)-1);%size of a mask pixel
2708                sizpy=(ObjectData.MaskY(1)-ObjectData.MaskY(end))/(nxy(1)-1);
2709                x_mask=ObjectData.MaskX(1):sizpx:ObjectData.MaskX(end); % pixel x coordinates for image display
2710                y_mask=ObjectData.MaskY(1):-sizpy:ObjectData.MaskY(end);% pixel x coordinates for image display
2711                %project on the positions of the scalar
2712                npxy=size(ObjectData.A);
2713                dxy(1)=(ObjectData.AY(end)-ObjectData.AY(1))/(npxy(1)-1);%grid mesh in y
2714                dxy(2)=(ObjectData.AX(end)-ObjectData.AX(1))/(npxy(2)-1);%grid mesh in x
2715                xi=ObjectData.AX(1):dxy(2):ObjectData.AX(end);
2716                yi=ObjectData.AY(1):dxy(1):ObjectData.AY(end);
2717                [XI,YI]=meshgrid(xi,yi);% creates the matrix of regular coordinates
2718                flag_mask = interp2(x_mask,y_mask,flag_mask,XI,YI);
2719            end
2720            AClass=class(ObjectData.A);
2721            ObjectData.A=flag_mask.*double(ObjectData.A);
2722            ObjectData.A=feval(AClass,ObjectData.A);
2723        end
2724        if ~isempty(ObjectData)
2725            %PlotType='none'; %default
2726            if imap==2 && isempty(view_field_handle)
2727                view_field(ObjectData)
2728            else
2729                [PlotType,PlotParamOut]=plot_field(ObjectData,haxes(imap),PlotParam{imap},PosColorbar{imap});
2730                if imap==1
2731                    errormsg=fill_GUI(PlotParamOut,handles.uvmat);
2732                else
2733                    errormsg=fill_GUI(PlotParamOut,view_field_handle);
2734                end
2735                for list={'Scalar','Vectors'}
2736                    if ~isfield(PlotParamOut,list{1})
2737                        set(plot_handles{imap}.(list{1}),'Visible','off')
2738                    end
2739                end
2740                if isfield(Field,'CoordMesh')&&~isempty(Field.CoordMesh)
2741                    ObjectData.CoordMesh=Field.CoordMesh; % gives an estimated mesh size (useful for mouse action on the plot)
2742                end
2743            end
2744        end
2745    end
2746   
2747    %% update the mask
2748    if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
2749        update_mask(handles,num_i1,num_i2);
2750    end
2751   
2752    %% prepare the menus of histograms and plot them (histogram of the whole volume in 3D case)
2753    menu_histo=(UvData.Field.ListVarName)';%list of field variables to be displayed for the menu of histogram display
2754    ind_skip=[];
2755    % nb_histo=1;
2756    Ustring='';
2757    Vstring='';
2758    % suppress coordinates from the histogram menu
2759    for ivar=1:numel(menu_histo)%l loop on field variables:
2760        if isfield(UvData.Field,'VarAttribute') && numel(UvData.Field.VarAttribute)>=ivar && isfield(UvData.Field.VarAttribute{ivar},'Role')
2761            Role=UvData.Field.VarAttribute{ivar}.Role;
2762            switch Role
2763                case {'coord_x','coord_y','coord_z','dimvar'}
2764                    ind_skip=[ind_skip ivar];
2765                case {'vector_x'}
2766                    Ustring=UvData.Field.ListVarName{ivar};
2767                    ind_skip=[ind_skip ivar];
2768                case {'vector_y'}
2769                    Vstring=UvData.Field.ListVarName{ivar};
2770                    ind_skip=[ind_skip ivar];
2771            end
2772        end
2773        DimCell=UvData.Field.VarDimName{ivar};
2774        DimName='';
2775        if ischar(DimCell)
2776            DimName=DimCell;
2777        elseif iscell(DimCell)&& numel(DimCell)==1
2778            DimName=DimCell{1};
2779        end
2780        if strcmp(DimName,menu_histo{ivar})
2781            ind_skip=[ind_skip ivar];
2782        end
2783    end
2784    menu_histo(ind_skip)=[];% remove skipped items
2785    if ~isempty(Ustring)
2786        menu_histo=[{[Ustring ',' Vstring]};menu_histo];% add U, V at the beginning if they exist
2787    end
2788   
2789    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2790    % display menus and plot histograms
2791    test_v=0;
2792    if ~isempty(menu_histo)
2793        set(handles.histo1_menu,'Value',1)
2794        set(handles.histo1_menu,'String',menu_histo)
2795        histo1_menu_Callback(handles.histo1_menu, [], handles)% plot first histogram
2796    end
2797end
2798
2799%------------------------------------------------------------------------
2800function histo1_menu_Callback(hObject, eventdata, handles)
2801%--------------------------------------------
2802histo_menu=get(handles.histo1_menu,'String');
2803histo_value=get(handles.histo1_menu,'Value');
2804FieldName=histo_menu{histo_value};
2805
2806UvData=get(handles.uvmat,'UserData');
2807Field=UvData.Field;
2808r=regexp(FieldName,'(?<var1>.*)(?<sep>,)(?<var2>.*)','names');
2809FieldName_2='';
2810if ~isempty(r)
2811    FieldName=r.var1;
2812    FieldName_2=r.var2;
2813end
2814if ~isfield(UvData.Field,FieldName)
2815    msgbox_uvmat('ERROR',['no field  ' FieldName ' for histogram'])
2816    return
2817end
2818FieldHisto=Field.(FieldName);
2819if isfield(Field,'FF') && ~isempty(Field.FF) && isequal(size(Field.FF),size(FieldHisto))
2820    indsel=find(Field.FF==0);%find values marked as false
2821    if ~isempty(indsel)
2822        FieldHisto=FieldHisto(indsel);
2823        if ~isempty(FieldName_2)
2824            FieldHisto(:,:,2)=Field.(FieldName_2)(indsel);
2825        end
2826    end
2827end
2828if isempty(Field)
2829    msgbox_uvmat('ERROR',['empty field ' FieldName])
2830else
2831    nxy=size(FieldHisto);
2832    Amin=double(min(min(min(FieldHisto))));%min of field value
2833    Amax=double(max(max(max(FieldHisto))));%max of field value
2834    if isequal(Amin,Amax)
2835        cla(handles.HistoAxes)
2836    else
2837        Histo.ListVarName={FieldName,'histo'};
2838        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
2839            Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
2840        else
2841            if numel(nxy)==2
2842                Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
2843            else
2844                Histo.VarDimName={FieldName,{FieldName,'component'}}; %dimensions for the histogram
2845            end
2846        end
2847        %unit
2848        units=[]; %default
2849        for ivar=1:numel(Field.ListVarName)
2850            if strcmp(Field.ListVarName{ivar},FieldName)
2851                if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'units')
2852                    units=Field.VarAttribute{ivar}.units;
2853                    break
2854                end
2855            end
2856        end
2857        if ~isempty(units)
2858            Histo.VarAttribute{1}.units=units;
2859        end
2860        eval(['Histo.' FieldName '=linspace(Amin,Amax,50);'])%absissa values for histo
2861        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
2862            C=reshape(double(FieldHisto),1,[]);% reshape in a vector
2863            Histo.histo(:,1)=hist(C, Histo.(FieldName));  %calculate histogram
2864        else
2865            for col=1:size(FieldHisto,3)
2866                B=FieldHisto(:,:,col);
2867                C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector
2868                Histo.histo(:,col)=hist(C, Histo.(FieldName));  %calculate histogram
2869            end
2870        end
2871        plot_field(Histo,handles.HistoAxes);
2872        hlegend=legend;
2873        if isempty(FieldName_2)
2874        set(hlegend,'String',FieldName)
2875        else
2876            set(hlegend,'String',{FieldName;FieldName_2})
2877        end
2878    end
2879end
2880
2881%-------------------------------------------------------------------
2882% --- translate coordinate to matrix index
2883%-------------------------------------------------------------------
2884function [indx,indy]=pos2ind(x0,rangx0,nxy)
2885indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel 
2886indy=1+round((nxy(1)-1)*(y12-rangy0(1))/(rangy0(2)-rangy0(1)));% index y of pixel
2887
2888
2889%-------------------------------------------------------------------
2890% --- Executes on button press in 'CheckZoom'.
2891%-------------------------------------------------------------------
2892function CheckZoom_Callback(hObject, eventdata, handles)
2893
2894if (get(handles.CheckZoom,'Value') == 1);
2895    set(handles.CheckZoom,'BackgroundColor',[1 1 0])
2896    set(handles.CheckFixLimits,'Value',1)% propose by default fixed limits for the plotting axes
2897    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2898else
2899    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
2900end
2901
2902%-------------------------------------------------------------------
2903% --- Executes on button press in 'CheckFixLimits'.
2904%-------------------------------------------------------------------
2905function CheckFixLimits_Callback(hObject, eventdata, handles)
2906test=get(handles.CheckFixLimits,'Value');
2907if test
2908    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2909else
2910    set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
2911    update_plot(handles);
2912end
2913
2914%-------------------------------------------------------------------
2915% --- Executes on button press in CheckFixAspectRatio.
2916function CheckFixAspectRatio_Callback(hObject, eventdata, handles)
2917%-------------------------------------------------------------------
2918if get(handles.CheckFixAspectRatio,'Value')
2919%     set(handles.CheckFixAspectRatio,'BackgroundColor',[1 1 0])
2920    update_plot(handles);
2921else
2922%     set(handles.CheckFixAspectRatio,'BackgroundColor',[0.7 0.7 0.7])
2923    update_plot(handles);
2924end
2925
2926%-------------------------------------------------------------------
2927function num_AspectRatio_Callback(hObject, eventdata, handles)
2928%-------------------------------------------------------------------
2929set(handles.CheckFixAspectRatio,'Value',1)% select the fixed aspect ratio button
2930% set(handles.CheckFixAspectRatio,'BackgroundColor',[1 1 0])% mark in yellow
2931update_plot(handles);
2932%-------------------------------------------------------------------
2933
2934%-------------------------------------------------------------------
2935
2936
2937
2938%-------------------------------------------------------------------
2939%----Executes on button press in 'record': records the current flags of manual correction.
2940%-------------------------------------------------------------------
2941function record_Callback(hObject, eventdata, handles)
2942% [filebase,num_i1,num_j1,num_i2,num_j2,Ext,NomType,SubDir]=read_input_file(handles);
2943[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
2944FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
2945%FileName=read_file_boxes(handles);
2946[erread,message]=fileattrib(FileName);
2947if ~isempty(message) && ~isequal(message.UserWrite,1)
2948     msgbox_uvmat('ERROR',['no writting access to ' FileName])
2949     return
2950end
2951test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
2952test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
2953if ~test_civ2 && ~test_civ1
2954    msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
2955end
2956if test_civ2
2957    nbname='nb_vectors2';
2958   flagname='vec2_FixFlag';
2959   attrname='fix2';
2960end
2961if test_civ1
2962    nbname='nb_vectors';
2963   flagname='vec_FixFlag';
2964   attrname='fix';
2965end
2966%write fix flags in the netcdf file
2967UvData=get(handles.uvmat,'UserData');
2968hhh=which('netcdf.open');% look for built-in matlab netcdf library
2969if ~isequal(hhh,'')% case of new builtin Matlab netcdf library
2970    nc=netcdf.open(FileName,'NC_WRITE');
2971    netcdf.reDef(nc);
2972    netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),attrname,1);
2973    dimid = netcdf.inqDimID(nc,nbname);
2974    try
2975        varid = netcdf.inqVarID(nc,flagname);% look for already existing fixflag variable
2976    catch
2977        varid=netcdf.defVar(nc,flagname,'double',dimid);%create fixflag variable if it does not exist
2978    end
2979    netcdf.endDef(nc);
2980    netcdf.putVar(nc,varid,UvData.PlotAxes.FF);
2981    netcdf.close(nc); 
2982else %old netcdf library
2983    netcdf_toolbox(FileName,AxeData,attrname,nbname,flagname)
2984end
2985
2986%-------------------------------------------------------------------
2987%----Correct the netcdf file, using toolbox (old versions of Matlab).
2988%-------------------------------------------------------------------
2989function netcdf_toolbox(FileName,AxeData,attrname,nbname,flagname)
2990nc=netcdf(FileName,'write'); %open netcdf file
2991result=redef(nc);
2992eval(['nc.' attrname '=1;']);
2993theDim=nc(nbname) ;% get the number of velocity vectors
2994nb_vectors=size(theDim);
2995var_FixFlag=ncvar(flagname,nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag
2996var_FixFlag(1:nb_vectors)=AxeData.FF;%
2997fin=close(nc);
2998
2999%-------------------------------------------------------------------
3000% --- Executes on button press in SubField
3001function SubField_Callback(hObject, eventdata, handles)
3002%-------------------------------------------------------------------
3003UvData=get(handles.uvmat,'UserData');
3004if get(handles.SubField,'Value')==0% if the subfield button is desactivated   
3005    set(handles.RootPath_1,'String','')
3006    set(handles.RootFile_1,'String','')
3007    set(handles.SubDir_1,'String','');
3008    set(handles.FileIndex_1,'String','');
3009    set(handles.FileExt_1,'String','');
3010    set(handles.RootPath_1,'Visible','off')
3011    set(handles.RootFile_1,'Visible','off')
3012    set(handles.SubDir_1,'Visible','off');
3013    set(handles.NomType_1,'Visible','off');
3014    set(handles.abs_time_1,'Visible','off')
3015    set(handles.FileIndex_1,'Visible','off');
3016    set(handles.FileExt_1,'Visible','off');
3017    set(handles.FieldName_1,'Value',1);%set to blank state
3018    set(handles.VelType_1,'Value',1);%set to blank state
3019    set(handles.num_Opacity,'String','')% desactivate opacity setting
3020    FieldList=get(handles.FieldName,'String');
3021    if numel(FieldList)>1   % if a choice of fields exists
3022        set(handles.FieldName_1,'Value',1)% set second field choice to blank
3023        set(handles.FieldName_1,'String',[{''};FieldList])% reproduce the menu FieldName plus a blank option
3024    else
3025        set(handles.FieldName_1,'String',{''})% set second field choice to blank
3026    end
3027    if ~strcmp(get(handles.VelType,'Visible'),'on')
3028        set(handles.VelType_1,'Visible','off')
3029    end
3030    if isfield(UvData,'XmlData_1')
3031        UvData=rmfield(UvData,'XmlData_1');
3032    end
3033    set(handles.uvmat,'UserData',UvData);
3034    transform_fct_list=get(handles.TransformName,'String');
3035    transform_fct=transform_fct_list(get(handles.TransformName,'Value'));
3036    if strcmp(transform_fct,'sub_field')
3037        set(handles.TransformName,'Value',1)%suppress the sub_field transform
3038        transform_fct_Callback(hObject, eventdata, handles);
3039    else
3040        run0_Callback(hObject, eventdata, handles)
3041    end 
3042else
3043    MenuBrowse_1_Callback(hObject, eventdata, handles)
3044end
3045
3046%------------------------------------------------------------------------
3047% --- read the data displayed for the input rootfile windows (new): TODO use read_GUI
3048
3049function [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles)
3050%------------------------------------------------------------------------
3051InputFile=read_GUI(handles.InputFile);
3052RootPath=InputFile.RootPath;
3053SubDir=regexprep(InputFile.SubDir,'/|\','');
3054RootFile=regexprep(InputFile.RootFile,'/|\','');
3055FileIndices=InputFile.FileIndex;
3056FileExt=InputFile.FileExt;
3057
3058
3059%------------------------------------------------------------------------
3060% ---- read the data displayed for the second input rootfile windows
3061function [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1,NomType_1]=read_file_boxes_1(handles)
3062%------------------------------------------------------------------------
3063RootPath_1=get(handles.RootPath_1,'String'); % read the data from the file1_input window
3064if isequal(get(handles.RootPath_1,'Visible'),'off') || isequal(RootPath_1,'"')
3065    RootPath_1=get(handles.RootPath,'String');
3066end;
3067SubDir_1=get(handles.SubDir_1,'String');
3068if isequal(get(handles.SubDir_1,'Visible'),'off')|| isequal(SubDir_1,'"')
3069    SubDir_1=get(handles.SubDir,'String');
3070end
3071SubDir_1=regexprep(SubDir_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3072RootFile_1=get(handles.RootFile_1,'String');
3073if isequal(get(handles.RootFile_1,'Visible'),'off') || isequal(RootFile_1,'"')
3074    RootFile_1=get(handles.RootFile,'String');
3075end
3076RootFile_1=regexprep(RootFile_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3077FileIndex_1=get(handles.FileIndex_1,'String');
3078if isequal(get(handles.FileIndex_1,'Visible'),'off')|| isequal(FileIndex_1,'"')
3079    FileIndex_1=get(handles.FileIndex,'String');
3080end
3081FileExt_1=get(handles.FileExt_1,'String');
3082if isequal(get(handles.FileExt_1,'Visible'),'off') || isequal(FileExt_1,'"')
3083    FileExt_1=get(handles.FileExt,'String');%read FileExt by default
3084end
3085NomType_1=get(handles.NomType_1,'String');
3086if isequal(get(handles.NomType_1,'Visible'),'off') || isequal(NomType_1,'"')
3087    NomType_1=get(handles.NomType,'String');%read FileExt by default
3088end
3089%------------------------------------------------------------------------
3090% --- Executes on menu selection FieldName
3091function FieldName_Callback(hObject, eventdata, handles)
3092%------------------------------------------------------------------------
3093UvData=get(handles.uvmat,'UserData');
3094list_fields=get(handles.FieldName,'String');% list menu fields
3095index_fields=get(handles.FieldName,'Value');% selected string index
3096field= list_fields{index_fields(1)}; % selected string
3097
3098%% fill the coordinates and variables from selections in get_field
3099if isequal(field,'get_field...')
3100    ParamIn=[];
3101    if strcmp(get(handles.VelType,'Visible'),'on')
3102        % we use the civ choice as default input
3103        ParamIn.SwitchVarIndexTime='attribute';
3104        ListVelType=get(handles.VelType,'String');
3105        VelType=ListVelType{get(handles.VelType,'Value')};
3106        switch VelType
3107            case 'civ1'
3108                 ParamIn.TimeVarName='Civ1_Time';
3109                 ParamIn.vector_x='Civ1_U';
3110                 ParamIn.vector_y='Civ1_V';
3111                 ParamIn.vec_color='Civ1_C';               
3112            case 'filter1'
3113                 ParamIn.TimeVarName='Civ1_Time';
3114                 ParamIn.vector_x='Civ1_U_smooth';
3115                 ParamIn.vector_y='Civ1_V_smooth';
3116            case 'civ2'
3117                 ParamIn.TimeVarName='Civ2_Time';
3118                 ParamIn.vector_x='Civ2_U';
3119                 ParamIn.vector_y='Civ2_V';
3120            case 'filter2'
3121                 ParamIn.TimeVarName='Civ2_Time';
3122                 ParamIn.vector_x='Civ2_U_smooth';
3123                 ParamIn.vector_y='Civ2_V_smooth';
3124                 ParamIn.vec_color='Civ2_C';
3125        end
3126    end
3127    set(handles.FixVelType,'visible','off')
3128    set(handles.VelType,'Visible','off')
3129    set(handles.VelType_1,'Visible','off')
3130    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3131    FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3132%     hget_field=findobj(allchild(0),'name','get_field');
3133%     if ~isempty(hget_field)
3134%         delete(hget_field)
3135%     end
3136    GetFieldData=get_field(FileName,ParamIn);
3137    FieldList={};
3138    VecColorList={};
3139    XName=GetFieldData.XVarName;
3140    if GetFieldData.CheckVector
3141        UName=GetFieldData.PanelVectors.vector_x;
3142        VName=GetFieldData.PanelVectors.vector_y;
3143        XName=GetFieldData.XVarName;
3144        YName=GetFieldData.YVarName;
3145        CName=GetFieldData.PanelVectors.vec_color;
3146        [FieldList,VecColorList]=set_field_list(UName,VName,CName);
3147    elseif GetFieldData.CheckScalar
3148        AName=GetFieldData.PanelScalar.scalar;
3149        XName=GetFieldData.XVarName;
3150        YName=GetFieldData.YVarName;
3151        FieldList={AName};
3152    elseif GetFieldData.CheckPlot1D;
3153        YName=GetFieldData.CheckPlot1D.ordinate;
3154    end
3155    set(handles.Coord_x,'String',{XName})
3156    set(handles.Coord_y,'String',{YName})
3157    set(handles.FieldName,'Value',1)
3158    set(handles.FieldName,'String',[FieldList; {'get_field...'}]);
3159    set(handles.ColorScalar,'Value',1)
3160    set(handles.ColorScalar,'String',VecColorList);
3161    UvData.FileType{1}='netcdf';
3162    set(handles.uvmat,'UserData',UvData)
3163    run0_Callback(hObject, eventdata, handles)
3164    return %no further action
3165end
3166
3167
3168
3169%read the rootfile input display
3170[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3171FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3172[tild,tild,tild,i1,i2,j1,j2,tild,NomType]=fileparts_uvmat(['xxx' get(handles.FileIndex,'String') FileExt]);
3173if isequal(field,'image')
3174    if  isfield(UvData.Field,'Civ2_ImageA')%get the corresponding input image in the netcdf file
3175        imagename=UvData.Field.Civ2_ImageA;
3176    elseif isfield(UvData.Field,'Civ1_ImageA')%
3177        imagename=UvData.Field.Civ1_ImageA;
3178    else
3179        SubDirBase=regexprep(SubDir,'\..*','');%take the root part of SubDir, before the first dot '.'
3180        imagename=fullfile_uvmat(RootPath,SubDirBase,RootFile,'.png',NomType,i1,[],j1,[]);
3181    end
3182    if ~exist(imagename,'file')
3183        [FileName,PathName] = uigetfile( ...
3184            {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3185            '*.jpg',' jpeg image files'; ...
3186            '*.png','.png image files'; ...
3187            '*.tif','.tif image files'; ...
3188            '*.avi;*.AVI','.avi movie files'; ...
3189            '*.vol','.volume images (png)'; ...
3190            '*.*',  'All Files (*.*)'}, ...
3191            'Pick an image',imagename);
3192        if ~ischar(FileName),return,end %abandon if the browser is cancelled
3193        imagename=[PathName FileName];
3194    end
3195     % display the selected field and related information
3196    display_file_name(handles,imagename)%display the image
3197    return
3198else
3199    ext=get(handles.FileExt,'String');
3200    if ~isequal(ext,'.nc') %find the new NomType if the previous display was not already a netcdf file
3201        [FileName,PathName] = uigetfile( ...
3202            {'*.nc', ' (*.nc)';
3203            '*.nc',' netcdf files'; ...
3204            '*.*',  'All Files (*.*)'}, ...
3205            'Pick a netcdf file',FileBase);
3206        if ~ischar(FileName),return,end %abandon if the browser is cancelled
3207        FullFileName=[PathName FileName];
3208        % display the selected field and related information
3209        display_file_name( handles,FullFileName)
3210        return
3211    end
3212end
3213indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
3214set(handles.FileIndex,'String',indices)
3215
3216%common to Fields_1_Callback
3217list_fields_1=get(handles.FieldName_1,'String');% list menu fields
3218field_1='';
3219if ~isempty(list_fields_1)
3220field_1= list_fields_1{get(handles.FieldName_1,'Value')}; % selected string
3221end
3222if isequal(field,'image')||isequal(field_1,'image')
3223    set(handles.TitleNpxy,'Visible','on')% visible npx,pxcm... buttons
3224    set(handles.num_Npx,'Visible','on')
3225    set(handles.num_Npy,'Visible','on')
3226else
3227    set(handles.TitleNpxy,'Visible','off')% visible npx,pxcm... buttons
3228    set(handles.num_Npx,'Visible','off')
3229    set(handles.num_Npy,'Visible','off')
3230end
3231if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3232    run0_Callback(hObject, eventdata, handles)
3233end
3234
3235%---------------------------------------------------
3236% --- Executes on menu selection FieldName
3237function FieldName_1_Callback(hObject, eventdata, handles)
3238%-------------------------------------------------
3239%% read input data
3240check_new=~get(handles.SubField,'Value'); %check_new=1 if a second field was not previously entered
3241UvData=get(handles.uvmat,'UserData');
3242if check_new && isfield(UvData,'XmlData')
3243    UvData.XmlData{2}=UvData.XmlData{1};
3244end
3245if isfield(UvData,'Field_1')
3246    UvData=rmfield(UvData,'Field_1');% remove the stored second field (a new one needs to be read)
3247end
3248UvData.FileName_1='';% desactivate the use of a constant second file
3249list_fields=get(handles.FieldName,'String');% list menu fields
3250field= list_fields{get(handles.FieldName,'Value')}; % selected string
3251list_fields=get(handles.FieldName_1,'String');% list menu fields
3252field_1= list_fields{get(handles.FieldName_1,'Value')}; % selected string for the second field
3253if isempty(field_1)%||(numel(UvData.FileType)>=2 && strcmp(UvData.FileType{2},'image'))
3254    set(handles.SubField,'Value',0)
3255    SubField_Callback(hObject, eventdata, handles)
3256    return
3257else
3258    set(handles.SubField,'Value',1)%state that a second field is now entered
3259end
3260
3261%% read the rootfile input display
3262[RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
3263FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
3264[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
3265switch field_1
3266    case 'get_field...'
3267        set_veltype_display(0) % no veltype display
3268        hget_field=findobj(allchild(0),'name','get_field_1');
3269        if ~isempty(hget_field)
3270            delete(hget_field)
3271        end
3272        hget_field=get_field(FileName_1);
3273        set(hget_field,'name','get_field_1')
3274        hhget_field=guidata(hget_field);
3275        set(hhget_field.list_fig,'Value',1)
3276        set(hhget_field.list_fig,'String',{'uvmat'})
3277        if check_new
3278            UvData.FileType{2}=UvData.FileType{1};
3279            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3280              set(handles.uvmat,'UserData',UvData)
3281        end
3282    case 'image'
3283        % get the image name corresponding to the current netcdf name (no unique correspondance)
3284        if  isfield(UvData.Field,'Civ2_ImageA')%get the corresponding input image in the netcdf file
3285            imagename=UvData.Field.Civ2_ImageA;
3286        elseif isfield(UvData.Field,'Civ1_ImageA')%
3287            imagename=UvData.Field.Civ1_ImageA;
3288        else
3289            SubDirBase=regexprep(SubDir_1,'\..*','');%take the root part of SubDir, before the first dot '.'
3290            imagename=fullfile_uvmat(RootPath_1,SubDirBase,RootFile_1,'.png',get(handles.NomType,'String'),i1,[],j1);
3291        end
3292        if ~exist(imagename,'file') % browse for images if it is not found
3293            [FileName,PathName] = uigetfile( ...
3294                {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3295                '*.jpg',' jpeg image files'; ...
3296                '*.png','.png image files'; ...
3297                '*.tif','.tif image files'; ...
3298                '*.avi;*.AVI','.avi movie files'; ...
3299                '*.vol','.volume images (png)'; ...
3300                '*.*',  'All Files (*.*)'}, ...
3301                'Pick an image',imagename);
3302            if ~ischar(FileName),return,end %abandon if the browser is cancelled
3303            imagename=[PathName FileName];
3304        end
3305        if ~ischar(imagename)% quit if the browser has  been closed
3306            set(handles.SubField,'Value',0)
3307        else %valid browser input:  display the selected image
3308            set(handles.TitleNpxy,'Visible','on')% visible npx,pxcm... buttons
3309            set(handles.num_Npx,'Visible','on')
3310            set(handles.num_Npy,'Visible','on')
3311            display_file_name(handles,imagename,2)%display the imag
3312        end
3313    otherwise
3314        check_refresh=1;
3315        if check_new% if a second field was not previously entered, we just read another field in the first input file
3316            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3317            set(handles.FileExt_1,'String',get(handles.FileExt,'String'))
3318           
3319            UvData.FileType{2}=UvData.FileType{1};
3320            UvData.XmlData{2}= UvData.XmlData{1};
3321            transform=get(handles.TransformPath,'UserData');
3322             if (~isa(transform,'function_handle')||nargin(transform)<3)
3323                set(handles.uvmat,'UserData',UvData)
3324                set(handles.TransformName,'value',2); % set transform fct to 'sub_field' if the current fct does not accept two input fields
3325                transform_fct_Callback(hObject, eventdata, handles)% activate transform_fct_Callback and refresh current plot
3326                 check_refresh=0;
3327             end             
3328        end
3329        if ~isequal(field,'image')
3330            set(handles.TitleNpxy,'Visible','off')% visible npx,pxcm... buttons
3331            set(handles.num_Npx,'Visible','off')
3332            set(handles.num_Npy,'Visible','off')
3333        end
3334        set(handles.uvmat,'UserData',UvData)
3335 
3336        if check_refresh && ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3337            run0_Callback(hObject, eventdata, handles)
3338        end
3339end
3340
3341%------------------------------------------------------------------------
3342% --- set the visibility of relevant velocity type menus:
3343function menu=set_veltype_display(Civ,FileType)
3344%------------------------------------------------------------------------
3345if ~exist('FileType','var')
3346    FileType='civx';
3347end
3348switch FileType
3349    case 'civx'
3350        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3351        if isequal(Civ,0)
3352            imax=0;
3353        elseif isequal(Civ,1) || isequal(Civ,2)
3354            imax=1;
3355        elseif isequal(Civ,3)
3356            imax=3;
3357        elseif isequal(Civ,4) || isequal(Civ,5)
3358            imax=4;
3359        elseif isequal(Civ,6) %patch2
3360            imax=6;
3361        end
3362    case 'civdata'
3363        menu={'civ1';'filter1';'civ2';'filter2'};
3364        if isequal(Civ,0)
3365            imax=0;
3366        elseif isequal(Civ,1) || isequal(Civ,2)
3367            imax=1;
3368        elseif isequal(Civ,3)
3369            imax=2;
3370        elseif isequal(Civ,4) || isequal(Civ,5)
3371            imax=3;
3372        elseif isequal(Civ,6) %patch2
3373            imax=4;
3374        end
3375end
3376menu=menu(1:imax);
3377
3378%------------------------------------------------------------------------
3379% --- Executes on button press in FixVelType.
3380function FixVelType_Callback(hObject, eventdata, handles)
3381%------------------------------------------------------------------------
3382% refresh the current plot if the fixed  veltype is unselected
3383if ~get(handles.FixVelType,'Value')
3384    run0_Callback(hObject, eventdata, handles)
3385end
3386
3387%------------------------------------------------------------------------
3388% --- Executes on button press in VelType.
3389function VelType_Callback(hObject, eventdata, handles)
3390%------------------------------------------------------------------------
3391set(handles.FixVelType,'Value',1)
3392run0_Callback(hObject, eventdata, handles)
3393
3394%------------------------------------------------------------------------
3395% --- Executes on choice selection in VelType_1.
3396function VelType_1_Callback(hObject, eventdata, handles)
3397%------------------------------------------------------------------------
3398set(handles.FixVelType,'Value',1)% the velocity type is now imposed by the GUI (not automatic)
3399UvData=get(handles.uvmat,'UserData');
3400set(handles.run0,'BackgroundColor',[1 1 0])%paint run0 button in yellow to indicate its activation
3401drawnow   
3402InputFile=read_GUI(handles.InputFile);% read the input file parameters
3403[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
3404[RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
3405FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];% name of the first input file
3406
3407check_refresh=0;
3408if isempty(InputFile.VelType_1)
3409        FileName_1='';% we plot the first input field without the second field
3410        set(handles.SubField,'Value',0)
3411        SubField_Callback(hObject, eventdata, handles)% activate SubField_Callback and refresh current plot, removing the second field
3412elseif get(handles.SubField,'Value')% if subfield is already 'on'
3413     FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];% name of the second input file
3414     check_refresh=1;%will refresh the current plot
3415else% we introduce the same file (with a different field) for the second series
3416     FileName_1=FileName;% we compare two fields in the same file
3417     UvData.FileType{2}=UvData.FileType{1};
3418     UvData.XmlData{2}= UvData.XmlData{1};
3419     set(handles.SubField,'Value',1)
3420     transform=get(handles.TransformPath,'UserData');
3421     if (~isa(transform,'function_handle')||nargin(transform)<3)
3422        set(handles.uvmat,'UserData',UvData)
3423        set(handles.TransformName,'value',2); % set transform fct to 'sub_field' if the current fct does not accept two input fields
3424        transform_fct_Callback(hObject, eventdata, handles)% activate transform_fct_Callback and refresh current plot
3425     else
3426         check_refresh=1;
3427     end 
3428end
3429
3430% refresh the current plot if it has not been done previously
3431if check_refresh
3432    UvData.FileName_1='';% desactivate the use of a constant second file
3433    set(handles.uvmat,'UserData',UvData)
3434    num_i1=stra2num(get(handles.i1,'String'));
3435    num_i2=stra2num(get(handles.i2,'String'));
3436    num_j1=stra2num(get(handles.j1,'String'));
3437    num_j2=stra2num(get(handles.j2,'String'));
3438    [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(['xx' FileIndex_1]);
3439    errormsg=refresh_field(handles,FileName,FileName_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1);
3440    if ~isempty(errormsg)
3441        msgbox_uvmat('ERROR',errormsg);
3442    else
3443        set(handles.i1,'BackgroundColor',[1 1 1])
3444        set(handles.i2,'BackgroundColor',[1 1 1])
3445        set(handles.j1,'BackgroundColor',[1 1 1])
3446        set(handles.j2,'BackgroundColor',[1 1 1])
3447        set(handles.FileIndex,'BackgroundColor',[1 1 1])
3448        set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
3449    end
3450    set(handles.run0,'BackgroundColor',[1 0 0])
3451end
3452
3453
3454%-----------------------------------------------------------------------
3455% --- reset civ buttons
3456function reset_vel_type(handles_civ0,handle1)
3457%-----------------------------------------------------------------------
3458for ibutton=1:length(handles_civ0)
3459    set(handles_civ0(ibutton),'BackgroundColor',[0.831 0.816 0.784])
3460    set(handles_civ0(ibutton),'Value',0)
3461end
3462if exist('handle1','var')%handles of selected button
3463        set(handle1,'BackgroundColor',[1 1 0]) 
3464end
3465
3466%-----------------------------------------------------------------------
3467% --- Executes on button press in MENUVOLUME.
3468function VOLUME_Callback(hObject, eventdata, handles)
3469%-----------------------------------------------------------------------
3470%errordlg('command VOL not implemented yet')
3471if ishandle(handles.UVMAT_title)
3472    delete(handles.UVMAT_title)
3473end
3474UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3475if isequal(get(handles.VOLUME,'Value'),1)
3476    set(handles.CheckZoom,'Value',0)
3477    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3478    set(handles.edit_vect,'Value',0)
3479    edit_vect_Callback(hObject, eventdata, handles)
3480    set(handles.edit_object,'Value',0)
3481    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3482%     set(handles.cal,'Value',0)
3483%     set(handles.cal,'BackgroundColor',[0 1 0])
3484    set(handles.edit_vect,'Value',0)
3485    edit_vect_Callback(hObject, eventdata, handles)
3486    %initiate set_object GUI
3487    data.Name='VOLUME';
3488    if isfield(UvData,'CoordType')
3489        data.CoordType=UvData.CoordType;
3490    end
3491    if isfield(UvData.Field,'CoordMesh')&~isempty(UvData.Field.CoordMesh)
3492        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
3493        data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
3494        data.DX=UvData.Field.CoordMesh;
3495        data.DY=UvData.Field.CoordMesh;
3496    elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3497        np=size(UvData.Field.A);
3498        meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
3499        meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
3500        data.RangeY=max(meshx,meshy);
3501        data.RangeX=max(meshx,meshy);
3502        data.DX=max(meshx,meshy);
3503    end
3504    data.ParentButton=handles.VOLUME;
3505    PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
3506    [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes,
3507                                                      % associate the set_object interface handle to the plotting axes
3508    %set(hset_object,'Position',get(handles.uvmat,'Position')+UvData.OpenParam.PosSetObject)
3509    UvData.MouseAction='create_object';
3510else
3511    set(handles.VOLUME,'BackgroundColor',[0 1 0])
3512end
3513set(handles.uvmat,'UserData',UvData)
3514
3515%-------------------------------------------------------
3516function edit_vect_Callback(hObject, eventdata, handles)
3517%-------------------------------------------------------
3518%
3519if isequal(get(handles.edit_vect,'Value'),1)
3520    VelTypeMenu=get(handles.VelType,'String');
3521    VelType=VelTypeMenu{get(handles.VelType,'Value')};
3522    if ~strcmp(VelType,'civ2') && ~strcmp(VelType,'civ1')
3523        msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
3524    end
3525    set(handles.record,'Visible','on')
3526    set(handles.edit_vect,'BackgroundColor',[1 1 0])
3527    set(handles.edit_object,'Value',0)
3528    set(handles.CheckZoom,'Value',0)
3529    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3530    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3531    set(gcf,'Pointer','arrow')
3532else
3533    set(handles.record,'Visible','off')
3534    set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7])
3535end
3536
3537%----------------------------------------------
3538function save_mask_Callback(hObject, eventdata, handles)
3539%-----------------------------------------------------------------------
3540UvData=get(handles.uvmat,'UserData');
3541
3542flag=1;
3543npx=size(UvData.Field.A,2);
3544npy=size(UvData.Field.A,1);
3545xi=0.5:npx-0.5;
3546yi=0.5:npy-0.5;
3547[Xi,Yi]=meshgrid(xi,yi);
3548if isfield(UvData,'Object')
3549    for iobj=1:length(UvData.Object)
3550        ObjectData=UvData.Object{iobj};
3551        if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
3552            flagobj=1;
3553            testphys=0; %coordinates in pixels by default
3554            if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys')
3555                if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
3556                    Calib=UvData.XmlData{1}.GeometryCalib;
3557                    testphys=1;
3558                end
3559            end
3560            if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style')
3561                if isequal(ObjectData.Type,'polygon')
3562                    X=ObjectData.Coord(:,1);
3563                    Y=ObjectData.Coord(:,2);
3564                    if testphys
3565                        [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
3566                    end
3567                    flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside                 
3568                elseif isequal(ObjectData.Type,'ellipse')
3569                    if testphys
3570                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3571                    end
3572                    RangeX=max(ObjectData.RangeX);
3573                    RangeY=max(ObjectData.RangeY);
3574                    X2Max=RangeX*RangeX;
3575                    Y2Max=RangeY*RangeY;
3576                    distX=(Xi-ObjectData.Coord(1,1));
3577                    distY=(Yi-ObjectData.Coord(1,2));
3578                    flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
3579                elseif isequal(ObjectData.Type,'rectangle')
3580                    if testphys
3581                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3582                    end
3583                    distX=abs(Xi-ObjectData.Coord(1,1));
3584                    distY=abs(Yi-ObjectData.Coord(1,2));
3585                    flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
3586                end
3587                if isequal(ObjectData.ProjMode,'mask_outside')
3588                    flagobj=~flagobj;
3589                end
3590                flag=flag & flagobj;
3591            end
3592        end
3593    end
3594end
3595% flag=~flag;
3596%mask name
3597RootPath=get(handles.RootPath,'String');
3598RootFile=get(handles.RootFile,'String');
3599RootFile=regexprep(RootFile,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3600filebase=fullfile(RootPath,RootFile);
3601list=get(handles.masklevel,'String');
3602masknumber=num2str(length(list));
3603maskindex=get(handles.masklevel,'Value');
3604mask_name=fullfile_uvmat(RootPath,SubDir,[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
3605%mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
3606imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
3607imflag=flipdim(imflag,1);
3608% imflag=uint8(255*flag);% =0 for flag=0 (vectors=0 when 20<imflag<200)
3609msgbox_uvmat('CONFIRMATION',[mask_name ' saved'])
3610imwrite(imflag,mask_name,'BitDepth',8);
3611
3612%display the mask
3613figure;
3614vec=linspace(0,1,256);%define a linear greyscale colormap
3615map=[vec' vec' vec'];
3616colormap(map)
3617
3618image(imflag);
3619
3620%-------------------------------------------------------------------
3621%-------------------------------------------------------------------
3622%  - FUNCTIONS FOR SETTING PLOTTING PARAMETERS
3623
3624%------------------------------------------------------------------
3625%-------------------------------------------------------------
3626% --- Executes on selection change in TransformName.
3627
3628function TransformName_Callback(hObject, eventdata, handles)
3629%-------------------------------------------------------------
3630UvData=get(handles.uvmat,'UserData');
3631menu=get(handles.TransformName,'String');refresh
3632ichoice=get(handles.TransformName,'Value');%item number in the menu
3633transform_name=menu{ichoice};% choice of the transform fct
3634list_path=get(handles.TransformName,'UserData');
3635
3636%% add a new item to the menu if the option 'more...' has been selected
3637prev_path=fullfile(get(handles.TransformPath,'String'));
3638if ~exist(prev_path,'dir')
3639    prev_path=fullfile(fileparts(which('uvmat')),'transform_field');
3640end
3641if strcmp(transform_name,'more...');
3642    [FileName, PathName] = uigetfile( ...
3643        {'*.m', ' (*.m)';
3644        '*.m',  '.m files '; ...
3645        '*.*', 'All Files (*.*)'}, ...
3646        'Pick the transform function', prev_path);
3647    if ~ischar(FileName),return,end %abandon if the browser is cancelled
3648    path_transform_fct =fullfile(PathName,FileName);
3649    if isempty(regexp(FileName,'\.m$'))% detect file extension .m
3650        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3651        return
3652    else
3653        transform_name=regexprep(FileName,'\.m','');
3654    end
3655    ichoice=find(strcmp(transform_name,menu),1);%look for the selected fct in the existing menu
3656    if isempty(ichoice)% if the item is not found, add it to the menu (before 'more...' and select it)
3657        menu=[menu(1:end-1);{transform_name};{'more...'}];
3658        ichoice=numel(menu)-1;   
3659    end
3660    list_path{ichoice}=PathName;%update the list fo fct paths
3661    set(handles.TransformName,'String',menu)
3662    set(handles.TransformName,'Value',ichoice)
3663   
3664    % save the new menu in the personal file 'uvmat_perso.mat'
3665    dir_perso=prefdir;%personal Matalb directory
3666    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3667    if exist(profil_perso,'file')
3668        nb_builtin=UvData.OpenParam.NbBuiltin;% number of 'builtin' (basic) transform fcts in uvmat
3669        if nb_builtin<numel(list_path)
3670        for ilist=nb_builtin+1:numel(list_path)
3671            transform_fct{ilist-nb_builtin}=[fullfile(list_path{ilist},menu{ilist}) '.m'];
3672        end
3673        save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
3674        end
3675    end
3676end
3677
3678%% create the function handle of the selected fct
3679
3680if isempty(list_path{ichoice})% case of no selected fct
3681    transform_handle=[];
3682else
3683    if ~exist(list_path{ichoice},'dir')
3684        msgbox_uvmat('ERROR','invalid fct path: select the transform fct again with the option more...')
3685        return
3686    end
3687    current_dir=pwd;%current working dir
3688    cd(list_path{ichoice})
3689    transform_handle=str2func(transform_name);
3690    cd(current_dir)
3691end
3692set(handles.TransformPath,'String',list_path{ichoice})
3693set(handles.TransformPath,'UserData',transform_handle)
3694set(handles.TransformName,'UserData',list_path)
3695
3696%% update the ToolTip string of the menu TransformName with the first line of the selected fct file
3697if isempty(list_path{ichoice})% case of no selected fct
3698    set(handles.TransformName,'ToolTipString','transform_fct:choose a transform function')
3699else
3700    try
3701        [fid,errormsg] =fopen([fullfile(list_path{ichoice},transform_name) '.m']);
3702        InputText=textscan(fid,'%s',1,'delimiter','\n');
3703        fclose(fid)
3704        set(handles.TransformName,'ToolTipString',['transform_fct: ' InputText{1}{1}])% put the first line of the selected function as tooltip help
3705    end
3706end
3707
3708%% adapt the GUI to the input/output conditions of the selected transform fct
3709DataOut=[];
3710CoordUnit='';
3711CoordUnitPrev='';
3712if isfield(UvData,'Field')&&isfield(UvData.Field,'CoordUnit')
3713    CoordUnitPrev=UvData.Field.CoordUnit;
3714end
3715if ~isempty(list_path{ichoice})
3716    if nargin(transform_handle)>1 && isfield(UvData,'XmlData')&&~isempty(UvData.XmlData)
3717        XmlData=UvData.XmlData{1};
3718        DataOut=feval(transform_handle,'*',XmlData);
3719        if isfield(DataOut,'CoordUnit')
3720            CoordUnit=DataOut.CoordUnit;
3721        end
3722        if isfield(DataOut,'InputFieldType')
3723            UvData.InputFieldType=DataOut.InputFieldType;
3724        end
3725    else
3726        DataOut=feval(transform_handle,'*');
3727    end
3728end
3729
3730
3731%% delete drawn objects if the output CooordUnit is different from the previous one
3732if ~strcmp(CoordUnit,CoordUnitPrev)
3733    set(handles.CheckFixLimits,'Value',0)
3734set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
3735    hother=findobj('Tag','proj_object');%find all the proj objects
3736    for iobj=1:length(hother)
3737        delete_object(hother(iobj))
3738    end
3739    hother=findobj('Tag','DeformPoint');%find all the proj objects
3740    for iobj=1:length(hother)
3741        delete_object(hother(iobj))
3742    end
3743    hh=findobj('Tag','calib_points');
3744    if ~isempty(hh)
3745        delete(hh)
3746    end
3747    hhh=findobj('Tag','calib_marker');
3748    if ~isempty(hhh)
3749        delete(hhh)
3750    end
3751%     if isfield(UvData,'Object')
3752%         UvData.Object=UvData.Object(1);
3753%     end
3754    set(handles.ListObject,'Value',1)
3755    set(handles.ListObject,'String',{''})
3756    set(handles.ListObject_1,'Value',1)
3757    set(handles.ListObject_1,'String',{''})
3758    set(handles.ViewObject,'value',0)
3759    ViewObject_Callback(hObject, eventdata, handles)
3760    set(handles.ViewField,'value',0)
3761    ViewField_Callback(hObject, eventdata, handles)
3762    set(handles.edit_object,'Value',0)
3763    edit_object_Callback(hObject, eventdata, handles)
3764    UvData.Object={[]};
3765end
3766set(handles.uvmat,'UserData',UvData)
3767
3768%% refresh the current plot
3769if isempty(list_path{ichoice}) || nargin(transform_handle)<3
3770    set(handles.SubField,'Value',0)
3771    SubField_Callback(hObject, eventdata, handles)
3772else
3773    run0_Callback(hObject, eventdata, handles)
3774end
3775
3776%------------------------------------------------
3777%CALLBACKS FOR PLOTTING PARAMETERS
3778%-------------------------------------------------
3779%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3780% Plot coordinates
3781%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3782%------------------------------------------------------------------------
3783function num_MinX_Callback(hObject, eventdata, handles)
3784%------------------------------------------------------------------------
3785set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3786set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3787update_plot(handles);
3788
3789%------------------------------------------------------------------------
3790function num_MaxX_Callback(hObject, eventdata, handles)
3791%------------------------------------------------------------------------
3792set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3793set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3794update_plot(handles);
3795
3796%------------------------------------------------------------------------
3797function num_MinY_Callback(hObject, eventdata, handles)
3798%------------------------------------------
3799set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3800set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3801update_plot(handles);
3802
3803%------------------------------------------------------------------------
3804function num_MaxY_Callback(hObject, eventdata, handles)
3805%------------------------------------------------------------------------
3806set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3807set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3808update_plot(handles);
3809
3810%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3811% Scalar or image representation
3812%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3813%------------------------------------------------------------------------
3814function num_MinA_Callback(hObject, eventdata, handles)
3815%------------------------------------------
3816set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3817set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3818MinA=str2double(get(handles.num_MinA,'String'));
3819MaxA=str2double(get(handles.num_MaxA,'String'));
3820if MinA>MaxA% switch minA and maxA in case of error
3821    MinA_old=MinA;
3822    MinA=MaxA;
3823    MaxA=MinA_old;
3824    set(handles.num_MinA,'String',num2str(MinA,5));
3825    set(handles.num_MaxA,'String',num2str(MaxA,5));
3826end
3827update_plot(handles);
3828
3829%------------------------------------------------------------------------
3830function num_MaxA_Callback(hObject, eventdata, handles)
3831%------------------------------------------------------------------------
3832set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3833set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3834MinA=str2double(get(handles.num_MinA,'String'));
3835MaxA=str2double(get(handles.num_MaxA,'String'));
3836if MinA>MaxA% switch minA and maxA in case of error
3837        MinA_old=MinA;
3838    MinA=MaxA;
3839    MaxA=MinA_old;
3840    set(handles.num_MinA,'String',num2str(MinA,5));
3841    set(handles.num_MaxA,'String',num2str(MaxA,5));
3842end
3843update_plot(handles);
3844
3845%------------------------------------------------------------------------
3846function CheckFixScalar_Callback(hObject, eventdata, handles)
3847%------------------------------------------------------------------------
3848test=get(handles.CheckFixScalar,'Value');
3849if test
3850    set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3851else
3852    set(handles.CheckFixScalar,'BackgroundColor',[0.7 0.7 0.7])
3853    update_plot(handles);
3854end
3855
3856%-------------------------------------------------------------------
3857function CheckBW_Callback(hObject, eventdata, handles)
3858%-------------------------------------------------------------------
3859update_plot(handles);
3860
3861%-------------------------------------------------------------------
3862function num_Opacity_Callback(hObject, eventdata, handles)
3863update_plot(handles);
3864%-------------------------------------------------------------------
3865
3866%-------------------------------------------------------------------
3867function ListContour_Callback(hObject, eventdata, handles)
3868%-------------------------------------------------------------------
3869val=get(handles.ListContour,'Value');
3870if val==2
3871    set(handles.interval_txt,'Visible','on')
3872    set(handles.num_IncrA,'Visible','on')
3873else
3874    set(handles.interval_txt,'Visible','off')
3875    set(handles.num_IncrA,'Visible','off')
3876end
3877update_plot(handles);
3878
3879%-------------------------------------------------------------------
3880function num_IncrA_Callback(hObject, eventdata, handles)
3881%-------------------------------------------------------------------
3882update_plot(handles);
3883
3884
3885%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3886% Vector representation
3887%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3888%-------------------------------------------------------------------
3889function CheckHideWarning_Callback(hObject, eventdata, handles)
3890%-------------------------------------------------------------------
3891update_plot(handles);
3892
3893%-------------------------------------------------------------------
3894function CheckHideFalse_Callback(hObject, eventdata, handles)
3895%-------------------------------------------------------------------
3896update_plot(handles);
3897
3898%-------------------------------------------------------------------
3899function num_VecScale_Callback(hObject, eventdata, handles)
3900%-------------------------------------------------------------------
3901set(handles.CheckFixVectors,'Value',1);
3902set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3903update_plot(handles);
3904
3905%-------------------------------------------------------------------
3906function CheckFixVectors_Callback(hObject, eventdata, handles)
3907%-------------------------------------------------------------------
3908test=get(handles.CheckFixVectors,'Value');
3909if test
3910    set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3911else
3912    update_plot(handles);
3913    %set(handles.num_VecScale,'String',num2str(ScalOut.num_VecScale,3))
3914    set(handles.CheckFixVectors,'BackgroundColor',[0.7 0.7 0.7])
3915end
3916
3917%------------------------------------------------------------------------
3918% --- Executes on selection change in CheckDecimate4 (nb_vec/4).
3919function CheckDecimate4_Callback(hObject, eventdata, handles)
3920%------------------------------------------------------------------------
3921if isequal(get(handles.CheckDecimate4,'Value'),1)
3922    set(handles.CheckDecimate16,'Value',0)
3923end
3924update_plot(handles);
3925
3926%------------------------------------------------------------------------
3927% --- Executes on selection change in CheckDecimate16 (nb_vec/16).
3928function CheckDecimate16_Callback(hObject, eventdata, handles)
3929%------------------------------------------------------------------------
3930if isequal(get(handles.CheckDecimate16,'Value'),1)
3931    set(handles.CheckDecimate4,'Value',0)
3932end
3933update_plot(handles);
3934
3935%------------------------------------------------------------------------
3936% --- Executes on selection change in ColorCode menu
3937function ColorCode_Callback(hObject, eventdata, handles)
3938%------------------------------------------------------------------------
3939% edit the choice for color code
3940update_color_code_boxes(handles);
3941update_plot(handles);
3942
3943%------------------------------------------------------------------------
3944function update_color_code_boxes(handles)
3945%------------------------------------------------------------------------
3946list_code=get(handles.ColorCode,'String');% list menu fields
3947colcode= list_code{get(handles.ColorCode,'Value')}; % selected field
3948enable_slider='off';%default
3949enable_bounds='off';%default
3950enable_scalar='off';%default
3951switch colcode
3952    case {'rgb','bgr'}
3953        enable_slider='on';
3954        enable_bounds='on';
3955        enable_scalar='on';
3956    case '64 colors'
3957        enable_bounds='on';
3958        enable_scalar='on';
3959end
3960set(handles.Slider1,'Visible',enable_slider)
3961set(handles.Slider2,'Visible', enable_slider)
3962set(handles.num_ColCode1,'Visible',enable_slider)
3963set(handles.num_ColCode2,'Visible',enable_slider)
3964set(handles.TitleColCode1,'Visible',enable_slider)
3965set(handles.TitleColCode2,'Visible',enable_slider)
3966set(handles.CheckFixVecColor,'Visible',enable_bounds)
3967set(handles.num_MinVec,'Visible',enable_bounds)
3968set(handles.num_MaxVec,'Visible',enable_bounds)
3969set(handles.ColorScalar,'Visible',enable_scalar)
3970set_vec_col_bar(handles)
3971
3972%------------------------------------------------------------------
3973% --- Executes on selection change in ColorScalar: choice of the color code.
3974function ColorScalar_Callback(hObject, eventdata, handles)
3975%------------------------------------------------------------------
3976% edit the choice for color code
3977list_scalar=get(handles.ColorScalar,'String');% list menu fields
3978col_scalar= list_scalar{get(handles.ColorScalar,'Value')}; % selected field
3979if isequal(col_scalar,'ima_cor')
3980    set(handles.CheckFixVecColor,'Value',1)%fixed scale by default
3981    ColorCode='rgb';
3982    set(handles.num_MinVec,'String','0')
3983    set(handles.num_MaxVec,'String','1')
3984    set(handles.num_ColCode1,'String','0.333')
3985    set(handles.num_ColCode2,'String','0.666')
3986else
3987    set(handles.CheckFixVecColor,'Value',0)%auto scale between min,max by default
3988    ColorCode='64 colors';
3989end
3990ColorCodeList=get(handles.ColorCode,'String');
3991ichoice=find(strcmp(ColorCode,ColorCodeList),1);
3992set(handles.ColorCode,'Value',ichoice)% set color code in the menu
3993
3994update_color_code_boxes(handles);
3995%replot the current graph
3996run0_Callback(hObject, eventdata, handles)
3997
3998%----------------------------------------------------------------
3999% -- Executes on slider movement to set the color code
4000%
4001function Slider1_Callback(hObject, eventdata, handles)
4002%------------------------------------------------------------------
4003slider1=get(handles.Slider1,'Value');
4004min_val=str2num(get(handles.num_MinVec,'String'));
4005max_val=str2num(get(handles.num_MaxVec,'String'));
4006col=min_val+(max_val-min_val)*slider1;
4007set(handles.num_ColCode1,'String',num2str(col))
4008if(get(handles.Slider2,'Value') < col)%move also the second slider at the same value if needed
4009    set(handles.Slider2,'Value',col)
4010    set(handles.num_ColCode2,'String',num2str(col))
4011end
4012set_vec_col_bar(handles)
4013update_plot(handles);
4014
4015%----------------------------------------------------------------
4016% Executes on slider movement to set the color code
4017%----------------------------------------------------------------
4018function Slider2_Callback(hObject, eventdata, handles)
4019slider2=get(handles.Slider2,'Value');
4020min_val=str2num(get(handles.num_MinVec,'String'));
4021max_val=str2num(get(handles.num_MaxVec,'String'));
4022col=min_val+(max_val-min_val)*slider2;
4023set(handles.num_ColCode2,'String',num2str(col))
4024if(get(handles.Slider1,'Value') > col)%move also the first slider at the same value if needed
4025    set(handles.Slider1,'Value',col)
4026    set(handles.num_ColCode1,'String',num2str(col))
4027end
4028set_vec_col_bar(handles)
4029update_plot(handles);
4030
4031%----------------------------------------------------------------
4032% --- Execute on return carriage on the edit box corresponding to slider 1
4033%----------------------------------------------------------------
4034function num_ColCode1_Callback(hObject, eventdata, handles)
4035set_vec_col_bar(handles)
4036update_plot(handles);
4037
4038%----------------------------------------------------------------
4039% --- Execute on return carriage on the edit box corresponding to slider 2
4040%----------------------------------------------------------------
4041function num_ColCode2_Callback(hObject, eventdata, handles)
4042set_vec_col_bar(handles)
4043update_plot(handles);
4044%------------------------------------------------------------------------
4045%-------------------------------------------------------
4046% --- Executes on button press in CheckFixVecColor.
4047%-------------------------------------------------------
4048function VecColBar_Callback(hObject, eventdata, handles)
4049set_vec_col_bar(handles)
4050
4051%------------------------------------------------------------------------
4052% --- Executes on button press in CheckFixVecColor.
4053function CheckFixVecColor_Callback(hObject, eventdata, handles)
4054%------------------------------------------------------------------------
4055if ~get(handles.CheckFixVecColor,'Value')
4056    update_plot(handles);
4057end
4058
4059%------------------------------------------------------------------------
4060% --- Executes on selection change in num_MaxVec.
4061function num_MinVec_Callback(hObject, eventdata, handles)
4062%------------------------------------------------------------------------
4063max_vec_Callback(hObject, eventdata, handles)
4064
4065%------------------------------------------------------------------------
4066% --- Executes on selection change in num_MaxVec.
4067function num_MaxVec_Callback(hObject, eventdata, handles)
4068%------------------------------------------------------------------------
4069set(handles.CheckFixVecColor,'Value',1)
4070CheckFixVecColor_Callback(hObject, eventdata, handles)
4071min_val=str2num(get(handles.num_MinVec,'String'));
4072max_val=str2num(get(handles.num_MaxVec,'String'));
4073slider1=get(handles.Slider1,'Value');
4074slider2=get(handles.Slider2,'Value');
4075colcode1=min_val+(max_val-min_val)*slider1;
4076colcode2=min_val+(max_val-min_val)*slider2;
4077set(handles.num_ColCode1,'String',num2str(colcode1))
4078set(handles.num_ColCode2,'String',num2str(colcode2))
4079update_plot(handles);
4080
4081%------------------------------------------------------------------------
4082% --- update the display of color code for vectors (on vecColBar)
4083function set_vec_col_bar(handles)
4084%------------------------------------------------------------------------
4085%get the image of the color display button 'VecColBar' in pixels
4086set(handles.VecColBar,'Unit','pixel');
4087pos_vert=get(handles.VecColBar,'Position');
4088set(handles.VecColBar,'Unit','Normalized');
4089width=ceil(pos_vert(3));
4090height=ceil(pos_vert(4));
4091
4092%get slider indications
4093list=get(handles.ColorCode,'String');
4094ichoice=get(handles.ColorCode,'Value');
4095colcode.ColorCode=list{ichoice};
4096colcode.MinVec=str2num(get(handles.num_MinVec,'String'));
4097colcode.MaxVec=str2num(get(handles.num_MaxVec,'String'));
4098test3color=strcmp(colcode.ColorCode,'rgb') || strcmp(colcode.ColorCode,'bgr');
4099if test3color
4100    colcode.ColCode1=str2num(get(handles.num_ColCode1,'String'));
4101    colcode.ColCode2=str2num(get(handles.num_ColCode2,'String'));
4102end
4103vec_C=colcode.MinVec+(colcode.MaxVec-colcode.MinVec)*(0.5:width-0.5)/width;%sample of vec_C values from min to max
4104[colorlist,col_vec]=set_col_vec(colcode,vec_C);
4105oneheight=ones(1,height);
4106A1=colorlist(col_vec,1)*oneheight;
4107A2=colorlist(col_vec,2)*oneheight;
4108A3=colorlist(col_vec,3)*oneheight;
4109A(:,:,1)=A1';
4110A(:,:,2)=A2';
4111A(:,:,3)=A3';
4112set(handles.VecColBar,'Cdata',A)
4113
4114%-------------------------------------------------------------------
4115function update_plot(handles)
4116%-------------------------------------------------------------------
4117UvData=get(handles.uvmat,'UserData');
4118AxeData=UvData.PlotAxes;% retrieve the current plotted data
4119PlotParam=read_GUI(handles.uvmat);
4120[tild,PlotParamOut]= plot_field(AxeData,handles.PlotAxes,PlotParam);
4121errormsg=fill_GUI(PlotParamOut,handles.uvmat);
4122%write_plot_param(handles,PlotParamOut); %update the auto plot parameters
4123
4124%------------------------------------------------------------------------
4125%------------------------------------------------------------------------
4126%   SELECTION AND EDITION OF PROJECTION OBJECTS
4127%------------------------------------------------------------------------
4128%------------------------------------------------------------------------
4129
4130% --- Executes on selection change in ListObject_1.
4131function ListObject_1_Callback(hObject, eventdata, handles)
4132list_str=get(handles.ListObject,'String');
4133UvData=get(handles.uvmat,'UserData');
4134ObjectData=UvData.Object{get(handles.ListObject_1,'Value')};
4135
4136%% update the projection plot on uvmat
4137ProjData= proj_field(UvData.Field,ObjectData);%project the current input field on object ObjectData
4138plot_field(ProjData,handles.PlotAxes,read_GUI(handles.uvmat));% plot the projected field;
4139%replot all the objects within the new projected field
4140for IndexObj=1:numel(list_str)
4141        hobject=UvData.Object{IndexObj}.DisplayHandle.uvmat;
4142        if isempty(hobject) || ~ishandle(hobject)
4143            hobject=handles.PlotAxes;
4144        end
4145        if isequal(IndexObj,get(handles.ListObject,'Value'))
4146            objectcolor='m'; %paint in magenta the currently selected object in ListObject
4147        else
4148            objectcolor='b';
4149        end
4150        UvData.Object{IndexObj}.DisplayHandle.uvmat=plot_object(UvData.Object{IndexObj},ObjectData,hobject,objectcolor);%draw the object in uvmat     
4151end
4152set(handles.uvmat,'UserData',UvData)
4153
4154%% display the object parameters if the GUI set_object is already opened
4155if ~get(handles.ViewObject,'Value')
4156    ZBounds=0; % default
4157    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4158        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4159        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4160    end
4161    ObjectData.Name=list_str{get(handles.ListObject_1,'Value')};
4162    set_object(ObjectData,[],ZBounds);
4163    set(handles.ViewObject,'Value',1)% show that the selected object in ListObject_1 is currently visualised
4164end
4165
4166%  desactivate the edit object mode
4167set(handles.edit_object,'Value',0)
4168set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])
4169
4170%------------------------------------------------------------------------
4171% --- Executes on selection change in ListObject.
4172function ListObject_Callback(hObject, eventdata, handles)
4173%------------------------------------------------------------------------
4174list_str=get(handles.ListObject,'String');
4175IndexObj=get(handles.ListObject,'Value');%present object selection
4176
4177%% The object  is displayed in set_object if this GUI is already opened
4178UvData=get(handles.uvmat,'UserData');
4179ObjectData=UvData.Object{IndexObj};
4180hset_object=findobj(allchild(0),'tag','set_object');
4181if ~isempty(hset_object)
4182    ZBounds=0; % default
4183    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4184        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4185        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4186    end
4187    ObjectData.Name=list_str{IndexObj};
4188    set_object(ObjectData,[],ZBounds);
4189    set(handles.ViewField,'Value',1)% show that the selected object in ListObject is currently visualised
4190end
4191
4192%%  desactivate the edit object mode
4193set(handles.edit_object,'Value',0)
4194set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])
4195
4196%% update the  plot on view_field if view_field is already openened
4197hview_field=findobj(allchild(0),'tag','view_field');
4198if isempty(hview_field)
4199    hhview_field.PlotAxes=[];
4200else
4201    Data=get(hview_field,'UserData');
4202    hhview_field=guidata(hview_field);
4203    ProjData= proj_field(UvData.Field,ObjectData);%project the current interface field on ObjectData
4204    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.PlotAxes,read_GUI(hview_field));%read plotting parameters on the uvmat interface
4205   
4206    %write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
4207    haxes=findobj(hview_field,'tag','axes3');
4208    pos=get(hview_field,'Position'); 
4209    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
4210        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
4211        pos_table=get(h_TableDisplay,'Position');
4212        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
4213        drawnow% needed to change position before the next command
4214        set(hview_field,'UserData',Data);% restore the previously stored GUI position after GUI resizing
4215    else
4216        set(hview_field,'Position',Data.GUISize)% return to the previously stored GUI position and size
4217    end
4218end
4219
4220%% update the color of the graphic object representation: the selected object in magenta, others in blue
4221update_object_color(handles.PlotAxes,hhview_field.PlotAxes,UvData.Object{IndexObj}.DisplayHandle.uvmat)
4222
4223%------------------------------------------------------------------------
4224%--- update the color representation of objects (indicating the selected ones)
4225function update_object_color(axes_uvmat,axes_view_field,DisplayHandle)
4226%------------------------------------------------------------------------
4227if isempty(axes_view_field)% case with no view_field plot
4228hother=[findobj(axes_uvmat,'Tag','proj_object');findobj(axes_uvmat,'Tag','DeformPoint')];%find all the proj object and deform point representations
4229else
4230hother=[findobj(axes_uvmat,'Tag','proj_object') ;findobj(axes_view_field,'Tag','proj_object');... %find all the proj object representations
4231findobj(axes_uvmat,'Tag','DeformPoint'); findobj(axes_view_field,'Tag','DeformPoint')];%find all the deform point representations
4232end
4233for iobj=1:length(hother)
4234    if isequal(get(hother(iobj),'Type'),'rectangle')||isequal(get(hother(iobj),'Type'),'patch')
4235        set(hother(iobj),'EdgeColor','b')
4236        if isequal(get(hother(iobj),'FaceColor'),'m')
4237            set(hother(iobj),'FaceColor','b')
4238        end
4239    elseif isequal(get(hother(iobj),'Type'),'image')
4240        Acolor=get(hother(iobj),'CData');
4241        Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2));
4242        set(hother(iobj),'CData',Acolor);
4243    else
4244        set(hother(iobj),'Color','b')
4245    end
4246    set(hother(iobj),'Selected','off')
4247end
4248if ishandle(DisplayHandle)
4249    linetype=get(DisplayHandle,'Type');
4250    if isequal(linetype,'line')
4251        set(DisplayHandle,'Color','m'); %set the selected object to magenta color
4252    elseif isequal(linetype,'rectangle')
4253        set(DisplayHandle,'EdgeColor','m'); %set the selected object to magenta color
4254    elseif isequal(linetype,'patch')
4255        set(DisplayHandle,'FaceColor','m'); %set the selected object to magenta color
4256    end
4257    SubObjectData=get(DisplayHandle,'UserData');
4258    if isfield(SubObjectData,'SubObject') & ishandle(SubObjectData.SubObject)
4259        for iobj=1:length(SubObjectData.SubObject)
4260            hsub=SubObjectData.SubObject(iobj);
4261            if isequal(get(hsub,'Type'),'rectangle')
4262                set(hsub,'EdgeColor','m'); %set the selected object to magenta color
4263            elseif isequal(get(hsub,'Type'),'image')
4264                Acolor=get(hsub,'CData');
4265                Acolor(:,:,1)=Acolor(:,:,3);
4266                set(hsub,'CData',Acolor);
4267            else
4268                set(hsub,'Color','m')
4269            end
4270        end
4271    end
4272    if isfield(SubObjectData,'DeformPoint') & ishandle(SubObjectData.DeformPoint)
4273        set(SubObjectData.DeformPoint,'Color','m')
4274    end
4275end
4276
4277%-------------------------------------------------------------------
4278% --- Executes on selection change in edit_object.
4279function edit_object_Callback(hObject, eventdata, handles)
4280%-------------------------------------------------------------------
4281hset_object=findobj(allchild(0),'Tag','set_object');
4282if get(handles.edit_object,'Value')
4283    set(handles.edit_object,'BackgroundColor',[1,1,0]) 
4284    %suppress the other options
4285    set(handles.CheckZoom,'Value',0)
4286    CheckZoom_Callback(hObject, eventdata, handles)
4287    hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4288    if ishandle(hgeometry_calib)
4289        hhgeometry_calib=guidata(hgeometry_calib);
4290        set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4291        set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4292    end
4293    set(handles.ViewObject,'value',1)
4294    ViewObject_Callback(hObject, eventdata, handles)
4295else % desctivate object edit mode
4296    set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4297    if ~isempty(hset_object)% open the
4298        hhset_object=guidata(hset_object);
4299        set(hhset_object.PLOT,'enable','off');
4300        set(get(hset_object,'children'),'enable','inactive')
4301    end
4302end
4303
4304
4305%------------------------------------------------------------------------
4306% --- Executes on button press in ViewObject.
4307function ViewObject_Callback(hObject, eventdata, handles)
4308%------------------------------------------------------------------------
4309check_view=get(handles.ViewObject,'Value');
4310
4311if check_view %activate set_object   
4312    IndexObj=get(handles.ListObject,'Value');
4313    list_object=get(handles.ListObject,'String');
4314    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4315    UvData.Object{IndexObj}.Name=list_object{IndexObj};
4316    if numel(UvData.Object)<IndexObj;% error in UvData
4317        msgbox_uvmat('ERROR','invalid object list')
4318        return
4319    end
4320    ZBounds=0; % default
4321    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4322        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4323        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4324    end
4325%     set(handles.ListObject_1,'Value',IndexObj);%restore ListObject selection after set_object deletion
4326    data=UvData.Object{IndexObj};
4327    if ~isfield(data,'Type')% default plane
4328        data.Type='plane';
4329    end
4330%     if isfield(UvData,'Field')
4331%         Field=UvData.Field;
4332%         if isfield(UvData.Field,'Mesh')&&~isempty(UvData.Field.Mesh)
4333%             data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
4334%             if strcmp(data.Type,'line')||strcmp(data.Type,'polyline')
4335%                 data.RangeY=UvData.Field.Mesh;
4336%             else
4337%                 data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
4338%             end
4339%             data.DX=UvData.Field.Mesh;
4340%             data.DY=UvData.Field.Mesh;
4341%         end
4342%         if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
4343%             data.Coord=[0 0 0]; %default
4344%         end
4345%         if isfield(Field,'CoordUnit')
4346%             data.CoordUnit=Field.CoordUnit;
4347%         end
4348%     end
4349    hset_object=set_object(data,[],ZBounds);
4350    hhset_object=guidata(hset_object);
4351    if get(handles.edit_object,'Value')% edit mode
4352        set(hhset_object.PLOT,'Enable','on')
4353        set(get(hset_object,'children'),'enable','on')
4354    else
4355        set(hhset_object.PLOT,'Enable','off')
4356        set(get(hset_object,'children'),'enable','inactive')% deactivate the GUI except SAVE
4357        set(hhset_object.SAVE,'Enable','on')
4358    end
4359else
4360    hset_object=findobj(allchild(0),'tag','set_object');
4361    if ~isempty(hset_object)
4362        delete(hset_object)% delete existing version of set_object
4363    end
4364end
4365 
4366
4367%------------------------------------------------------------------------
4368% --- Executes on button press in ViewField.
4369function ViewField_Callback(hObject, eventdata, handles)
4370%------------------------------------------------------------------------
4371check_view=get(handles.ViewField,'Value');
4372
4373if check_view
4374    IndexObj=get(handles.ListObject,'Value');
4375    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4376    if numel(UvData.Object)<IndexObj(end);% error in UvData
4377        msgbox_uvmat('ERROR','invalid object list')
4378        return
4379    end
4380    ZBounds=0; % default
4381    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4382        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4383        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4384    end
4385    set(handles.ListObject,'Value',IndexObj);%restore ListObject selection after set_object deletion
4386    if ~isfield(UvData.Object{IndexObj(1)},'Type')% default plane
4387        UvData.Object{IndexObj(1)}.Type='plane';
4388    end
4389    list_object=get(handles.ListObject,'String');
4390    UvData.Object{IndexObj(end)}.Name=list_object{IndexObj(end)};
4391   
4392    %% show the projection of the selected object on view_field
4393    ProjData= proj_field(UvData.Field,UvData.Object{IndexObj});%project the current field on ObjectData
4394    hview_field=findobj(allchild(0),'tag','view_field');
4395    if isempty(hview_field)
4396        hview_field=view_field;
4397    end
4398    hhview_field=guidata(hview_field);
4399    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.PlotAxes,read_GUI(hview_field));%read plotting parameters on the GUI view_field);
4400    errormsg=fill_GUI(PlotParam,hview_field);
4401    for list={'Scalar','Vectors'}
4402        if ~isfield(PlotParam,list{1})
4403            set(hhview_field.(list{1}),'Visible','off')
4404        end
4405    end
4406    %write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
4407    haxes=findobj(hview_field,'tag','axes3');
4408    pos=get(hview_field,'Position');
4409    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
4410        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
4411        pos_table=get(h_TableDisplay,'Position');
4412        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
4413    else
4414        Data=get(hview_field,'UserData');
4415        set(hview_field,'Position',Data.GUISize)% restore the size of view_field for plots
4416    end
4417else
4418    hview_field=findobj(allchild(0),'tag','view_field');
4419    if ~isempty(hview_field)
4420        delete(hview_field)% delete existing version of set_object
4421    end
4422end
4423
4424
4425%------------------------------------------------------------------------
4426% --- Executes on button press in delete_object.
4427function delete_object_Callback(hObject, eventdata, handles)
4428%------------------------------------------------------------------------
4429IndexObj=get(handles.ListObject,'Value');%projection object selected for view_field
4430IndexObj_1=get(handles.ListObject_1,'Value');%projection object selected for uvmat plot
4431if IndexObj>1 && ~isequal(IndexObj,IndexObj_1) % do not delete the object used for the uvmat plot
4432    delete_object(IndexObj)
4433end
4434
4435%------------------------------------------------------------------------
4436%------------------------------------------------------------------------
4437%  II - TOOLS FROM THE UPPER MENU BAR
4438%------------------------------------------------------------------------
4439%------------------------------------------------------------------------
4440
4441%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4442% Export  Menu Callbacks
4443%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4444%------------------------------------------------------------------------
4445% --- Executes on button press in Menu/Export/field in workspace.
4446function MenuExportField_Callback(hObject, eventdata, handles)
4447%------------------------------------------------------------------------
4448global Data_uvmat
4449Data_uvmat=get(handles.uvmat,'UserData');
4450evalin('base','global Data_uvmat')%make CurData global in the workspace
4451display('current field :')
4452evalin('base','Data_uvmat') %display CurData in the workspace
4453commandwindow; %brings the Matlab command window to the front
4454
4455%------------------------------------------------------------------------
4456% --- Executes on button press in Menu/Export/extract figure.
4457function MenuExportFigure_Callback(hObject, eventdata, handles)
4458%------------------------------------------------------------------------
4459% huvmat=get(handles.MenuExport,'parent');
4460hfig=figure;
4461copyobj(handles.PlotAxes,hfig);
4462map=colormap(handles.PlotAxes);
4463colormap(map);%transmit the current colormap to the zoom fig
4464colorbar
4465
4466% --------------------------------------------------------------------
4467function MenuExportAxis_Callback(hObject, eventdata, handles)
4468ListFig=findobj(allchild(0),'Type','figure');
4469nb_option=0;
4470menu={};
4471for ilist=1:numel(ListFig)
4472    FigName=get(ListFig(ilist),'name');
4473    if isempty(FigName)
4474        FigName=['figure ' num2str(ListFig(ilist))];
4475    end
4476    if ~strcmp(FigName,'uvmat')
4477        ListAxes=findobj(ListFig(ilist),'Type','axes');
4478        ListTags=get(ListAxes,'Tag');
4479        if ~isempty(ListTags) && ~isempty(find(~strcmp('Colorbar',ListTags), 1))
4480            ListAxes=ListAxes(~strcmp('Colorbar',ListTags));
4481            if numel(ListAxes)==1
4482                nb_option=nb_option+1;
4483                menu{nb_option}=FigName ;
4484                AxesHandle(nb_option)=ListAxes;
4485            else
4486                nb_axis=0;
4487                for iaxes=1:numel(ListAxes)
4488                    nb_axis=nb_axis+1;
4489                    nb_option=nb_option+1;
4490                    menu{nb_option}=[FigName '_' num2str(nb_axis)];
4491                    AxesHandle(nb_option)=ListAxes(nb_axis);
4492                end
4493            end
4494        end
4495    end
4496end
4497if isempty(menu)
4498    answer=msgbox_uvmat('INPUT_Y-N','no existing plotting axes available, create new figure?');
4499    if strcmp(answer,'Yes')
4500        hfig=figure;
4501        copyobj(handles.PlotAxes,hfig);
4502    else
4503        return
4504    end
4505    map=colormap(handles.PlotAxes);
4506    colormap(map);%transmit the current colormap to the zoom fig
4507    colorbar
4508else
4509    answer=msgbox_uvmat('INPUT_MENU','select a figure/axis on which the current uvmat plot will be exported',menu);
4510    if isempty(answer)
4511        return
4512    else
4513        axes(AxesHandle(answer))
4514        hold on
4515        hchild=get(handles.PlotAxes,'children');
4516        copyobj(hchild,gca);
4517    end
4518end
4519
4520
4521%------------------------------------------------------------------------
4522% --------------------------------------------------------------------
4523function MenuExportMovie_Callback(hObject, eventdata, handles)
4524% --------------------------------------------------------------------
4525set(handles.MenuExportMovie,'BusyAction','queue')% activate the button
4526huvmat=get(handles.run0,'parent');
4527UvData=get(huvmat,'UserData');
4528%[xx,xx,FileBase]=read_file_boxes(handles);
4529[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
4530FileBase=fullfile(RootPath,RootFile);
4531 %read the current input file name
4532prompt = {'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)'};
4533dlg_title = 'select properties of the output avi movie';
4534num_lines= 1;
4535def     = {[FileBase '_out.avi'];'10';'1';'[0.03 0.05 0.95 0.92]';'10'};
4536answer = inputdlg(prompt,dlg_title,num_lines,def,'on');
4537aviname=answer{1};
4538fps=str2double(answer{2});
4539% check for existing file with output name aviname
4540if exist(aviname,'file')
4541    backup=aviname;
4542    testexist=2;
4543    while testexist==2
4544        backup=[backup '~'];
4545        testexist=exist(backup,'file');     
4546    end
4547    [success,message]=copyfile(aviname,backup);%make backup of the existing file
4548    if isequal(success,1)
4549        delete(aviname)%delete existing file
4550    else
4551        msgbox_uvmat('ERROR',message)
4552        return
4553    end
4554end
4555%create avi open
4556aviobj=avifile(aviname,'Compression','None','fps',fps);
4557
4558%display first view for tests
4559newfig=figure;
4560newaxes=copyobj(handles.PlotAxes,newfig);%new plotting axes in the new figure
4561set(newaxes,'Tag','movieaxes')
4562nbpix=[512 384]*str2double(answer{3});
4563set(gcf,'Position',[1 1 nbpix])% resolution XVGA
4564set(newaxes,'Position',eval(answer{4}));
4565map=colormap(handles.PlotAxes);
4566colormap(map);%transmit the current colormap to the zoom fig
4567msgbox_uvmat('INPUT_Y-N',{['adjust figure ' num2str(newfig) ' with its matlab edit menu '] ;...
4568        ['then press OK to get the avi movie as a copy of figure ' num2str(newfig) ' display']});
4569UvData.plotaxes=newaxes;% the axis in the new figure becomes the current main plotting axes
4570set(huvmat,'UserData',UvData);
4571increment=str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d
4572set(handles.STOP,'Visible','on')
4573set(handles.speed,'Visible','on')
4574set(handles.speed_txt,'Visible','on')
4575set(handles.Movie,'BusyAction','queue')
4576
4577%imin=str2double(get(handles.i1,'String'));
4578imax=str2double(answer{5});
4579% if isfield(UvData,'Time')
4580htitle=get(newaxes,'Title');
4581xlim=get(newaxes,'XLim');
4582ylim=get(newaxes,'YLim');
4583set(htitle,'Position',[xlim(2)+0.07*(xlim(2)-xlim(1)) ylim(2)-0.05*(ylim(2)-ylim(1)) 0])
4584time_str=get(handles.abs_time,'String');
4585set(htitle,'String',['t=' time_str])
4586set(handles.speed,'Value',1)
4587for i=1:imax
4588    if get(handles.speed,'Value')~=0 && isequal(get(handles.MenuExportMovie,'BusyAction'),'queue') % enable STOP command
4589            runpm(hObject,eventdata,handles,increment)% run plus
4590            drawnow
4591            time_str=get(handles.abs_time,'String');
4592            if ishandle(htitle)
4593             set(htitle,'String',['t=' time_str])
4594            end
4595            mov=getframe(newfig);
4596            aviobj=addframe(aviobj,mov);
4597    end
4598end
4599aviobj=close(aviobj);
4600UvData=rmfield(UvData,'plotaxes');
4601%UvData.Object{1}.plotaxes=handles.PlotAxes;
4602set(huvmat,'UserData',UvData);
4603msgbox_uvmat('CONFIRMATION',{['movie ' aviname ' created '];['with ' num2str(imax) ' frames']})
4604
4605
4606%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4607% Projection Objects Menu Callbacks
4608%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4609
4610% -----------------------------------------------------------------------
4611function Menupoints_Callback(hObject, eventdata, handles)
4612%------------------------------------------------------------------------
4613data.Type='points';
4614data.ProjMode='projection';%default
4615data.ProjModeMenu={};% do not restrict ProjMode menus
4616create_object(data,handles)
4617
4618% -----------------------------------------------------------------------
4619function Menuline_Callback(hObject, eventdata, handles)
4620%------------------------------------------------------------------------
4621data.Type='line';
4622data.ProjMode='projection';%default
4623data.ProjModeMenu={};% do not restrict ProjMode menus
4624create_object(data,handles)
4625
4626%------------------------------------------------------------------------
4627function Menupolyline_Callback(hObject, eventdata, handles)
4628%------------------------------------------------------------------------
4629data.Type='polyline';
4630data.ProjMode='projection';%default
4631data.ProjModeMenu={};% do not restrict ProjMode menus
4632create_object(data,handles)
4633
4634%------------------------------------------------------------------------
4635function Menupolygon_Callback(hObject, eventdata, handles)
4636%------------------------------------------------------------------------
4637data.Type='polygon';
4638data.ProjMode='inside';%default
4639data.ProjModeMenu={};% do not restrict ProjMode menus
4640create_object(data,handles)
4641
4642%------------------------------------------------------------------------
4643function Menurectangle_Callback(hObject, eventdata, handles)
4644%------------------------------------------------------------------------
4645data.Type='rectangle';
4646data.ProjMode='inside';%default
4647data.ProjModeMenu={};% do not restrict ProjMode menus
4648create_object(data,handles)
4649
4650%------------------------------------------------------------------------
4651function Menuellipse_Callback(hObject, eventdata, handles)
4652%------------------------------------------------------------------------
4653data.Type='ellipse';
4654data.ProjMode='inside';%default
4655data.ProjModeMenu={};% do not restrict ProjMode menus
4656create_object(data,handles)
4657
4658%------------------------------------------------------------------------
4659function MenuMaskObject_Callback(hObject, eventdata, handles)
4660%------------------------------------------------------------------------
4661data.Type='polygon';
4662data.TypeMenu={'polygon'};
4663data.ProjMode='mask_inside';%default
4664data.ProjModeMenu={'mask_inside';'mask_outside'};
4665create_object(data,handles)
4666
4667%------------------------------------------------------------------------
4668function Menuplane_Callback(hObject, eventdata, handles)
4669%------------------------------------------------------------------------
4670data.Type='plane';
4671data.ProjMode='projection';%default
4672data.ProjModeMenu={};% do not restrict ProjMode menus
4673create_object(data,handles)
4674
4675%------------------------------------------------------------------------
4676function Menuvolume_Callback(hObject, eventdata, handles)
4677%------------------------------------------------------------------------
4678data.Type='volume';
4679data.ProjMode='interp_lin';%default
4680data.ProjModeMenu={};
4681% set(handles.create,'Visible','on')
4682% set(handles.create,'Value',1)
4683% VOLUME_Callback(hObject,eventdata,handles)data.ProjModeMenu={};
4684create_object(data,handles)
4685
4686%------------------------------------------------------------------------
4687% --- generic function used for the creation of a projection object
4688function create_object(data,handles)
4689%------------------------------------------------------------------------
4690% desactivate geometric calibration if opened
4691hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4692if ishandle(hgeometry_calib)
4693    hhgeometry_calib=guidata(hgeometry_calib);
4694    set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4695    set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4696end
4697set(handles.edit_object,'Value',0); %suppress the object edit mode
4698set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4699ListObject=get(handles.ListObject,'String');
4700if isempty(ListObject)
4701    ListObject={''};
4702end
4703if ~strcmp(ListObject{end},'')
4704    ListObject=[ListObject;{''}]; %append a blank to the list (if nort already done) to indicate the creation of a new object
4705    set(handles.ListObject,'String',ListObject)
4706end
4707IndexObj=length(ListObject);
4708set(handles.ListObject,'Value',IndexObj)
4709UvData=get(handles.uvmat,'UserData');
4710UvData.Object{IndexObj}=[]; %create a new empty object
4711UvData.Object{IndexObj}.DisplayHandle.uvmat=handles.PlotAxes; % axes for plot_object
4712UvData.Object{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation
4713data.Name=data.Type;% default name=type
4714data.Coord=[0 0]; %default
4715if isfield(UvData,'Field')
4716    Field=UvData.Field;
4717    if isfield(UvData.Field,'CoordMesh')&&~isempty(UvData.Field.CoordMesh)
4718        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
4719        if strcmp(data.Type,'line')||strcmp(data.Type,'polyline')||strcmp(data.Type,'points')
4720            data.RangeY=UvData.Field.CoordMesh;
4721        else
4722            data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
4723        end
4724        data.DX=UvData.Field.CoordMesh;
4725        data.DY=UvData.Field.CoordMesh;
4726    end
4727    if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
4728         data.Coord=[0 0 0]; %default
4729    end
4730    if isfield(Field,'CoordUnit')
4731        data.CoordUnit=Field.CoordUnit;
4732    end
4733end
4734if ishandle(handles.UVMAT_title)
4735    delete(handles.UVMAT_title)%delete the initial display of uvmat if no field has been entered
4736end
4737hset_object=set_object(data,handles);% call the set_object interface
4738hhset_object=guidata(hset_object);
4739hchild=get(hset_object,'children');
4740set(hchild,'enable','on')
4741set(handles.uvmat,'UserData',UvData)
4742set(handles.CheckZoom,'Value',0) %desactivate the zoom for object creation by the mouse
4743CheckZoom_Callback(handles.uvmat, [], handles)
4744set(handles.delete_object,'Visible','on')
4745
4746%------------------------------------------------------------------------
4747function MenuBrowseObject_Callback(hObject, eventdata, handles)
4748%------------------------------------------------------------------------
4749%get the object file
4750[FileName, PathName, filterindex] = uigetfile( ...
4751       {'*.xml;*.mat', ' (*.xml,*.mat)';
4752       '*.xml',  '.xml files '; ...
4753        '*.mat',  '.mat matlab files '}, ...
4754        'Pick an xml Object file',get(handles.RootPath,'String'));
4755fileinput=[PathName FileName];%complete file name
4756sizf=size(fileinput);
4757if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
4758
4759%read the file
4760[data,heading]=xml2struct(fileinput);
4761if ~strcmp(heading,'ProjObject')
4762    msgbox_uvmat('WARNING','The xml file does not have the heading ProjObject for projection objects')
4763end
4764[tild,data.Name]=fileparts(FileName);% object name set as file name
4765ListObject=get(handles.ListObject,'String');
4766if ~strcmp(ListObject{end},'')
4767    ListObject=[ListObject;{''}]; %append a blank to the list (if not already done) to indicate the creation of a new object
4768    set(handles.ListObject,'String',ListObject)
4769end
4770IndexObj=length(ListObject);
4771
4772UvData=get(handles.uvmat,'UserData');
4773UvData.Object{IndexObj}=[]; %create a new empty object
4774UvData.Object{IndexObj}.DisplayHandle.uvmat=[]; %no plot handle before plot_field operation
4775UvData.Object{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation
4776set(handles.uvmat,'UserData',UvData)
4777set(handles.ListObject,'Value',IndexObj)
4778hset_object=set_object(data);% call the set_object interface
4779set(get(hset_object,'children'),'enable','on')% enable edit action on elements on GUI set_object
4780set(handles.edit_object,'Value',0); %suppress the object edit mode
4781set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4782set(handles.delete_object,'Visible','on')
4783
4784
4785%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4786% MenuEdit Callbacks
4787%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4788%------------------------------------------------------------------------
4789function MenuEditObject_Callback(hObject, eventdata, handles)
4790%------------------------------------------------------------------------
4791set(handles.edit_object,'Value',1)
4792edit_Callback(hObject, eventdata, handles)
4793
4794%------------------------------------------------------------------------
4795function MenuEditVectors_Callback(hObject, eventdata, handles)
4796%------------------------------------------------------------------------
4797set(handles.edit_vect,'Visible','on')
4798set(handles.edit_vect,'Value',1)
4799edit_vect_Callback(hObject, eventdata, handles)
4800
4801%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4802% MenuTools Callbacks
4803%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4804%------------------------------------------------------------------------
4805function MenuCalib_Callback(hObject, eventdata, handles)
4806%------------------------------------------------------------------------
4807
4808UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4809
4810%suppress competing options
4811set(handles.CheckZoom,'Value',0)
4812set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
4813set(handles.ListObject,'Value',1)     
4814% initiate display of GUI geometry_calib
4815data=[]; %default
4816if isfield(UvData,'CoordType')
4817    data.CoordType=UvData.CoordType;
4818end
4819[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
4820FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
4821set(handles.view_xml,'Backgroundcolor',[1 1 0])%indicate the reading of the current xml file by geometry_calib
4822pos_uvmat=get(handles.uvmat,'Position');
4823pos_cal(1)=pos_uvmat(1)+UvData.OpenParam.PosGeometryCalib(1)*pos_uvmat(3);
4824pos_cal(2)=pos_uvmat(2)+UvData.OpenParam.PosGeometryCalib(2)*pos_uvmat(4);
4825pos_cal(3:4)=UvData.OpenParam.PosGeometryCalib(3:4).* pos_uvmat(3:4);
4826geometry_calib(FileName,pos_cal);% call the geometry_calib interface   
4827set(handles.view_xml,'Backgroundcolor',[1 1 1])%indicate the end of reading of the current xml file by geometry_calib
4828set(handles.MenuCalib,'checked','on')% indicate that MenuCalib is activated, test used by mouse action
4829
4830
4831%-----------------------------------------------------------------------
4832function MenuLIFCalib_Callback(hObject, eventdata, handles)
4833%------------------------------------------------------------------------
4834%% read UvData properties stored on the uvmat interface
4835UvData=get(handles.uvmat,'UserData');
4836if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
4837    XmlData=UvData.XmlData{1};
4838else
4839    msgbox_uvmat('ERROR','geometric calibration needed: use Tools/geometric calibration in the menu bar');
4840    return
4841end
4842
4843%% read lines currently drawn
4844ListObj=UvData.Object;
4845select=zeros(1,numel(ListObj));
4846for iobj=1:numel(ListObj);
4847    if isfield(ListObj{iobj},'Type') && strcmp(ListObj{iobj}.Type,'line')
4848        select(iobj)=1;
4849    end
4850end
4851val=find(select);
4852if numel(val)<2
4853    msgbox_uvmat('ERROR','light rays must be defined by at least two lines created by Projection object/line in the menu bar');
4854    return
4855else
4856    set(handles.ListObject,'Value',val);% show the selected lines on the list
4857    ObjectData=UvData.Object(val);
4858    for iobj=1:length(ObjectData)
4859%         if isfield(ObjectData{iobj},'Coord')
4860            xA(iobj)=ObjectData{iobj}.Coord(1,1);
4861            yA(iobj)=ObjectData{iobj}.Coord(1,2);
4862            xB(iobj)=ObjectData{iobj}.Coord(2,1);
4863            yB(iobj)=ObjectData{iobj}.Coord(2,2);
4864%         end
4865    end
4866end
4867
4868%% find the origin as intersection of the two first lines (see http://www.ahristov.com/tutorial/geometry-games/intersection-lines.html )
4869x1=xA(1);x2=xB(1);
4870x3=xA(2);x4=xB(2);
4871y1=yA(1);y2=yB(1);
4872y3=yA(2);y4=yB(2);
4873D = (x1-x2)*(y3-y4) -(y1-y2)*(x3-x4);
4874if D==0
4875    msgbox_uvmat('ERROR','the two lines are parallel');
4876    return
4877end
4878x0=((x3-x4)*(x1*y2-y1*x2)-(x1-x2)*(x3*y4-y3*x4))/D;
4879y0=((y3-y4)*(x1*y2-y1*x2)-(y1-y2)*(x3*y4-y3*x4))/D;
4880XmlData.Illumination.Origin=[x0 y0];
4881XmlData.PolarCentre=[x0 y0];
4882
4883%% display the current image in polar coordinates with origin at the  illumination source
4884currentdir=pwd; 
4885uvmatpath=fileparts(which('uvmat'));
4886cd(fullfile(uvmatpath,'transform_field'));
4887phys_polar=str2func('phys_polar');
4888cd(currentdir)
4889DataOut=phys_polar(UvData.Field,XmlData);
4890view_field(DataOut);
4891
4892%% use the third line for reference luminosity
4893if numel(val)==3
4894    x_ref=linspace(ObjectData{3}.Coord(1,1),ObjectData{3}.Coord(2,1),10);
4895    y_ref=linspace(ObjectData{3}.Coord(1,2),ObjectData{3}.Coord(2,2),10);
4896    x_ref=x_ref-x0;
4897    y_ref=y_ref-y0;
4898    [theta_ref,r_ref] = cart2pol(x_ref,y_ref);%theta_ref  and r_ref are the polar coordinates of the points on the line
4899    theta_ref=theta_ref*180/pi;
4900    figure
4901    plot(theta_ref,r_ref)
4902    azimuth_ima=linspace(DataOut.AY(1),DataOut.AY(2),size(DataOut.A,1));%profile of x index on the transformed image
4903    dist_source = interp1(theta_ref,r_ref,azimuth_ima);
4904    dist_source_pixel=round(size(DataOut.A,2)*(dist_source-DataOut.AX(1))/(DataOut.AX(2)-DataOut.AX(1)));
4905    line_nan= isnan(dist_source_pixel);
4906    dist_source_pixel(line_nan)=1;
4907    width=20; %number of pixels used for reference
4908    DataOut.A=double(DataOut.A);
4909    Anorm=zeros(size(DataOut.A));
4910    Aval=mean(mean(DataOut.A));
4911    for iline=1:size(DataOut.A,1)
4912        lum(iline)=mean(DataOut.A(iline,dist_source_pixel(iline):dist_source_pixel(iline)+width));
4913        Anorm(iline,:)=uint16(Aval*DataOut.A(iline,:)/lum(iline));
4914    end
4915    lum(line_nan)=NaN;
4916    figure
4917    plot(1:size(DataOut.A,1),lum)
4918end
4919ImaName=regexprep([get(handles.RootFile,'String') get(handles.FileIndex,'String')],'//','');
4920NewImageName=fullfile(get(handles.RootPath,'String'),'polar',[ImaName get(handles.FileExt,'String')]);
4921imwrite(Anorm,NewImageName,'BitDepth',16)
4922
4923%% record the origin in the xml file
4924XmlFileName=find_imadoc(get(handles.RootPath,'String'),get(handles.SubDir,'String'),get(handles.RootFile,'String'),get(handles.FileExt,'String'));
4925answer=msgbox_uvmat('INPUT_Y-N','save the illumination origin in the current xml file?');
4926if strcmp(answer,'Yes')
4927    t=xmltree(XmlFileName); %read the file
4928    title=get(t,1,'name');
4929    if ~strcmp(title,'ImaDoc')
4930        msgbox_uvmat('ERROR','wrong xml file');
4931        return
4932    end
4933    % backup the output file if it already exist, and read it
4934    backupfile=XmlFileName;
4935    testexist=2;
4936    while testexist==2
4937        backupfile=[backupfile '~'];
4938        testexist=exist(backupfile,'file');
4939    end
4940    [success,message]=copyfile(XmlFileName,backupfile);%make backup
4941    if success~=1
4942        errormsg=['errror in xml file backup: ' message];
4943        return
4944    end
4945    uid_illumination=find(t,'ImaDoc/Illumination');
4946    if isempty(uid_illumination)  %if GeometryCalib does not already exists, create it
4947        [t,uid_illumination]=add(t,1,'element','Illumination');
4948    end
4949    uid_origin=find(t,'ImaDoc/Illumination/Origin');
4950    if ~isempty(uid_origin)  %if GeometryCalib does not already exists, create it
4951         t=delete(t,uid_origin);
4952    end
4953    % save the illumination origin
4954    t=struct2xml(XmlData.Illumination,t,uid_illumination);
4955    save(t,XmlFileName);
4956end
4957   
4958
4959
4960%------------------------------------------------------------------------
4961function MenuMask_Callback(hObject, eventdata, handles)
4962%------------------------------------------------------------------------
4963UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4964ListObj=UvData.Object;
4965select=zeros(1,numel(ListObj));
4966for iobj=1:numel(ListObj);
4967    if strcmp(ListObj{iobj}.ProjMode,'mask_inside')||strcmp(ListObj{iobj}.ProjMode,'mask_outside')
4968        select(iobj)=1;
4969    end
4970end
4971val=find(select);
4972if isempty(val)
4973    msgbox_uvmat('ERROR','polygons must be first created by Projection object/mask polygon in the menu bar');
4974    return
4975else
4976    set(handles.ListObject,'Value',val);
4977    flag=1;
4978    npx=size(UvData.Field.A,2);
4979    npy=size(UvData.Field.A,1);
4980    xi=0.5:npx-0.5;
4981    yi=0.5:npy-0.5;
4982    [Xi,Yi]=meshgrid(xi,yi);
4983%     if isfield(UvData,'Object')
4984        for iobj=1:length(UvData.Object)
4985            ObjectData=UvData.Object{iobj};
4986            if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
4987                flagobj=1;
4988                testphys=0; %coordinates in pixels by default
4989                if isfield(ObjectData,'CoordUnit') && ~isequal(ObjectData.CoordUnit,'pixel')
4990                    if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
4991                        Calib=UvData.XmlData{1}.GeometryCalib;
4992                        testphys=1;
4993                    end
4994                end
4995                if isfield(ObjectData,'Coord')&& isfield(ObjectData,'Type')
4996                    if isequal(ObjectData.Type,'polygon')
4997                        X=ObjectData.Coord(:,1);
4998                        Y=ObjectData.Coord(:,2);
4999                        if testphys
5000                            pos=[X Y zeros(size(X))];
5001                            if isfield(Calib,'SliceCoord') && length(Calib.SliceCoord)>=3
5002                                if isfield(Calib,'SliceAngle')&&~isequal(Calib.SliceAngle,[0 0 0])
5003                                    om=norm(Calib.SliceAngle);%norm of rotation angle in radians
5004                                    OmAxis=Calib.SliceAngle/om; %unit vector marking the rotation axis
5005                                    cos_om=cos(pi*om/180);
5006                                    sin_om=sin(pi*om/180);
5007                                    pos=cos_om*pos+sin_om*cross(OmAxis,pos)+(1-cos_om)*(OmAxis*pos')*OmAxis;
5008                                end
5009                                pos(:,1)=pos(:,1)+Calib.SliceCoord(1);
5010                                pos(:,2)=pos(:,2)+Calib.SliceCoord(2);
5011                                pos(:,3)=pos(:,3)+Calib.SliceCoord(3);
5012                            end                           
5013                            [X,Y]=px_XYZ(Calib,pos(:,1),pos(:,2),pos(:,3));
5014                        end
5015                        flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside
5016                    elseif isequal(ObjectData.Type,'ellipse')
5017                        if testphys
5018                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
5019                        end
5020                        RangeX=max(ObjectData.RangeX);
5021                        RangeY=max(ObjectData.RangeY);
5022                        X2Max=RangeX*RangeX;
5023                        Y2Max=RangeY*RangeY;
5024                        distX=(Xi-ObjectData.Coord(1,1));
5025                        distY=(Yi-ObjectData.Coord(1,2));
5026                        flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
5027                    elseif isequal(ObjectData.Type,'rectangle')
5028                        if testphys
5029                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
5030                        end
5031                        distX=abs(Xi-ObjectData.Coord(1,1));
5032                        distY=abs(Yi-ObjectData.Coord(1,2));
5033                        flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
5034                    end
5035                    if isequal(ObjectData.ProjMode,'mask_outside')
5036                        flagobj=~flagobj;
5037                    end
5038                    flag=flag & flagobj;
5039                end
5040            end
5041        end
5042%     end
5043    %mask name
5044    RootPath=get(handles.RootPath,'String');
5045    SubDir=get(handles.SubDir,'String');
5046    RootFile=get(handles.RootFile,'String');
5047    if ~isempty(RootFile)&&(isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
5048        RootFile(1)=[];
5049    end
5050    list=get(handles.masklevel,'String');
5051    masknumber=num2str(length(list));
5052    maskindex=get(handles.masklevel,'Value');
5053   % mask_name=fullfile_uvmat(RootPath,'',[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
5054    mask_name=fullfile_uvmat(RootPath,[SubDir '.mask'],'mask','.png','_1',maskindex);
5055    imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
5056    imflag=flipdim(imflag,1);
5057
5058    %display the mask
5059    hfigmask=figure;
5060    set(hfigmask,'Name','mask image')
5061    vec=linspace(0,1,256);%define a linear greyscale colormap
5062    map=[vec' vec' vec'];
5063    colormap(map)
5064    image(imflag);
5065    answer=msgbox_uvmat('INPUT_TXT','mask file name:', mask_name);
5066    if ~strcmp(answer,'Cancel')
5067        mask_dir=fileparts(answer);
5068        if ~exist(mask_dir,'dir')
5069            [xx,msg1]=mkdir(mask_dir);
5070            if ~strcmp(msg1,'')
5071                errormsg=['cannot create ' mask_dir ': ' msg1];%error message for directory creation
5072                return
5073            end
5074        end
5075        imwrite(imflag,answer,'BitDepth',8);
5076    end
5077    set(handles.ListObject,'Value',1)
5078end
5079
5080%------------------------------------------------------------------------
5081%-- open the GUI set_grid.fig to create grid
5082function MenuGrid_Callback(hObject, eventdata, handles)
5083%------------------------------------------------------------------------
5084%suppress the other options if grid is chosen
5085set(handles.edit_vect,'Value',0)
5086edit_vect_Callback(hObject, eventdata, handles)
5087set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
5088set(handles.ListObject,'Value',1)     
5089
5090%prepare display of the set_grid GUI
5091[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
5092FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
5093UvData=get(handles.uvmat,'UserData');
5094% CoordList=get(handles.TransformName,'String');
5095% val=get(handles.TransformName,'Value');
5096set_grid(FileName,UvData.Field);% call the set_object interface
5097
5098
5099%------------------------------------------------------------------------
5100function MenuRuler_Callback(hObject, eventdata, handles)
5101%------------------------------------------------------------------------
5102set(handles.CheckZoom,'Value',0)
5103CheckZoom_Callback(handles.uvmat, [], handles)
5104set(handles.MenuRuler,'checked','on')
5105UvData=get(handles.uvmat,'UserData');
5106UvData.MouseAction='ruler';
5107set(handles.uvmat,'UserData',UvData);
5108
5109%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
5110% MenuRun Callbacks
5111%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
5112
5113%------------------------------------------------------------------------
5114% open the GUI 'series'
5115function MenuSeries_Callback(hObject, eventdata, handles)
5116%------------------------------------------------------------------------
5117[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
5118Param.FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];%first input file name
5119if isequal(get(handles.SubField,'Value'),1)
5120    [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
5121    FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
5122    if ~isequal(FileName_1,Param.FileName)
5123        Param.FileName_1=FileName_1;%second input file name if relevant
5124    end
5125end
5126Param.NomType=get(handles.NomType,'String');
5127Param.NomType_1=get(handles.NomType_1,'String');
5128Param.CheckFixPair=get(handles.CheckFixPair,'Value');
5129UvData=get(handles.uvmat,'UserData');
5130if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'Time')
5131    Param.Time=UvData.XmlData{1}.Time;
5132end
5133if isequal(get(handles.scan_i,'Value'),1)
5134    Param.incr_i=str2num(get(handles.num_IndexIncrement,'String'));
5135elseif isequal(get(handles.scan_j,'Value'),1)
5136    Param.incr_j=str2num(get(handles.num_IndexIncrement,'String'));
5137end
5138
5139%% transfer fields and coordinate names
5140Param.list_fields=get(handles.FieldName,'String');% list menu fields
5141FieldName=Param.list_fields{get(handles.FieldName,'Value')};
5142ind_image=find(strcmp('image',Param.list_fields));
5143if ~isempty(ind_image) && numel(Param.list_fields)>1
5144    Param.list_fields(ind_image)=[]; %suppress  'image' option
5145end
5146Param.index_fields=find(strcmp(FieldName,Param.list_fields));% selected string index
5147Param.list_fields_1=get(handles.FieldName_1,'String');% list menu fields
5148if ischar(Param.list_fields_1),Param.list_fields_1={Param.list_fields_1};end
5149FieldName_1=Param.list_fields_1{get(handles.FieldName_1,'Value')};
5150ind_image=find(strcmp('image',Param.list_fields_1));
5151if ~isempty(ind_image) && numel(Param.list_fields_1)>1
5152    Param.list_fields_1(ind_image)=[]; %suppress  'image' option
5153end
5154Param.index_fields_1=find(strcmp(FieldName_1,Param.list_fields_1));% selected string index
5155TransformList=get(handles.TransformName,'String');
5156Param.TransformName=TransformList{get(handles.TransformName,'Value')};
5157Param.Coord_x_str=get(handles.Coord_x,'String');
5158Param.Coord_x_val=get(handles.Coord_x,'Value');
5159Param.Coord_y_str=get(handles.Coord_y,'String');
5160Param.Coord_y_val=get(handles.Coord_y,'Value');
5161series(Param); %run the series interface
5162
5163%------------------------------------------------------------------------
5164% -- open the GUI civ.fig for PIV
5165function MenuPIV_Callback(hObject, eventdata, handles)
5166%------------------------------------------------------------------------
5167 [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
5168 FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
5169civ(FileName);% interface de civ(not in the uvmat file)
5170
5171% --------------------------------------------------------------------
5172function MenuHelp_Callback(hObject, eventdata, handles)
5173% --------------------------------------------------------------------
5174path_to_uvmat=which ('uvmat');% check the path of uvmat
5175pathelp=fileparts(path_to_uvmat);
5176helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
5177if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
5178else
5179    addpath (fullfile(pathelp,'uvmat_doc'))
5180    web(helpfile);
5181end
5182
5183% --- Executes on selection change in Coord_y.
5184function Coord_y_Callback(hObject, eventdata, handles)
5185
5186% --- Executes on selection change in Coord_x.
5187function Coord_x_Callback(hObject, eventdata, handles)
5188
5189
5190% --- Executes on button press in CheckColorBar.
5191function CheckColorBar_Callback(hObject, eventdata, handles)
5192
5193
5194
5195function TransformPath_Callback(hObject, eventdata, handles)
5196% hObject    handle to TransformPath (see GCBO)
5197% eventdata  reserved - to be defined in a future version of MATLAB
5198% handles    structure with handles and user data (see GUIDATA)
5199
5200% Hints: get(hObject,'String') returns contents of TransformPath as text
5201%        str2double(get(hObject,'String')) returns contents of TransformPath as a double
5202
5203
5204%TODO: use to modify fill_GUI
5205%'write_plot_param': update the plotting parameters on the uvmat or view_field interface after a plotting operation
5206function write_plot_param(handles,PlotParam)
5207%% coordinates
5208if isempty(PlotParam.Coordinates)
5209    set(handles.Coordinates,'Visible','off')
5210    set(handles.PlotAxes,'Visible','off')
5211    set(handles.text_display,'Visible','off')
5212    set(handles.TableDisplay,'Visible','on')
5213else
5214    set(handles.Coordinates,'Visible','on')
5215    set(handles.PlotAxes,'Visible','on')
5216    set(handles.text_display,'Visible','on')
5217    if isfield(handles,'TableDisplay')
5218    set(handles.TableDisplay,'Visible','off')
5219    end
5220    Coordinates=PlotParam.Coordinates;
5221    if isfield(Coordinates,'CheckFixAspectRatio')
5222        if Coordinates.CheckFixAspectRatio
5223            set(handles.CheckFixAspectRatio,'Value',1)
5224        else
5225            set(handles.CheckFixAspectRatio,'Value',0)
5226 
5227        end
5228    end
5229    if isfield(Coordinates,'AspectRatio')
5230        set(handles.num_AspectRatio,'String',num2str(Coordinates.AspectRatio))
5231    end
5232    if isfield(Coordinates,'MinX')
5233        set(handles.num_MinX,'String',num2str(Coordinates.MinX,4));
5234        set(handles.num_MaxX,'String',num2str(Coordinates.MaxX,4));
5235        set(handles.num_MinY,'String',num2str(Coordinates.MinY,4));
5236        set(handles.num_MaxY,'String',num2str(Coordinates.MaxY,4));
5237    else
5238        set(handles.num_MinX,'String','');
5239        set(handles.num_MaxX,'String','');
5240        set(handles.num_MinY,'String','');
5241        set(handles.num_MaxY,'String','');
5242    end
5243end
5244
5245%% scalar or image parameters
5246if isfield(PlotParam,'Scalar')
5247    set(handles.Scalar,'Visible','on')
5248    if isfield(PlotParam.Scalar,'MaxA')
5249        set(handles.num_MaxA,'String',num2str(PlotParam.Scalar.MaxA,3));
5250    end
5251    if isfield(PlotParam.Scalar,'MinA')
5252        set(handles.num_MinA,'String',num2str(PlotParam.Scalar.MinA,3));
5253    end   
5254    if isfield(PlotParam.Scalar,'IncrA')
5255        set(handles.num_IncrA,'String',num2str(PlotParam.Scalar.IncrA,3))
5256    end
5257    set(handles.CheckBW,'Value',PlotParam.Scalar.CheckBW)
5258    if isfield(PlotParam.Scalar,'Opacity')&&isfield(handles,'num_Opacity')
5259        set(handles.num_Opacity,'String',num2str(PlotParam.Scalar.Opacity))
5260    end
5261else
5262    set(handles.Scalar,'Visible','off')
5263end
5264
5265%% parameter for vector field
5266if isfield(PlotParam,'Vectors')
5267    set(handles.Vectors,'Visible','on')
5268    if isfield(PlotParam.Vectors,'VecScale')
5269        set(handles.num_VecScale,'String',num2str(PlotParam.Vectors.VecScale,3))
5270    end
5271    if isfield(PlotParam.Vectors,'MinC')&& isfield(PlotParam.Vectors,'MaxC')
5272        MinC=PlotParam.Vectors.MinC;
5273        MaxC=PlotParam.Vectors.MaxC;
5274        set(handles.num_MinVec,'String', num2str(MinC,3));
5275        set(handles.num_MaxVec,'String',num2str(MaxC,3));
5276        list=get(handles.ColorCode,'String');
5277        ichoice=get(handles.ColorCode,'Value');
5278        color_option=list{ichoice};
5279        test3color=strcmp(color_option,'rgb')||strcmp(color_option,'bgr');
5280        if test3color% need to update color thresholds
5281            set(handles.num_ColCode1,'Visible','on')
5282            set(handles.num_ColCode2,'Visible','on')
5283            set(handles.Slider1,'Visible','on')
5284            set(handles.Slider2,'Visible','on')
5285            %ColCode1=MinC+(MaxC-MinC)*PlotParam.Vectors.ColCode1;
5286            %ColCode2=MinC+(MaxC-MinC)*PlotParam.Vectors.ColCode2;
5287%             ColCode1=MinC+(MaxC-MinC)*PlotParam.Vectors.ColCode1;
5288            %ColCode2=MinC+(MaxC-MinC)*PlotParam.Vectors.ColCode2;
5289            set(handles.num_ColCode1,'String',num2str(PlotParam.Vectors.ColCode1,3))
5290            set(handles.num_ColCode2,'String',num2str(PlotParam.Vectors.ColCode2,3))
5291            set(handles.Slider1,'Value',(PlotParam.Vectors.ColCode1-MinC)/(MaxC-MinC))
5292            set(handles.Slider2,'Value',(PlotParam.Vectors.ColCode2-MinC)/(MaxC-MinC))
5293        else
5294            set(handles.num_ColCode1,'Visible','off')
5295            set(handles.num_ColCode2,'Visible','off')
5296            set(handles.Slider1,'Visible','off')
5297            set(handles.Slider2,'Visible','off')
5298        end
5299    end
5300else
5301    set(handles.Vectors,'Visible','off')
5302    if isfield(handles,'edit_vect')
5303        set(handles.edit_vect,'Visible','off')
5304        set(handles.record,'Visible','off')
5305    end
5306end
5307
5308
5309
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