source: trunk/src/uvmat.m @ 589

Last change on this file since 589 was 589, checked in by sommeria, 8 years ago

various minor corrections made

File size: 221.2 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%                       .PosSetObject: position of set_object
35%                       .PosGeometryCalib: size of set_object
36%                       .NbBuiltin: nbre of functions always displayed in transform_fct menu
37%          .Object: cell array of structures representing the current projection objects, as produced by 'set_object.m'={[]} by default
38%          .NewSeries: =0/1 flag telling whether a new field series has been opened
39%          .FileName_1: name of the current second field (used to detect a  constant field during file scanning)
40%          .FileType: current file type, as defined by the fct  get_file_type.m)
41%          .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
42%          .MovieObject: current movie object
43%          .TimeUnit: unit for time
44%          .XmlData: cell array of 1 or 2 structures representing the xml files associated with the input fieldname (containing timing  and geometry calibration)
45%          .Field: cell array of 1 or 2 structures representing the current  input field(s)
46%          .PlotAxes: field structure representing the current field plotted  on the main axes  (used for mouse operations)
47%          .HistoAxes: idem for histogram axes
48
49% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%   DATA FLOW  (for run0_Callback) %%%%%%%%%%%%%%%%%%%%:
50%
51%
52% 1) Input filenames are determined by MenuBrowse (first field), MenuBrowse_1
53% (second field), or by the stored file name .FileName_1, or as an input of uvmat.
54% 2) These functions call 'uvmat/display_file_name.m' which detects the file series, and fills the file index boxes
55% 3) Then 'uvmat/update_rootinfo.m' Updates information about a new field series (indices to scan, timing, calibration from an xml file)
56% 4) Then fieldname are opened and visualised by the main sub-function 'uvmat/refresh_field.m'
57% The function first reads the name of the input file(s) (one or two) from the edit boxes  of the GUI
58% It then reads the input file(s) with the function read_field.m and perform the following list of operations:
59%
60%    %%%%%%%%  structure of uvmat/refresh_field.m %%%%%%%%
61%
62%           Main input open       second input open_1       
63%                    |                   | 
64%             read_field.m            read_field.m
65%                    |                   |
66%                 Field{1}            Field{2}               
67%                    |                   |                                 
68%                    --->transform fct<---             transform (e.g. phys.m) and combine input fieldname 
69%                            |                                   
70%                        (tps_coeff_field.m)               calculate tps coefficients (for filter projection or spatial derivatives).
71%                            |
72%                       UvData.Field-------------->histogram
73%               _____________|____________
74%              |                          |                   
75%        proj_field.m               proj_field.m       project the field on the projection objects (use calc_field.m)           
76%              |                          |
77%         UvData.PlotAxes          ViewData.PlotAxes (on view_field)
78%              |                          |
79%       plot_field.m (uvmat)       plot_field.m (view_field)      plot the projected fieldname
80%
81%
82%%%%%%%%%%%%%%    SCALARS: %%%%%%%%%%%%??%%%
83% scalars are displayed either as an image or countour plot, either as a color of
84% velocity vectors. The scalar values in the first case is represented by
85% UvData.Field.A, and by UvData.Field.C in the second case. The corresponding set of X
86% and Y coordinates are represented by UvData.Field.AX and UvData.Field.AY, and .X and
87% .Y for C (the same as velocity vectors). If A is a nxxny matrix (scalar
88% on a regtular grid), then .AX andf.AY contains only two elements, represneting the
89% coordinates of the four image corners. The scalar name is represented by
90% the strings .AName and/or .CName.
91% If the scalar exists in an input open (image or scalar stored under its
92% name in a netcdf open), it is directly read at the level of Field{1}or Field{2}.
93% Else only its name AName is recorded in Field{i}, and its field is then calculated
94%by the fuction calc_scal after the coordinate transform or after projection on an edit_object
95     
96% Properties attached to plotting figures (standard Matlab properties):
97%    'CurrentAxes'= gca or get(gcf,'CurrentAxes');
98%    'CurrentPoint'=get(gcf,'CurrentPoint'): figure coordinates of the point over which the mouse is positioned
99%    'CurrentCharacter'=get(gcf,'CurrentCharacter'): last character typed  over the figure where the mouse is positioned
100%    'WindowButtonMotionFcn': function permanently called by mouse motion over the figure
101%    'KeyPressFcn': function called by pressing a key on the key board
102%    'WindowButtonDownFcn':  function called by pressing the mouse over the  figure
103%    'WindowButtonUpFcn': function called by releasing  the mouse pressure over the  figure
104
105% Properties attached to plotting axes:
106%    'CurrentPoint'=get(gca,'CurrentPoint'); (standard Matlab) same as for the figure, but position in plot coordinates.
107%     AxeData:=get(gca,'UserData');
108%     AxeData.Drawing  = create: create a new object
109%                       = deform: modify an existing object by moving its defining create
110%                      = off: no current drawing action
111%                     = translate: translate an existing object
112%                    = calibration: move a calibration point
113%                    = CheckZoom: isolate a subregion for CheckZoom in=1 if an object is being currently drawn, 0 else (set to 0 by releasing mouse button)
114%            .CurrentOrigin: Origin of a curently drawn edit_object
115%            .CurrentLine: currently drawn menuline (A REVOIR)
116%            .CurrentObject: handle of the currently drawn edit_object
117%            .CurrentRectZoom: current rectangle used for CheckZoom
118
119% Properties attached to projection objects (create, menuline, menuplane...):
120%    'Tag'='proj_object': for all projection objects
121%    ObjectData.Type=...: style of projection object:
122%              .ProjMode
123%              .Coord: defines the position of the object
124%              .XMin,YMin....
125%              .XMax,YMax....
126%              .DX,DY,DZ
127%              .Phi, .Theta, .Psi : Euler angles
128%              .X,.Y,.U,.V.... : field data projected on the object
129%              .IndexObj: index in the list of UvData.Object
130           %during plotting
131%               .plotaxes: handles of the current axes used to plot the  result of field projection on the object
132%               .plothandle: vector of handle(s) of the object graphic represnetation in all the opened plotting axes
133% To each projection object #iobj, corresponds an axis
134% Object{iobj}.plotaxes and nbobj representation graphs  Object{iobj}.plothandles(:) (where nbobj is the
135% nbre of current objects opened in uvmat. Note that Object{iobj}.plothandles(iobj)=[] : an object is not represented in its own projection field;
136
137%------------------------------------------------------------------------
138%------------------------------------------------------------------------
139%  I - MAIN FUNCTION uvmat
140%------------------------------------------------------------------------
141%------------------------------------------------------------------------
142function varargout = uvmat(varargin)
143
144% Begin initialization code - DO NOT EDIT
145gui_Singleton = 1;
146gui_State = struct('gui_Name',          mfilename, ...
147                   'gui_Singleton',     gui_Singleton, ...
148                   'gui_OpeningFcn',    @uvmat_OpeningFcn, ...
149                   'gui_OutputFcn',     @uvmat_OutputFcn, ...
150                   'gui_LayoutFcn',     [], ...
151                   'gui_Callback',      []);
152if nargin && ischar(varargin{1})&& ~isempty(regexp(varargin{1},'_Callback','once'))
153    gui_State.gui_Callback = str2func(varargin{1});
154end
155
156if nargout
157    varargout{1:nargout} = gui_mainfcn(gui_State, varargin{:});
158else
159    gui_mainfcn(gui_State, varargin{:});
160end
161% End initialization code - DO NOT EDIT
162
163%------------------------------------------------------------------------
164% --- Executes just before the GUI uvmat is made visible.
165function uvmat_OpeningFcn(hObject, eventdata, handles, input )
166%------------------------------------------------------------------------
167
168%% Choose default command menuline output for uvmat (standard GUI)
169handles.output = hObject;
170
171%% Update handles structure (standard GUI)
172guidata(hObject, handles);
173
174%% add the path to uvmat (useful if uvmat has been opened in the working directory and a working directory change occured)
175path_uvmat=fileparts(which('uvmat'));
176
177%% set the position of colorbar and ancillary GUIs:
178set(hObject,'Units','Normalized')
179movegui(hObject,'center')
180%UvData.OpenParam.PosColorbar=[0.8450    0.0900    0.0190    0.3600];
181UvData.OpenParam.PosColorbar=[0.805 0.022 0.019 0.445];
182UvData.OpenParam.PosSetObject=[-0.05 -0.03 0.3 0.7]; %position for set_object
183UvData.OpenParam.PosGeometryCalib=[0.95 -0.03 0.28 1 ];%position for geometry_calib (TO IMPROVE)
184% UvData.OpenParam.CalSize=[0.28 1];
185% UvData.PlotAxes=[];%initiate the record of plotted field
186% UvData.axes2=[];
187% UvData.axes1=[];
188AxeData.LimEditBox=1; %initialise AxeData
189set(handles.PlotAxes,'UserData',AxeData)
190
191%% set functions for the mouse and keyboard
192set(hObject,'KeyPressFcn',{'keyboard_callback',handles})%set keyboard action function
193set(hObject,'WindowButtonMotionFcn',{'mouse_motion',handles})%set mouse action functio
194set(hObject,'WindowButtonDownFcn',{'mouse_down'})%set mouse click action function
195set(hObject,'WindowButtonUpFcn',{'mouse_up',handles})
196set(hObject,'DeleteFcn',{@closefcn})%
197
198%% initialisation
199% set(handles.ListObject,'Value',1)% default: empty projection objectproj_field
200% set(handles.ListObject,'String',{''})
201% set(handles.ListObject_1,'Value',1)% default: empty projection objectproj_field
202% set(handles.ListObject_1,'String',{''})
203set(handles.FieldName,'Value',1)
204set(handles.FieldName,'string',{''})
205UvData.Object={[]};
206
207%% TRANSFORM menu: builtin fcts
208transform_menu={'';'sub_field';'phys';'phys_polar'};
209UvData.OpenParam.NbBuiltin=numel(transform_menu); %number of functions
210transform_path=fullfile(path_uvmat,'transform_field');
211path_list=cell(UvData.OpenParam.NbBuiltin,1);
212path_list{1}='';
213for ilist=2:UvData.OpenParam.NbBuiltin
214path_list{ilist}=transform_path; % set transform_path to the path_list
215end
216
217%% load the list of previously browsed files in menus Open, Open_1 and transform_fct
218 dir_perso=prefdir; % path to the directory .matlab containing the personal data of the current user
219 profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmat_perso.mat' in .matlab
220 if exist(profil_perso,'file')
221     h=load (profil_perso);
222     if isfield(h,'MenuFile')% load the menu of previously opened files
223         for ifile=1:min(length(h.MenuFile),5)
224             set(handles.(['MenuFile_' num2str(ifile)]),'Label',h.MenuFile{ifile});
225             set(handles.(['MenuFile_' num2str(ifile) '_1']),'Label',h.MenuFile{ifile});
226         end
227     end
228     if isfield(h,'RootPath')
229         set(handles.RootPath,'UserData',h.RootPath); %store the previous campaign in the UserData of RootPath
230     end
231     if isfield(h,'transform_fct') && iscell(h.transform_fct) % load the menu of transform fct set by user
232         for ilist=1:length(h.transform_fct);
233             if exist(h.transform_fct{ilist},'file')
234                 [path,file]=fileparts(h.transform_fct{ilist});
235                 transform_menu=[transform_menu; {file}];
236                 path_list=[path_list; {path}];
237             end
238         end
239     end
240 end
241transform_menu=[transform_menu;{'more...'}];%append the option more.. to the menu
242set(handles.transform_fct,'String',transform_menu)% display the menu of transform fcts
243set(handles.transform_fct,'UserData',path_list)% store the corresponding list of path in UserData of uicontrol transform_fct
244set(handles.path_transform,'String','')
245set(handles.path_transform,'UserData',[])
246
247%% case of an input argument for uvmat
248testinputfield=0;
249inputfile=[];
250Field=[];
251if exist('input','var')
252    if ishandle(handles.UVMAT_title)
253        delete(handles.UVMAT_title)
254    end   
255    if isstruct(input)
256        if isfield(input,'InputFile')
257            inputfile=input.InputFile;
258        end
259        if isfield(input,'TimeIndex')
260            set(handles.i1,num2str(input.TimeIndex))
261        end
262        if isfield(input,'FieldsString')
263            UvData.FieldsString=input.FieldsString;
264        end
265    elseif ischar(input)% file name introduced as input
266           inputfile=input;
267    elseif isnumeric(input)%simple matrix introduced as input
268        sizinput=size(input);
269        if sizinput(1)<=1 || sizinput(2)<=1
270            msgbox_uvmat('ERROR','bad input for uvmat: file name, structure or numerical matrix accepted')
271            return
272        end
273        UvData.Field.ListVarName={'A','coord_y','coord_x'};
274        UvData.Field.VarDimName={{'coord_y','coord_x'},'cord_y','coord_x'};
275        UvData.Field.A=input;
276        UvData.Field.coord_x=[0.5 size(input,2)-0.5];
277        UvData.Field.coord_y=[size(input,1)-0.5 0.5];
278        testinputfield=1;
279    end
280else
281    %% check the path and date of modification of all functions in uvmat
282    path_to_uvmat=which ('uvmat');% check the path detected for source file uvmat
283    [infomsg,date_str,svn_info]=check_files;%check the path of the functions called by uvmat.m   
284    date_str=['last modification: ' date_str];
285    if ishandle(handles.UVMAT_title)
286        set(handles.UVMAT_title,'String',...
287            [{'Copyright  LEGI UMR 5519 /CNRS-UJF-Grenoble INP, 2010'};...
288            {'GNU General Public License'};...
289            {path_to_uvmat};...
290            {date_str};...
291            infomsg]);
292    end
293end
294set(handles.uvmat,'UserData',UvData)
295if ~isempty(inputfile)
296    %%%%% display the input field %%%%%%%
297    display_file_name(handles,inputfile)
298    %%%%%%%
299end
300
301set_vec_col_bar(handles) %update the display of color code for vectors
302
303%------------------------------------------------------------------------
304% --- Outputs from this function are returned to the command menuline.
305function varargout = uvmat_OutputFcn(hObject, eventdata, handles)
306varargout{1} = handles.output;% the only output argument is the handle to the GUI figure
307
308%------------------------------------------------------------------------
309% --- executed when closing uvmat: delete or desactivate the associated figures if exist
310function closefcn(gcbo,eventdata)
311%------------------------------------------------------------------------
312hh=findobj(allchild(0),'tag','view_field');
313if ~isempty(hh)
314    delete(hh)
315end
316hh=findobj(allchild(0),'tag','geometry_calib');
317if ~isempty(hh)
318    delete(hh)
319end
320hh=findobj(allchild(0),'tag','set_object');
321if ~isempty(hh)
322    hhh=findobj(hh,'tag','PLOT');
323    set(hhh,'enable','off')
324end
325
326%------------------------------------------------------------------------
327%------------------------------------------------------------------------
328%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
329% automatically sets the global properties when the rootfile name is introduced
330% then activate the view-field action if selected
331% it is activated either by clicking on the RootPath window or by the
332% browser
333%------------------------------------------------------------------------
334%------------------------------------------------------------------------
335% --- Executes on the menu Open/Browse...
336% search the files, recognize their type according to their name and fill the rootfile input windows
337function MenuBrowse_Callback(hObject, eventdata, handles)
338[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
339oldfile=fullfile(RootPath,SubDir);
340if isempty(oldfile) %loads the previously stored file name and set it as default in the file_input box
341    oldfile=get(handles.RootPath,'UserData');
342end
343[FileName, PathName] = uigetfile({'*.*','All Files(*.*)'},'Pick a file',oldfile);
344if ~ischar(FileName),return,end %abandon if the browser is cancelled
345fileinput=[PathName FileName];%complete file name
346
347%% display the selected field and related information
348display_file_name( handles,fileinput)
349
350% -----------------------------------------------------------------------
351% --- Executes on the menu Open/Browse campaign...
352% search the file inside a campaign, using the GUI view_data
353function MenuBrowseCampaign_Callback(hObject, eventdata, handles)
354% -----------------------------------------------------------------------
355RootPath=get(handles.RootPath,'String');
356if isempty(RootPath)
357    RootPath=get(handles.RootPath,'UserData');%use Rootpath recored from the personal file at uvmat opening
358end
359CampaignPath=fileparts(fileparts(RootPath));
360DirFull = uigetdir(CampaignPath,'Select a Campaign dir, then press OK');
361if ~ischar(DirFull)|| ~exist(DirFull,'dir')
362    return
363end
364OutPut=browse_data(DirFull);% open the GUI browse_data to get select a campaign dir, experiment and device
365if ~isfield(OutPut,'Campaign')
366    return
367end
368DirName=fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.Device{1});
369hdir=dir(DirName); %list files and dirs
370for ilist=1:numel(hdir)
371    if ~isequal(hdir(ilist).isdir,1)%look for files, not dir
372        FileName=hdir(ilist).name;
373        FileType=get_file_type(fullfile(DirName,FileName));
374        switch FileType
375            case {'image','multimage','civx','civdata','netcdf'}
376            break
377        end
378    end
379end
380
381%% display the selected field and related information
382display_file_name( handles,fullfile(DirName,FileName))
383
384% -----------------------------------------------------------------------
385% --- Open again the file whose name has been recorded in MenuFile_1
386function MenuFile_1_Callback(hObject, eventdata, handles)
387%------------------------------------------------------------------------
388fileinput=get(handles.MenuFile_1,'Label');
389display_file_name( handles,fileinput)
390
391% -----------------------------------------------------------------------
392% --- Open again the file whose name has been recorded in MenuFile_2
393function MenuFile_2_Callback(hObject, eventdata, handles)
394%------------------------------------------------------------------------
395fileinput=get(handles.MenuFile_2,'Label');
396display_file_name(handles,fileinput)
397
398% -----------------------------------------------------------------------
399% --- Open again the file whose name has been recorded in MenuFile_3
400function MenuFile_3_Callback(hObject, eventdata, handles)
401%------------------------------------------------------------------------
402fileinput=get(handles.MenuFile_3,'Label');
403display_file_name(handles,fileinput)
404
405% -----------------------------------------------------------------------
406% --- Open again the file whose name has been recorded in MenuFile_4
407function MenuFile_4_Callback(hObject, eventdata, handles)
408%------------------------------------------------------------------------
409fileinput=get(handles.MenuFile_4,'Label');
410display_file_name(handles,fileinput)
411
412% -----------------------------------------------------------------------
413% --- Open again the file whose name has been recorded in MenuFile_5
414function MenuFile_5_Callback(hObject, eventdata, handles)
415%------------------------------------------------------------------------
416fileinput=get(handles.MenuFile_5,'Label');
417display_file_name(handles,fileinput)
418
419%------------------------------------------------------------------------
420% --- Executes on the menu Open/Browse_1 for the second input field,
421%     search the files, recognize their type according to their name and fill the rootfile input windows
422function MenuBrowse_1_Callback(hObject, eventdata, handles)
423%------------------------------------------------------------------------
424RootPath=get(handles.RootPath,'String');
425[FileName, PathName] = uigetfile({'*.*','All Files(*.*)'},'Pick a file',RootPath);
426if ~ischar(FileName),return,end %abandon if the browser is cancelled
427fileinput_1=[PathName FileName];%complete file name
428
429% refresh the current displayed field
430set(handles.SubField,'Value',1)
431display_file_name(handles,fileinput_1,2)
432
433%update list of recent files in the menubar
434MenuFile_1=fileinput_1;
435MenuFile_2=get(handles.MenuFile_1,'Label');
436MenuFile_3=get(handles.MenuFile_2,'Label');
437MenuFile_4=get(handles.MenuFile_3,'Label');
438MenuFile_5=get(handles.MenuFile_4,'Label');
439set(handles.MenuFile_1,'Label',MenuFile_1)
440set(handles.MenuFile_2,'Label',MenuFile_2)
441set(handles.MenuFile_3,'Label',MenuFile_3)
442set(handles.MenuFile_4,'Label',MenuFile_4)
443set(handles.MenuFile_5,'Label',MenuFile_5)
444set(handles.MenuFile_1_1,'Label',MenuFile_1)
445set(handles.MenuFile_2_1,'Label',MenuFile_2)
446set(handles.MenuFile_3_1,'Label',MenuFile_3)
447set(handles.MenuFile_4_1,'Label',MenuFile_4)
448set(handles.MenuFile_5_1,'Label',MenuFile_5)
449% dir_perso=prefdir;
450% profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
451% if exist(profil_perso,'file')
452%     save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
453% else
454%     txt=ver('MATLAB');
455%     Release=txt.Release;
456%     relnumb=str2double(Release(3:4));
457%     if relnumb >= 14
458%         save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
459%     else
460%         save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
461%     end
462% end
463
464% --------------------------------------------------------------------
465function MenuBrowseCampaign_1_Callback(hObject, eventdata, handles)
466% -----------------------------------------------------------------------
467CampaignPath=fileparts(fileparts(get(handles.RootPath,'String')));
468DirFull = uigetdir(CampaignPath,'Select a Campaign dir, then press OK');
469if ~ischar(DirFull)|| ~exist(DirFull,'dir')
470    return
471end
472OutPut=browse_data(DirFull);% open the GUI browse_data to get select a campaign dir, experiment and device
473if ~isfield(OutPut,'Campaign')
474    return
475end
476DirName=fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.Device{1});
477hdir=dir(DirName); %list files and dirs
478for ilist=1:numel(hdir)
479    if ~isequal(hdir(ilist).isdir,1)%look for files, not dir
480        FileName=hdir(ilist).name;
481        FileType=get_file_type(fullfile(DirName,FileName));
482        switch FileType
483            case {'image','multimage','civx','civdata','netcdf'}
484            break
485        end
486    end
487end
488
489%% display the selected field and related information
490set(handles.SubField,'Value',1)
491display_file_name( handles,fullfile(DirName,FileName),2)
492
493% -----------------------------------------------------------------------
494% --- Open again as second field the file whose name has been recorded in MenuFile_1
495function MenuFile_1_1_Callback(hObject, eventdata, handles)
496% -----------------------------------------------------------------------
497fileinput_1=get(handles.MenuFile_1_1,'Label');
498set(handles.SubField,'Value',1)
499display_file_name(handles,fileinput_1,2)
500
501% -----------------------------------------------------------------------
502% --- Open again as second field the file whose name has been recorded in MenuFile_2
503function MenuFile_2_1_Callback(hObject, eventdata, handles)
504% -----------------------------------------------------------------------
505fileinput_1=get(handles.MenuFile_2_1,'Label');
506set(handles.SubField,'Value',1)
507display_file_name(handles,fileinput_1,2)
508
509% -----------------------------------------------------------------------
510% --- Open again as second field the file whose name has been recorded in MenuFile_3
511function MenuFile_3_1_Callback(hObject, eventdata, handles)
512% -----------------------------------------------------------------------
513fileinput_1=get(handles.MenuFile_3_1,'Label');
514set(handles.SubField,'Value',1)
515display_file_name(handles,fileinput_1,2)
516
517% -----------------------------------------------------------------------
518% --- Open again as second field the file whose name has been recorded in MenuFile_4
519function MenuFile_4_1_Callback(hObject, eventdata, handles)
520% -----------------------------------------------------------------------
521fileinput_1=get(handles.MenuFile_4_1,'Label');
522set(handles.SubField,'Value',1)
523display_file_name(handles,fileinput_1,2)
524
525% -----------------------------------------------------------------------
526% --- Open again as second field the file whose name has been recorded in MenuFile_5
527function MenuFile_5_1_Callback(hObject, eventdata, handles)
528% -----------------------------------------------------------------------
529fileinput_1=get(handles.MenuFile_5_1,'Label');
530set(handles.SubField,'Value',1)
531display_file_name(handles,fileinput_1,2)
532
533%------------------------------------------------------------------------
534% --- Called by action in RootPath edit box
535function RootPath_Callback(hObject,eventdata,handles)
536%------------------------------------------------------------------------
537% read the current input file name:
538[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
539if ~exist(fullfile(RootPath,SubDir),'dir')
540    msgbox_uvmat('ERROR',['directory ' fullfile(RootPath,SubDir) ' does not exist'])
541    return
542end
543% detect the file type, get the movie object if relevant, and look for the corresponding file series:
544[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
545% initiate the input file series and refresh the current field view:
546update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,1);
547
548%-----------------------------------------------------------------------
549% --- Called by action in RootPath_1 edit box
550function RootPath_1_Callback(hObject,eventdata,handles)
551% -----------------------------------------------------------------------
552% update_rootinfo_1(hObject,eventdata,handles)
553[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
554if ~exist(fullfile(RootPath,SubDir),'dir')
555    msgbox_uvmat('ERROR',['directory ' fullfile(RootPath,SubDir) ' does not exist'])
556    return
557end
558% detect the file type, get the movie object if relevant, and look for the corresponding file series:
559[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
560% initiate the input file series and refresh the current field view:
561update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,2);
562
563%------------------------------------------------------------------------
564% --- Called by action in RootFile edit box
565function SubDir_Callback(hObject, eventdata, handles)
566%------------------------------------------------------------------------
567%refresh the menu of input fieldname
568Fields_Callback(hObject, eventdata, handles);
569% refresh the current field view
570run0_Callback(hObject, eventdata, handles);
571
572%------------------------------------------------------------------------
573% --- Called by action in RootFile edit box
574function RootFile_Callback(hObject, eventdata, handles)
575%------------------------------------------------------------------------
576RootPath_Callback(hObject,eventdata,handles)
577
578%-----------------------------------------------------------------------
579% --- Called by action in RootFile_1 edit box
580function RootFile_1_Callback(hObject, eventdata, handles)
581% -----------------------------------------------------------------------
582RootPath_1_Callback(hObject,eventdata,handles)
583
584%------------------------------------------------------------------------
585% --- Called by action in FileIndex edit box
586function FileIndex_Callback(hObject, eventdata, handles)
587%------------------------------------------------------------------------
588[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
589set(handles.i1,'String',num2str(i1));
590set(handles.i2,'String',num2str(i2));
591set(handles.j1,'String',num2str(j1));
592set(handles.j2,'String',num2str(j2));
593
594% refresh the current field view
595run0_Callback(hObject, eventdata, handles)
596
597%------------------------------------------------------------------------
598% --- Called by action in FileIndex_1 edit box
599function FileIndex_1_Callback(hObject, eventdata, handles)
600%------------------------------------------------------------------------
601run0_Callback(hObject, eventdata, handles)
602
603%------------------------------------------------------------------------
604% --- Called by action in NomType edit box
605function NomType_Callback(hObject, eventdata, handles)
606%------------------------------------------------------------------------
607i1=str2num(get(handles.i1,'String'));
608i2=str2num(get(handles.i2,'String'));
609j1=str2num(get(handles.j1,'String'));
610j2=str2num(get(handles.j2,'String'));
611FileIndex=fullfile_uvmat('','','','',get(handles.NomType,'String'),i1,i2,j1,j2);
612set(handles.FileIndex,'String',FileIndex)
613% refresh the current settings and refresh the field view
614RootPath_Callback(hObject,eventdata,handles)
615
616%------------------------------------------------------------------------
617% --- Called by action in NomType edit box
618function NomType_1_Callback(hObject, eventdata, handles)
619%------------------------------------------------------------------------
620i1=str2num(get(handles.i1,'String'));
621i2=str2num(get(handles.i2,'String'));
622j1=str2num(get(handles.j1,'String'));
623j2=str2num(get(handles.j2,'String'));
624FileIndex=fullfile_uvmat('','','','',get(handles.NomType_1,'String'),i1,i2,j1,j2);
625set(handles.FileIndex_1,'String',FileIndex)
626% refresh the current settings and refresh the field view
627RootPath_1_Callback(hObject,eventdata,handles)
628
629%------------------------------------------------------------------------
630% --- Fills the edit boxes RootPath, RootFile,NomType...from an input file name 'fileinput'
631function display_file_name(handles,fileinput,index)
632%------------------------------------------------------------------------
633%% look for the input file existence
634if ~exist(fileinput,'file')
635    msgbox_uvmat('ERROR',['input file ' fileinput  ' does not exist'])
636    return
637end
638
639%% set the mouse pointer to 'watch'
640set(handles.uvmat,'Pointer','watch')
641set(handles.RootPath,'BackgroundColor',[1 1 0])
642drawnow
643
644%% define the relevant handles for the first field series (index=1) or the second file series (index=2)
645if ~exist('index','var')
646    index=1;
647end
648if index==1
649    handles_RootPath=handles.RootPath;
650    handles_SubDir=handles.SubDir;
651    handles_RootFile=handles.RootFile;
652    handles_FileIndex=handles.FileIndex;
653    handles_NomType=handles.NomType;
654    handles_FileExt=handles.FileExt;
655elseif index==2
656    handles_RootPath=handles.RootPath_1;
657    handles_SubDir=handles.SubDir_1;
658    handles_RootFile=handles.RootFile_1;
659    handles_FileIndex=handles.FileIndex_1;
660    handles_NomType=handles.NomType_1;
661    handles_FileExt=handles.FileExt_1;
662    set(handles.RootPath_1,'Visible','on')
663    set(handles.RootFile_1,'Visible','on')
664    set(handles.SubDir_1,'Visible','on');
665    set(handles.FileIndex_1,'Visible','on');
666    set(handles.FileExt_1,'Visible','on');
667    set(handles.NomType_1,'Visible','on');
668end
669
670%% detect root name, nomenclature and indices in the input file name:
671[FilePath,FileName,FileExt]=fileparts(fileinput);
672% detect the file type, get the movie object if relevant, and look for the corresponding file series:
673% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
674[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
675
676%% open the file or fill the GUI uvmat according to the detected file type
677switch FileType
678    case ''
679        msgbox_uvmat('ERROR','invalid input file type')
680    case 'txt'
681        edit(fileinput)
682    case 'figure'                           %display matlab figure
683        hfig=open(fileinput);
684        set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
685        set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
686        set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
687    case 'xml'                % edit xml files
688        t=xmltree(fileinput);
689        % the xml file marks a project or project link, open datatree_browser
690        if strcmp(get(t,1,'name'),'Project')&& exist(regexprep(fileinput,'.xml$',''),'dir')
691            datatree_browser(fileinput)
692        else % other xml file, open the xml editor
693            editxml(fileinput);
694        end
695    case 'xls'% Excel file opended by editxml
696        editxml(fileinput);
697    otherwise
698        set(handles_RootPath,'String',RootPath);
699        rootname=fullfile(RootPath,SubDir,RootFile);
700        set(handles_SubDir,'String',['/' SubDir]);
701        set(handles_RootFile,'String',['/' RootFile]); %display the separator
702        indices=fileinput(length(rootname)+1:end);
703        indices(end-length(FileExt)+1:end)=[]; %remove extension
704        set(handles_FileIndex,'String',indices);
705        set(handles_NomType,'String',NomType);
706        set(handles_FileExt,'String',FileExt);
707        if index==1
708            % fill file index counters if the first file series is opened
709            set(handles.i1,'String',num2str(i1));
710            set(handles.i2,'String',num2str(i2));
711            set(handles.j1,'String',num2stra(j1,NomType));
712            set(handles.j2,'String',num2stra(j2,NomType));
713        else %read the current field index to synchronise with the first series
714            i1_s=str2num(get(handles.i1,'String'));
715            i2_0=str2num(get(handles.i2,'String'));
716            if ~isempty(i2_0)
717                i2_s=i2_0;
718            else
719               i2_s=i2;
720            end
721            j1_0=stra2num(get(handles.j1,'String'));
722            if ~isempty(j1_0)
723                j1_s=j1_0;
724            else
725                j1_s=j1;
726            end
727            j2_0=stra2num(get(handles.j2,'String'));
728            if ~isempty(j2_0)
729                j2_s=j2_0;
730            else
731                j2_s=j2;
732            end
733        end
734       
735        % synchronise indices of the second  input file if it exists
736        if get(handles.SubField,'Value')==1% if the subfield button is activated, update the field numbers
737            Input=read_GUI(handles.InputFile);
738            if ~isfield(Input,'RootPath_1')||strcmp(Input.RootPath_1,'"')
739                Input.RootPath_1=Input.RootPath;
740            end
741            if ~isfield(Input,'SubDir_1')||strcmp(Input.SubDir_1,'"')
742                Input.SubDir_1=Input.SubDir;
743            end
744            if ~isfield(Input,'RootFile_1')||strcmp(Input.RootFile_1,'"')
745                Input.RootFile_1=Input.RootFile;
746            end
747            if ~isfield(Input,'FileExt_1')||strcmp(Input.FileExt_1,'"')
748                Input.FileExt_1=Input.FileExt;
749            end
750            if ~isfield(Input,'NomType_1')||strcmp(Input.NomType_1,'"')
751                Input.NomType_1=Input.NomType;
752            end
753            %updtate the indices of the second field series to correspond to the newly opened one
754            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);
755            if exist(FileName_1,'file')
756                FileIndex_1=fullfile_uvmat('','','','',Input.NomType_1,i1_s,i2_s,j1_s,j2_s);
757            else
758                FileIndex_1=fullfile_uvmat('','','','',Input.NomType_1,i1,i2,j1,j2);
759                msgbox_uvmat('WARNING','unable to synchronise the indices of the two series')
760            end
761            set(handles.FileIndex_1,'String',FileIndex_1)
762        end
763       
764        %enable other menus
765        set(handles.MenuOpen_1,'Enable','on')
766        set(handles.MenuFile_1_1,'Enable','on')
767        set(handles.MenuFile_2_1,'Enable','on')
768        set(handles.MenuFile_3_1,'Enable','on')
769        set(handles.MenuFile_4_1,'Enable','on')
770        set(handles.MenuFile_5_1,'Enable','on')
771        set(handles.MenuExport,'Enable','on')
772        set(handles.MenuExportFigure,'Enable','on')
773        set(handles.MenuExportMovie,'Enable','on')
774        set(handles.MenuTools,'Enable','on')
775
776        % initiate input file series and refresh the current field view:     
777        update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,index);
778
779end
780
781%% update list of recent files in the menubar and save it for future opening
782MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
783    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
784str_find=strcmp(fileinput,MenuFile);
785if isempty(find(str_find,1))
786    MenuFile=[{fileinput};MenuFile];%insert the current file if not already in the list
787end
788for ifile=1:min(length(MenuFile),5)
789    set(handles.(['MenuFile_' num2str(ifile)]),'Label',MenuFile{ifile});
790    set(handles.(['MenuFile_' num2str(ifile) '_1']),'Label',MenuFile{ifile});
791end
792dir_perso=prefdir;
793profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
794if exist(profil_perso,'file')
795    save (profil_perso,'MenuFile','RootPath','-append'); %store the file names for future opening of uvmat
796else
797    save (profil_perso,'MenuFile','RootPath','-V6'); %store the file names for future opening of uvmat
798end
799
800%% set back the mouse pointer to arrow
801set(handles.uvmat,'Pointer','arrow')
802
803
804%------------------------------------------------------------------------
805% --- Update information about a new field series (indices to scan, timing,
806%     calibration from an xml file, then refresh current plots
807
808function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,VideoObject,index)
809%------------------------------------------------------------------------
810%% define the relevant handles depending on the index (1=first file series, 2= second file series)
811if ~exist('index','var')
812    index=1;
813end
814if index==1
815    handles_RootPath=handles.RootPath;
816    handles_Fields=handles.FieldName;
817elseif index==2
818    handles_RootPath=handles.RootPath_1;
819    handles_Fields=handles.FieldName_1;
820end
821
822set(handles_RootPath,'BackgroundColor',[1 1 0])
823drawnow
824set(handles.FieldName,'UserData',[])% reinialize data from uvmat opening
825UvData=get(handles.uvmat,'UserData');%huvmat=handles of the uvmat interface
826UvData.NewSeries=1; %flag for run0: begin a new series
827UvData.FileName_1='';% name of the current second field (used to detect a  constant field during file scanning)
828UvData.FileType{index}=FileType;
829UvData.i1_series{index}=i1_series;
830UvData.i2_series{index}=i2_series;
831UvData.j1_series{index}=j1_series;
832UvData.j2_series{index}=j2_series;
833set(handles.FixVelType,'Value',0); %desactivate fixed veltype
834if index==1
835    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
836else
837    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
838end
839FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
840FileBase=fullfile(RootPath,RootFile);
841if ~exist(FileName,'file')
842   msgbox_uvmat('ERROR',['input file ' FileName ' not found']);
843    return
844end
845
846%% read timing and total frame number from the current file (movie files) !! may be overrid by xml file
847XmlData.Time=[];%default
848XmlData.GeometryCalib=[];%default
849TimeUnit='';%default
850Time=[];
851% testima=0; %test for image input
852imainfo=[];
853ColorType='falsecolor'; %default
854% hhh=[];
855UvData.MovieObject{index}=VideoObject;
856if ~isempty(VideoObject)
857    imainfo=get(VideoObject);
858%     testima=1;
859    TimeUnit='s';
860    if isempty(j1_series); %frame index along i
861        Time=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)';
862    else
863        Time=ones(size(i1_series,1),1)*(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate);
864    end
865    set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FrameRate) 'ms']);%display the elementary time interval in millisec
866    ColorType='truecolor';
867elseif ~isempty(FileExt(2:end))&&(~isempty(imformats(FileExt(2:end))) || isequal(FileExt,'.vol'))%&& isequal(NomType,'*')% multi-frame image
868%     testima=1;
869    if ~isequal(SubDir,'')
870        imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]);
871    else
872        imainfo=imfinfo([FileBase FileIndices FileExt]);
873    end
874    ColorType=imainfo.ColorType;%='truecolor' for color images
875end
876if isfield(imainfo,'Width') && isfield(imainfo,'Height')
877    if length(imainfo)>1
878        set(handles.num_Npx,'String',num2str(imainfo(1).Width));%fills nbre of pixels x box
879        set(handles.num_Npy,'String',num2str(imainfo(1).Height));%fills nbre of pixels x box
880    else
881        set(handles.num_Npx,'String',num2str(imainfo.Width));%fills nbre of pixels x box
882        set(handles.num_Npy,'String',num2str(imainfo.Height));%fills nbre of pixels x box
883    end
884else
885    set(handles.num_Npx,'String','');%fills nbre of pixels x box
886    set(handles.num_Npy,'String','');%fills nbre of pixels x box
887end
888set(handles.CheckBW,'Value',strcmp(ColorType,'grayscale'))% select handles.CheckBW if grayscale image
889
890%% read parameters (time, geometric calibration..) from a documentation file (.xml advised)
891XmlFileName=find_imadoc(RootPath,SubDir,RootFile,FileExt);
892[tild,tild,DocExt]=fileparts(XmlFileName);
893warntext='';%default warning message
894NbSlice=1;%default
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])
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        set(handles.view_xml,'Visible','off')
907    else
908        set(handles.view_xml,'String',['view ' DocExt])   
909        XmlData=XmlDataRead;
910        if isfield(XmlData,'TimeUnit')
911            if isfield(XmlData,'TimeUnit')&& ~isempty(XmlData.TimeUnit)
912                TimeUnit=XmlData.TimeUnit;
913            end
914        end
915        set(handles.view_xml,'BackgroundColor',[1 1 1])
916        drawnow
917        if isfield(XmlData, 'GeometryCalib') && ~isempty(XmlData.GeometryCalib)
918            if isfield(XmlData.GeometryCalib,'VolumeScan') && isequal(XmlData.GeometryCalib.VolumeScan,'y')
919                set (handles.slices,'String','volume')
920            end
921            hgeometry_calib=findobj('tag','geometry_calib');
922            if ~isempty(hgeometry_calib)
923                GUserData=get(hgeometry_calib,'UserData');
924                if ~(isfield(GUserData,'XmlInputFile') && strcmp(GUserData.XmlInputFile,XmlFileName))
925                    answer=msgbox_uvmat('INPUT_Y-N','replace the display of geometry_calib with the new input data?');
926                    if strcmp(answer,'Yes')
927                        geometry_calib(XmlFileName);%diplay the new calibration points and parameters in geometry_calib
928                    end
929                end
930            end
931        end
932    end
933end
934if ~(isfield(XmlData,'Time')&& ~isempty(XmlData.Time))
935    XmlData.Time=Time; %time set by video
936end
937
938%% store last index in handles.lat_i and .last_j
939nbfield=max(max(max(i2_series)));
940if isempty(nbfield)
941    nbfield=max(max(max(i1_series)));
942end
943nbfield_j=max(max(max(j2_series)));
944if isempty(nbfield_j)
945    nbfield_j=max(max(max(j1_series)));
946end
947if ~isempty(XmlData.Time)
948    %transform .Time to a column vector if it is a line vector the nomenclature uses a single index
949    if isequal(size(XmlData.Time,1),1)
950        %NomType=get(handles.NomType,'String');
951        XmlData.Time=(XmlData.Time)';
952    end
953end
954last_i_cell=get(handles.last_i,'String');
955if isempty(nbfield)
956    last_i_cell{index}='';
957else
958    last_i_cell{index}=num2str(nbfield);
959end
960set(handles.last_i,'String',last_i_cell)
961last_j_cell=get(handles.last_j,'String');
962if isempty(nbfield_j)
963     last_j_cell{index}='';
964else
965     last_j_cell{index}=num2str(nbfield_j);
966end
967set(handles.last_j,'String',last_j_cell);
968
969%% store geometric calibration in UvData
970if isfield(XmlData,'GeometryCalib')
971    GeometryCalib=XmlData.GeometryCalib;
972    if isempty(GeometryCalib)
973        set(handles.pxcm,'String','')
974        set(handles.pycm,'String','')
975        set(handles.transform_fct,'Value',1); %  no transform by default
976    else
977        if (isfield(GeometryCalib,'R')&& ~isequal(GeometryCalib.R(2,1),0) && ~isequal(GeometryCalib.R(1,2),0)) ||...
978            (isfield(GeometryCalib,'kappa1')&& ~isequal(GeometryCalib.kappa1,0))
979            set(handles.pxcm,'String','var')
980            set(handles.pycm,'String','var')
981        elseif isfield(GeometryCalib,'fx_fy')
982            pixcmx=GeometryCalib.fx_fy(1);%*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx);
983            pixcmy=GeometryCalib.fx_fy(2);%*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy);
984            set(handles.pxcm,'String',num2str(pixcmx))
985            set(handles.pycm,'String',num2str(pixcmy))
986        end
987        if ~get(handles.CheckFixLimits,'Value')
988            set(handles.transform_fct,'Value',3); % phys transform by default if fixedLimits is off
989        end
990        if isfield(GeometryCalib,'SliceCoord')           
991           siz=size(GeometryCalib.SliceCoord);
992           if siz(1)>1
993               NbSlice=siz(1);
994               set(handles.slices,'Visible','on')
995               set(handles.slices,'Value',1)
996           end
997           if isfield(GeometryCalib,'VolumeScan') && isequal(GeometryCalib.VolumeScan,'y')
998               set(handles.num_NbSlice,'Visible','off')
999           else
1000               set(handles.num_NbSlice,'Visible','on')
1001               set(handles.num_NbSlice,'String',num2str(NbSlice))
1002           end
1003           slices_Callback([],[], handles)
1004        end           
1005    end
1006end
1007
1008%% update the data attached to the uvmat interface
1009if ~isempty(TimeUnit)
1010    set(handles.time_txt,'String',['time (' TimeUnit ')'])
1011end
1012UvData.TimeUnit=TimeUnit;
1013UvData.XmlData{index}=XmlData;
1014UvData.NewSeries=1;
1015% UvData.MovieObject=MovieObject;
1016
1017%display warning message
1018if ~isequal(warntext,'')
1019    msgbox_uvmat('WARNING',warntext);
1020end
1021
1022%% set default options in menu 'FieldName'
1023switch FileType
1024    case {'civx','civdata'}
1025%         [FieldList,ColorList]=calc_field;
1026        [FieldList,ColorList]=set_field_list('U','V','C');
1027        set(handles_Fields,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data
1028        set(handles_Fields,'Value',2) % set menu to 'velocity
1029        if index==1
1030            set(handles.FieldName_1,'Value',1);
1031            set(handles.FieldName_1,'String',[{''};{'image'};FieldList;{'get_field...'}]);%standard menu for civx data reproduced for the second field
1032        end
1033        set(handles.ColorScalar,'Value',1)
1034        set(handles.ColorScalar,'String',ColorList)
1035        set(handles.Vectors,'Visible','on')
1036        set(handles.Coord_x,'Value',1);
1037        set(handles.Coord_x,'String',{'X'});
1038        set(handles.Coord_y,'Value',1);
1039        set(handles.Coord_y,'String',{'Y'});
1040    case 'netcdf'
1041        set(handles_Fields,'Value',1)
1042        set(handles_Fields,'String',{'get_field...'})
1043        hget_field=get_field(FileName);
1044        hhget_field=guidata(hget_field);
1045        get_field('RUN_Callback',hhget_field.RUN,[],hhget_field);
1046    otherwise
1047        set(handles_Fields,'Value',1) % set menu to 'image'
1048        set(handles_Fields,'String',{'image'})
1049        set(handles.Coord_x,'Value',1);
1050        set(handles.Coord_x,'String',{'AX'});
1051        set(handles.Coord_y,'Value',1);
1052        set(handles.Coord_y,'String',{'AY'});
1053end
1054set(handles.uvmat,'UserData',UvData)
1055
1056%% set index navigation options and refresh plots
1057scan_option='i';%default
1058state_j='off'; %default
1059if index==2
1060    if get(handles.scan_j,'Value')
1061        scan_option='j'; %keep the scan option for the second file series
1062    end
1063    if strcmp(get(handles.j1,'Visible'),'on')
1064        state_j='on';
1065    end
1066end
1067[ref_j,ref_i]=find(squeeze(i1_series(1,:,:)));
1068if ~isempty(j1_series)
1069        state_j='on';
1070        if index==1
1071            if isequal(ref_i,ref_i(1)*ones(size(ref_j)))% if ref_i is always equal to its first value
1072                scan_option='j'; %scan j indext               
1073            end
1074        end
1075end
1076if isequal(scan_option,'i')
1077    diff_ref_i=diff(ref_i,1);
1078    if isempty(diff_ref_i)
1079        diff_ref_i=1;
1080    end
1081    if isequal (diff_ref_i,diff_ref_i(1)*ones(size(diff_ref_i)))
1082        set(handles.num_IndexIncrement,'String',num2str(diff_ref_i(1)))
1083    end
1084     set(handles.scan_i,'Value',1)
1085     scan_i_Callback([],[], handles);
1086else
1087    diff_ref_j=diff(ref_j);
1088    if isempty(diff_ref_j)
1089        diff_ref_j=1;
1090    end
1091    if isequal (diff_ref_j,diff_ref_j(1)*ones(size(diff_ref_j)))
1092        set(handles.num_IndexIncrement,'String',num2str(diff_ref_j(1)))
1093    end
1094     set(handles.scan_j,'Value',1)
1095     scan_j_Callback([],[], handles);
1096end
1097set(handles.scan_j,'Visible',state_j)
1098set(handles.j1,'Visible',state_j)
1099set(handles.j2,'Visible',state_j)
1100set(handles.last_j,'Visible',state_j);
1101set(handles.frame_j,'Visible',state_j);
1102set(handles.j_text,'Visible',state_j);
1103if ~isempty(i2_series)||~isempty(j2_series)
1104    set(handles.CheckFixPair,'Visible','on')
1105elseif index==1
1106    set(handles.CheckFixPair,'Visible','off')
1107end
1108
1109%% apply the effect of the transform fct and view the field 
1110transform=get(handles.path_transform,'UserData');
1111if index==2 && (~isa(transform,'function_handle')||nargin(transform)<3)
1112    set(handles.transform_fct,'value',2); % set transform to sub_field if the current fct doe not accept two input fields
1113end
1114transform_fct_Callback([],[],handles)
1115mask_test=get(handles.CheckMask,'value');
1116if mask_test
1117    MaskData=get(handles.CheckMask,'UserData');
1118    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1119          delete(MaskData.maskhandle)    %delete old mask
1120    end
1121    CheckMask_Callback([],[],handles)
1122end
1123
1124%------------------------------------------------------------------------
1125% --- switch file index scanning options scan_i and scan_j in an exclusive way
1126function scan_i_Callback(hObject, eventdata, handles)
1127%------------------------------------------------------------------------
1128if get(handles.scan_i,'Value')==1
1129%     set(handles.scan_i,'BackgroundColor',[1 1 0])
1130    set(handles.scan_j,'Value',0)
1131else
1132%     set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1133    set(handles.scan_j,'Value',1)
1134end
1135scan_j_Callback(hObject, eventdata, handles)
1136
1137%------------------------------------------------------------------------
1138% --- switch file index scanning options scan_i and scan_j in an exclusive way
1139function scan_j_Callback(hObject, eventdata, handles)
1140%------------------------------------------------------------------------
1141if get(handles.scan_j,'Value')==1
1142%     set(handles.scan_j,'BackgroundColor',[1 1 0])
1143    set(handles.scan_i,'Value',0)
1144%     set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1145%     NomType=get(handles.NomType,'String');
1146%     switch NomType
1147%     case {'_1_1-2','#_ab','%3dab'},% pair with j index
1148%         set(handles.CheckFixPair,'Visible','on')% option fixed pair on/off made visible (choice of avaible pair with buttons + and - if ='off')
1149%     otherwise
1150%         set(handles.CheckFixPair,'Visible','off')
1151%     end
1152else
1153%     set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
1154    set(handles.scan_i,'Value',1)
1155%     set(handles.scan_i,'BackgroundColor',[1 1 0])
1156    set(handles.CheckFixPair,'Visible','off')
1157end
1158
1159%------------------------------------------------------------------------
1160function i1_Callback(hObject, eventdata, handles)
1161%------------------------------------------------------------------------
1162update_ij(handles,1)
1163
1164%------------------------------------------------------------------------
1165function i2_Callback(hObject, eventdata, handles)
1166%------------------------------------------------------------------------
1167update_ij(handles,2)
1168
1169%------------------------------------------------------------------------
1170function j1_Callback(hObject, eventdata, handles)
1171%------------------------------------------------------------------------
1172update_ij(handles,3)
1173
1174%------------------------------------------------------------------------
1175function j2_Callback(hObject, eventdata, handles)
1176%------------------------------------------------------------------------
1177update_ij(handles,4)
1178
1179%------------------------------------------------------------------------
1180%--- update the index display after action on edit boxes i1, i2, j1 or j2
1181function update_ij(handles,index_rank)
1182NomType=get(handles.NomType,'String');
1183indices=get(handles.FileIndex,'String');
1184[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(indices);% the indices for the second series taken from FileIndex
1185switch index_rank
1186    case 1
1187        indices=fullfile_uvmat('','','','',NomType,stra2num(get(handles.i1,'String')),i2,j1,j2);
1188        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
1189    case 2
1190        indices=fullfile_uvmat('','','','',NomType,i1,stra2num(get(handles.i2,'String')),j1,j2);
1191        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
1192    case 3
1193        indices=fullfile_uvmat('','','','',NomType,i1,i2,stra2num(get(handles.j1,'String')),j2);
1194        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
1195    case 4
1196        indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,stra2num(get(handles.j2,'String')));
1197        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
1198end
1199set(handles.FileIndex,'String',indices)
1200set(handles.FileIndex,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation
1201% update the second index if relevant
1202if strcmp(get(handles.FileIndex_1,'Visible'),'on')
1203    NomType_1=get(handles.NomType_1,'String');
1204    indices_1=get(handles.FileIndex_1,'String');
1205    [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
1206    switch index_rank
1207        case 1
1208            indices_1=fullfile_uvmat('','','','',NomType_1,stra2num(get(handles.i1,'String')),i2_1,j1_1,j2_1);
1209        case 2
1210            indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,stra2num(get(handles.i2,'String')),j1_1,j2_1);
1211        case 3
1212            indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,i2_1,stra2num(get(handles.j1,'String')),j2_1);
1213        case 4
1214            indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,i2_1,j1_1,stra2num(get(handles.j2,'String')));
1215    end
1216    set(handles.FileIndex_1,'String',indices_1)
1217    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
1218end
1219   
1220%------------------------------------------------------------------------
1221
1222%------------------------------------------------------------------------
1223function slices_Callback(hObject, eventdata, handles)
1224%------------------------------------------------------------------------
1225if strcmp(get(handles.slices,'String'),'slices')
1226    if get(handles.slices,'Value')==1
1227        set(handles.num_NbSlice,'Visible','on')
1228        set(handles.z_text,'Visible','on')
1229        set(handles.z_index,'Visible','on')
1230        num_NbSlice_Callback(hObject, eventdata, handles)
1231    else
1232        set(handles.num_NbSlice,'Visible','off')
1233        set(handles.z_text,'Visible','off')
1234        set(handles.z_index,'Visible','off')
1235        set(handles.masklevel,'Value',1)
1236        set(handles.masklevel,'String',{'1'})
1237    end
1238end
1239
1240%------------------------------------------------------------------------
1241function num_NbSlice_Callback(hObject, eventdata, handles)
1242%------------------------------------------------------------------------
1243mode=get(handles.slices,'String');
1244nb_slice_str=get(handles.num_NbSlice,'String');
1245if strcmp(mode,'volume')
1246    z=stra2num(get(handles.j1,'String'));
1247else
1248    num=str2double(get(handles.i1,'String'));
1249    nbslice=str2double(get(handles.num_NbSlice,'String'));
1250    z=mod(num-1,nbslice)+1;
1251end
1252set(handles.z_index,'String',num2str(z))
1253for ilist=1:nbslice
1254    list_index{ilist,1}=num2str(ilist);
1255end   
1256set(handles.masklevel,'String',list_index)
1257set(handles.masklevel,'Value',z)
1258
1259%------------------------------------------------------------------------
1260% --- Executes on button press in view_xml.
1261function view_xml_Callback(hObject, eventdata, handles)
1262%------------------------------------------------------------------------
1263%[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles);
1264 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1265FileBase=fullfile(RootPath,RootFile);
1266option=get(handles.view_xml,'String');
1267if isequal(option,'view .xml')
1268    FileXml=fullfile(RootPath,[SubDir '.xml']);
1269    if ~exist(FileXml,'file')% case of civ files , removes the extension for subdir
1270        FileXml=fullfile(RootPath,[regexprep(SubDir,'\..+$','') '.xml']);
1271    end
1272    heditxml=editxml(FileXml);
1273end
1274
1275%------------------------------------------------------------------------
1276% --- Executes on button press in CheckMask.
1277function CheckMask_Callback(hObject, eventdata, handles)
1278%------------------------------------------------------------------------
1279%case of view mask selection
1280if isequal(get(handles.CheckMask,'Value'),1)
1281     [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1282     FileBase=fullfile(RootPath,RootFile);
1283    num_i1=stra2num(get(handles.i1,'String'));
1284    num_j1=stra2num(get(handles.j1,'String'));
1285    currentdir=pwd; 
1286    cd(RootPath);
1287    maskfiles=dir('*_*mask_*.png');%look for a mask file
1288    cd(currentdir);%come back to the working directory
1289    mdetect=0;
1290    if ~isempty(maskfiles)
1291        for ilist=1:length(maskfiles)
1292            maskname=maskfiles(ilist).name;% take the first mask file in the list
1293            [tild,tild,tild,tild,tild,tild,tild,MaskExt,Mask_NomType{ilist}]=fileparts_uvmat(maskname);
1294             [tild,Name]=fileparts(maskname);
1295            Namedouble=double(Name);
1296            val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1297            ind_mask=findstr('mask',Name);
1298            i=ind_mask-1;
1299            while val(i)==0 && i>0
1300                i=i-1;
1301            end
1302            nbmask_str=str2num(Name(i+1:ind_mask-1));
1303            if ~isempty(nbmask_str)
1304                nbslice(ilist)=nbmask_str; % number of different masks (slices)
1305            end
1306        end
1307        if isequal(min(nbslice),max(nbslice))
1308            nbslice=nbslice(1);
1309        else
1310            msgbox_uvmat('ERROR','several inconsistent mask sets coexist in the current image directory')
1311            return
1312        end
1313        if ~isempty(nbslice) && Name(i)=='_'
1314            Mask.Base=[FileBase Name(i:ind_mask+3)];
1315            Mask.NbSlice=nbslice;
1316            num_i1=mod(num_i1-1,nbslice)+1;
1317            Mask.NomType=regexprep(Mask_NomType{1},'0','');%remove '0' in nom type for masks
1318            [RootPath,RootFile]=fileparts(Mask.Base);
1319            maskname=fullfile_uvmat(RootPath,'',RootFile,'.png',Mask.NomType,num_i1,[],num_j1);
1320            %maskname=name_generator(Mask.Base,num_i1,num_j1,'.png',Mask.NomType);%
1321            mdetect=exist(maskname,'file');
1322            if mdetect
1323                set(handles.num_NbSlice,'String',Name(i+1:ind_mask-1));
1324                 set(handles.num_NbSlice,'BackgroundColor',[1 1 0])
1325                set(handles.CheckMask,'UserData',Mask);
1326                set(handles.CheckMask,'BackgroundColor',[1 1 0])
1327                if nbslice > 1
1328                    set(handles.slices,'value',1)
1329                    slices_Callback(hObject, eventdata, handles)
1330                end
1331            end
1332        end
1333    end
1334    errormsg=[];%default
1335    if mdetect==0
1336        [FileName, PathName, filterindex] = uigetfile( ...
1337            {'*.png', ' (*.png)';
1338            '*.png',  '.png files '; ...
1339            '*.*', 'All Files (*.*)'}, ...
1340            'Pick a mask file *.png',FileBase);
1341        if ~ischar(FileName),return,end %abandon if the browser is cancelled
1342        maskname=fullfile(PathName,FileName);
1343        [RootDir,SubDir,RootFile,tild,tild,tild,tild,tild,Mask.NomType]=fileparts_uvmat(maskname);
1344        Mask.Base=fullfile(RootDir,SubDir,RootFile);
1345        Mask.NbSlice=1;
1346        set(handles.CheckMask,'UserData',Mask);
1347        set(handles.CheckMask,'BackgroundColor',[1 1 0])
1348    end
1349    if isempty(errormsg)
1350        errormsg=update_mask(handles,num_i1,num_j1);
1351    end
1352    if ~isempty(errormsg)
1353            set(handles.CheckMask,'Value',0)
1354            set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1355     end
1356else % desactivate mask display
1357    MaskData=get(handles.CheckMask,'UserData');
1358    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1359          delete(MaskData.maskhandle)   
1360    end
1361    set(handles.CheckMask,'UserData',[])   
1362    UvData=get(handles.uvmat,'UserData');
1363    if isfield(UvData,'MaskName')
1364        UvData=rmfield(UvData,'MaskName');
1365        set(handles.uvmat,'UserData',UvData)
1366    end
1367    set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1368end
1369
1370%------------------------------------------------------------------------
1371function errormsg=update_mask(handles,num_i1,num_j1)
1372%------------------------------------------------------------------------
1373errormsg=[];%default
1374MaskData=get(handles.CheckMask,'UserData');
1375if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1376    uistack(MaskData.maskhandle,'top');
1377end
1378num_i1_mask=mod(num_i1-1,MaskData.NbSlice)+1;
1379[RootPath,RootFile]=fileparts(MaskData.Base);
1380MaskName=fullfile_uvmat(RootPath,'',RootFile,'.png',MaskData.NomType,num_i1_mask,[],num_j1);
1381UvData=get(handles.uvmat,'UserData');
1382%update mask image if the mask is new
1383if ~ (isfield(UvData,'MaskName') && isequal(UvData.MaskName,MaskName))
1384    UvData.MaskName=MaskName; %update the recorded name on UvData
1385    set(handles.uvmat,'UserData',UvData);
1386    if ~exist(MaskName,'file')
1387        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1388            delete(MaskData.maskhandle)   
1389        end
1390    else
1391        %read mask image
1392        [Mask,tild,errormsg] = read_field(MaskName,'image');
1393%         Mask.AName='image';
1394%         Mask.A=imread(MaskName);
1395        if ~isempty(errormsg)
1396            return
1397        end
1398        npxy=size(Mask.A);
1399        if length(npxy)>2
1400            errormsg=[MaskName ' is not a grey scale image'];
1401            return
1402        elseif ~isa(Mask.A,'uint8')
1403            errormsg=[MaskName ' is not a 8 bit grey level image'];
1404            return
1405        end
1406%         Mask.AX=[0.5 npxy(2)-0.5];
1407%         Mask.AY=[npxy(1)-0.5 0.5 ];
1408%         Mask.CoordUnit='pixel';
1409        if isequal(get(handles.slices,'Value'),1)
1410           NbSlice=str2num(get(handles.num_NbSlice,'String'));
1411           num_i1=str2num(get(handles.i1,'String'));
1412           Mask.ZIndex=mod(num_i1-1,NbSlice)+1;
1413        end
1414        %px to phys or other transform on field
1415         menu_transform=get(handles.transform_fct,'String');
1416        choice_value=get(handles.transform_fct,'Value');
1417        transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1418        transform=get(handles.path_transform,'UserData');
1419        if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
1420            if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
1421                Calib=UvData.XmlData{1}.GeometryCalib;
1422                Mask=transform(Mask,UvData.XmlData{1});
1423            end
1424        end
1425        flagmask=Mask.A < 200;
1426       
1427        %make brown color image
1428        imflag(:,:,1)=0.9*flagmask;
1429        imflag(:,:,2)=0.7*flagmask;
1430        imflag(:,:,3)=zeros(size(flagmask));
1431       
1432        %update mask image
1433        hmask=[]; %default
1434        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1435            hmask=MaskData.maskhandle;
1436        end
1437        if ~isempty(hmask)
1438            set(hmask,'CData',imflag)   
1439            set(hmask,'AlphaData',flagmask*0.6)
1440            set(hmask,'XData',Mask.AX);
1441            set(hmask,'YData',Mask.AY);
1442%             uistack(hmask,'top')
1443        else
1444            axes(handles.PlotAxes)
1445            hold on   
1446            MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*ones(size(flagmask)));
1447            set(handles.CheckMask,'UserData',MaskData)
1448        end
1449    end
1450end
1451
1452%------------------------------------------------------------------------
1453%------------------------------------------------------------------------
1454% III - MAIN REFRESH FUNCTIONS : 'FRAME PLOT'
1455%------------------------------------------------------------------------
1456
1457%------------------------------------------------------------------------
1458% --- Executes on button press in runplus: make one step forward and call
1459% --- run0. The step forward is along the fieldname series 1 or 2 depending on
1460% --- the scan_i and scan_j check box (exclusive each other)
1461function runplus_Callback(hObject, eventdata, handles)
1462%------------------------------------------------------------------------
1463set(handles.runplus,'BackgroundColor',[1 1 0])%paint the command button in yellow
1464drawnow
1465%TODO: introduce the option: increment ='*' to move to the next available view
1466increment=str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d
1467% if isnan(increment)
1468%     set(handles.num_IndexIncrement,'String','1')%default value
1469%     increment=1;
1470% end
1471errormsg=runpm(hObject,eventdata,handles,increment);
1472if ~isempty(errormsg)
1473    msgbox_uvmat('ERROR',errormsg);
1474end
1475set(handles.runplus,'BackgroundColor',[1 0 0])%paint the command button back to red
1476
1477%------------------------------------------------------------------------
1478% --- Executes on button press in runmin: make one step backward and call
1479% --- run0. The step backward is along the fieldname series 1 or 2 depending on
1480% --- the scan_i and scan_j check box (exclusive each other)
1481function runmin_Callback(hObject, eventdata, handles)
1482%------------------------------------------------------------------------
1483set(handles.runmin,'BackgroundColor',[1 1 0])%paint the command button in yellow
1484drawnow
1485increment=-str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d
1486% if isnan(increment)
1487%     set(handles.num_IndexIncrement,'String','1')%default value
1488%     increment=1;
1489% end
1490errormsg=runpm(hObject,eventdata,handles,increment);
1491if ~isempty(errormsg)
1492    msgbox_uvmat('ERROR',errormsg);
1493end
1494set(handles.runmin,'BackgroundColor',[1 0 0])%paint the command button back to red
1495
1496%------------------------------------------------------------------------
1497% -- Executes on button press in Movie: make a series of +> steps
1498function Movie_Callback(hObject, eventdata, handles)
1499%------------------------------------------------------------------------
1500set(handles.Movie,'BackgroundColor',[1 1 0])%paint the command button in yellow
1501drawnow
1502increment=str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d
1503% if isnan(increment)
1504%     set(handles.num_IndexIncrement,'String','1')%default value
1505%     increment=1;
1506% end
1507set(handles.STOP,'Visible','on')
1508set(handles.speed,'Visible','on')
1509set(handles.speed_txt,'Visible','on')
1510set(handles.Movie,'BusyAction','queue')
1511UvData=get(handles.uvmat,'UserData');
1512
1513while get(handles.Movie,'Value')==1 && get(handles.speed,'Value')~=0 && isequal(get(handles.Movie,'BusyAction'),'queue') % enable STOP command
1514        errormsg=runpm(hObject,eventdata,handles,increment);
1515        if ~isempty(errormsg)
1516            set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1517            return
1518        end
1519        pause(1.02-get(handles.speed,'Value'))% wait for next image
1520end
1521if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1522    UvData.aviobj=close(UvData.aviobj);
1523   set(handles.uvmat,'UserData',UvData);
1524end
1525set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1526
1527%------------------------------------------------------------------------
1528% -- Executes on button press in Movie: make a series of <- steps
1529function MovieBackward_Callback(hObject, eventdata, handles)
1530%------------------------------------------------------------------------
1531set(handles.MovieBackward,'BackgroundColor',[1 1 0])%paint the command button in yellow
1532drawnow
1533increment=-str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d
1534set(handles.STOP,'Visible','on')
1535set(handles.speed,'Visible','on')
1536set(handles.speed_txt,'Visible','on')
1537set(handles.MovieBackward,'BusyAction','queue')
1538UvData=get(handles.uvmat,'UserData');
1539
1540while get(handles.MovieBackward,'Value')==1 && get(handles.speed,'Value')~=0 && isequal(get(handles.MovieBackward,'BusyAction'),'queue') % enable STOP command
1541        errormsg=runpm(hObject,eventdata,handles,increment);
1542        if ~isempty(errormsg)
1543            set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1544            return
1545        end
1546        pause(1.02-get(handles.speed,'Value'))% wait for next image
1547end
1548if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1549    UvData.aviobj=close(UvData.aviobj);
1550   set(handles.uvmat,'UserData',UvData);
1551end
1552set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1553
1554%------------------------------------------------------------------------
1555function STOP_Callback(hObject, eventdata, handles)
1556%------------------------------------------------------------------------
1557set(handles.movie_pair,'BusyAction','Cancel')
1558set(handles.movie_pair,'value',0)
1559set(handles.Movie,'BusyAction','Cancel')
1560set(handles.MovieBackward,'BusyAction','Cancel')
1561set(handles.MenuExportMovie,'BusyAction','Cancel')
1562set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1563set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1564set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1565
1566%------------------------------------------------------------------------
1567% --- function activated by runplus and run minus
1568function errormsg=runpm(hObject,eventdata,handles,increment)
1569%------------------------------------------------------------------------
1570errormsg='';%default
1571%% check for movie pair status
1572movie_status=get(handles.movie_pair,'Value');
1573if isequal(movie_status,1)
1574    STOP_Callback(hObject, eventdata, handles)%interrupt movie pair if active
1575end
1576
1577%% read the current input file name(s) and field indices
1578InputFile=read_GUI(handles.InputFile);
1579InputFile.RootFile=regexprep(InputFile.RootFile,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1580InputFile.SubDir=regexprep(InputFile.SubDir,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1581FileExt=InputFile.FileExt;
1582NomType=get(handles.NomType,'String');
1583i1=str2num(get(handles.i1,'String'));%read the field indices (for movie, it is not given by the file name)
1584i2=[];%default
1585if strcmp(get(handles.i2,'Visible'),'on')
1586    i2=str2num(get(handles.i2,'String'));
1587end
1588j1=[];
1589if strcmp(get(handles.j1,'Visible'),'on')
1590    j1=stra2num(get(handles.j1,'String'));
1591end
1592j2=j1;
1593if strcmp(get(handles.j2,'Visible'),'on')
1594    j2=stra2num(get(handles.j2,'String'));
1595end
1596sub_value= get(handles.SubField,'Value');
1597if sub_value % a second input file has been entered
1598     [InputFile.RootPath_1,InputFile.SubDir_1,InputFile.RootFile_1,InputFile.FileIndex_1,InputFile.FileExt_1,InputFile.NomType_1]=read_file_boxes_1(handles);   
1599    [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
1600else
1601    filename_1=[];
1602end   
1603
1604%% increment (or decrement) the field indices and update the input filename(s)
1605if isempty(increment)
1606    set(handles.CheckFixPair,'Value',0)
1607end
1608CheckFixPair=get(handles.CheckFixPair,'Value')||(isempty(i2)&&isempty(j2));
1609
1610% the pair i1-i2 or j1-j2 is imposed (check box CheckFixPair selected)
1611        i1_1=i1;
1612        i2_1=i2;
1613        j1_1=j1;
1614        j2_1=j2;
1615if CheckFixPair
1616    if get(handles.scan_i,'Value')==1% case of scanning along index i
1617        i1=i1+increment;
1618        i2=i2+increment;
1619        if sub_value
1620            i1_1=i1_1+increment;
1621            i2_1=i2_1+increment;
1622        end
1623       
1624    else % case of scanning along index j (burst numbers)
1625        j1=j1+increment;
1626        j2=j2+increment;
1627        if sub_value
1628            j1_1=j1_1+increment;
1629            j2_1=j2_1+increment;
1630        end
1631    end
1632   
1633% the pair i1-i2 or j1-j2 is free (check box CheckFixPair not selected): the list of existing indices recorded in UvData is used
1634else
1635    UvData=get(handles.uvmat,'UserData');
1636    ref_i=i1;
1637    if ~isempty(i2)
1638        ref_i=floor((i1+i2)/2);% current reference index i
1639    end
1640    ref_j=1;
1641    if ~isempty(j1)
1642        ref_j=j1;
1643        if ~isempty(j2)
1644            ref_j=floor((j1+j2)/2);% current reference index j
1645        end
1646    end
1647    if ~isempty(increment)
1648        if get(handles.scan_i,'Value')==1% case of scanning along index i
1649            ref_i=ref_i+increment;% increment the current reference index i
1650        else % case of scanning along index j (burst numbers)
1651            ref_j=ref_j+increment;% increment the current reference index j if scan_j option is used
1652        end
1653    else % free increment
1654        runaction=get(gcbo,'tag');
1655        if strcmp(runaction,'runplus')||strcmp(runaction,'Movie')% if runplus or movie is activated
1656            step=1;
1657        else
1658            step=-1;
1659        end
1660        if get(handles.scan_i,'Value')==1% case of scanning along index i
1661            ref_i=ref_i+step;
1662            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
1663                ref_i=ref_i+step;
1664            end
1665        else % case of scanning along index j (burst numbers)
1666            ref_j=ref_j+step;
1667            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
1668                ref_j=ref_j+step;
1669            end
1670        end
1671    end
1672    if ref_i<0
1673        errormsg='minimum i index reached';
1674    elseif ref_j<0
1675        errormsg='minimum j index reached';
1676    elseif ref_i+1>size(UvData.i1_series{1},3)
1677        errormsg='maximum i index reached (reload the input file to update the index bound)';
1678    elseif ref_j+1>size(UvData.i1_series{1},2)
1679        errormsg='maximum j index reached (reload the input file to update the index bound)';
1680    end
1681    if ~isempty(errormsg),return,end
1682    siz=size(UvData.i1_series{1});
1683    ref_indices=ref_i*siz(1)*siz(2)+ref_j*siz(1)+1:ref_i*siz(1)*siz(2)+(ref_j+1)*siz(1);
1684    i1_subseries=UvData.i1_series{1}(ref_indices);
1685    ref_indices=ref_indices(i1_subseries>0);
1686    if isempty(ref_indices)% case of pairs (free index i)
1687        ref_indices=ref_i*siz(1)*siz(2)+1:(ref_i+1)*siz(1)*siz(2);
1688        i1_subseries=UvData.i1_series{1}(ref_indices);
1689        ref_indices=ref_indices(i1_subseries>0);
1690    end
1691    if isempty(ref_indices),errormsg='no next frame: set num_IndexIncrement =''*'' to reach the next existing file';return
1692    end
1693    i1=UvData.i1_series{1}(ref_indices(end));
1694    if ~isempty(UvData.i2_series{1})
1695        i2=UvData.i2_series{1}(ref_indices(end));
1696    end
1697    if ~isempty(UvData.j1_series{1})
1698        j1=UvData.j1_series{1}(ref_indices(end));
1699    end
1700    if ~isempty(UvData.j2_series{1})
1701        j2=UvData.j2_series{1}(ref_indices(end));
1702    end
1703   
1704    % case of a second file series
1705    if sub_value
1706        ref_i_1=i1_1;
1707        if ~isempty(i2_1)
1708            ref_i_1=floor((i1_1+i2_1)/2);% current reference index i
1709        end
1710        ref_j_1=1;
1711        if ~isempty(j1_1)
1712            ref_j_1=j1_1;
1713            if ~isempty(j2_1)
1714                ref_j_1=floor((j1_1+j2_1)/2);% current reference index j
1715            end
1716        end
1717        if ~isempty(increment)
1718            if get(handles.scan_i,'Value')==1% case of scanning along index i
1719                ref_i_1=ref_i_1+increment;% increment the current reference index i
1720            else % case of scanning along index j (burst numbers)
1721                ref_j_1=ref_j_1+increment;% increment the current reference index j if scan_j option is used
1722            end
1723        else % free increment, synchronise the ref indices with the first series
1724            ref_i_1=ref_i;
1725            ref_j_1=ref_j;
1726        end
1727        if numel(UvData.i1_series)==1
1728            UvData.i1_series{2}=UvData.i1_series{1};
1729            UvData.j1_series{2}=UvData.j1_series{1};
1730            UvData.i2_series{2}=UvData.i2_series{1};
1731            UvData.j2_series{2}=UvData.j2_series{1};
1732        end
1733        if ref_i_1<0
1734            errormsg='minimum i index reached';
1735        elseif ref_j_1<0
1736            errormsg='minimum j index reached';
1737        elseif ref_i_1+1>size(UvData.i1_series{2},3)
1738            errormsg='maximum i index reached for the second series (reload the input file to update the index bound)';
1739        elseif ref_j_1+1>size(UvData.i1_series{2},2)
1740            errormsg='maximum j index reached for the second series(reload the input file to update the index bound)';
1741        end
1742        if ~isempty(errormsg),return,end
1743        siz=size(UvData.i1_series{2});
1744        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);
1745        i1_subseries=UvData.i1_series{2}(ref_indices);
1746        ref_indices=ref_indices(i1_subseries>0);
1747        if isempty(ref_indices)% case of pairs (free index i)
1748            ref_indices=ref_i_1*siz(1)*siz(2)+1:(ref_i_1+1)*siz(1)*siz(2);
1749            i1_subseries=UvData.i1_series{2}(ref_indices);
1750            ref_indices=ref_indices(i1_subseries>0);
1751        end
1752        i1_1=UvData.i1_series{2}(ref_indices(end));
1753        if ~isempty(UvData.i2_series{2})
1754            i2_1=UvData.i2_series{2}(ref_indices(end));
1755        end
1756        if ~isempty(UvData.j1_series{2})
1757            j1_1=UvData.j1_series{2}(ref_indices(end));
1758        end
1759        if ~isempty(UvData.j2_series{2})
1760            j2_1=UvData.j2_series{1}(ref_indices(end));
1761        end   
1762    else% the second series (if needed) is the same file as the first
1763        i1_1=i1;
1764        i2_1=i2;
1765        j1_1=j1;
1766        j2_1=j2;
1767    end
1768end
1769filename=fullfile_uvmat(InputFile.RootPath,InputFile.SubDir,InputFile.RootFile,FileExt,NomType,i1,i2,j1,j2);
1770if sub_value
1771    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);
1772end
1773
1774%% refresh plots
1775errormsg=refresh_field(handles,filename,filename_1,i1,i2,j1,j2,i1_1,i2_1,j1_1,j2_1);
1776
1777%% update the index counters if the index move is successfull
1778if isempty(errormsg)
1779    set(handles.i1,'String',num2stra(i1,NomType,1));
1780    if isequal(i2,i1)
1781        set(handles.i2,'String','');
1782    else
1783        set(handles.i2,'String',num2stra(i2,NomType,1));
1784    end
1785    set(handles.j1,'String',num2stra(j1,NomType,2));
1786    if isequal(j2,j1)
1787        set(handles.j2,'String','');
1788    else
1789        set(handles.j2,'String',num2stra(j2,NomType,2));
1790    end
1791    indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1792    set(handles.FileIndex,'String',indices);
1793    if ~isempty(filename_1)
1794        indices_1=fullfile_uvmat('','','','',InputFile.NomType_1,i1_1,i2_1,j1_1,j2_1);
1795        set(handles.FileIndex_1,'String',indices_1);
1796    end
1797    if isequal(movie_status,1)
1798        set(handles.movie_pair,'Value',1)
1799        movie_pair_Callback(hObject, eventdata, handles); %reactivate moviepair if it was activated
1800    end
1801end
1802
1803%------------------------------------------------------------------------
1804% --- Executes on button press in movie_pair: create an alternating movie with two view
1805function movie_pair_Callback(hObject, eventdata, handles)
1806%------------------------------------------------------------------------
1807%% stop movie action if the movie_pair button is off
1808if ~get(handles.movie_pair,'value')
1809    set(handles.movie_pair,'BusyAction','Cancel')%stop movie pair if button is 'off'
1810    set(handles.i2,'String','')
1811    set(handles.j2,'String','')
1812    return
1813else
1814    set(handles.movie_pair,'BusyAction','queue')
1815end
1816
1817%% initialisation
1818set(handles.movie_pair,'BackgroundColor',[1 1 0])%paint the command button in yellow
1819drawnow
1820list_fields=get(handles.FieldName,'String');% list menu fields
1821index_fields=get(handles.FieldName,'Value');% selected string index
1822FieldName=list_fields{index_fields}; % selected field
1823UvData=get(handles.uvmat,'UserData');
1824if isequal(FieldName,'image')
1825    index=1;
1826    [RootPath,SubDir,RootFile,FileIndices,Ext]=read_file_boxes(handles);
1827    NomType=get(handles.NomType,'String');
1828else
1829    list_fields=get(handles.FieldName_1,'String');% list menu fields
1830    index_fields=get(handles.FieldName_1,'Value');% selected string index
1831    FieldName=list_fields{index_fields}; % selected field
1832    if isequal(FieldName,'image')
1833        index=2;
1834        [RootPath,tild,RootFile,FileIndex_1,Ext,NomType]=read_file_boxes_1(handles);
1835    else
1836        msgbox_uvmat('ERROR','an image or movie must be first introduced as input')
1837        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1838        set(handles.movie_pair,'Value',0)
1839        return
1840    end
1841end
1842num_i1=str2num(get(handles.i1,'String'));
1843num_j1=stra2num(get(handles.j1,'String'));
1844num_i2=str2num(get(handles.i2,'String'));
1845num_j2=stra2num(get(handles.j2,'String'));
1846imaname_1='';
1847if isempty(num_j2)
1848    if isempty(num_i2)
1849        if strcmp(get(handles.j2,'Visible'),'on') %if the j box is visible
1850            imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,Ext,NomType,num_i1,[],num_j1+1);
1851        end
1852        if exist(imaname_1,'file')
1853            num_j2=num_j1+1;
1854            set(handles.j2,'String',num2str(num_j2));
1855        else
1856            imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,Ext,NomType,num_i1+1,[],num_j1);
1857            if exist(imaname_1,'file')
1858                num_i2=num_i1+1;
1859                set(handles.i2,'String',num2str(num_i2));
1860            else
1861                msgbox_uvmat('ERROR', 'a second image index i2 or j2 is needed to show the pair as a movie')
1862                set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1863                set(handles.movie_pair,'Value',0)
1864                return
1865            end
1866        end
1867    else
1868        num_j2=num_j1;%repeat the index i1 by default
1869    end
1870end
1871if isempty(num_i2)
1872    num_i2=num_i1;%repeat the index i1 by default
1873end
1874imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,Ext,NomType,num_i2,[],num_j2);
1875if strcmp(NomType,'*')
1876    num_frame=num_i2;
1877else
1878    num_frame=num_j2;
1879end
1880if ~exist(imaname_1,'file')
1881      msgbox_uvmat('ERROR',['second input open (-)  ' imaname_1 ' not found']);
1882      set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1883       set(handles.movie_pair,'Value',0)
1884      return
1885end
1886
1887%% get the first image
1888%Field.AName='image';
1889if index==1
1890    Field_a=UvData.Field;% movie on the second field
1891else
1892    Field_a=UvData.Field_1;% movie on the first field
1893end
1894
1895%% read the second image
1896MovieObject=[];
1897if numel(UvData.MovieObject)>=index
1898    MovieObject=UvData.MovieObject{index};
1899end
1900[Field_b,ParamOut,errormsg] = read_field(imaname_1,UvData.FileType{index},MovieObject,num_frame);
1901% Field_b.AX=Field_a.AX;
1902% Field_b.AY=Field_a.AY;
1903% % z index
1904% nbslice=str2double(get(handles.num_NbSlice,'String'));
1905% if ~isempty(nbslice)
1906%     Field_b.ZIndex=mod(num_i2-1,nbslice)+1;
1907% end
1908% Field_b.CoordUnit='pixel';
1909%
1910% %% determine the input file type
1911% if (test_1 && isfield(UvData,'MovieObject')&& numel(UvData.MovieObject>=2))||(~test_1 && ~isempty(UvData.MovieObject{1}))
1912%     FileType='movie';
1913% elseif isequal(lower(Ext),'.avi')
1914%     FileType='avi';
1915% elseif isequal(lower(Ext),'.vol')
1916%     FileType='vol';
1917% else
1918%    form=imformats(Ext(2:end));
1919%    if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
1920%        if isequal(NomType,'*');
1921%            FileType='multimage';
1922%        else
1923%            FileType='image';
1924%        end
1925%    end
1926% end
1927% switch FileType
1928%         case 'movie'
1929%             if test_1
1930%                 Field_b.A=read(UvData.MovieObject{2},num_i2);
1931%             else
1932%                 Field_b.A=read(UvData.MovieObject{1},num_i2);
1933%             end
1934%         case 'avi'
1935%             mov=aviread(imaname_1,num_i2);
1936%             Field_b.A=frame2im(mov(1));
1937%         case 'vol'
1938%             Field_b.A=imread(imaname_1);
1939%         case 'multimage'
1940%             Field_b.A=imread(imaname_1,num_i2);
1941%         case 'image'
1942%             Field_b.A=imread(imaname_1);
1943% end
1944% if get(handles.slices,'Value')
1945%     Field.ZIndex=str2double(get(handles.z_index,'String'));
1946% end
1947
1948%px to phys or other transform on field
1949transform=get(handles.path_transform,'UserData');
1950if  ~isempty(transform)
1951    if isfield(UvData,'XmlData') && numel(UvData.XmlData)>=index %use geometry calib recorded from the ImaDoc xml file as first priority
1952        if index==2
1953        Field_a=transform(Field_a,UvData.XmlData{index});%the first field has been stored without transform
1954        end
1955        Field_b=transform(Field_b,UvData.XmlData{index});
1956    end
1957end
1958
1959 % make movie until movie speed is set to 0 or STOP is activated
1960hima=findobj(handles.PlotAxes,'Tag','ima');% %handles.PlotAxes =main plotting window (A GENERALISER)
1961set(handles.STOP,'Visible','on')
1962set(handles.speed,'Visible','on')
1963set(handles.speed_txt,'Visible','on')
1964while get(handles.speed,'Value')~=0 && isequal(get(handles.movie_pair,'BusyAction'),'queue')%isequal(get(handles.run0,'BusyAction'),'queue'); % enable STOP command
1965    % read and plot the series of images in non erase mode
1966    set(hima,'CData',Field_b.A);
1967    pause(1.02-get(handles.speed,'Value'));% wait for next image
1968    set(hima,'CData',Field_a.A);
1969    pause(1.02-get(handles.speed,'Value'));% wait for next image
1970end
1971set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1972 set(handles.movie_pair,'Value',0)
1973
1974%------------------------------------------------------------------------
1975% --- Executes on button press in run0.
1976function run0_Callback(hObject, eventdata, handles)
1977%------------------------------------------------------------------------
1978set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
1979drawnow
1980[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
1981filename=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
1982filename_1='';%default
1983FileIndex_1='';
1984if get(handles.SubField,'Value')
1985    [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
1986    filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
1987end
1988num_i1=stra2num(get(handles.i1,'String'));
1989num_i2=stra2num(get(handles.i2,'String'));
1990num_j1=stra2num(get(handles.j1,'String'));
1991num_j2=stra2num(get(handles.j2,'String'));
1992[tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(FileIndex_1);
1993
1994errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1);
1995
1996if ~isempty(errormsg)
1997      msgbox_uvmat('ERROR',errormsg);
1998else
1999    set(handles.i1,'BackgroundColor',[1 1 1])
2000    set(handles.i2,'BackgroundColor',[1 1 1])
2001    set(handles.j1,'BackgroundColor',[1 1 1])
2002    set(handles.j2,'BackgroundColor',[1 1 1])
2003    set(handles.FileIndex,'BackgroundColor',[1 1 1])
2004    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
2005end   
2006set(handles.run0,'BackgroundColor',[1 0 0])
2007
2008
2009%------------------------------------------------------------------------
2010% --- read the input files and refresh all the plots, including projection.
2011% OUTPUT:
2012%  errormsg: error message char string  =[] by default
2013% INPUT:
2014% filename: first input file (=[] in the absence of input file)
2015% filename_1: second input file (=[] in the asbsenc of secodn input file)
2016% num_i1,num_i2,num_j1,num_j2; frame indices
2017% Field: structure describing an optional input field (then replace the input file)
2018
2019function errormsg=refresh_field(handles,FileName,FileName_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1)
2020%------------------------------------------------------------------------
2021
2022%% initialisation
2023abstime=[];
2024abstime_1=[];
2025dt=[];
2026if ~exist('Field','var')
2027    Field={};
2028end
2029UvData=get(handles.uvmat,'UserData');
2030if ishandle(handles.UVMAT_title) %remove title panel on uvmat
2031    delete(handles.UVMAT_title)
2032end
2033
2034%% determine the main input file information for action
2035if ~exist(FileName,'file')
2036    errormsg=['input file ' FileName ' does not exist'];
2037    return
2038end
2039NomType=get(handles.NomType,'String');
2040NomType_1='';
2041if strcmp(get(handles.NomType_1,'Visible'),'on')
2042    NomType_1=get(handles.NomType_1,'String');
2043end
2044%update the z position index
2045mode_slice=get(handles.slices,'String');
2046if strcmp(mode_slice,'volume')
2047    z_index=num_j1;
2048    set(handles.z_index,'String',num2str(z_index))
2049else
2050    nbslice=str2num(get(handles.num_NbSlice,'String'));
2051    z_index=mod(num_i1-1,nbslice)+1;
2052    set(handles.z_index,'String',num2str(z_index))
2053end
2054% refresh menu for save_mask if relevant
2055masknumber=get(handles.masklevel,'String');
2056if length(masknumber)>=z_index
2057    set(handles.masklevel,'Value',z_index)
2058end
2059
2060%% test for need of tps
2061check_proj_tps=0;
2062if  (strcmp(UvData.FileType{1},'civdata')||strcmp(UvData.FileType{1},'civx'))
2063    for iobj=1:numel(UvData.Object)
2064        if isfield(UvData.Object{iobj},'ProjMode')&& strcmp(UvData.Object{iobj}.ProjMode,'interp_tps')
2065            check_proj_tps=1;
2066            break
2067        end
2068    end
2069end
2070
2071%% read the first input field
2072ParamIn.ColorVar='';%default variable name for vector color
2073frame_index=1;%default
2074FieldName='';%default
2075VelType='';%default
2076switch UvData.FileType{1}
2077    case {'civx','civdata','netcdf'};
2078        list_fields=get(handles.FieldName,'String');% list menu fields
2079        FieldName= list_fields{get(handles.FieldName,'Value')}; % selected field
2080        % if get_field... is selected, the GUI get_field will be used to enter fields
2081        if ~strcmp(FieldName,'get_field...')
2082            if get(handles.FixVelType,'Value')
2083                VelTypeList=get(handles.VelType,'String');
2084                VelType=VelTypeList{get(handles.VelType,'Value')};
2085            end
2086        end
2087        % case of input vector field, get the scalar used for vector color
2088        if ~isempty(regexp(FieldName,'^vec('))
2089            list_code=get(handles.ColorCode,'String');% list menu fields
2090            index_code=get(handles.ColorCode,'Value');% selected string index
2091            if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2092                list_code=get(handles.ColorScalar,'String');% list menu fields
2093                index_code=get(handles.ColorScalar,'Value');% selected string index
2094                ParamIn.ColorVar= list_code{index_code}; % selected field
2095            end
2096        end
2097    case {'video','mmreader'}
2098        ParamIn=UvData.MovieObject{1};     
2099        if ~strcmp(NomType,'*')
2100            frame_index=num_j1;%frame index for movies or multimage
2101        else
2102            frame_index=num_i1;
2103        end
2104    case 'multimage'
2105        if ~strcmp(NomType,'*')
2106            frame_index=num_j1;%frame index for movies or multimage
2107        else
2108            frame_index=num_i1;
2109        end
2110    case 'vol' %TODO: update
2111        if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2112            ParamIn.Npy=UvData.XmlData.Npy;
2113            ParamIn.Npx=UvData.XmlData.Npx;
2114        else           
2115            errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2116            return
2117        end
2118end
2119if isstruct (ParamIn)
2120    ParamIn.FieldName=FieldName;
2121    ParamIn.VelType=VelType;
2122    XNameMenu=get(handles.Coord_x,'String');
2123    ParamIn.Coord_x=XNameMenu(get(handles.Coord_x,'Value'));
2124    YNameMenu=get(handles.Coord_y,'String');
2125    ParamIn.Coord_y=YNameMenu(get(handles.Coord_y,'Value'));
2126end
2127check_tps = 0;         
2128if strcmp(UvData.FileType{1},'civdata')&&~strcmp(ParamIn.FieldName,'velocity')&&~strcmp(ParamIn.FieldName,'get_field...')
2129       check_tps=1;%tps needed to get the requested field
2130end
2131[Field{1},ParamOut,errormsg] = read_field(FileName,UvData.FileType{1},ParamIn,frame_index);
2132if ~isempty(errormsg)
2133    errormsg=['uvmat / refresh_field / read_field( ' FileName ') / ' errormsg];
2134    return
2135end 
2136if isfield(ParamOut,'Npx')&& isfield(ParamOut,'Npy')
2137    set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2138    set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2139end
2140if isfield(ParamOut,'TimeIndex')% case of time obtained from get_field
2141    set(handles.i1,'String',num2str(ParamOut.TimeIndex))
2142end
2143if isfield(ParamOut,'TimeValue')
2144    Field{1}.Time=ParamOut.TimeValue;% case of time obtained from get_field
2145end
2146Field{1}.ZIndex=z_index; %used for multiplane 3D calibration
2147
2148
2149%% choose and read a second field FileName_1 if defined
2150VelType_1=[];%default
2151FieldName_1=[];
2152ParamIn_1=[];
2153ParamOut_1=[];
2154frame_index_1=1;
2155if ~isempty(FileName_1)
2156    if ~exist(FileName_1,'file')
2157        errormsg=['second file ' FileName_1 ' does not exist'];
2158        return
2159    end
2160   % Name=FileName_1;
2161    switch UvData.FileType{2}
2162        case {'civx','civdata','netcdf'};
2163            list_fields=get(handles.FieldName_1,'String');% list menu fields
2164            if ischar(list_fields),list_fields={list_fields};end
2165            FieldName_1= list_fields{get(handles.FieldName_1,'Value')}; % selected field
2166            if ~strcmp(FieldName,'get_field...')
2167                if get(handles.FixVelType,'Value')
2168                    VelTypeList=get(handles.VelType_1,'String');
2169                    VelType_1=VelTypeList{get(handles.VelType_1,'Value')};% read the velocity type.
2170                end
2171            end
2172            if strcmp(FieldName_1,'velocity')&& strcmp(get(handles.ColorCode,'Visible'),'on')
2173                list_code=get(handles.ColorCode,'String');% list menu fields
2174                index_code=get(handles.ColorCode,'Value');% selected string index
2175                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2176                    list_code=get(handles.ColorScalar,'String');% list menu fields
2177                    index_code=get(handles.ColorScalar,'Value');% selected string index
2178                    ParamIn_1.ColorVar= list_code{index_code}; % selected field for vector color display                 
2179                end
2180            end
2181        case {'video','mmreader'}
2182            ParamIn_1=UvData.MovieObject{2};
2183                        if ~strcmp(NomType_1,'*')
2184                frame_index_1=j1_1;%frame index for movies or multimage
2185            else
2186                frame_index_1=i1_1;
2187            end 
2188         case 'multimage'
2189            if ~strcmp(NomType_1,'*')
2190                frame_index_1=j1_1;%frame index for movies or multimage
2191            else
2192                frame_index_1=i1_1;
2193            end   
2194        case 'vol' %TODO: update
2195            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2196                ParamIn_1.Npy=UvData.XmlData.Npy;
2197                ParamIn_1.Npx=UvData.XmlData.Npx;
2198            else
2199                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2200                return
2201            end
2202    end
2203    if isequal(get(handles.NomType_1,'Visible'),'on')
2204    NomType_1=get(handles.NomType_1,'String');
2205    else
2206        NomType_1=get(handles.NomType,'String');
2207    end
2208    test_keepdata_1=0;% test for keeping the previous stored data if the input files are unchanged
2209    if ~isequal(NomType_1,'*')&& isfield(UvData,'FileName_1')
2210           test_keepdata_1= strcmp(FileName_1,UvData.FileName_1) ;
2211    end
2212    if test_keepdata_1
2213        Field{2}=UvData.Field_1;% keep the stored field
2214        ParamOut_1=UvData.ParamOut_1;
2215    else
2216        if isempty(ParamIn_1) || isstruct(ParamIn_1)
2217        ParamIn_1.FieldName=FieldName_1;
2218        ParamIn_1.VelType=VelType_1;
2219        ParamIn_1.GUIName='get_field_1';
2220        end 
2221        [Field{2},ParamOut_1,errormsg] = read_field(FileName_1,UvData.FileType{2},ParamIn_1,frame_index_1);
2222        if ~isempty(errormsg)
2223            errormsg=['error in reading ' FieldName_1 ' in ' FileName_1 ': ' errormsg];
2224            return
2225        end
2226        if isstruct(ParamOut_1)&&~strcmp(ParamOut_1.FieldName,'get_field...')&& (strcmp(UvData.FileType{2},'civdata')||strcmp(UvData.FileType{2},'civx'))...
2227                &&~strcmp(ParamOut_1.FieldName,'velocity') && ~strcmp(ParamOut_1.FieldName,'get_field...')
2228            if ~check_proj_tps
2229             %   Field{2}=calc_field([{ParamOut_1.FieldName} {ParamOut_1.ColorVar}],Field{2});
2230            end
2231        end
2232    end
2233    Field{2}.ZIndex=z_index;%used for multi-plane 3D calibration
2234end
2235
2236%% update uvmat interface
2237if isfield(ParamOut,'Npx')
2238    set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2239    set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2240elseif isfield(ParamOut_1,'Npx')
2241    set(handles.num_Npx,'String',num2str(ParamOut_1.Npx));% display image size on the interface
2242    set(handles.num_Npy,'String',num2str(ParamOut_1.Npy));
2243end
2244
2245%% update the display menu for the first velocity type (first menuline)
2246test_veltype=0;
2247% if ~isequal(FileType,'netcdf')|| isequal(FieldName,'get_field...')
2248if (strcmp(UvData.FileType{1},'civx')||strcmp(UvData.FileType{1},'civdata'))&& ~strcmp(FieldName,'get_field...')
2249    test_veltype=1;
2250    set(handles.VelType,'Visible','on')
2251    set(handles.VelType_1,'Visible','on')
2252    set(handles.FixVelType,'Visible','on')
2253    menu=set_veltype_display(ParamOut.CivStage,UvData.FileType{1});
2254    index_menu=strcmp(ParamOut.VelType,menu);%look for VelType in  the menu
2255    index_val=find(index_menu,1);
2256    if isempty(index_val)
2257        index_val=1;
2258    end
2259    set(handles.VelType,'Value',index_val)
2260    if ~get(handles.SubField,'value')
2261        set(handles.VelType,'String',menu)
2262        set(handles.VelType_1,'Value',1)
2263        set(handles.VelType_1,'String',[{''};menu])
2264    end
2265else
2266    set(handles.VelType,'Visible','off')
2267end
2268% display the FieldName menu from the input file and pick the selected one:
2269% if isstruct(ParamOut)
2270%     field_index=strcmp(ParamOut.FieldName,ParamOut.FieldList);
2271%     set(handles.FieldName,'String',ParamOut.FieldList); %update the field menu
2272%     set(handles.FieldName,'Value',find(field_index,1))
2273% end
2274
2275%% update the display menu for the second velocity type (second menuline)
2276test_veltype_1=0;
2277if isempty(FileName_1)
2278    %     set(handles.FieldName_1,'Value',1); %update the field menu
2279    %     if isstruct(ParamOut)
2280    %     set(handles.FieldName_1,'String',[{''};ParamOut.FieldList]); %update the field menu
2281    %     end
2282elseif ~test_keepdata_1
2283    if (~strcmp(UvData.FileType{2},'netcdf')&&~strcmp(UvData.FileType{2},'civdata')&&~strcmp(UvData.FileType{2},'civx'))|| isequal(FieldName_1,'get_field...')
2284        set(handles.VelType_1,'Visible','off')
2285    else
2286        test_veltype_1=1;
2287        set(handles.VelType_1,'Visible','on')
2288        menu=set_veltype_display(ParamOut_1.CivStage,UvData.FileType{2});
2289        index_menu=strcmp(ParamOut_1.VelType,menu);
2290        set(handles.VelType_1,'Value',1+find(index_menu,1))
2291        set(handles.VelType_1,'String',[{''};menu])
2292    end
2293    % update the second field menu: the same quantity
2294    if isstruct(ParamOut_1)
2295%        set(handles.FieldName_1,'String',[{''};ParamOut_1.FieldList]); %update the field menu
2296        % display the FieldName menu from the input file and pick the selected one:
2297        FieldList=get(handles.FieldName_1,'String');
2298        field_index=strcmp(ParamOut_1.FieldName,FieldList);
2299        if ~isempty(field_index)
2300            set(handles.FieldName_1,'Value',find(field_index,1))
2301        end
2302    end
2303end
2304if test_veltype||test_veltype_1
2305    set(handles.FixVelType,'Visible','on')
2306else
2307    set(handles.FixVelType,'Visible','off')
2308end
2309
2310% field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
2311% set(handles.FieldName,'String',ParamOut.FieldList); %update the field menu
2312% set(handles.FieldName,'Value',find(field_index,1))
2313   
2314%% introduce w as background image by default for a new series (only for nbdim=2)
2315if ~isfield(UvData,'NewSeries')
2316    UvData.NewSeries=1;
2317end
2318%put W as background image by default if NbDim=2:
2319if  UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W) && ~isequal(Field{1}.NbDim,3);
2320        set(handles.SubField,'Value',1);
2321        set(handles.RootPath_1,'String','"')
2322        set(handles.RootFile_1,'String','"')
2323        set(handles.SubDir_1,'String','"');
2324         indices=fullfile_uvmat('','','','',NomType,num_i1,num_i2,num_j1,num_j2);
2325        set(handles.FileIndex_1,'String',indices)
2326        set(handles.FileExt_1,'String','"');
2327        set(handles.FieldName_1,'Visible','on');
2328        set(handles.FieldName_1,'Visible','on');
2329        set(handles.RootPath_1,'Visible','on')
2330        set(handles.RootFile_1,'Visible','on')
2331        set(handles.SubDir_1,'Visible','on');
2332        set(handles.FileIndex_1,'Visible','on');
2333        set(handles.FileExt_1,'Visible','on');
2334        set(handles.FieldName_1,'Visible','on');
2335        Field{1}.AName='w';
2336end           
2337
2338%% display time
2339testimedoc=0;
2340TimeUnit='';
2341if isfield(Field{1},'Time')
2342    abstime=Field{1}.Time;%time read from the netcdf input file
2343end
2344if numel(Field)==2 && isfield(Field{2},'Time')
2345    abstime_1=Field{2}.Time;%time read from the netcdf input file
2346end
2347if isfield(Field{1},'Dt')
2348    dt=Field{1}.Dt;%dt read from the netcdf input file
2349    if isfield(Field{1},'TimeUnit')
2350       TimeUnit=Field{1}.TimeUnit;
2351    end
2352elseif numel(Field)==2 && isfield(Field{2},'Dt')%dt obtained from the second field if not defined in the first
2353    dt=Field{2}.Dt;%dt read from the netcdf input file
2354    if isfield(Field{2},'TimeUnit')
2355       TimeUnit=Field{2}.TimeUnit;
2356    end
2357end
2358% time from xml file overset previous result
2359if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'Time')
2360    if isempty(num_i2)||isnan(num_i2)
2361        num_i2=num_i1;
2362    end
2363    if isempty(num_j1)||isnan(num_j1)
2364        num_j1=1;
2365    end
2366    if isempty(num_j2)||isnan(num_j2)
2367        num_j2=num_j1;
2368    end
2369    siz=size(UvData.XmlData{1}.Time);
2370    if ~isempty(num_i1)&& ~isempty(num_i2) && num_i1>0 &&siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2371        abstime=(UvData.XmlData{1}.Time(num_i1,num_j1)+UvData.XmlData{1}.Time(num_i2,num_j2))/2;%overset the time read from files
2372        dt=(UvData.XmlData{1}.Time(num_i2,num_j2)-UvData.XmlData{1}.Time(num_i1,num_j1));
2373        Field{1}.Dt=dt;
2374        if isfield(UvData.XmlData{1},'TimeUnit')
2375            TimeUnit=UvData.XmlData{1}.TimeUnit;
2376        end
2377    end
2378    if numel(UvData.XmlData)==2
2379        if isempty(i2_1)
2380            i2_1=num_i1;
2381        end
2382        if isempty(j1_1)
2383            j1_1=1;
2384        end
2385        if isempty(j2_1)
2386            j2_1=j1_1;
2387        end
2388        siz=size(UvData.XmlData{2}.Time);
2389        if ~isempty(i1_1) && siz(1)>=max(i1_1,i2_1) && siz(2)>=max(j1_1,j2_1)
2390            abstime_1=(UvData.XmlData{2}.Time(i1_1,j1_1)+UvData.XmlData{2}.Time(i2_1,j2_1))/2;%overset the time read from files
2391            Field{2}.Dt=(UvData.XmlData{2}.Time(i2_1,j2_1)-UvData.XmlData{2}.Time(i1_1,j1_1));
2392        end
2393    end
2394end
2395if ~isequal(numel(abstime),1)
2396    abstime=[];
2397end
2398if ~isequal(numel(abstime_1),1)
2399      abstime_1=[];
2400end 
2401set(handles.abs_time,'String',num2str(abstime,5))
2402set(handles.abs_time_1,'String',num2str(abstime_1,5))
2403if isempty(dt)||isequal(dt,0)
2404    set(handles.Dt_txt,'String','')
2405else
2406    if  isempty(TimeUnit)
2407        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  10^(-3)'] )
2408    else
2409        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  m' TimeUnit] )
2410    end
2411end
2412
2413
2414%% store the current open names, fieldname and vel types in uvmat interface
2415UvData.FileName_1=FileName_1;
2416UvData.ParamOut_1=ParamOut_1;
2417if numel(Field)==2
2418UvData.Field_1=Field{2}; %store the second field for possible use at next RUN
2419end
2420
2421%% apply coordinate transform or other user fct
2422transform=get(handles.path_transform,'UserData');
2423if isempty(transform)
2424    UvData.Field=Field{1};
2425else
2426    XmlData=[];%default
2427    XmlData_1=[];%default
2428    if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority
2429        XmlData=UvData.XmlData{1};
2430        if numel(UvData.XmlData)==2
2431            XmlData_1=UvData.XmlData{2};
2432        end
2433    end
2434    transform=get(handles.path_transform,'UserData');
2435    switch nargin(transform)
2436        case 4
2437            if length(Field)==2
2438                UvData.Field=transform(Field{1},XmlData,Field{2},XmlData_1);
2439            else
2440                UvData.Field=transform(Field{1},XmlData);
2441            end
2442        case 3
2443            if length(Field)==2
2444                UvData.Field=transform(Field{1},XmlData,Field{2});
2445            else
2446                UvData.Field=transform(Field{1},XmlData);
2447            end
2448        case 2
2449            UvData.Field=transform(Field{1},XmlData);
2450        case 1
2451            UvData.Field=transform(Field{1});
2452    end
2453end
2454
2455%% calculate tps coefficients if needed
2456UvData.Field=tps_coeff_field(UvData.Field,check_proj_tps);
2457
2458%% analyse input field
2459%test_x=0;
2460%test_z=0;% test for unstructured z coordinate
2461%[errormsg,ListDimName,DimValue,VarDimIndex]=check_field_structure(UvData.Field);% check the input field structure
2462% if ~isempty(errormsg)
2463%     errormsg=['error in uvmat/refresh_field/check_field_structure: ' errormsg];% display error
2464%     return
2465% end
2466[CellInfo,NbDimArray,errormsg]=find_field_cells(UvData.Field);% analyse  the input field structure
2467if ~isempty(errormsg)
2468    errormsg=['uvmat /refresh_field / find_field_cells / ' errormsg];% display error
2469    return
2470end
2471
2472NbDim=max(NbDimArray);% spatial dimension of the input field
2473imax=find(NbDimArray==NbDim);% indices of field cells to consider
2474if isfield(UvData.Field,'NbDim')
2475    NbDim=double(UvData.Field.NbDim);% deal with plane fields containing z coordinates
2476end
2477
2478%UvData.Field=get_bounds(UvData.Field);
2479
2480%% get bounds and mesh (needed  to propose default options for projection objects)
2481if NbDim>1
2482    CoordMax=zeros(numel(imax),NbDim);
2483    CoordMin=zeros(numel(imax),NbDim);
2484    Mesh=zeros(1,numel(imax));
2485    for ind=1:numel(imax)
2486        if strcmp(CellInfo{imax(ind)}.CoordType,'tps')
2487            CoordName=UvData.Field.ListVarName{CellInfo{imax(ind)}.CoordIndex};% X,Y coordinates in a single variable
2488            CoordMax(ind,NbDim)=max(max(UvData.Field.(CoordName)(1:end-3,1,:),[],1),[],3);% max of x component (2D case)
2489            CoordMax(ind,NbDim-1)=max(max(UvData.Field.(CoordName)(1:end-3,2,:),[],1),[],3);% max of y component (2D case)
2490            CoordMin(ind,NbDim)=min(min(UvData.Field.(CoordName)(1:end-3,1,:),[],1),[],3);
2491            CoordMin(ind,NbDim-1)=min(min(UvData.Field.(CoordName)(1:end-3,2,:),[],1),[],3);% min of y component (2D case)
2492        else
2493            XName=UvData.Field.ListVarName{CellInfo{imax(ind)}.CoordIndex(end)};
2494            YName=UvData.Field.ListVarName{CellInfo{imax(ind)}.CoordIndex(end-1)};
2495            CoordMax(ind,NbDim)=max(max(UvData.Field.(XName)));
2496            CoordMin(ind,NbDim)=min(min(UvData.Field.(XName)));
2497            CoordMax(ind,NbDim-1)=max(max(UvData.Field.(YName)));
2498            CoordMin(ind,NbDim-1)=min(min(UvData.Field.(YName)));
2499            %         test_x=1;%test for unstructured coordinates
2500            if NbDim==3
2501                ZName=UvData.Field.ListVarName{CellInfo{imax(ind)}.CoordIndex(1)};
2502                CoordMax(imax(ind),1)=max(max(UvData.Field.(ZName)));
2503                CoordMin(ind,1)=min(min(UvData.Field.(ZName)));
2504            end
2505        end
2506        switch CellInfo{imax(ind)}.CoordType
2507           
2508            case {'scattered','tps'} %unstructured coordinates
2509                NbPoints=CellInfo{imax(ind)}.CoordSize;% total nbre of points
2510                Mesh(ind)=(prod(CoordMax(ind,:)-CoordMin(ind,:))/NbPoints)^(1/NbDim); %(volume or area per point)^(1/NbDim)
2511            case 'grid'%structured coordinate
2512                NbPoints=CellInfo{imax(ind)}.CoordSize;% nbre of points in each direction
2513                Mesh(ind)=min((CoordMax(ind,:)-CoordMin(ind,:))./(NbPoints-1));               
2514        end
2515    end
2516    UvData.Field.CoordMesh=min(Mesh);
2517    UvData.Field.XMax=max(CoordMax(ind,end));
2518    UvData.Field.XMin=min(CoordMin(ind,end));
2519    UvData.Field.YMax=max(CoordMax(ind,end-1));
2520    UvData.Field.YMin=max(CoordMin(ind,end-1));
2521    if NbDim==3
2522        UvData.Field.ZMax=max(CoordMax(ind,1));
2523        UvData.Field.ZMin=max(CoordMin(ind,1));
2524    end
2525    % adjust the mesh to a value 1, 2 , 5 *10^n
2526    ord=10^(floor(log10(UvData.Field.CoordMesh)));%order of magnitude
2527    if UvData.Field.CoordMesh/ord>=5
2528        UvData.Field.CoordMesh=5*ord;
2529    elseif UvData.Field.CoordMesh/ord>=2
2530        UvData.Field.CoordMesh=2*ord;
2531    else
2532        UvData.Field.CoordMesh=ord;
2533    end
2534    % default projection plane
2535    if isempty(UvData.Object{1})
2536        UvData.Object{1}.Type='plane';%main plotting plane
2537        UvData.Object{1}.ProjMode='projection';%main plotting plane
2538        UvData.Object{1}.DisplayHandle.uvmat=[]; %plane not visible in uvmat
2539        UvData.Object{1}.DisplayHandle.view_field=[]; %plane not visible in uvmat
2540    end
2541    %% 3D case (menuvolume)
2542    if NbDim==3% && UvData.NewSeries
2543        test_set_object=1;
2544        hset_object=findobj(allchild(0),'tag','set_object');% look for the set_object GUI
2545        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
2546        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
2547        if ~isempty(hset_object) %if set_object is detected
2548            delete(hset_object);% delete the GUI set_object if it does not fit
2549        end
2550        if test_set_object% reinitiate the GUI set_object
2551            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
2552            UvData.Object{1}.NbDim=NbDim;%test for 3D objects
2553            UvData.Object{1}.RangeZ=UvData.Field.CoordMesh;%main plotting plane
2554            UvData.Object{1}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen
2555            UvData.Object{1}.Angle=[0 0 0];
2556            UvData.Object{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR
2557            UvData.Object{1}.Name='1-PLANE';
2558            UvData.Object{1}.enable_plot=1;
2559            set_object(UvData.Object{1},handles,ZBounds);
2560            set(handles.ListObject,'Value',1);
2561            set(handles.ListObject,'String',{'1-PLANE'});
2562            set(handles.edit_object,'Value',1)% put the plane in edit mode to enable the z cursor
2563            edit_object_Callback([],[], handles)
2564        end
2565        %multilevel case (single menuplane in a 3D space)
2566    elseif isfield(UvData,'Z')
2567        if isfield(UvData,'CoordType')&& isequal(UvData.CoordType,'phys') && isfield(UvData,'XmlData')
2568            XmlData=UvData.XmlData{1};
2569            if isfield(XmlData,'PlanePos')
2570                UvData.Object{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:);
2571            end
2572            if isfield(XmlData,'PlaneAngle')
2573                siz=size(XmlData.PlaneAngle);
2574                indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning)
2575                UvData.Object{1}.PlaneAngle=XmlData.PlaneAngle(indangle,:);
2576            end
2577        elseif isfield(UvData,'ZIndex')
2578            UvData.Object{1}.ZObject=UvData.ZIndex;
2579        end
2580    end
2581end
2582
2583testnewseries=UvData.NewSeries;
2584UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback)
2585set(handles.uvmat,'UserData',UvData)
2586
2587%% reset the min and max of scalar if only the mask is displayed(TODO: check the need)
2588% if isfield(UvData,'Mask')&& ~isfield(UvData,'A')
2589%     set(handles.num_MinA,'String','0')
2590%     set(handles.num_MaxA,'String','255')
2591% end
2592
2593%% usual 1D (x,y) plots
2594if NbDim<=1
2595    set(handles.Objects,'Visible','off')
2596    set(handles.ListObject_1_title,'Visible','off')
2597    set(handles.ListObject_1,'Visible','off')
2598    [PlotType,PlotParamOut]=plot_field(UvData.Field,handles.PlotAxes,read_GUI(handles.uvmat));
2599    write_plot_param(handles,PlotParamOut) %update the auto plot parameters
2600   
2601%% 2D or 3D fieldname are generally projected
2602else
2603    set(handles.Objects,'Visible','on')
2604    set(handles.ListObject_1_title,'Visible','on')
2605    set(handles.ListObject_1,'Visible','on')
2606   
2607    %% Plot the projections on the selected  projection objects
2608    % main projection object (uvmat display)
2609    list_object=get(handles.ListObject_1,'String');
2610    if isequal(list_object,{''})||isequal(list_object,' ')%refresh list of objects if the menu is empty
2611        set(handles.ListObject,'Value',1)
2612        set(handles.ListObject,'String',{'plane'})
2613        UvData.Object{1}.Type='plane';%main plotting plane
2614        UvData.Object{1}.ProjMode='projection';%main plotting plane
2615        UvData.Object{1}.DisplayHandle.uvmat=[]; %plane not visible in uvmat
2616        UvData.Object{1}.DisplayHandle.view_field=[]; %plane not visible in uvmat
2617        set(handles.ListObject_1,'Value',1)
2618        set(handles.ListObject_1,'String',{'plane'})
2619    end
2620    IndexObj(1)=get(handles.ListObject_1,'Value');%selected projection object for main view
2621    if IndexObj(1)> numel(UvData.Object)
2622        IndexObj(1)=1;%select the first object if the selected one does not exist
2623        set(handles.ListObject_1,'Value',1)
2624    end
2625    IndexObj(2)=get(handles.ListObject,'Value');%selected projection object for main view
2626    if isequal(IndexObj(2),IndexObj(1))
2627        IndexObj(2)=[];
2628    end
2629    plot_handles{1}=handles;
2630    if isfield(UvData,'plotaxes')%case of movies
2631        haxes(1)=UvData.plotaxes;
2632    else
2633        haxes(1)=handles.PlotAxes;
2634    end
2635    PlotParam{1}=read_GUI(handles.uvmat);
2636    %default settings if vectors not visible
2637    if ~isfield(PlotParam{1},'Vectors')
2638        PlotParam{1}.Vectors.MaxVec=1;
2639        PlotParam{1}.Vectors.MinVec=0;
2640        PlotParam{1}.Vectors.CheckFixVecColor=1;
2641        PlotParam{1}.Vectors.ColCode1=0.33;
2642        PlotParam{1}.Vectors.ColCode2=0.66;
2643        PlotParam{1}.Vectors.ColorScalar={''};
2644        PlotParam{1}.Vectors.ColorCode= {'rgb'};
2645    end
2646    PosColorbar{1}=UvData.OpenParam.PosColorbar;%prescribe the colorbar position on the uvmat interface
2647   
2648    %% second projection object (view_field display)
2649    if length( IndexObj)>=2
2650        view_field_handle=findobj(allchild(0),'tag','view_field');%handles of the view_field GUI
2651        if ~isempty(view_field_handle)
2652            plot_handles{2}=guidata(view_field_handle);
2653            haxes(2)=plot_handles{2}.PlotAxes;
2654            PlotParam{2}=read_GUI(handles.uvmat);%read plotting parameters on the uvmat interface
2655            PosColorbar{2}='*'; %TODO: deal with colorbar position on view_field
2656        end
2657    end
2658   
2659    %% loop on the projection objects: one or two
2660   
2661    for imap=1:numel(IndexObj)
2662        iobj=IndexObj(imap);
2663        [ObjectData,errormsg]=proj_field(UvData.Field,UvData.Object{iobj});% project field on the object
2664        if ~isempty(errormsg)
2665            return
2666        end
2667        if testnewseries
2668            PlotParam{imap}.Scalar.CheckBW=[]; %B/W option depends on the input field (image or scalar)
2669            if isfield(ObjectData,'CoordUnit')
2670                PlotParam{imap}.Coordinates.CheckFixAspectRatio=1;% set x and y scaling equal if CoordUnit is defined (common unit for x and y)
2671                PlotParam{imap}.Coordinates.AspectRatio=1; %set aspect ratio to 1
2672            end
2673        end
2674        %use of mask (TODO: check)
2675        if isfield(ObjectData,'NbDim') && isequal(ObjectData.NbDim,2) && isfield(ObjectData,'Mask') && isfield(ObjectData,'A')
2676            flag_mask=double(ObjectData.Mask>200);%=0 for masked regions
2677            AX=ObjectData.AX;%x coordiantes for the scalar field
2678            AY=ObjectData.AY;%y coordinates for the scalar field
2679            MaskX=ObjectData.MaskX;%x coordiantes for the mask
2680            MaskY=ObjectData.MaskY;%y coordiantes for the mask
2681            if ~isequal(MaskX,AX)||~isequal(MaskY,AY)
2682                nxy=size(flag_mask);
2683                sizpx=(ObjectData.MaskX(end)-ObjectData.MaskX(1))/(nxy(2)-1);%size of a mask pixel
2684                sizpy=(ObjectData.MaskY(1)-ObjectData.MaskY(end))/(nxy(1)-1);
2685                x_mask=ObjectData.MaskX(1):sizpx:ObjectData.MaskX(end); % pixel x coordinates for image display
2686                y_mask=ObjectData.MaskY(1):-sizpy:ObjectData.MaskY(end);% pixel x coordinates for image display
2687                %project on the positions of the scalar
2688                npxy=size(ObjectData.A);
2689                dxy(1)=(ObjectData.AY(end)-ObjectData.AY(1))/(npxy(1)-1);%grid mesh in y
2690                dxy(2)=(ObjectData.AX(end)-ObjectData.AX(1))/(npxy(2)-1);%grid mesh in x
2691                xi=ObjectData.AX(1):dxy(2):ObjectData.AX(end);
2692                yi=ObjectData.AY(1):dxy(1):ObjectData.AY(end);
2693                [XI,YI]=meshgrid(xi,yi);% creates the matrix of regular coordinates
2694                flag_mask = interp2(x_mask,y_mask,flag_mask,XI,YI);
2695            end
2696            AClass=class(ObjectData.A);
2697            ObjectData.A=flag_mask.*double(ObjectData.A);
2698            ObjectData.A=feval(AClass,ObjectData.A);
2699        end
2700        if ~isempty(ObjectData)
2701            %PlotType='none'; %default
2702            if imap==2 && isempty(view_field_handle)
2703                view_field(ObjectData)
2704            else
2705                [PlotType,PlotParamOut]=plot_field(ObjectData,haxes(imap),PlotParam{imap},PosColorbar{imap});
2706                write_plot_param(plot_handles{imap},PlotParamOut) %update the auto plot parameters
2707                if isfield(Field,'CoordMesh')&&~isempty(Field.CoordMesh)
2708                    ObjectData.CoordMesh=Field.CoordMesh; % gives an estimated mesh size (useful for mouse action on the plot)
2709                end
2710            end
2711        end
2712    end
2713   
2714    %% update the mask
2715    if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
2716        update_mask(handles,num_i1,num_i2);
2717    end
2718   
2719    %% prepare the menus of histograms and plot them (histogram of the whole volume in 3D case)
2720    menu_histo=(UvData.Field.ListVarName)';%list of field variables to be displayed for the menu of histogram display
2721    ind_skip=[];
2722    % nb_histo=1;
2723    Ustring='';
2724    Vstring='';
2725    % suppress coordinates from the histogram menu
2726    for ivar=1:numel(menu_histo)%l loop on field variables:
2727        if isfield(UvData.Field,'VarAttribute') && numel(UvData.Field.VarAttribute)>=ivar && isfield(UvData.Field.VarAttribute{ivar},'Role')
2728            Role=UvData.Field.VarAttribute{ivar}.Role;
2729            switch Role
2730                case {'coord_x','coord_y','coord_z','dimvar'}
2731                    ind_skip=[ind_skip ivar];
2732                case {'vector_x'}
2733                    Ustring=UvData.Field.ListVarName{ivar};
2734                    ind_skip=[ind_skip ivar];
2735                case {'vector_y'}
2736                    Vstring=UvData.Field.ListVarName{ivar};
2737                    ind_skip=[ind_skip ivar];
2738            end
2739        end
2740        DimCell=UvData.Field.VarDimName{ivar};
2741        DimName='';
2742        if ischar(DimCell)
2743            DimName=DimCell;
2744        elseif iscell(DimCell)&& numel(DimCell)==1
2745            DimName=DimCell{1};
2746        end
2747        if strcmp(DimName,menu_histo{ivar})
2748            ind_skip=[ind_skip ivar];
2749        end
2750    end
2751    menu_histo(ind_skip)=[];% remove skipped items
2752    if ~isempty(Ustring)
2753        menu_histo=[{[Ustring ',' Vstring]};menu_histo];% add U, V at the beginning if they exist
2754    end
2755   
2756    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2757    % display menus and plot histograms
2758    test_v=0;
2759    if ~isempty(menu_histo)
2760        set(handles.histo1_menu,'Value',1)
2761        set(handles.histo1_menu,'String',menu_histo)
2762        histo1_menu_Callback(handles.histo1_menu, [], handles)% plot first histogram
2763    end
2764end
2765
2766%------------------------------------------------------------------------
2767function histo1_menu_Callback(hObject, eventdata, handles)
2768%--------------------------------------------
2769histo_menu=get(handles.histo1_menu,'String');
2770histo_value=get(handles.histo1_menu,'Value');
2771FieldName=histo_menu{histo_value};
2772
2773UvData=get(handles.uvmat,'UserData');
2774Field=UvData.Field;
2775r=regexp(FieldName,'(?<var1>.*)(?<sep>,)(?<var2>.*)','names');
2776FieldName_2='';
2777if ~isempty(r)
2778    FieldName=r.var1;
2779    FieldName_2=r.var2;
2780end
2781if ~isfield(UvData.Field,FieldName)
2782    msgbox_uvmat('ERROR',['no field  ' FieldName ' for histogram'])
2783    return
2784end
2785FieldHisto=Field.(FieldName);
2786if isfield(Field,'FF') && ~isempty(Field.FF) && isequal(size(Field.FF),size(FieldHisto))
2787    indsel=find(Field.FF==0);%find values marked as false
2788    if ~isempty(indsel)
2789        FieldHisto=FieldHisto(indsel);
2790        if ~isempty(FieldName_2)
2791            FieldHisto(:,:,2)=Field.(FieldName_2)(indsel);
2792        end
2793    end
2794end
2795if isempty(Field)
2796    msgbox_uvmat('ERROR',['empty field ' FieldName])
2797else
2798    nxy=size(FieldHisto);
2799    Amin=double(min(min(min(FieldHisto))));%min of field value
2800    Amax=double(max(max(max(FieldHisto))));%max of field value
2801    if isequal(Amin,Amax)
2802        cla(handles.HistoAxes)
2803    else
2804        Histo.ListVarName={FieldName,'histo'};
2805        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
2806            Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
2807        else
2808            if numel(nxy)==2
2809                Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
2810            else
2811                Histo.VarDimName={FieldName,{FieldName,'component'}}; %dimensions for the histogram
2812            end
2813        end
2814        %unit
2815        units=[]; %default
2816        for ivar=1:numel(Field.ListVarName)
2817            if strcmp(Field.ListVarName{ivar},FieldName)
2818                if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'units')
2819                    units=Field.VarAttribute{ivar}.units;
2820                    break
2821                end
2822            end
2823        end
2824        if ~isempty(units)
2825            Histo.VarAttribute{1}.units=units;
2826        end
2827        eval(['Histo.' FieldName '=linspace(Amin,Amax,50);'])%absissa values for histo
2828        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
2829            C=reshape(double(FieldHisto),1,[]);% reshape in a vector
2830            Histo.histo(:,1)=hist(C, Histo.(FieldName));  %calculate histogram
2831        else
2832            for col=1:size(FieldHisto,3)
2833                B=FieldHisto(:,:,col);
2834                C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector
2835                Histo.histo(:,col)=hist(C, Histo.(FieldName));  %calculate histogram
2836            end
2837        end
2838        plot_field(Histo,handles.HistoAxes);
2839        hlegend=legend;
2840        if isempty(FieldName_2)
2841        set(hlegend,'String',FieldName)
2842        else
2843            set(hlegend,'String',{FieldName;FieldName_2})
2844        end
2845    end
2846end
2847
2848%-------------------------------------------------------------------
2849% --- translate coordinate to matrix index
2850%-------------------------------------------------------------------
2851function [indx,indy]=pos2ind(x0,rangx0,nxy)
2852indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel 
2853indy=1+round((nxy(1)-1)*(y12-rangy0(1))/(rangy0(2)-rangy0(1)));% index y of pixel
2854
2855
2856%-------------------------------------------------------------------
2857% --- Executes on button press in 'CheckZoom'.
2858%-------------------------------------------------------------------
2859function CheckZoom_Callback(hObject, eventdata, handles)
2860
2861if (get(handles.CheckZoom,'Value') == 1);
2862    set(handles.CheckZoom,'BackgroundColor',[1 1 0])
2863    set(handles.CheckFixLimits,'Value',1)% propose by default fixed limits for the plotting axes
2864    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2865else
2866    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
2867end
2868
2869%-------------------------------------------------------------------
2870% --- Executes on button press in 'CheckFixLimits'.
2871%-------------------------------------------------------------------
2872function CheckFixLimits_Callback(hObject, eventdata, handles)
2873test=get(handles.CheckFixLimits,'Value');
2874if test
2875    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2876else
2877    set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
2878    update_plot(handles);
2879end
2880
2881%-------------------------------------------------------------------
2882% --- Executes on button press in CheckFixAspectRatio.
2883function CheckFixAspectRatio_Callback(hObject, eventdata, handles)
2884%-------------------------------------------------------------------
2885if get(handles.CheckFixAspectRatio,'Value')
2886%     set(handles.CheckFixAspectRatio,'BackgroundColor',[1 1 0])
2887    update_plot(handles);
2888else
2889%     set(handles.CheckFixAspectRatio,'BackgroundColor',[0.7 0.7 0.7])
2890    update_plot(handles);
2891end
2892
2893%-------------------------------------------------------------------
2894function num_AspectRatio_Callback(hObject, eventdata, handles)
2895%-------------------------------------------------------------------
2896set(handles.CheckFixAspectRatio,'Value',1)% select the fixed aspect ratio button
2897% set(handles.CheckFixAspectRatio,'BackgroundColor',[1 1 0])% mark in yellow
2898update_plot(handles);
2899%-------------------------------------------------------------------
2900
2901%-------------------------------------------------------------------
2902
2903
2904
2905%-------------------------------------------------------------------
2906%----Executes on button press in 'record': records the current flags of manual correction.
2907%-------------------------------------------------------------------
2908function record_Callback(hObject, eventdata, handles)
2909% [filebase,num_i1,num_j1,num_i2,num_j2,Ext,NomType,SubDir]=read_input_file(handles);
2910[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
2911FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
2912%FileName=read_file_boxes(handles);
2913[erread,message]=fileattrib(FileName);
2914if ~isempty(message) && ~isequal(message.UserWrite,1)
2915     msgbox_uvmat('ERROR',['no writting access to ' FileName])
2916     return
2917end
2918test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
2919test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
2920if ~test_civ2 && ~test_civ1
2921    msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
2922end
2923if test_civ2
2924    nbname='nb_vectors2';
2925   flagname='vec2_FixFlag';
2926   attrname='fix2';
2927end
2928if test_civ1
2929    nbname='nb_vectors';
2930   flagname='vec_FixFlag';
2931   attrname='fix';
2932end
2933%write fix flags in the netcdf file
2934UvData=get(handles.uvmat,'UserData');
2935hhh=which('netcdf.open');% look for built-in matlab netcdf library
2936if ~isequal(hhh,'')% case of new builtin Matlab netcdf library
2937    nc=netcdf.open(FileName,'NC_WRITE');
2938    netcdf.reDef(nc);
2939    netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),attrname,1);
2940    dimid = netcdf.inqDimID(nc,nbname);
2941    try
2942        varid = netcdf.inqVarID(nc,flagname);% look for already existing fixflag variable
2943    catch
2944        varid=netcdf.defVar(nc,flagname,'double',dimid);%create fixflag variable if it does not exist
2945    end
2946    netcdf.endDef(nc);
2947    netcdf.putVar(nc,varid,UvData.PlotAxes.FF);
2948    netcdf.close(nc); 
2949else %old netcdf library
2950    netcdf_toolbox(FileName,AxeData,attrname,nbname,flagname)
2951end
2952
2953%-------------------------------------------------------------------
2954%----Correct the netcdf file, using toolbox (old versions of Matlab).
2955%-------------------------------------------------------------------
2956function netcdf_toolbox(FileName,AxeData,attrname,nbname,flagname)
2957nc=netcdf(FileName,'write'); %open netcdf file
2958result=redef(nc);
2959eval(['nc.' attrname '=1;']);
2960theDim=nc(nbname) ;% get the number of velocity vectors
2961nb_vectors=size(theDim);
2962var_FixFlag=ncvar(flagname,nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag
2963var_FixFlag(1:nb_vectors)=AxeData.FF;%
2964fin=close(nc);
2965
2966%-------------------------------------------------------------------
2967% --- Executes on button press in SubField
2968function SubField_Callback(hObject, eventdata, handles)
2969%-------------------------------------------------------------------
2970UvData=get(handles.uvmat,'UserData');
2971if get(handles.SubField,'Value')==0% if the subfield button is desactivated   
2972    set(handles.RootPath_1,'String','')
2973    set(handles.RootFile_1,'String','')
2974    set(handles.SubDir_1,'String','');
2975    set(handles.FileIndex_1,'String','');
2976    set(handles.FileExt_1,'String','');
2977    set(handles.RootPath_1,'Visible','off')
2978    set(handles.RootFile_1,'Visible','off')
2979    set(handles.SubDir_1,'Visible','off');
2980    set(handles.NomType_1,'Visible','off');
2981    set(handles.abs_time_1,'Visible','off')
2982    set(handles.FileIndex_1,'Visible','off');
2983    set(handles.FileExt_1,'Visible','off');
2984    set(handles.FieldName_1,'Value',1);%set to blank state
2985    set(handles.VelType_1,'Value',1);%set to blank state
2986    set(handles.num_Opacity,'String','')% desactivate opacity setting
2987    FieldList=get(handles.FieldName,'String');
2988    if numel(FieldList)>1   % if a choice of fields exists
2989        set(handles.FieldName_1,'Value',1)% set second field choice to blank
2990        set(handles.FieldName_1,'String',[{''};FieldList])% reproduce the menu FieldName plus a blank option
2991    else
2992        set(handles.FieldName_1,'String',{''})% set second field choice to blank
2993    end
2994    if ~strcmp(get(handles.VelType,'Visible'),'on')
2995        set(handles.VelType_1,'Visible','off')
2996    end
2997    if isfield(UvData,'XmlData_1')
2998        UvData=rmfield(UvData,'XmlData_1');
2999    end
3000    set(handles.uvmat,'UserData',UvData);
3001    transform_fct_list=get(handles.transform_fct,'String');
3002    transform_fct=transform_fct_list(get(handles.transform_fct,'Value'));
3003    if strcmp(transform_fct,'sub_field')
3004        set(handles.transform_fct,'Value',1)%suppress the sub_field transform
3005        transform_fct_Callback(hObject, eventdata, handles);
3006    else
3007        run0_Callback(hObject, eventdata, handles)
3008    end 
3009else
3010    MenuBrowse_1_Callback(hObject, eventdata, handles)
3011end
3012
3013%------------------------------------------------------------------------
3014% --- read the data displayed for the input rootfile windows (new): TODO use read_GUI
3015
3016function [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles)
3017%------------------------------------------------------------------------
3018InputFile=read_GUI(handles.InputFile);
3019RootPath=InputFile.RootPath;
3020SubDir=regexprep(InputFile.SubDir,'/|\','');
3021RootFile=regexprep(InputFile.RootFile,'/|\','');
3022FileIndices=InputFile.FileIndex;
3023FileExt=InputFile.FileExt;
3024
3025
3026%------------------------------------------------------------------------
3027% ---- read the data displayed for the second input rootfile windows
3028function [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1,NomType_1]=read_file_boxes_1(handles)
3029%------------------------------------------------------------------------
3030RootPath_1=get(handles.RootPath_1,'String'); % read the data from the file1_input window
3031if isequal(get(handles.RootPath_1,'Visible'),'off') || isequal(RootPath_1,'"')
3032    RootPath_1=get(handles.RootPath,'String');
3033end;
3034SubDir_1=get(handles.SubDir_1,'String');
3035if isequal(get(handles.SubDir_1,'Visible'),'off')|| isequal(SubDir_1,'"')
3036    SubDir_1=get(handles.SubDir,'String');
3037end
3038SubDir_1=regexprep(SubDir_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3039RootFile_1=get(handles.RootFile_1,'String');
3040if isequal(get(handles.RootFile_1,'Visible'),'off') || isequal(RootFile_1,'"')
3041    RootFile_1=get(handles.RootFile,'String');
3042end
3043RootFile_1=regexprep(RootFile_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3044FileIndex_1=get(handles.FileIndex_1,'String');
3045if isequal(get(handles.FileIndex_1,'Visible'),'off')|| isequal(FileIndex_1,'"')
3046    FileIndex_1=get(handles.FileIndex,'String');
3047end
3048FileExt_1=get(handles.FileExt_1,'String');
3049if isequal(get(handles.FileExt_1,'Visible'),'off') || isequal(FileExt_1,'"')
3050    FileExt_1=get(handles.FileExt,'String');%read FileExt by default
3051end
3052NomType_1=get(handles.NomType_1,'String');
3053if isequal(get(handles.NomType_1,'Visible'),'off') || isequal(NomType_1,'"')
3054    NomType_1=get(handles.NomType,'String');%read FileExt by default
3055end
3056%------------------------------------------------------------------------
3057% --- Executes on menu selection FieldName
3058function FieldName_Callback(hObject, eventdata, handles)
3059%------------------------------------------------------------------------
3060UvData=get(handles.uvmat,'UserData');
3061list_fields=get(handles.FieldName,'String');% list menu fields
3062index_fields=get(handles.FieldName,'Value');% selected string index
3063field= list_fields{index_fields(1)}; % selected string
3064
3065%% fill the coordinates and variables from selections in get_field
3066if isequal(field,'get_field...')
3067    ParamIn=[];
3068    if strcmp(get(handles.VelType,'Visible'),'on')
3069        % we use the civ choice as default input
3070        ParamIn.SwitchVarIndexTime='attribute';
3071        ListVelType=get(handles.VelType,'String');
3072        VelType=ListVelType{get(handles.VelType,'Value')};
3073        switch VelType
3074            case 'civ1'
3075                 ParamIn.TimeVarName='Civ1_Time';
3076                 ParamIn.vector_x='Civ1_U';
3077                 ParamIn.vector_y='Civ1_V';
3078                 ParamIn.vec_color='Civ1_C';               
3079            case 'filter1'
3080                 ParamIn.TimeVarName='Civ1_Time';
3081                 ParamIn.vector_x='Civ1_U_smooth';
3082                 ParamIn.vector_y='Civ1_V_smooth';
3083            case 'civ2'
3084                 ParamIn.TimeVarName='Civ2_Time';
3085                 ParamIn.vector_x='Civ2_U';
3086                 ParamIn.vector_y='Civ2_V';
3087            case 'filter2'
3088                 ParamIn.TimeVarName='Civ2_Time';
3089                 ParamIn.vector_x='Civ2_U_smooth';
3090                 ParamIn.vector_y='Civ2_V_smooth';
3091                 ParamIn.vec_color='Civ2_C';
3092        end
3093    end
3094    set(handles.FixVelType,'visible','off')
3095    set(handles.VelType,'Visible','off')
3096    set(handles.VelType_1,'Visible','off')
3097    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3098    FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3099%     hget_field=findobj(allchild(0),'name','get_field');
3100%     if ~isempty(hget_field)
3101%         delete(hget_field)
3102%     end
3103    GetFieldData=get_field(FileName,ParamIn);
3104    FieldList={};
3105    VecColorList={};
3106    XName='';
3107    YName='';
3108    if GetFieldData.CheckVector
3109        UName=GetFieldData.PanelVectors.vector_x;
3110        VName=GetFieldData.PanelVectors.vector_y;
3111        XName=GetFieldData.XVarName;
3112        YName=GetFieldData.YVarName;
3113        CName=GetFieldData.PanelVectors.vec_color;
3114        [FieldList,VecColorList]=set_field_list(UName,VName,CName);
3115%         FieldList={['vec(' UName ',' VName ')'];...
3116%             ['norm(' UName ',' VName ')'];...
3117%             ['curl(' UName ',' VName ')'];...
3118%             ['div(' UName ',' VName ')'];...
3119%             ['strain(' UName ',' VName ')']};
3120%         VecColorList={['norm(' UName ',' VName ')'];...
3121%             UName;...
3122%             VName};...
3123%             if ~isempty(CName)
3124%             VecColorList=[{CName};VecColorList];
3125%             end
3126    end
3127    if GetFieldData.CheckScalar
3128        AName=GetFieldData.PanelScalar.scalar;
3129        XName=GetFieldData.XVarName;
3130        YName=GetFieldData.YVarName;
3131        FieldList={AName};
3132    end
3133    if GetFieldData.CheckPlot1D
3134        XName=GetFieldData.CheckPlot1D.abscissa;
3135        YName=GetFieldData.CheckPlot1D.ordinate;
3136    end
3137    set(handles.Coord_x,'String',{XName})
3138    set(handles.Coord_y,'String',{YName})
3139    set(handles.FieldName,'Value',1)
3140    set(handles.FieldName,'String',[FieldList; {'get_field...'}]);
3141    set(handles.ColorScalar,'Value',1)
3142    set(handles.ColorScalar,'String',VecColorList);
3143    UvData.FileType{1}='netcdf';
3144    set(handles.uvmat,'UserData',UvData)
3145    run0_Callback(hObject, eventdata, handles)
3146    return %no further action
3147end
3148
3149
3150
3151%read the rootfile input display
3152[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3153FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3154[tild,tild,tild,i1,i2,j1,j2,tild,NomType]=fileparts_uvmat(['xxx' get(handles.FileIndex,'String') FileExt]);
3155if isequal(field,'image')
3156    if  isfield(UvData.Field,'Civ2_ImageA')%get the corresponding input image in the netcdf file
3157        imagename=UvData.Field.Civ2_ImageA;
3158    elseif isfield(UvData.Field,'Civ1_ImageA')%
3159        imagename=UvData.Field.Civ1_ImageA;
3160    else
3161        SubDirBase=regexprep(SubDir,'\..*','');%take the root part of SubDir, before the first dot '.'
3162        imagename=fullfile_uvmat(RootPath,SubDirBase,RootFile,'.png',NomType,i1,[],j1,[]);
3163    end
3164    if ~exist(imagename,'file')
3165        [FileName,PathName] = uigetfile( ...
3166            {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3167            '*.jpg',' jpeg image files'; ...
3168            '*.png','.png image files'; ...
3169            '*.tif','.tif image files'; ...
3170            '*.avi;*.AVI','.avi movie files'; ...
3171            '*.vol','.volume images (png)'; ...
3172            '*.*',  'All Files (*.*)'}, ...
3173            'Pick an image',imagename);
3174        if ~ischar(FileName),return,end %abandon if the browser is cancelled
3175        imagename=[PathName FileName];
3176    end
3177     % display the selected field and related information
3178    display_file_name(handles,imagename)%display the image
3179    return
3180else
3181    ext=get(handles.FileExt,'String');
3182    if ~isequal(ext,'.nc') %find the new NomType if the previous display was not already a netcdf file
3183        [FileName,PathName] = uigetfile( ...
3184            {'*.nc', ' (*.nc)';
3185            '*.nc',' netcdf files'; ...
3186            '*.*',  'All Files (*.*)'}, ...
3187            'Pick a netcdf file',FileBase);
3188        if ~ischar(FileName),return,end %abandon if the browser is cancelled
3189        FullFileName=[PathName FileName];
3190        % display the selected field and related information
3191        display_file_name( handles,FullFileName)
3192        return
3193    end
3194end
3195indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
3196set(handles.FileIndex,'String',indices)
3197
3198%common to Fields_1_Callback
3199list_fields_1=get(handles.FieldName_1,'String');% list menu fields
3200field_1='';
3201if ~isempty(list_fields_1)
3202field_1= list_fields_1{get(handles.FieldName_1,'Value')}; % selected string
3203end
3204if isequal(field,'image')||isequal(field_1,'image')
3205    set(handles.TitleNpxy,'Visible','on')% visible npx,pxcm... buttons
3206    set(handles.num_Npx,'Visible','on')
3207    set(handles.num_Npy,'Visible','on')
3208else
3209    set(handles.TitleNpxy,'Visible','off')% visible npx,pxcm... buttons
3210    set(handles.num_Npx,'Visible','off')
3211    set(handles.num_Npy,'Visible','off')
3212end
3213if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3214    run0_Callback(hObject, eventdata, handles)
3215end
3216
3217%---------------------------------------------------
3218% --- Executes on menu selection FieldName
3219function FieldName_1_Callback(hObject, eventdata, handles)
3220%-------------------------------------------------
3221%% read input data
3222check_new=~get(handles.SubField,'Value'); %check_new=1 if a second field was not previously entered
3223UvData=get(handles.uvmat,'UserData');
3224if check_new && isfield(UvData,'XmlData')
3225    UvData.XmlData{2}=UvData.XmlData{1};
3226end
3227if isfield(UvData,'Field_1')
3228    UvData=rmfield(UvData,'Field_1');% remove the stored second field (a new one needs to be read)
3229end
3230UvData.FileName_1='';% desactivate the use of a constant second file
3231list_fields=get(handles.FieldName,'String');% list menu fields
3232field= list_fields{get(handles.FieldName,'Value')}; % selected string
3233list_fields=get(handles.FieldName_1,'String');% list menu fields
3234field_1= list_fields{get(handles.FieldName_1,'Value')}; % selected string for the second field
3235if isempty(field_1)%||(numel(UvData.FileType)>=2 && strcmp(UvData.FileType{2},'image'))
3236    set(handles.SubField,'Value',0)
3237    SubField_Callback(hObject, eventdata, handles)
3238    return
3239else
3240    set(handles.SubField,'Value',1)%state that a second field is now entered
3241end
3242
3243%% read the rootfile input display
3244[RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
3245FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
3246[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
3247switch field_1
3248    case 'get_field...'
3249        set_veltype_display(0) % no veltype display
3250        hget_field=findobj(allchild(0),'name','get_field_1');
3251        if ~isempty(hget_field)
3252            delete(hget_field)
3253        end
3254        hget_field=get_field(FileName_1);
3255        set(hget_field,'name','get_field_1')
3256        hhget_field=guidata(hget_field);
3257        set(hhget_field.list_fig,'Value',1)
3258        set(hhget_field.list_fig,'String',{'uvmat'})
3259        if check_new
3260            UvData.FileType{2}=UvData.FileType{1};
3261            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3262              set(handles.uvmat,'UserData',UvData)
3263        end
3264    case 'image'
3265        % get the image name corresponding to the current netcdf name (no unique correspondance)
3266        if  isfield(UvData.Field,'Civ2_ImageA')%get the corresponding input image in the netcdf file
3267            imagename=UvData.Field.Civ2_ImageA;
3268        elseif isfield(UvData.Field,'Civ1_ImageA')%
3269            imagename=UvData.Field.Civ1_ImageA;
3270        else
3271            SubDirBase=regexprep(SubDir_1,'\..*','');%take the root part of SubDir, before the first dot '.'
3272            imagename=fullfile_uvmat(RootPath_1,SubDirBase,RootFile_1,'.png',get(handles.NomType,'String'),i1,[],j1);
3273        end
3274        if ~exist(imagename,'file') % browse for images if it is not found
3275            [FileName,PathName] = uigetfile( ...
3276                {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3277                '*.jpg',' jpeg image files'; ...
3278                '*.png','.png image files'; ...
3279                '*.tif','.tif image files'; ...
3280                '*.avi;*.AVI','.avi movie files'; ...
3281                '*.vol','.volume images (png)'; ...
3282                '*.*',  'All Files (*.*)'}, ...
3283                'Pick an image',imagename);
3284            if ~ischar(FileName),return,end %abandon if the browser is cancelled
3285            imagename=[PathName FileName];
3286        end
3287        if ~ischar(imagename)% quit if the browser has  been closed
3288            set(handles.SubField,'Value',0)
3289        else %valid browser input:  display the selected image
3290            set(handles.TitleNpxy,'Visible','on')% visible npx,pxcm... buttons
3291            set(handles.num_Npx,'Visible','on')
3292            set(handles.num_Npy,'Visible','on')
3293            display_file_name(handles,imagename,2)%display the imag
3294        end
3295    otherwise
3296        check_refresh=1;
3297        if check_new% if a second field was not previously entered, we just read another field in the first input file
3298            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3299            set(handles.FileExt_1,'String',get(handles.FileExt,'String'))
3300           
3301            UvData.FileType{2}=UvData.FileType{1};
3302            UvData.XmlData{2}= UvData.XmlData{1};
3303            transform=get(handles.path_transform,'UserData');
3304             if (~isa(transform,'function_handle')||nargin(transform)<3)
3305                set(handles.uvmat,'UserData',UvData)
3306                set(handles.transform_fct,'value',2); % set transform fct to 'sub_field' if the current fct does not accept two input fields
3307                transform_fct_Callback(hObject, eventdata, handles)% activate transform_fct_Callback and refresh current plot
3308                 check_refresh=0;
3309             end             
3310        end
3311        if ~isequal(field,'image')
3312            set(handles.TitleNpxy,'Visible','off')% visible npx,pxcm... buttons
3313            set(handles.num_Npx,'Visible','off')
3314            set(handles.num_Npy,'Visible','off')
3315        end
3316        set(handles.uvmat,'UserData',UvData)
3317 
3318        if check_refresh && ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3319            run0_Callback(hObject, eventdata, handles)
3320        end
3321end
3322
3323%------------------------------------------------------------------------
3324% --- set the visibility of relevant velocity type menus:
3325function menu=set_veltype_display(Civ,FileType)
3326%------------------------------------------------------------------------
3327if ~exist('FileType','var')
3328    FileType='civx';
3329end
3330switch FileType
3331    case 'civx'
3332        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3333        if isequal(Civ,0)
3334            imax=0;
3335        elseif isequal(Civ,1) || isequal(Civ,2)
3336            imax=1;
3337        elseif isequal(Civ,3)
3338            imax=3;
3339        elseif isequal(Civ,4) || isequal(Civ,5)
3340            imax=4;
3341        elseif isequal(Civ,6) %patch2
3342            imax=6;
3343        end
3344    case 'civdata'
3345        menu={'civ1';'filter1';'civ2';'filter2'};
3346        if isequal(Civ,0)
3347            imax=0;
3348        elseif isequal(Civ,1) || isequal(Civ,2)
3349            imax=1;
3350        elseif isequal(Civ,3)
3351            imax=2;
3352        elseif isequal(Civ,4) || isequal(Civ,5)
3353            imax=3;
3354        elseif isequal(Civ,6) %patch2
3355            imax=4;
3356        end
3357end
3358menu=menu(1:imax);
3359
3360%------------------------------------------------------------------------
3361% --- Executes on button press in FixVelType.
3362function FixVelType_Callback(hObject, eventdata, handles)
3363%------------------------------------------------------------------------
3364% refresh the current plot if the fixed  veltype is unselected
3365if ~get(handles.FixVelType,'Value')
3366    run0_Callback(hObject, eventdata, handles)
3367end
3368
3369%------------------------------------------------------------------------
3370% --- Executes on button press in VelType.
3371function VelType_Callback(hObject, eventdata, handles)
3372%------------------------------------------------------------------------
3373set(handles.FixVelType,'Value',1)
3374run0_Callback(hObject, eventdata, handles)
3375
3376%------------------------------------------------------------------------
3377% --- Executes on choice selection in VelType_1.
3378function VelType_1_Callback(hObject, eventdata, handles)
3379%------------------------------------------------------------------------
3380set(handles.FixVelType,'Value',1)% the velocity type is now imposed by the GUI (not automatic)
3381UvData=get(handles.uvmat,'UserData');
3382set(handles.run0,'BackgroundColor',[1 1 0])%paint run0 button in yellow to indicate its activation
3383drawnow   
3384InputFile=read_GUI(handles.InputFile);% read the input file parameters
3385[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
3386[RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
3387FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];% name of the first input file
3388
3389check_refresh=0;
3390if isempty(InputFile.VelType_1)
3391        FileName_1='';% we plot the first input field without the second field
3392        set(handles.SubField,'Value',0)
3393        SubField_Callback(hObject, eventdata, handles)% activate SubField_Callback and refresh current plot, removing the second field
3394elseif get(handles.SubField,'Value')% if subfield is already 'on'
3395     FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];% name of the second input file
3396     check_refresh=1;%will refresh the current plot
3397else% we introduce the same file (with a different field) for the second series
3398     FileName_1=FileName;% we compare two fields in the same file
3399     UvData.FileType{2}=UvData.FileType{1};
3400     UvData.XmlData{2}= UvData.XmlData{1};
3401     set(handles.SubField,'Value',1)
3402     transform=get(handles.path_transform,'UserData');
3403     if (~isa(transform,'function_handle')||nargin(transform)<3)
3404        set(handles.uvmat,'UserData',UvData)
3405        set(handles.transform_fct,'value',2); % set transform fct to 'sub_field' if the current fct does not accept two input fields
3406        transform_fct_Callback(hObject, eventdata, handles)% activate transform_fct_Callback and refresh current plot
3407     else
3408         check_refresh=1;
3409     end 
3410end
3411
3412% refresh the current plot if it has not been done previously
3413if check_refresh
3414    UvData.FileName_1='';% desactivate the use of a constant second file
3415    set(handles.uvmat,'UserData',UvData)
3416    num_i1=stra2num(get(handles.i1,'String'));
3417    num_i2=stra2num(get(handles.i2,'String'));
3418    num_j1=stra2num(get(handles.j1,'String'));
3419    num_j2=stra2num(get(handles.j2,'String'));
3420    [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(['xx' FileIndex_1]);
3421    errormsg=refresh_field(handles,FileName,FileName_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1);
3422    if ~isempty(errormsg)
3423        msgbox_uvmat('ERROR',errormsg);
3424    else
3425        set(handles.i1,'BackgroundColor',[1 1 1])
3426        set(handles.i2,'BackgroundColor',[1 1 1])
3427        set(handles.j1,'BackgroundColor',[1 1 1])
3428        set(handles.j2,'BackgroundColor',[1 1 1])
3429        set(handles.FileIndex,'BackgroundColor',[1 1 1])
3430        set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
3431    end
3432    set(handles.run0,'BackgroundColor',[1 0 0])
3433end
3434
3435
3436%-----------------------------------------------------------------------
3437% --- reset civ buttons
3438function reset_vel_type(handles_civ0,handle1)
3439%-----------------------------------------------------------------------
3440for ibutton=1:length(handles_civ0)
3441    set(handles_civ0(ibutton),'BackgroundColor',[0.831 0.816 0.784])
3442    set(handles_civ0(ibutton),'Value',0)
3443end
3444if exist('handle1','var')%handles of selected button
3445        set(handle1,'BackgroundColor',[1 1 0]) 
3446end
3447
3448%-----------------------------------------------------------------------
3449% --- Executes on button press in MENUVOLUME.
3450function VOLUME_Callback(hObject, eventdata, handles)
3451%-----------------------------------------------------------------------
3452%errordlg('command VOL not implemented yet')
3453if ishandle(handles.UVMAT_title)
3454    delete(handles.UVMAT_title)
3455end
3456UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3457if isequal(get(handles.VOLUME,'Value'),1)
3458    set(handles.CheckZoom,'Value',0)
3459    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3460    set(handles.edit_vect,'Value',0)
3461    edit_vect_Callback(hObject, eventdata, handles)
3462    set(handles.edit_object,'Value',0)
3463    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3464%     set(handles.cal,'Value',0)
3465%     set(handles.cal,'BackgroundColor',[0 1 0])
3466    set(handles.edit_vect,'Value',0)
3467    edit_vect_Callback(hObject, eventdata, handles)
3468    %initiate set_object GUI
3469    data.Name='VOLUME';
3470    if isfield(UvData,'CoordType')
3471        data.CoordType=UvData.CoordType;
3472    end
3473    if isfield(UvData.Field,'CoordMesh')&~isempty(UvData.Field.CoordMesh)
3474        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
3475        data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
3476        data.DX=UvData.Field.CoordMesh;
3477        data.DY=UvData.Field.CoordMesh;
3478    elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3479        np=size(UvData.Field.A);
3480        meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
3481        meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
3482        data.RangeY=max(meshx,meshy);
3483        data.RangeX=max(meshx,meshy);
3484        data.DX=max(meshx,meshy);
3485    end
3486    data.ParentButton=handles.VOLUME;
3487    PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
3488    [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes,
3489                                                      % associate the set_object interface handle to the plotting axes
3490    set(hset_object,'Position',get(handles.uvmat,'Position')+UvData.OpenParam.PosSetObject)
3491    UvData.MouseAction='create_object';
3492else
3493    set(handles.VOLUME,'BackgroundColor',[0 1 0])
3494end
3495set(handles.uvmat,'UserData',UvData)
3496
3497%-------------------------------------------------------
3498function edit_vect_Callback(hObject, eventdata, handles)
3499%-------------------------------------------------------
3500%
3501if isequal(get(handles.edit_vect,'Value'),1)
3502    VelTypeMenu=get(handles.VelType,'String');
3503    VelType=VelTypeMenu{get(handles.VelType,'Value')};
3504    if ~strcmp(VelType,'civ2') && ~strcmp(VelType,'civ1')
3505        msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
3506    end
3507    set(handles.record,'Visible','on')
3508    set(handles.edit_vect,'BackgroundColor',[1 1 0])
3509    set(handles.edit_object,'Value',0)
3510    set(handles.CheckZoom,'Value',0)
3511    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3512    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3513    set(gcf,'Pointer','arrow')
3514else
3515    set(handles.record,'Visible','off')
3516    set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7])
3517end
3518
3519%----------------------------------------------
3520function save_mask_Callback(hObject, eventdata, handles)
3521%-----------------------------------------------------------------------
3522UvData=get(handles.uvmat,'UserData');
3523
3524flag=1;
3525npx=size(UvData.Field.A,2);
3526npy=size(UvData.Field.A,1);
3527xi=0.5:npx-0.5;
3528yi=0.5:npy-0.5;
3529[Xi,Yi]=meshgrid(xi,yi);
3530if isfield(UvData,'Object')
3531    for iobj=1:length(UvData.Object)
3532        ObjectData=UvData.Object{iobj};
3533        if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
3534            flagobj=1;
3535            testphys=0; %coordinates in pixels by default
3536            if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys')
3537                if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
3538                    Calib=UvData.XmlData{1}.GeometryCalib;
3539                    testphys=1;
3540                end
3541            end
3542            if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style')
3543                if isequal(ObjectData.Type,'polygon')
3544                    X=ObjectData.Coord(:,1);
3545                    Y=ObjectData.Coord(:,2);
3546                    if testphys
3547                        [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
3548                    end
3549                    flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside                 
3550                elseif isequal(ObjectData.Type,'ellipse')
3551                    if testphys
3552                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3553                    end
3554                    RangeX=max(ObjectData.RangeX);
3555                    RangeY=max(ObjectData.RangeY);
3556                    X2Max=RangeX*RangeX;
3557                    Y2Max=RangeY*RangeY;
3558                    distX=(Xi-ObjectData.Coord(1,1));
3559                    distY=(Yi-ObjectData.Coord(1,2));
3560                    flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
3561                elseif isequal(ObjectData.Type,'rectangle')
3562                    if testphys
3563                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3564                    end
3565                    distX=abs(Xi-ObjectData.Coord(1,1));
3566                    distY=abs(Yi-ObjectData.Coord(1,2));
3567                    flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
3568                end
3569                if isequal(ObjectData.ProjMode,'mask_outside')
3570                    flagobj=~flagobj;
3571                end
3572                flag=flag & flagobj;
3573            end
3574        end
3575    end
3576end
3577% flag=~flag;
3578%mask name
3579RootPath=get(handles.RootPath,'String');
3580RootFile=get(handles.RootFile,'String');
3581RootFile=regexprep(RootFile,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3582filebase=fullfile(RootPath,RootFile);
3583list=get(handles.masklevel,'String');
3584masknumber=num2str(length(list));
3585maskindex=get(handles.masklevel,'Value');
3586mask_name=fullfile_uvmat(RootPath,SubDir,[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
3587%mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
3588imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
3589imflag=flipdim(imflag,1);
3590% imflag=uint8(255*flag);% =0 for flag=0 (vectors=0 when 20<imflag<200)
3591msgbox_uvmat('CONFIRMATION',[mask_name ' saved'])
3592imwrite(imflag,mask_name,'BitDepth',8);
3593
3594%display the mask
3595figure;
3596vec=linspace(0,1,256);%define a linear greyscale colormap
3597map=[vec' vec' vec'];
3598colormap(map)
3599
3600image(imflag);
3601
3602%-------------------------------------------------------------------
3603%-------------------------------------------------------------------
3604%  - FUNCTIONS FOR SETTING PLOTTING PARAMETERS
3605
3606%------------------------------------------------------------------
3607%-------------------------------------------------------------
3608% --- Executes on selection change in transform_fct.
3609
3610function transform_fct_Callback(hObject, eventdata, handles)
3611%-------------------------------------------------------------
3612UvData=get(handles.uvmat,'UserData');
3613menu=get(handles.transform_fct,'String');refresh
3614ichoice=get(handles.transform_fct,'Value');%item number in the menu
3615transform_name=menu{ichoice};% choice of the transform fct
3616list_path=get(handles.transform_fct,'UserData');
3617
3618%% add a new item to the menu if the option 'more...' has been selected
3619prev_path=fullfile(get(handles.path_transform,'String'));
3620if ~exist(prev_path,'dir')
3621    prev_path=fullfile(fileparts(which('uvmat')),'transform_field');
3622end
3623if strcmp(transform_name,'more...');
3624    [FileName, PathName] = uigetfile( ...
3625        {'*.m', ' (*.m)';
3626        '*.m',  '.m files '; ...
3627        '*.*', 'All Files (*.*)'}, ...
3628        'Pick the transform function', prev_path);
3629    if ~ischar(FileName),return,end %abandon if the browser is cancelled
3630    path_transform_fct =fullfile(PathName,FileName);
3631    if isempty(regexp(FileName,'\.m$'))% detect file extension .m
3632        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3633        return
3634    else
3635        transform_name=regexprep(FileName,'\.m','');
3636    end
3637    ichoice=find(strcmp(transform_name,menu),1);%look for the selected fct in the existing menu
3638    if isempty(ichoice)% if the item is not found, add it to the menu (before 'more...' and select it)
3639        menu=[menu(1:end-1);{transform_name};{'more...'}];
3640        ichoice=numel(menu)-1;   
3641    end
3642    list_path{ichoice}=PathName;%update the list fo fct paths
3643    set(handles.transform_fct,'String',menu)
3644    set(handles.transform_fct,'Value',ichoice)
3645   
3646    % save the new menu in the personal file 'uvmat_perso.mat'
3647    dir_perso=prefdir;%personal Matalb directory
3648    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3649    if exist(profil_perso,'file')
3650        nb_builtin=UvData.OpenParam.NbBuiltin;% number of 'builtin' (basic) transform fcts in uvmat
3651        if nb_builtin<numel(list_path)
3652        for ilist=nb_builtin+1:numel(list_path)
3653            transform_fct{ilist-nb_builtin}=[fullfile(list_path{ilist},menu{ilist}) '.m'];
3654        end
3655        save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
3656        end
3657    end
3658end
3659
3660%% create the function handle of the selected fct
3661
3662if isempty(list_path{ichoice})% case of no selected fct
3663    transform_handle=[];
3664else
3665    if ~exist(list_path{ichoice},'dir')
3666        msgbox_uvmat('ERROR','invalid fct path: select the transform fct again with the option more...')
3667        return
3668    end
3669    current_dir=pwd;%current working dir
3670    cd(list_path{ichoice})
3671    transform_handle=str2func(transform_name);
3672    cd(current_dir)
3673end
3674set(handles.path_transform,'String',list_path{ichoice})
3675set(handles.path_transform,'UserData',transform_handle)
3676set(handles.transform_fct,'UserData',list_path)
3677
3678%% update the ToolTip string of the menu transform_fct with the first line of the selected fct file
3679if isempty(list_path{ichoice})% case of no selected fct
3680    set(handles.transform_fct,'ToolTipString','transform_fct:choose a transform function')
3681else
3682    try
3683        [fid,errormsg] =fopen([fullfile(list_path{ichoice},transform_name) '.m']);
3684        InputText=textscan(fid,'%s',1,'delimiter','\n');
3685        fclose(fid)
3686        set(handles.transform_fct,'ToolTipString',['transform_fct: ' InputText{1}{1}])% put the first line of the selected function as tooltip help
3687    end
3688end
3689
3690%% adapt the GUI to the input/output conditions of the selected transform fct
3691DataOut=[];
3692CoordUnit='';
3693CoordUnitPrev='';
3694if isfield(UvData,'Field')&&isfield(UvData.Field,'CoordUnit')
3695    CoordUnitPrev=UvData.Field.CoordUnit;
3696end
3697if ~isempty(list_path{ichoice})
3698    if nargin(transform_handle)>1 && isfield(UvData,'XmlData')&&~isempty(UvData.XmlData)
3699        XmlData=UvData.XmlData{1};
3700        DataOut=feval(transform_handle,'*',XmlData);
3701        if isfield(DataOut,'CoordUnit')
3702            CoordUnit=DataOut.CoordUnit;
3703        end
3704        if isfield(DataOut,'InputFieldType')
3705            UvData.InputFieldType=DataOut.InputFieldType;
3706        end
3707    else
3708        DataOut=feval(transform_handle,'*');
3709    end
3710end
3711
3712
3713%% delete drawn objects if the output CooordUnit is different from the previous one
3714if ~strcmp(CoordUnit,CoordUnitPrev)
3715    set(handles.CheckFixLimits,'Value',0)
3716set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
3717    hother=findobj('Tag','proj_object');%find all the proj objects
3718    for iobj=1:length(hother)
3719        delete_object(hother(iobj))
3720    end
3721    hother=findobj('Tag','DeformPoint');%find all the proj objects
3722    for iobj=1:length(hother)
3723        delete_object(hother(iobj))
3724    end
3725    hh=findobj('Tag','calib_points');
3726    if ~isempty(hh)
3727        delete(hh)
3728    end
3729    hhh=findobj('Tag','calib_marker');
3730    if ~isempty(hhh)
3731        delete(hhh)
3732    end
3733%     if isfield(UvData,'Object')
3734%         UvData.Object=UvData.Object(1);
3735%     end
3736    set(handles.ListObject,'Value',1)
3737    set(handles.ListObject,'String',{''})
3738    set(handles.ListObject_1,'Value',1)
3739    set(handles.ListObject_1,'String',{''})
3740    set(handles.ViewObject,'value',0)
3741    ViewObject_Callback(hObject, eventdata, handles)
3742    set(handles.ViewField,'value',0)
3743    ViewField_Callback(hObject, eventdata, handles)
3744    set(handles.edit_object,'Value',0)
3745    edit_object_Callback(hObject, eventdata, handles)
3746    UvData.Object={[]};
3747end
3748set(handles.uvmat,'UserData',UvData)
3749
3750%% refresh the current plot
3751if isempty(list_path{ichoice}) || nargin(transform_handle)<3
3752    set(handles.SubField,'Value',0)
3753    SubField_Callback(hObject, eventdata, handles)
3754else
3755    run0_Callback(hObject, eventdata, handles)
3756end
3757
3758%------------------------------------------------
3759%CALLBACKS FOR PLOTTING PARAMETERS
3760%-------------------------------------------------
3761%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3762% Plot coordinates
3763%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3764%------------------------------------------------------------------------
3765function num_MinX_Callback(hObject, eventdata, handles)
3766%------------------------------------------------------------------------
3767set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3768set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3769update_plot(handles);
3770
3771%------------------------------------------------------------------------
3772function num_MaxX_Callback(hObject, eventdata, handles)
3773%------------------------------------------------------------------------
3774set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3775set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3776update_plot(handles);
3777
3778%------------------------------------------------------------------------
3779function num_MinY_Callback(hObject, eventdata, handles)
3780%------------------------------------------
3781set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3782set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3783update_plot(handles);
3784
3785%------------------------------------------------------------------------
3786function num_MaxY_Callback(hObject, eventdata, handles)
3787%------------------------------------------------------------------------
3788set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3789set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3790update_plot(handles);
3791
3792%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3793% Scalar or image representation
3794%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3795%------------------------------------------------------------------------
3796function num_MinA_Callback(hObject, eventdata, handles)
3797%------------------------------------------
3798set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3799set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3800MinA=str2double(get(handles.num_MinA,'String'));
3801MaxA=str2double(get(handles.num_MaxA,'String'));
3802if MinA>MaxA% switch minA and maxA in case of error
3803    MinA_old=MinA;
3804    MinA=MaxA;
3805    MaxA=MinA_old;
3806    set(handles.num_MinA,'String',num2str(MinA,5));
3807    set(handles.num_MaxA,'String',num2str(MaxA,5));
3808end
3809update_plot(handles);
3810
3811%------------------------------------------------------------------------
3812function num_MaxA_Callback(hObject, eventdata, handles)
3813%------------------------------------------------------------------------
3814set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3815set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3816MinA=str2double(get(handles.num_MinA,'String'));
3817MaxA=str2double(get(handles.num_MaxA,'String'));
3818if MinA>MaxA% switch minA and maxA in case of error
3819        MinA_old=MinA;
3820    MinA=MaxA;
3821    MaxA=MinA_old;
3822    set(handles.num_MinA,'String',num2str(MinA,5));
3823    set(handles.num_MaxA,'String',num2str(MaxA,5));
3824end
3825update_plot(handles);
3826
3827%------------------------------------------------------------------------
3828function CheckFixScalar_Callback(hObject, eventdata, handles)
3829%------------------------------------------------------------------------
3830test=get(handles.CheckFixScalar,'Value');
3831if test
3832    set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3833else
3834    set(handles.CheckFixScalar,'BackgroundColor',[0.7 0.7 0.7])
3835    update_plot(handles);
3836end
3837
3838%-------------------------------------------------------------------
3839function CheckBW_Callback(hObject, eventdata, handles)
3840%-------------------------------------------------------------------
3841update_plot(handles);
3842
3843%-------------------------------------------------------------------
3844function num_Opacity_Callback(hObject, eventdata, handles)
3845update_plot(handles);
3846%-------------------------------------------------------------------
3847
3848%-------------------------------------------------------------------
3849function ListContour_Callback(hObject, eventdata, handles)
3850%-------------------------------------------------------------------
3851val=get(handles.ListContour,'Value');
3852if val==2
3853    set(handles.interval_txt,'Visible','on')
3854    set(handles.num_IncrA,'Visible','on')
3855else
3856    set(handles.interval_txt,'Visible','off')
3857    set(handles.num_IncrA,'Visible','off')
3858end
3859update_plot(handles);
3860
3861%-------------------------------------------------------------------
3862function num_IncrA_Callback(hObject, eventdata, handles)
3863%-------------------------------------------------------------------
3864update_plot(handles);
3865
3866
3867%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3868% Vector representation
3869%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3870%-------------------------------------------------------------------
3871function CheckHideWarning_Callback(hObject, eventdata, handles)
3872%-------------------------------------------------------------------
3873update_plot(handles);
3874
3875%-------------------------------------------------------------------
3876function CheckHideFalse_Callback(hObject, eventdata, handles)
3877%-------------------------------------------------------------------
3878update_plot(handles);
3879
3880%-------------------------------------------------------------------
3881function num_VecScale_Callback(hObject, eventdata, handles)
3882%-------------------------------------------------------------------
3883set(handles.CheckFixVectors,'Value',1);
3884set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3885update_plot(handles);
3886
3887%-------------------------------------------------------------------
3888function CheckFixVectors_Callback(hObject, eventdata, handles)
3889%-------------------------------------------------------------------
3890test=get(handles.CheckFixVectors,'Value');
3891if test
3892    set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3893else
3894    update_plot(handles);
3895    %set(handles.num_VecScale,'String',num2str(ScalOut.num_VecScale,3))
3896    set(handles.CheckFixVectors,'BackgroundColor',[0.7 0.7 0.7])
3897end
3898
3899%------------------------------------------------------------------------
3900% --- Executes on selection change in CheckDecimate4 (nb_vec/4).
3901function CheckDecimate4_Callback(hObject, eventdata, handles)
3902%------------------------------------------------------------------------
3903if isequal(get(handles.CheckDecimate4,'Value'),1)
3904    set(handles.CheckDecimate16,'Value',0)
3905end
3906update_plot(handles);
3907
3908%------------------------------------------------------------------------
3909% --- Executes on selection change in CheckDecimate16 (nb_vec/16).
3910function CheckDecimate16_Callback(hObject, eventdata, handles)
3911%------------------------------------------------------------------------
3912if isequal(get(handles.CheckDecimate16,'Value'),1)
3913    set(handles.CheckDecimate4,'Value',0)
3914end
3915update_plot(handles);
3916
3917%------------------------------------------------------------------------
3918% --- Executes on selection change in ColorCode menu
3919function ColorCode_Callback(hObject, eventdata, handles)
3920%------------------------------------------------------------------------
3921% edit the choice for color code
3922update_color_code_boxes(handles);
3923update_plot(handles);
3924
3925%------------------------------------------------------------------------
3926function update_color_code_boxes(handles)
3927%------------------------------------------------------------------------
3928list_code=get(handles.ColorCode,'String');% list menu fields
3929colcode= list_code{get(handles.ColorCode,'Value')}; % selected field
3930enable_slider='off';%default
3931enable_bounds='off';%default
3932enable_scalar='off';%default
3933switch colcode
3934    case {'rgb','bgr'}
3935        enable_slider='on';
3936        enable_bounds='on';
3937        enable_scalar='on';
3938    case '64 colors'
3939        enable_bounds='on';
3940        enable_scalar='on';
3941end
3942set(handles.Slider1,'Visible',enable_slider)
3943set(handles.Slider2,'Visible', enable_slider)
3944set(handles.num_ColCode1,'Visible',enable_slider)
3945set(handles.num_ColCode2,'Visible',enable_slider)
3946set(handles.TitleColCode1,'Visible',enable_slider)
3947set(handles.TitleColCode2,'Visible',enable_slider)
3948set(handles.CheckFixVecColor,'Visible',enable_bounds)
3949set(handles.num_MinVec,'Visible',enable_bounds)
3950set(handles.num_MaxVec,'Visible',enable_bounds)
3951set(handles.ColorScalar,'Visible',enable_scalar)
3952set_vec_col_bar(handles)
3953
3954%------------------------------------------------------------------
3955% --- Executes on selection change in ColorScalar: choice of the color code.
3956function ColorScalar_Callback(hObject, eventdata, handles)
3957%------------------------------------------------------------------
3958% edit the choice for color code
3959list_scalar=get(handles.ColorScalar,'String');% list menu fields
3960col_scalar= list_scalar{get(handles.ColorScalar,'Value')}; % selected field
3961if isequal(col_scalar,'ima_cor')
3962    set(handles.CheckFixVecColor,'Value',1)%fixed scale by default
3963    ColorCode='rgb';
3964    set(handles.num_MinVec,'String','0')
3965    set(handles.num_MaxVec,'String','1')
3966    set(handles.num_ColCode1,'String','0.333')
3967    set(handles.num_ColCode2,'String','0.666')
3968else
3969    set(handles.CheckFixVecColor,'Value',0)%auto scale between min,max by default
3970    ColorCode='64 colors';
3971end
3972ColorCodeList=get(handles.ColorCode,'String');
3973ichoice=find(strcmp(ColorCode,ColorCodeList),1);
3974set(handles.ColorCode,'Value',ichoice)% set color code in the menu
3975
3976update_color_code_boxes(handles);
3977%replot the current graph
3978run0_Callback(hObject, eventdata, handles)
3979
3980%----------------------------------------------------------------
3981% -- Executes on slider movement to set the color code
3982%
3983function Slider1_Callback(hObject, eventdata, handles)
3984%------------------------------------------------------------------
3985slider1=get(handles.Slider1,'Value');
3986min_val=str2num(get(handles.num_MinVec,'String'));
3987max_val=str2num(get(handles.num_MaxVec,'String'));
3988col=min_val+(max_val-min_val)*slider1;
3989set(handles.num_ColCode1,'String',num2str(col))
3990if(get(handles.Slider2,'Value') < col)%move also the second slider at the same value if needed
3991    set(handles.Slider2,'Value',col)
3992    set(handles.num_ColCode2,'String',num2str(col))
3993end
3994set_vec_col_bar(handles)
3995update_plot(handles);
3996
3997%----------------------------------------------------------------
3998% Executes on slider movement to set the color code
3999%----------------------------------------------------------------
4000function Slider2_Callback(hObject, eventdata, handles)
4001slider2=get(handles.Slider2,'Value');
4002min_val=str2num(get(handles.num_MinVec,'String'));
4003max_val=str2num(get(handles.num_MaxVec,'String'));
4004col=min_val+(max_val-min_val)*slider2;
4005set(handles.num_ColCode2,'String',num2str(col))
4006if(get(handles.Slider1,'Value') > col)%move also the first slider at the same value if needed
4007    set(handles.Slider1,'Value',col)
4008    set(handles.num_ColCode1,'String',num2str(col))
4009end
4010set_vec_col_bar(handles)
4011update_plot(handles);
4012
4013%----------------------------------------------------------------
4014% --- Execute on return carriage on the edit box corresponding to slider 1
4015%----------------------------------------------------------------
4016function num_ColCode1_Callback(hObject, eventdata, handles)
4017set_vec_col_bar(handles)
4018update_plot(handles);
4019
4020%----------------------------------------------------------------
4021% --- Execute on return carriage on the edit box corresponding to slider 2
4022%----------------------------------------------------------------
4023function num_ColCode2_Callback(hObject, eventdata, handles)
4024set_vec_col_bar(handles)
4025update_plot(handles);
4026%------------------------------------------------------------------------
4027%-------------------------------------------------------
4028% --- Executes on button press in CheckFixVecColor.
4029%-------------------------------------------------------
4030function VecColBar_Callback(hObject, eventdata, handles)
4031set_vec_col_bar(handles)
4032
4033%------------------------------------------------------------------------
4034% --- Executes on button press in CheckFixVecColor.
4035function CheckFixVecColor_Callback(hObject, eventdata, handles)
4036%------------------------------------------------------------------------
4037if ~get(handles.CheckFixVecColor,'Value')
4038    update_plot(handles);
4039end
4040
4041%------------------------------------------------------------------------
4042% --- Executes on selection change in num_MaxVec.
4043function num_MinVec_Callback(hObject, eventdata, handles)
4044%------------------------------------------------------------------------
4045max_vec_Callback(hObject, eventdata, handles)
4046
4047%------------------------------------------------------------------------
4048% --- Executes on selection change in num_MaxVec.
4049function num_MaxVec_Callback(hObject, eventdata, handles)
4050%------------------------------------------------------------------------
4051set(handles.CheckFixVecColor,'Value',1)
4052CheckFixVecColor_Callback(hObject, eventdata, handles)
4053min_val=str2num(get(handles.num_MinVec,'String'));
4054max_val=str2num(get(handles.num_MaxVec,'String'));
4055slider1=get(handles.Slider1,'Value');
4056slider2=get(handles.Slider2,'Value');
4057colcode1=min_val+(max_val-min_val)*slider1;
4058colcode2=min_val+(max_val-min_val)*slider2;
4059set(handles.num_ColCode1,'String',num2str(colcode1))
4060set(handles.num_ColCode2,'String',num2str(colcode2))
4061update_plot(handles);
4062
4063%------------------------------------------------------------------------
4064% --- update the display of color code for vectors (on vecColBar)
4065function set_vec_col_bar(handles)
4066%------------------------------------------------------------------------
4067%get the image of the color display button 'VecColBar' in pixels
4068set(handles.VecColBar,'Unit','pixel');
4069pos_vert=get(handles.VecColBar,'Position');
4070set(handles.VecColBar,'Unit','Normalized');
4071width=ceil(pos_vert(3));
4072height=ceil(pos_vert(4));
4073
4074%get slider indications
4075list=get(handles.ColorCode,'String');
4076ichoice=get(handles.ColorCode,'Value');
4077colcode.ColorCode=list{ichoice};
4078colcode.MinVec=str2num(get(handles.num_MinVec,'String'));
4079colcode.MaxVec=str2num(get(handles.num_MaxVec,'String'));
4080test3color=strcmp(colcode.ColorCode,'rgb') || strcmp(colcode.ColorCode,'bgr');
4081if test3color
4082    colcode.ColCode1=str2num(get(handles.num_ColCode1,'String'));
4083    colcode.ColCode2=str2num(get(handles.num_ColCode2,'String'));
4084end
4085vec_C=colcode.MinVec+(colcode.MaxVec-colcode.MinVec)*(0.5:width-0.5)/width;%sample of vec_C values from min to max
4086[colorlist,col_vec]=set_col_vec(colcode,vec_C);
4087oneheight=ones(1,height);
4088A1=colorlist(col_vec,1)*oneheight;
4089A2=colorlist(col_vec,2)*oneheight;
4090A3=colorlist(col_vec,3)*oneheight;
4091A(:,:,1)=A1';
4092A(:,:,2)=A2';
4093A(:,:,3)=A3';
4094set(handles.VecColBar,'Cdata',A)
4095
4096%-------------------------------------------------------------------
4097function update_plot(handles)
4098%-------------------------------------------------------------------
4099UvData=get(handles.uvmat,'UserData');
4100AxeData=UvData.PlotAxes;% retrieve the current plotted data
4101PlotParam=read_GUI(handles.uvmat);
4102[tild,PlotParamOut]= plot_field(AxeData,handles.PlotAxes,PlotParam);
4103write_plot_param(handles,PlotParamOut); %update the auto plot parameters
4104
4105%------------------------------------------------------------------------
4106%------------------------------------------------------------------------
4107%   SELECTION AND EDITION OF PROJECTION OBJECTS
4108%------------------------------------------------------------------------
4109%------------------------------------------------------------------------
4110
4111% --- Executes on selection change in ListObject_1.
4112function ListObject_1_Callback(hObject, eventdata, handles)
4113list_str=get(handles.ListObject,'String');
4114UvData=get(handles.uvmat,'UserData');
4115ObjectData=UvData.Object{get(handles.ListObject_1,'Value')};
4116
4117%% update the projection plot on uvmat
4118ProjData= proj_field(UvData.Field,ObjectData);%project the current input field on object ObjectData
4119plot_field(ProjData,handles.PlotAxes,read_GUI(handles.uvmat));% plot the projected field;
4120%replot all the objects within the new projected field
4121for IndexObj=1:numel(list_str)
4122        hobject=UvData.Object{IndexObj}.DisplayHandle.uvmat;
4123        if isempty(hobject) || ~ishandle(hobject)
4124            hobject=handles.PlotAxes;
4125        end
4126        if isequal(IndexObj,get(handles.ListObject,'Value'))
4127            objectcolor='m'; %paint in magenta the currently selected object in ListObject
4128        else
4129            objectcolor='b';
4130        end
4131        UvData.Object{IndexObj}.DisplayHandle.uvmat=plot_object(UvData.Object{IndexObj},ObjectData,hobject,objectcolor);%draw the object in uvmat     
4132end
4133set(handles.uvmat,'UserData',UvData)
4134
4135%% display the object parameters if the GUI set_object is already opened
4136if ~get(handles.ViewObject,'Value')
4137    ZBounds=0; % default
4138    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4139        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4140        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4141    end
4142    ObjectData.Name=list_str{get(handles.ListObject_1,'Value')};
4143    set_object(ObjectData,[],ZBounds);
4144    set(handles.ViewObject,'Value',1)% show that the selected object in ListObject_1 is currently visualised
4145end
4146
4147%  desactivate the edit object mode
4148set(handles.edit_object,'Value',0)
4149set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])
4150
4151%------------------------------------------------------------------------
4152% --- Executes on selection change in ListObject.
4153function ListObject_Callback(hObject, eventdata, handles)
4154%------------------------------------------------------------------------
4155list_str=get(handles.ListObject,'String');
4156IndexObj=get(handles.ListObject,'Value');%present object selection
4157
4158%% The object  is displayed in set_object if this GUI is already opened
4159UvData=get(handles.uvmat,'UserData');
4160ObjectData=UvData.Object{IndexObj};
4161hset_object=findobj(allchild(0),'tag','set_object');
4162if ~isempty(hset_object)
4163    ZBounds=0; % default
4164    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4165        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4166        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4167    end
4168    ObjectData.Name=list_str{IndexObj};
4169    set_object(ObjectData,[],ZBounds);
4170    set(handles.ViewField,'Value',1)% show that the selected object in ListObject is currently visualised
4171end
4172
4173%%  desactivate the edit object mode
4174set(handles.edit_object,'Value',0)
4175set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])
4176
4177%% update the  plot on view_field if view_field is already openened
4178hview_field=findobj(allchild(0),'tag','view_field');
4179if isempty(hview_field)
4180    hhview_field.PlotAxes=[];
4181else
4182    Data=get(hview_field,'UserData');
4183    hhview_field=guidata(hview_field);
4184    ProjData= proj_field(UvData.Field,ObjectData);%project the current interface field on ObjectData
4185    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.PlotAxes,read_GUI(hview_field));%read plotting parameters on the uvmat interfachhview_fiel
4186    write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
4187    haxes=findobj(hview_field,'tag','axes3');
4188    pos=get(hview_field,'Position'); 
4189    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
4190        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
4191        pos_table=get(h_TableDisplay,'Position');
4192        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
4193        drawnow% needed to change position before the next command
4194        set(hview_field,'UserData',Data);% restore the previously stored GUI position after GUI resizing
4195    else
4196        set(hview_field,'Position',Data.GUISize)% return to the previously stored GUI position and size
4197    end
4198end
4199
4200%% update the color of the graphic object representation: the selected object in magenta, others in blue
4201update_object_color(handles.PlotAxes,hhview_field.PlotAxes,UvData.Object{IndexObj}.DisplayHandle.uvmat)
4202
4203%------------------------------------------------------------------------
4204%--- update the color representation of objects (indicating the selected ones)
4205function update_object_color(axes_uvmat,axes_view_field,DisplayHandle)
4206%------------------------------------------------------------------------
4207if isempty(axes_view_field)% case with no view_field plot
4208hother=[findobj(axes_uvmat,'Tag','proj_object');findobj(axes_uvmat,'Tag','DeformPoint')];%find all the proj object and deform point representations
4209else
4210hother=[findobj(axes_uvmat,'Tag','proj_object') ;findobj(axes_view_field,'Tag','proj_object');... %find all the proj object representations
4211findobj(axes_uvmat,'Tag','DeformPoint'); findobj(axes_view_field,'Tag','DeformPoint')];%find all the deform point representations
4212end
4213for iobj=1:length(hother)
4214    if isequal(get(hother(iobj),'Type'),'rectangle')||isequal(get(hother(iobj),'Type'),'patch')
4215        set(hother(iobj),'EdgeColor','b')
4216        if isequal(get(hother(iobj),'FaceColor'),'m')
4217            set(hother(iobj),'FaceColor','b')
4218        end
4219    elseif isequal(get(hother(iobj),'Type'),'image')
4220        Acolor=get(hother(iobj),'CData');
4221        Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2));
4222        set(hother(iobj),'CData',Acolor);
4223    else
4224        set(hother(iobj),'Color','b')
4225    end
4226    set(hother(iobj),'Selected','off')
4227end
4228if ishandle(DisplayHandle)
4229    linetype=get(DisplayHandle,'Type');
4230    if isequal(linetype,'line')
4231        set(DisplayHandle,'Color','m'); %set the selected object to magenta color
4232    elseif isequal(linetype,'rectangle')
4233        set(DisplayHandle,'EdgeColor','m'); %set the selected object to magenta color
4234    elseif isequal(linetype,'patch')
4235        set(DisplayHandle,'FaceColor','m'); %set the selected object to magenta color
4236    end
4237    SubObjectData=get(DisplayHandle,'UserData');
4238    if isfield(SubObjectData,'SubObject') & ishandle(SubObjectData.SubObject)
4239        for iobj=1:length(SubObjectData.SubObject)
4240            hsub=SubObjectData.SubObject(iobj);
4241            if isequal(get(hsub,'Type'),'rectangle')
4242                set(hsub,'EdgeColor','m'); %set the selected object to magenta color
4243            elseif isequal(get(hsub,'Type'),'image')
4244                Acolor=get(hsub,'CData');
4245                Acolor(:,:,1)=Acolor(:,:,3);
4246                set(hsub,'CData',Acolor);
4247            else
4248                set(hsub,'Color','m')
4249            end
4250        end
4251    end
4252    if isfield(SubObjectData,'DeformPoint') & ishandle(SubObjectData.DeformPoint)
4253        set(SubObjectData.DeformPoint,'Color','m')
4254    end
4255end
4256
4257%-------------------------------------------------------------------
4258% --- Executes on selection change in edit_object.
4259function edit_object_Callback(hObject, eventdata, handles)
4260%-------------------------------------------------------------------
4261hset_object=findobj(allchild(0),'Tag','set_object');
4262if get(handles.edit_object,'Value')
4263    set(handles.edit_object,'BackgroundColor',[1,1,0]) 
4264    %suppress the other options
4265    set(handles.CheckZoom,'Value',0)
4266    CheckZoom_Callback(hObject, eventdata, handles)
4267    hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4268    if ishandle(hgeometry_calib)
4269        hhgeometry_calib=guidata(hgeometry_calib);
4270        set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4271        set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4272    end
4273    set(handles.ViewObject,'value',1)
4274    ViewObject_Callback(hObject, eventdata, handles)
4275else % desctivate object edit mode
4276    set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4277    if ~isempty(hset_object)% open the
4278        hhset_object=guidata(hset_object);
4279        set(hhset_object.PLOT,'enable','off');
4280        set(get(hset_object,'children'),'enable','inactive')
4281    end
4282end
4283
4284
4285%------------------------------------------------------------------------
4286% --- Executes on button press in ViewObject.
4287function ViewObject_Callback(hObject, eventdata, handles)
4288%------------------------------------------------------------------------
4289check_view=get(handles.ViewObject,'Value');
4290
4291if check_view %activate set_object   
4292    IndexObj=get(handles.ListObject,'Value');
4293    list_object=get(handles.ListObject,'String');
4294    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4295    UvData.Object{IndexObj}.Name=list_object{IndexObj};
4296    if numel(UvData.Object)<IndexObj;% error in UvData
4297        msgbox_uvmat('ERROR','invalid object list')
4298        return
4299    end
4300    ZBounds=0; % default
4301    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4302        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4303        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4304    end
4305%     set(handles.ListObject_1,'Value',IndexObj);%restore ListObject selection after set_object deletion
4306    data=UvData.Object{IndexObj};
4307    if ~isfield(data,'Type')% default plane
4308        data.Type='plane';
4309    end
4310%     if isfield(UvData,'Field')
4311%         Field=UvData.Field;
4312%         if isfield(UvData.Field,'Mesh')&&~isempty(UvData.Field.Mesh)
4313%             data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
4314%             if strcmp(data.Type,'line')||strcmp(data.Type,'polyline')
4315%                 data.RangeY=UvData.Field.Mesh;
4316%             else
4317%                 data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
4318%             end
4319%             data.DX=UvData.Field.Mesh;
4320%             data.DY=UvData.Field.Mesh;
4321%         end
4322%         if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
4323%             data.Coord=[0 0 0]; %default
4324%         end
4325%         if isfield(Field,'CoordUnit')
4326%             data.CoordUnit=Field.CoordUnit;
4327%         end
4328%     end
4329    hset_object=set_object(data,[],ZBounds);
4330    hhset_object=guidata(hset_object);
4331    if get(handles.edit_object,'Value')% edit mode
4332        set(hhset_object.PLOT,'Enable','on')
4333        set(get(hset_object,'children'),'enable','on')
4334    else
4335        set(hhset_object.PLOT,'Enable','off')
4336        set(get(hset_object,'children'),'enable','inactive')% deactivate the GUI except SAVE
4337        set(hhset_object.SAVE,'Enable','on')
4338    end
4339else
4340    hset_object=findobj(allchild(0),'tag','set_object');
4341    if ~isempty(hset_object)
4342        delete(hset_object)% delete existing version of set_object
4343    end
4344end
4345 
4346
4347%------------------------------------------------------------------------
4348% --- Executes on button press in ViewField.
4349function ViewField_Callback(hObject, eventdata, handles)
4350%------------------------------------------------------------------------
4351check_view=get(handles.ViewField,'Value');
4352
4353if check_view
4354    IndexObj=get(handles.ListObject,'Value');
4355    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4356    if numel(UvData.Object)<IndexObj(end);% error in UvData
4357        msgbox_uvmat('ERROR','invalid object list')
4358        return
4359    end
4360    ZBounds=0; % default
4361    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4362        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4363        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4364    end
4365    set(handles.ListObject,'Value',IndexObj);%restore ListObject selection after set_object deletion
4366    if ~isfield(UvData.Object{IndexObj(1)},'Type')% default plane
4367        UvData.Object{IndexObj(1)}.Type='plane';
4368    end
4369    list_object=get(handles.ListObject,'String');
4370    UvData.Object{IndexObj(end)}.Name=list_object{IndexObj(end)};
4371   
4372    %% show the projection of the selected object on view_field
4373    ProjData= proj_field(UvData.Field,UvData.Object{IndexObj});%project the current field on ObjectData
4374    hview_field=findobj(allchild(0),'tag','view_field');
4375    if isempty(hview_field)
4376        hview_field=view_field;
4377    end
4378    hhview_field=guidata(hview_field);
4379    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.PlotAxes,read_GUI(hview_field));%read plotting parameters on the GUI view_field);
4380    write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
4381    haxes=findobj(hview_field,'tag','axes3');
4382    pos=get(hview_field,'Position');
4383    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
4384        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
4385        pos_table=get(h_TableDisplay,'Position');
4386        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
4387    else
4388        Data=get(hview_field,'UserData');
4389        set(hview_field,'Position',Data.GUISize)% restore the size of view_field for plots
4390    end
4391else
4392    hview_field=findobj(allchild(0),'tag','view_field');
4393    if ~isempty(hview_field)
4394        delete(hview_field)% delete existing version of set_object
4395    end
4396end
4397
4398
4399%------------------------------------------------------------------------
4400% --- Executes on button press in delete_object.
4401function delete_object_Callback(hObject, eventdata, handles)
4402%------------------------------------------------------------------------
4403IndexObj=get(handles.ListObject,'Value');%projection object selected for view_field
4404IndexObj_1=get(handles.ListObject_1,'Value');%projection object selected for uvmat plot
4405if IndexObj>1 && ~isequal(IndexObj,IndexObj_1) % do not delete the object used for the uvmat plot
4406    delete_object(IndexObj)
4407end
4408
4409%------------------------------------------------------------------------
4410%------------------------------------------------------------------------
4411%  II - TOOLS FROM THE UPPER MENU BAR
4412%------------------------------------------------------------------------
4413%------------------------------------------------------------------------
4414
4415%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4416% Export  Menu Callbacks
4417%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4418%------------------------------------------------------------------------
4419% --- Executes on button press in Menu/Export/field in workspace.
4420function MenuExportField_Callback(hObject, eventdata, handles)
4421%------------------------------------------------------------------------
4422global Data_uvmat
4423Data_uvmat=get(handles.uvmat,'UserData');
4424evalin('base','global Data_uvmat')%make CurData global in the workspace
4425display('current field :')
4426evalin('base','Data_uvmat') %display CurData in the workspace
4427commandwindow; %brings the Matlab command window to the front
4428
4429%------------------------------------------------------------------------
4430% --- Executes on button press in Menu/Export/extract figure.
4431function MenuExportFigure_Callback(hObject, eventdata, handles)
4432%------------------------------------------------------------------------
4433% huvmat=get(handles.MenuExport,'parent');
4434hfig=figure;
4435copyobj(handles.PlotAxes,hfig);
4436map=colormap(handles.PlotAxes);
4437colormap(map);%transmit the current colormap to the zoom fig
4438colorbar
4439
4440% --------------------------------------------------------------------
4441function MenuExportAxis_Callback(hObject, eventdata, handles)
4442ListFig=findobj(allchild(0),'Type','figure');
4443nb_option=0;
4444menu={};
4445for ilist=1:numel(ListFig)
4446    FigName=get(ListFig(ilist),'name');
4447    if isempty(FigName)
4448        FigName=['figure ' num2str(ListFig(ilist))];
4449    end
4450    if ~strcmp(FigName,'uvmat')
4451        ListAxes=findobj(ListFig(ilist),'Type','axes');
4452        ListTags=get(ListAxes,'Tag');
4453        if ~isempty(ListTags) && ~isempty(find(~strcmp('Colorbar',ListTags), 1))
4454            ListAxes=ListAxes(~strcmp('Colorbar',ListTags));
4455            if numel(ListAxes)==1
4456                nb_option=nb_option+1;
4457                menu{nb_option}=FigName ;
4458                AxesHandle(nb_option)=ListAxes;
4459            else
4460                nb_axis=0;
4461                for iaxes=1:numel(ListAxes)
4462                    nb_axis=nb_axis+1;
4463                    nb_option=nb_option+1;
4464                    menu{nb_option}=[FigName '_' num2str(nb_axis)];
4465                    AxesHandle(nb_option)=ListAxes(nb_axis);
4466                end
4467            end
4468        end
4469    end
4470end
4471if isempty(menu)
4472    answer=msgbox_uvmat('INPUT_Y-N','no existing plotting axes available, create new figure?');
4473    if strcmp(answer,'Yes')
4474        hfig=figure;
4475        copyobj(handles.PlotAxes,hfig);
4476    else
4477        return
4478    end
4479    map=colormap(handles.PlotAxes);
4480    colormap(map);%transmit the current colormap to the zoom fig
4481    colorbar
4482else
4483    answer=msgbox_uvmat('INPUT_MENU','select a figure/axis on which the current uvmat plot will be exported',menu);
4484    if isempty(answer)
4485        return
4486    else
4487        axes(AxesHandle(answer))
4488        hold on
4489        hchild=get(handles.PlotAxes,'children');
4490        copyobj(hchild,gca);
4491    end
4492end
4493
4494
4495%------------------------------------------------------------------------
4496% --------------------------------------------------------------------
4497function MenuExportMovie_Callback(hObject, eventdata, handles)
4498% --------------------------------------------------------------------
4499set(handles.MenuExportMovie,'BusyAction','queue')% activate the button
4500huvmat=get(handles.run0,'parent');
4501UvData=get(huvmat,'UserData');
4502%[xx,xx,FileBase]=read_file_boxes(handles);
4503[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
4504FileBase=fullfile(RootPath,RootFile);
4505 %read the current input file name
4506prompt = {'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)'};
4507dlg_title = 'select properties of the output avi movie';
4508num_lines= 1;
4509def     = {[FileBase '_out.avi'];'10';'1';'[0.03 0.05 0.95 0.92]';'10'};
4510answer = inputdlg(prompt,dlg_title,num_lines,def,'on');
4511aviname=answer{1};
4512fps=str2double(answer{2});
4513% check for existing file with output name aviname
4514if exist(aviname,'file')
4515    backup=aviname;
4516    testexist=2;
4517    while testexist==2
4518        backup=[backup '~'];
4519        testexist=exist(backup,'file');     
4520    end
4521    [success,message]=copyfile(aviname,backup);%make backup of the existing file
4522    if isequal(success,1)
4523        delete(aviname)%delete existing file
4524    else
4525        msgbox_uvmat('ERROR',message)
4526        return
4527    end
4528end
4529%create avi open
4530aviobj=avifile(aviname,'Compression','None','fps',fps);
4531
4532%display first view for tests
4533newfig=figure;
4534newaxes=copyobj(handles.PlotAxes,newfig);%new plotting axes in the new figure
4535set(newaxes,'Tag','movieaxes')
4536nbpix=[512 384]*str2double(answer{3});
4537set(gcf,'Position',[1 1 nbpix])% resolution XVGA
4538set(newaxes,'Position',eval(answer{4}));
4539map=colormap(handles.PlotAxes);
4540colormap(map);%transmit the current colormap to the zoom fig
4541msgbox_uvmat('INPUT_Y-N',{['adjust figure ' num2str(newfig) ' with its matlab edit menu '] ;...
4542        ['then press OK to get the avi movie as a copy of figure ' num2str(newfig) ' display']});
4543UvData.plotaxes=newaxes;% the axis in the new figure becomes the current main plotting axes
4544set(huvmat,'UserData',UvData);
4545increment=str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d
4546set(handles.STOP,'Visible','on')
4547set(handles.speed,'Visible','on')
4548set(handles.speed_txt,'Visible','on')
4549set(handles.Movie,'BusyAction','queue')
4550
4551%imin=str2double(get(handles.i1,'String'));
4552imax=str2double(answer{5});
4553% if isfield(UvData,'Time')
4554htitle=get(newaxes,'Title');
4555xlim=get(newaxes,'XLim');
4556ylim=get(newaxes,'YLim');
4557set(htitle,'Position',[xlim(2)+0.07*(xlim(2)-xlim(1)) ylim(2)-0.05*(ylim(2)-ylim(1)) 0])
4558time_str=get(handles.abs_time,'String');
4559set(htitle,'String',['t=' time_str])
4560set(handles.speed,'Value',1)
4561for i=1:imax
4562    if get(handles.speed,'Value')~=0 && isequal(get(handles.MenuExportMovie,'BusyAction'),'queue') % enable STOP command
4563            runpm(hObject,eventdata,handles,increment)% run plus
4564            drawnow
4565            time_str=get(handles.abs_time,'String');
4566            if ishandle(htitle)
4567             set(htitle,'String',['t=' time_str])
4568            end
4569            mov=getframe(newfig);
4570            aviobj=addframe(aviobj,mov);
4571    end
4572end
4573aviobj=close(aviobj);
4574UvData=rmfield(UvData,'plotaxes');
4575%UvData.Object{1}.plotaxes=handles.PlotAxes;
4576set(huvmat,'UserData',UvData);
4577msgbox_uvmat('CONFIRMATION',{['movie ' aviname ' created '];['with ' num2str(imax) ' frames']})
4578
4579
4580%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4581% Projection Objects Menu Callbacks
4582%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4583
4584% -----------------------------------------------------------------------
4585function Menupoints_Callback(hObject, eventdata, handles)
4586%------------------------------------------------------------------------
4587data.Type='points';
4588data.ProjMode='projection';%default
4589data.ProjModeMenu={};% do not restrict ProjMode menus
4590create_object(data,handles)
4591
4592% -----------------------------------------------------------------------
4593function Menuline_Callback(hObject, eventdata, handles)
4594%------------------------------------------------------------------------
4595data.Type='line';
4596data.ProjMode='projection';%default
4597data.ProjModeMenu={};% do not restrict ProjMode menus
4598create_object(data,handles)
4599
4600%------------------------------------------------------------------------
4601function Menupolyline_Callback(hObject, eventdata, handles)
4602%------------------------------------------------------------------------
4603data.Type='polyline';
4604data.ProjMode='projection';%default
4605data.ProjModeMenu={};% do not restrict ProjMode menus
4606create_object(data,handles)
4607
4608%------------------------------------------------------------------------
4609function Menupolygon_Callback(hObject, eventdata, handles)
4610%------------------------------------------------------------------------
4611data.Type='polygon';
4612data.ProjMode='inside';%default
4613data.ProjModeMenu={};% do not restrict ProjMode menus
4614create_object(data,handles)
4615
4616%------------------------------------------------------------------------
4617function Menurectangle_Callback(hObject, eventdata, handles)
4618%------------------------------------------------------------------------
4619data.Type='rectangle';
4620data.ProjMode='inside';%default
4621data.ProjModeMenu={};% do not restrict ProjMode menus
4622create_object(data,handles)
4623
4624%------------------------------------------------------------------------
4625function Menuellipse_Callback(hObject, eventdata, handles)
4626%------------------------------------------------------------------------
4627data.Type='ellipse';
4628data.ProjMode='inside';%default
4629data.ProjModeMenu={};% do not restrict ProjMode menus
4630create_object(data,handles)
4631
4632%------------------------------------------------------------------------
4633function MenuMaskObject_Callback(hObject, eventdata, handles)
4634%------------------------------------------------------------------------
4635data.Type='polygon';
4636data.TypeMenu={'polygon'};
4637data.ProjMode='mask_inside';%default
4638data.ProjModeMenu={'mask_inside';'mask_outside'};
4639create_object(data,handles)
4640
4641%------------------------------------------------------------------------
4642function Menuplane_Callback(hObject, eventdata, handles)
4643%------------------------------------------------------------------------
4644data.Type='plane';
4645data.ProjMode='projection';%default
4646data.ProjModeMenu={};% do not restrict ProjMode menus
4647create_object(data,handles)
4648
4649%------------------------------------------------------------------------
4650function Menuvolume_Callback(hObject, eventdata, handles)
4651%------------------------------------------------------------------------
4652data.Type='volume';
4653data.ProjMode='interp_lin';%default
4654data.ProjModeMenu={};
4655% set(handles.create,'Visible','on')
4656% set(handles.create,'Value',1)
4657% VOLUME_Callback(hObject,eventdata,handles)data.ProjModeMenu={};
4658create_object(data,handles)
4659
4660%------------------------------------------------------------------------
4661% --- generic function used for the creation of a projection object
4662function create_object(data,handles)
4663%------------------------------------------------------------------------
4664% desactivate geometric calibration if opened
4665hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4666if ishandle(hgeometry_calib)
4667    hhgeometry_calib=guidata(hgeometry_calib);
4668    set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4669    set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4670end
4671set(handles.edit_object,'Value',0); %suppress the object edit mode
4672set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4673ListObject=get(handles.ListObject,'String');
4674if isempty(ListObject)
4675    ListObject={''};
4676end
4677if ~strcmp(ListObject{end},'')
4678    ListObject=[ListObject;{''}]; %append a blank to the list (if nort already done) to indicate the creation of a new object
4679    set(handles.ListObject,'String',ListObject)
4680end
4681IndexObj=length(ListObject);
4682set(handles.ListObject,'Value',IndexObj)
4683UvData=get(handles.uvmat,'UserData');
4684UvData.Object{IndexObj}=[]; %create a new empty object
4685UvData.Object{IndexObj}.DisplayHandle.uvmat=handles.PlotAxes; % axes for plot_object
4686UvData.Object{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation
4687data.Name=data.Type;% default name=type
4688data.Coord=[0 0]; %default
4689if isfield(UvData,'Field')
4690    Field=UvData.Field;
4691    if isfield(UvData.Field,'CoordMesh')&&~isempty(UvData.Field.CoordMesh)
4692        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
4693        if strcmp(data.Type,'line')||strcmp(data.Type,'polyline')||strcmp(data.Type,'points')
4694            data.RangeY=UvData.Field.CoordMesh;
4695        else
4696            data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
4697        end
4698        data.DX=UvData.Field.CoordMesh;
4699        data.DY=UvData.Field.CoordMesh;
4700    end
4701    if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
4702         data.Coord=[0 0 0]; %default
4703    end
4704    if isfield(Field,'CoordUnit')
4705        data.CoordUnit=Field.CoordUnit;
4706    end
4707end
4708if ishandle(handles.UVMAT_title)
4709    delete(handles.UVMAT_title)%delete the initial display of uvmat if no field has been entered
4710end
4711hset_object=set_object(data,handles);% call the set_object interface
4712hhset_object=guidata(hset_object);
4713hchild=get(hset_object,'children');
4714set(hchild,'enable','on')
4715set(handles.uvmat,'UserData',UvData)
4716set(handles.CheckZoom,'Value',0) %desactivate the zoom for object creation by the mouse
4717CheckZoom_Callback(handles.uvmat, [], handles)
4718set(handles.delete_object,'Visible','on')
4719
4720%------------------------------------------------------------------------
4721function MenuBrowseObject_Callback(hObject, eventdata, handles)
4722%------------------------------------------------------------------------
4723%get the object file
4724[FileName, PathName, filterindex] = uigetfile( ...
4725       {'*.xml;*.mat', ' (*.xml,*.mat)';
4726       '*.xml',  '.xml files '; ...
4727        '*.mat',  '.mat matlab files '}, ...
4728        'Pick an xml Object file',get(handles.RootPath,'String'));
4729fileinput=[PathName FileName];%complete file name
4730sizf=size(fileinput);
4731if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
4732
4733%read the file
4734[data,heading]=xml2struct(fileinput);
4735if ~strcmp(heading,'ProjObject')
4736    msgbox_uvmat('WARNING','The xml file does not have the heading ProjObject for projection objects')
4737end
4738[tild,data.Name]=fileparts(FileName);% object name set as file name
4739ListObject=get(handles.ListObject,'String');
4740if ~strcmp(ListObject{end},'')
4741    ListObject=[ListObject;{''}]; %append a blank to the list (if not already done) to indicate the creation of a new object
4742    set(handles.ListObject,'String',ListObject)
4743end
4744IndexObj=length(ListObject);
4745
4746UvData=get(handles.uvmat,'UserData');
4747UvData.Object{IndexObj}=[]; %create a new empty object
4748UvData.Object{IndexObj}.DisplayHandle.uvmat=[]; %no plot handle before plot_field operation
4749UvData.Object{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation
4750set(handles.uvmat,'UserData',UvData)
4751set(handles.ListObject,'Value',IndexObj)
4752hset_object=set_object(data);% call the set_object interface
4753set(get(hset_object,'children'),'enable','on')% enable edit action on elements on GUI set_object
4754set(handles.edit_object,'Value',0); %suppress the object edit mode
4755set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4756set(handles.delete_object,'Visible','on')
4757
4758
4759%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4760% MenuEdit Callbacks
4761%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4762%------------------------------------------------------------------------
4763function MenuEditObject_Callback(hObject, eventdata, handles)
4764%------------------------------------------------------------------------
4765set(handles.edit_object,'Value',1)
4766edit_Callback(hObject, eventdata, handles)
4767
4768%------------------------------------------------------------------------
4769function MenuEditVectors_Callback(hObject, eventdata, handles)
4770%------------------------------------------------------------------------
4771set(handles.edit_vect,'Visible','on')
4772set(handles.edit_vect,'Value',1)
4773edit_vect_Callback(hObject, eventdata, handles)
4774
4775%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4776% MenuTools Callbacks
4777%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4778%------------------------------------------------------------------------
4779function MenuCalib_Callback(hObject, eventdata, handles)
4780%------------------------------------------------------------------------
4781
4782UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4783
4784%suppress competing options
4785set(handles.CheckZoom,'Value',0)
4786set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
4787set(handles.ListObject,'Value',1)     
4788% initiate display of GUI geometry_calib
4789data=[]; %default
4790if isfield(UvData,'CoordType')
4791    data.CoordType=UvData.CoordType;
4792end
4793[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
4794FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
4795set(handles.view_xml,'Backgroundcolor',[1 1 0])%indicate the reading of the current xml file by geometry_calib
4796pos_uvmat=get(handles.uvmat,'Position');
4797pos_cal(1)=pos_uvmat(1)+UvData.OpenParam.PosGeometryCalib(1)*pos_uvmat(3);
4798pos_cal(2)=pos_uvmat(2)+UvData.OpenParam.PosGeometryCalib(2)*pos_uvmat(4);
4799pos_cal(3:4)=UvData.OpenParam.PosGeometryCalib(3:4).* pos_uvmat(3:4);
4800geometry_calib(FileName,pos_cal);% call the geometry_calib interface   
4801set(handles.view_xml,'Backgroundcolor',[1 1 1])%indicate the end of reading of the current xml file by geometry_calib
4802set(handles.MenuCalib,'checked','on')% indicate that MenuCalib is activated, test used by mouse action
4803
4804
4805%-----------------------------------------------------------------------
4806function MenuLIFCalib_Callback(hObject, eventdata, handles)
4807%------------------------------------------------------------------------
4808%% read UvData properties stored on the uvmat interface
4809UvData=get(handles.uvmat,'UserData');
4810if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
4811    XmlData=UvData.XmlData{1};
4812else
4813    msgbox_uvmat('ERROR','geometric calibration needed: use Tools/geometric calibration in the menu bar');
4814    return
4815end
4816
4817%% read lines currently drawn
4818ListObj=UvData.Object;
4819select=zeros(1,numel(ListObj));
4820for iobj=1:numel(ListObj);
4821    if isfield(ListObj{iobj},'Type') && strcmp(ListObj{iobj}.Type,'line')
4822        select(iobj)=1;
4823    end
4824end
4825val=find(select);
4826if numel(val)<2
4827    msgbox_uvmat('ERROR','light rays must be defined by at least two lines created by Projection object/line in the menu bar');
4828    return
4829else
4830    set(handles.ListObject,'Value',val);% show the selected lines on the list
4831    ObjectData=UvData.Object(val);
4832    for iobj=1:length(ObjectData)
4833%         if isfield(ObjectData{iobj},'Coord')
4834            xA(iobj)=ObjectData{iobj}.Coord(1,1);
4835            yA(iobj)=ObjectData{iobj}.Coord(1,2);
4836            xB(iobj)=ObjectData{iobj}.Coord(2,1);
4837            yB(iobj)=ObjectData{iobj}.Coord(2,2);
4838%         end
4839    end
4840end
4841
4842%% find the origin as intersection of the two first lines (see http://www.ahristov.com/tutorial/geometry-games/intersection-lines.html )
4843x1=xA(1);x2=xB(1);
4844x3=xA(2);x4=xB(2);
4845y1=yA(1);y2=yB(1);
4846y3=yA(2);y4=yB(2);
4847D = (x1-x2)*(y3-y4) -(y1-y2)*(x3-x4);
4848if D==0
4849    msgbox_uvmat('ERROR','the two lines are parallel');
4850    return
4851end
4852x0=((x3-x4)*(x1*y2-y1*x2)-(x1-x2)*(x3*y4-y3*x4))/D;
4853y0=((y3-y4)*(x1*y2-y1*x2)-(y1-y2)*(x3*y4-y3*x4))/D;
4854XmlData.Illumination.Origin=[x0 y0];
4855XmlData.PolarCentre=[x0 y0];
4856
4857%% display the current image in polar coordinates with origin at the  illumination source
4858currentdir=pwd; 
4859uvmatpath=fileparts(which('uvmat'));
4860cd(fullfile(uvmatpath,'transform_field'));
4861phys_polar=str2func('phys_polar');
4862cd(currentdir)
4863DataOut=phys_polar(UvData.Field,XmlData);
4864view_field(DataOut);
4865
4866%% use the third line for reference luminosity
4867if numel(val)==3
4868    x_ref=linspace(ObjectData{3}.Coord(1,1),ObjectData{3}.Coord(2,1),10);
4869    y_ref=linspace(ObjectData{3}.Coord(1,2),ObjectData{3}.Coord(2,2),10);
4870    x_ref=x_ref-x0;
4871    y_ref=y_ref-y0;
4872    [theta_ref,r_ref] = cart2pol(x_ref,y_ref);%theta_ref  and r_ref are the polar coordinates of the points on the line
4873    theta_ref=theta_ref*180/pi;
4874    figure
4875    plot(theta_ref,r_ref)
4876    azimuth_ima=linspace(DataOut.AY(1),DataOut.AY(2),size(DataOut.A,1));%profile of x index on the transformed image
4877    dist_source = interp1(theta_ref,r_ref,azimuth_ima);
4878    dist_source_pixel=round(size(DataOut.A,2)*(dist_source-DataOut.AX(1))/(DataOut.AX(2)-DataOut.AX(1)));
4879    line_nan= isnan(dist_source_pixel);
4880    dist_source_pixel(line_nan)=1;
4881    width=20; %number of pixels used for reference
4882    DataOut.A=double(DataOut.A);
4883    Anorm=zeros(size(DataOut.A));
4884    Aval=mean(mean(DataOut.A));
4885    for iline=1:size(DataOut.A,1)
4886        lum(iline)=mean(DataOut.A(iline,dist_source_pixel(iline):dist_source_pixel(iline)+width));
4887        Anorm(iline,:)=uint16(Aval*DataOut.A(iline,:)/lum(iline));
4888    end
4889    lum(line_nan)=NaN;
4890    figure
4891    plot(1:size(DataOut.A,1),lum)
4892end
4893ImaName=regexprep([get(handles.RootFile,'String') get(handles.FileIndex,'String')],'//','');
4894NewImageName=fullfile(get(handles.RootPath,'String'),'polar',[ImaName get(handles.FileExt,'String')]);
4895imwrite(Anorm,NewImageName,'BitDepth',16)
4896
4897%% record the origin in the xml file
4898XmlFileName=find_imadoc(get(handles.RootPath,'String'),get(handles.SubDir,'String'),get(handles.RootFile,'String'),get(handles.FileExt,'String'));
4899answer=msgbox_uvmat('INPUT_Y-N','save the illumination origin in the current xml file?');
4900if strcmp(answer,'Yes')
4901    t=xmltree(XmlFileName); %read the file
4902    title=get(t,1,'name');
4903    if ~strcmp(title,'ImaDoc')
4904        msgbox_uvmat('ERROR','wrong xml file');
4905        return
4906    end
4907    % backup the output file if it already exist, and read it
4908    backupfile=XmlFileName;
4909    testexist=2;
4910    while testexist==2
4911        backupfile=[backupfile '~'];
4912        testexist=exist(backupfile,'file');
4913    end
4914    [success,message]=copyfile(XmlFileName,backupfile);%make backup
4915    if success~=1
4916        errormsg=['errror in xml file backup: ' message];
4917        return
4918    end
4919    uid_illumination=find(t,'ImaDoc/Illumination');
4920    if isempty(uid_illumination)  %if GeometryCalib does not already exists, create it
4921        [t,uid_illumination]=add(t,1,'element','Illumination');
4922    end
4923    uid_origin=find(t,'ImaDoc/Illumination/Origin');
4924    if ~isempty(uid_origin)  %if GeometryCalib does not already exists, create it
4925         t=delete(t,uid_origin);
4926    end
4927    % save the illumination origin
4928    t=struct2xml(XmlData.Illumination,t,uid_illumination);
4929    save(t,XmlFileName);
4930end
4931   
4932
4933
4934%------------------------------------------------------------------------
4935function MenuMask_Callback(hObject, eventdata, handles)
4936%------------------------------------------------------------------------
4937UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4938ListObj=UvData.Object;
4939select=zeros(1,numel(ListObj));
4940for iobj=1:numel(ListObj);
4941    if strcmp(ListObj{iobj}.ProjMode,'mask_inside')||strcmp(ListObj{iobj}.ProjMode,'mask_outside')
4942        select(iobj)=1;
4943    end
4944end
4945val=find(select);
4946if isempty(val)
4947    msgbox_uvmat('ERROR','polygons must be first created by Projection object/mask polygon in the menu bar');
4948    return
4949else
4950    set(handles.ListObject,'Value',val);
4951    flag=1;
4952    npx=size(UvData.Field.A,2);
4953    npy=size(UvData.Field.A,1);
4954    xi=0.5:npx-0.5;
4955    yi=0.5:npy-0.5;
4956    [Xi,Yi]=meshgrid(xi,yi);
4957%     if isfield(UvData,'Object')
4958        for iobj=1:length(UvData.Object)
4959            ObjectData=UvData.Object{iobj};
4960            if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
4961                flagobj=1;
4962                testphys=0; %coordinates in pixels by default
4963                if isfield(ObjectData,'CoordUnit') && ~isequal(ObjectData.CoordUnit,'pixel')
4964                    if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
4965                        Calib=UvData.XmlData{1}.GeometryCalib;
4966                        testphys=1;
4967                    end
4968                end
4969                if isfield(ObjectData,'Coord')&& isfield(ObjectData,'Type')
4970                    if isequal(ObjectData.Type,'polygon')
4971                        X=ObjectData.Coord(:,1);
4972                        Y=ObjectData.Coord(:,2);
4973                        if testphys
4974                            pos=[X Y zeros(size(X))];
4975                            if isfield(Calib,'SliceCoord') && length(Calib.SliceCoord)>=3
4976                                if isfield(Calib,'SliceAngle')&&~isequal(Calib.SliceAngle,[0 0 0])
4977                                    om=norm(Calib.SliceAngle);%norm of rotation angle in radians
4978                                    OmAxis=Calib.SliceAngle/om; %unit vector marking the rotation axis
4979                                    cos_om=cos(pi*om/180);
4980                                    sin_om=sin(pi*om/180);
4981                                    pos=cos_om*pos+sin_om*cross(OmAxis,pos)+(1-cos_om)*(OmAxis*pos')*OmAxis;
4982                                end
4983                                pos(:,1)=pos(:,1)+Calib.SliceCoord(1);
4984                                pos(:,2)=pos(:,2)+Calib.SliceCoord(2);
4985                                pos(:,3)=pos(:,3)+Calib.SliceCoord(3);
4986                            end                           
4987                            [X,Y]=px_XYZ(Calib,pos(:,1),pos(:,2),pos(:,3));
4988                        end
4989                        flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside
4990                    elseif isequal(ObjectData.Type,'ellipse')
4991                        if testphys
4992                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4993                        end
4994                        RangeX=max(ObjectData.RangeX);
4995                        RangeY=max(ObjectData.RangeY);
4996                        X2Max=RangeX*RangeX;
4997                        Y2Max=RangeY*RangeY;
4998                        distX=(Xi-ObjectData.Coord(1,1));
4999                        distY=(Yi-ObjectData.Coord(1,2));
5000                        flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
5001                    elseif isequal(ObjectData.Type,'rectangle')
5002                        if testphys
5003                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
5004                        end
5005                        distX=abs(Xi-ObjectData.Coord(1,1));
5006                        distY=abs(Yi-ObjectData.Coord(1,2));
5007                        flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
5008                    end
5009                    if isequal(ObjectData.ProjMode,'mask_outside')
5010                        flagobj=~flagobj;
5011                    end
5012                    flag=flag & flagobj;
5013                end
5014            end
5015        end
5016%     end
5017    %mask name
5018    RootPath=get(handles.RootPath,'String');
5019    SubDir=get(handles.SubDir,'String');
5020    RootFile=get(handles.RootFile,'String');
5021    if ~isempty(RootFile)&&(isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
5022        RootFile(1)=[];
5023    end
5024    list=get(handles.masklevel,'String');
5025    masknumber=num2str(length(list));
5026    maskindex=get(handles.masklevel,'Value');
5027   % mask_name=fullfile_uvmat(RootPath,'',[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
5028    mask_name=fullfile_uvmat(RootPath,[SubDir '.mask'],'mask','.png','_1',maskindex);
5029    imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
5030    imflag=flipdim(imflag,1);
5031
5032    %display the mask
5033    hfigmask=figure;
5034    set(hfigmask,'Name','mask image')
5035    vec=linspace(0,1,256);%define a linear greyscale colormap
5036    map=[vec' vec' vec'];
5037    colormap(map)
5038    image(imflag);
5039    answer=msgbox_uvmat('INPUT_TXT','mask file name:', mask_name);
5040    if ~strcmp(answer,'Cancel')
5041        mask_dir=fileparts(answer);
5042        if ~exist(mask_dir,'dir')
5043            [xx,msg1]=mkdir(mask_dir);
5044            if ~strcmp(msg1,'')
5045                errormsg=['cannot create ' mask_dir ': ' msg1];%error message for directory creation
5046                return
5047            end
5048        end
5049        imwrite(imflag,answer,'BitDepth',8);
5050    end
5051    set(handles.ListObject,'Value',1)
5052end
5053
5054%------------------------------------------------------------------------
5055%-- open the GUI set_grid.fig to create grid
5056function MenuGrid_Callback(hObject, eventdata, handles)
5057%------------------------------------------------------------------------
5058%suppress the other options if grid is chosen
5059set(handles.edit_vect,'Value',0)
5060edit_vect_Callback(hObject, eventdata, handles)
5061set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
5062set(handles.ListObject,'Value',1)     
5063
5064%prepare display of the set_grid GUI
5065[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
5066FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
5067UvData=get(handles.uvmat,'UserData');
5068% CoordList=get(handles.transform_fct,'String');
5069% val=get(handles.transform_fct,'Value');
5070set_grid(FileName,UvData.Field);% call the set_object interface
5071
5072
5073%------------------------------------------------------------------------
5074function MenuRuler_Callback(hObject, eventdata, handles)
5075%------------------------------------------------------------------------
5076set(handles.CheckZoom,'Value',0)
5077CheckZoom_Callback(handles.uvmat, [], handles)
5078set(handles.MenuRuler,'checked','on')
5079UvData=get(handles.uvmat,'UserData');
5080UvData.MouseAction='ruler';
5081set(handles.uvmat,'UserData',UvData);
5082
5083%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
5084% MenuRun Callbacks
5085%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
5086
5087%------------------------------------------------------------------------
5088% open the GUI 'series'
5089function MenuSeries_Callback(hObject, eventdata, handles)
5090%------------------------------------------------------------------------
5091series; %first display of the GUI to fill waiting time
5092[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
5093Param.FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];%first input file name
5094if isequal(get(handles.SubField,'Value'),1)
5095    [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
5096    FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
5097    if ~isequal(FileName_1,Param.FileName)
5098        Param.FileName_1=FileName_1;%second input file name if relevant
5099    end
5100end
5101Param.NomType=get(handles.NomType,'String');
5102Param.NomType_1=get(handles.NomType_1,'String');
5103Param.CheckFixPair=get(handles.CheckFixPair,'Value');
5104UvData=get(handles.uvmat,'UserData');
5105if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'Time')
5106    Param.Time=UvData.XmlData{1}.Time;
5107end
5108if isequal(get(handles.scan_i,'Value'),1)
5109    Param.incr_i=str2num(get(handles.num_IndexIncrement,'String'));
5110elseif isequal(get(handles.scan_j,'Value'),1)
5111    Param.incr_j=str2num(get(handles.num_IndexIncrement,'String'));
5112end
5113
5114%% transfer fields and coordinate names
5115Param.list_fields=get(handles.FieldName,'String');% list menu fields
5116FieldName=Param.list_fields{get(handles.FieldName,'Value')};
5117ind_image=find(strcmp('image',Param.list_fields));
5118if ~isempty(ind_image) && numel(Param.list_fields)>1
5119    Param.list_fields(ind_image)=[]; %suppress  'image' option
5120end
5121Param.index_fields=find(strcmp(FieldName,Param.list_fields));% selected string index
5122Param.list_fields_1=get(handles.FieldName_1,'String');% list menu fields
5123if ischar(Param.list_fields_1),Param.list_fields_1={Param.list_fields_1};end
5124FieldName_1=Param.list_fields_1{get(handles.FieldName_1,'Value')};
5125ind_image=find(strcmp('image',Param.list_fields_1));
5126if ~isempty(ind_image) && numel(Param.list_fields_1)>1
5127    Param.list_fields_1(ind_image)=[]; %suppress  'image' option
5128end
5129Param.index_fields_1=find(strcmp(FieldName_1,Param.list_fields_1));% selected string index
5130Param.transform_str=get(handles.transform_fct,'String');
5131Param.transform_val=get(handles.transform_fct,'Value');
5132Param.Coord_x_str=get(handles.Coord_x,'String');
5133Param.Coord_x_val=get(handles.Coord_x,'Value');
5134Param.Coord_y_str=get(handles.Coord_y,'String');
5135Param.Coord_y_val=get(handles.Coord_y,'Value');
5136series(Param); %run the series interface
5137
5138%------------------------------------------------------------------------
5139% -- open the GUI civ.fig for PIV
5140function MenuPIV_Callback(hObject, eventdata, handles)
5141%------------------------------------------------------------------------
5142 [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
5143 FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
5144civ(FileName);% interface de civ(not in the uvmat file)
5145
5146% --------------------------------------------------------------------
5147function MenuHelp_Callback(hObject, eventdata, handles)
5148% --------------------------------------------------------------------
5149path_to_uvmat=which ('uvmat');% check the path of uvmat
5150pathelp=fileparts(path_to_uvmat);
5151helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
5152if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
5153else
5154    addpath (fullfile(pathelp,'uvmat_doc'))
5155    web(helpfile);
5156end
5157
5158% --- Executes on selection change in Coord_y.
5159function Coord_y_Callback(hObject, eventdata, handles)
5160
5161% --- Executes on selection change in Coord_x.
5162function Coord_x_Callback(hObject, eventdata, handles)
5163
5164
5165% --- Executes on button press in CheckColorBar.
5166function CheckColorBar_Callback(hObject, eventdata, handles)
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