source: trunk/src/uvmat.m @ 635

Last change on this file since 635 was 635, checked in by sommeria, 8 years ago
File size: 229.5 KB
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1%'uvmat': function associated with the GUI 'uvmat.fig' for images and data field visualization
2%------------------------------------------------------------------------
3% function huvmat=uvmat(input)
4%
5%OUTPUT
6% huvmat=current handles of the GUI uvmat.fig
7%%
8%
9%INPUT:
10% input: input file name (if character chain), or input image matrix to
11% visualize, or Matlab structure representing  netcdf fieldname (with fieldname
12% ListVarName....)
13%
14%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
15%  Copyright Joel Sommeria,  2008, LEGI / CNRS-UJF-INPG, joel.sommeria@legi.grenoble-inp.fr.
16%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17%     This open is part of the toolbox UVMAT.
18%
19%     UVMAT is free software; you can redistribute it and/or modify
20%     it under the terms of the GNU General Public License as published by
21%     the Free Software Foundation; either version 2 of the License, or
22%     (at your option) any later version.
23%
24%     UVMAT is distributed in the hope that it will be useful,
25%     but WITHOUT ANY WARRANTY; without even the implied warranty of
26%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
27%     GNU General Public License (open UVMAT/COPYING.txt) for more details.
28%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
29%
30% Information stored on the interface:(use 'Export/field in workspace' in
31% the menu bar of uvmat to retrieve it)
32%          .OpenParam: structure containing parameters defined when uvmat is opened
33%                       .PosColorbar: position (1x4 vector)of the colorbar (relative to the fig uvmat)
34%                       .PosGeometryCalib: size of set_object
35%                       .NbBuiltin: nbre of functions always displayed in TransformName menu
36%          .ProjObject: cell array of structures representing the current projection objects, as produced by 'set_object.m'={[]} by default
37%          .NewSeries: =0/1 flag telling whether a new field series has been opened
38%          .FileName_1: name of the current second field (used to detect a  constant field during file scanning)
39%          .FileType: current file type, as defined by the fct  get_file_type.m)
40%          .i1_series,.i2_series,.j1_series,.j1_series: series of i1,i2,j1,j2 indices detected in the input dir,set by  the fct find_file_series
41%          .MovieObject: current movie object
42%          .TimeUnit: unit for time
43%          .XmlData: cell array of 1 or 2 structures representing the xml files associated with the input fieldname (containing timing  and geometry calibration)
44%          .Field: cell array of 1 or 2 structures representing the current  input field(s)
45%          .PlotAxes: field structure representing the current field plotted  on the main axes  (used for mouse operations)
46%          .HistoAxes: idem for histogram axes
47
48% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%   DATA FLOW  (for run0_Callback) %%%%%%%%%%%%%%%%%%%%:
49%
50%
51% 1) Input filenames are determined by MenuBrowse (first field), MenuBrowse_1
52% (second field), or by the stored file name .FileName_1, or as an input of uvmat.
53% 2) These functions call 'uvmat/display_file_name.m' which detects the file series, and fills the file index boxes
54% 3) Then 'uvmat/update_rootinfo.m' Updates information about a new field series (indices to scan, timing, calibration from an xml file)
55% 4) Then fieldname are opened and visualised by the main sub-function 'uvmat/refresh_field.m'
56% The function first reads the name of the input file(s) (one or two) from the edit boxes  of the GUI
57% It then reads the input file(s) with the function read_field.m and perform the following list of operations:
58%
59%    %%%%%%%%  structure of uvmat/refresh_field.m %%%%%%%%
60%
61%           Main input open       second input open_1       
62%                    |                   | 
63%             read_field.m            read_field.m
64%                    |                   |
65%                 Field{1}            Field{2}               
66%                    |                   |                                 
67%                    --->transform fct<---             transform (e.g. phys.m) and combine input fieldname 
68%                            |                                   
69%                        (tps_coeff_field.m)               calculate tps coefficients (for filter projection or spatial derivatives).
70%                            |
71%                       UvData.Field-------------->histogram
72%               _____________|____________
73%              |                          |                   
74%        proj_field.m               proj_field.m       project the field on the projection objects (use set_field_list.m)           
75%              |                          |
76%         UvData.PlotAxes          ViewData.PlotAxes (on view_field)
77%              |                          |
78%       plot_field.m (uvmat)       plot_field.m (view_field)      plot the projected fieldname
79%
80%
81%%%%%%%%%%%%%%    SCALARS: %%%%%%%%%%%%??%%%
82% scalars are displayed either as an image or countour plot, either as a color of
83% velocity vectors. The scalar values in the first case is represented by
84% UvData.Field.A, and by UvData.Field.C in the second case. The corresponding set of X
85% and Y coordinates are represented by UvData.Field.AX and UvData.Field.AY, and .X and
86% .Y for C (the same as velocity vectors). If A is a nxxny matrix (scalar
87% on a regtular grid), then .AX andf.AY contains only two elements, represneting the
88% coordinates of the four image corners. The scalar name is represented by
89% the strings .AName and/or .CName.
90% If the scalar exists in an input open (image or scalar stored under its
91% name in a netcdf open), it is directly read at the level of Field{1}or Field{2}.
92% Else only its name AName is recorded in Field{i}, and its field is then calculated
93%by the fuction calc_scal after the coordinate transform or after projection on an edit_object
94     
95% Properties attached to plotting figures (standard Matlab properties):
96%    'CurrentAxes'= gca or get(gcf,'CurrentAxes');
97%    'CurrentPoint'=get(gcf,'CurrentPoint'): figure coordinates of the point over which the mouse is positioned
98%    'CurrentCharacter'=get(gcf,'CurrentCharacter'): last character typed  over the figure where the mouse is positioned
99%    'WindowButtonMotionFcn': function permanently called by mouse motion over the figure
100%    'KeyPressFcn': function called by pressing a key on the key board
101%    'WindowButtonDownFcn':  function called by pressing the mouse over the  figure
102%    'WindowButtonUpFcn': function called by releasing  the mouse pressure over the  figure
103
104% Properties attached to plotting axes:
105%    'CurrentPoint'=get(gca,'CurrentPoint'); (standard Matlab) same as for the figure, but position in plot coordinates.
106%     AxeData:=get(gca,'UserData');
107%     AxeData.Drawing  = create: create a new object
108%                       = deform: modify an existing object by moving its defining create
109%                      = off: no current drawing action
110%                     = translate: translate an existing object
111%                    = calibration: move a calibration point
112%                    = CheckZoom: isolate a subregion for CheckZoom in=1 if an object is being currently drawn, 0 else (set to 0 by releasing mouse button)
113%            .CurrentOrigin: Origin of a curently drawn edit_object
114%            .CurrentLine: currently drawn menuline (A REVOIR)
115%            .CurrentObject: handle of the currently drawn edit_object
116%            .CurrentRectZoom: current rectangle used for CheckZoom
117
118% Properties attached to projection objects (create, menuline, menuplane...):
119%    'Tag'='proj_object': for all projection objects
120%    ObjectData.Type=...: style of projection object:
121%              .ProjMode
122%              .Coord: defines the position of the object
123%              .XMin,YMin....
124%              .XMax,YMax....
125%              .DX,DY,DZ
126%              .Phi, .Theta, .Psi : Euler angles
127%              .X,.Y,.U,.V.... : field data projected on the object
128%              .IndexObj: index in the list of UvData.ProjObject
129           %during plotting
130%               .plotaxes: handles of the current axes used to plot the  result of field projection on the object
131%               .plothandle: vector of handle(s) of the object graphic represnetation in all the opened plotting axes
132% To each projection object #iobj, corresponds an axis
133% Object{iobj}.plotaxes and nbobj representation graphs  Object{iobj}.plothandles(:) (where nbobj is the
134% nbre of current objects opened in uvmat. Note that Object{iobj}.plothandles(iobj)=[] : an object is not represented in its own projection field;
135
136%------------------------------------------------------------------------
137%------------------------------------------------------------------------
138%  I - MAIN FUNCTION uvmat
139%------------------------------------------------------------------------
140%------------------------------------------------------------------------
141function varargout = uvmat(varargin)
142
143% Begin initialization code - DO NOT EDIT
144gui_Singleton = 1;
145gui_State = struct('gui_Name',          mfilename, ...
146                   'gui_Singleton',     gui_Singleton, ...
147                   'gui_OpeningFcn',    @uvmat_OpeningFcn, ...
148                   'gui_OutputFcn',     @uvmat_OutputFcn, ...
149                   'gui_LayoutFcn',     [], ...
150                   'gui_Callback',      []);
151if nargin && ischar(varargin{1})&& ~isempty(regexp(varargin{1},'_Callback','once'))
152    gui_State.gui_Callback = str2func(varargin{1});
153end
154
155if nargout
156    varargout{1:nargout} = gui_mainfcn(gui_State, varargin{:});
157else
158    gui_mainfcn(gui_State, varargin{:});
159end
160% End initialization code - DO NOT EDIT
161
162%------------------------------------------------------------------------
163% --- Executes just before the GUI uvmat is made visible.
164function uvmat_OpeningFcn(hObject, eventdata, handles, input )
165%------------------------------------------------------------------------
166
167%% Choose default command menuline output for uvmat (standard GUI)
168handles.output = hObject;
169
170%% Update handles structure (standard GUI)
171guidata(hObject, handles);
172
173%% add the path to uvmat (useful if uvmat has been opened in the working directory and a working directory change occured)
174path_uvmat=fileparts(which('uvmat'));
175
176%% set the position of the GUI, colorbar and ancillary GUIs:
177set(hObject,'Units','pixels')%
178set(0,'Units','pixels');
179ScreenSize=get(0,'ScreenSize');%size of the current screen
180Width=1050;
181Height=700;
182%adjust to screen size (reduced by a min margin)
183RescaleFactor=min((ScreenSize(3)-80)/Width,(ScreenSize(4)-80)/Height);
184if RescaleFactor>1
185    RescaleFactor=RescaleFactor/2+1/2; %reduce the rescale factor to provide an increased margin for a big screen
186end
187Width=Width*RescaleFactor;
188Height=Height*RescaleFactor;
189LeftX=80*RescaleFactor;%position of the left fig side, in pixels (put to the left side, with some margin)
190LowY=round(ScreenSize(4)/2-Height/2); % put at the middle height on the screen
191set(hObject,'Position',[LeftX LowY Width Height])
192
193%set(hObject,'Units','Normalized')
194
195%UvData.OpenParam.PosColorbar=[0.8450    0.0900    0.0190    0.3600];
196UvData.OpenParam.PosColorbar=[0.805 0.022 0.019 0.445];
197%UvData.OpenParam.PosSetObject=[-0.05 -0.03 0.3 0.7]; %position for set_object
198UvData.OpenParam.PosGeometryCalib=[0.95 -0.03 0.28 1 ];%position for geometry_calib (TO IMPROVE)
199% UvData.OpenParam.CalSize=[0.28 1];
200% UvData.PlotAxes=[];%initiate the record of plotted field
201% UvData.axes2=[];
202% UvData.axes1=[];
203AxeData.LimEditBox=1; %initialise AxeData
204set(handles.PlotAxes,'UserData',AxeData)
205
206%% set functions for the mouse and keyboard
207set(hObject,'KeyPressFcn',{'keyboard_callback',handles})%set keyboard action function
208set(hObject,'WindowButtonMotionFcn',{'mouse_motion',handles})%set mouse action functio
209set(hObject,'WindowButtonDownFcn',{'mouse_down'})%set mouse click action function
210set(hObject,'WindowButtonUpFcn',{'mouse_up',handles})
211set(hObject,'DeleteFcn',{@closefcn})%
212
213%% initialisation
214set(handles.FieldName,'Value',1)
215set(handles.FieldName,'string',{''})
216UvData.ProjObject={[]};
217
218%% TRANSFORM menu: builtin fcts
219transform_menu={'';'sub_field';'phys';'phys_polar'};
220UvData.OpenParam.NbBuiltin=numel(transform_menu); %number of functions
221transform_path=fullfile(path_uvmat,'transform_field');
222path_list=cell(UvData.OpenParam.NbBuiltin,1);
223path_list{1}='';
224for ilist=2:UvData.OpenParam.NbBuiltin
225path_list{ilist}=transform_path; % set transform_path to the path_list
226end
227
228%% load the list of previously browsed files in menus Open, Open_1 and TransformName
229 dir_perso=prefdir; % path to the directory .matlab containing the personal data of the current user
230 profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmat_perso.mat' in .matlab
231 if exist(profil_perso,'file')
232     h=load (profil_perso);
233     if isfield(h,'MenuFile')% load the menu of previously opened files
234         for ifile=1:min(length(h.MenuFile),5)
235             set(handles.(['MenuFile_' num2str(ifile)]),'Label',h.MenuFile{ifile});
236             set(handles.(['MenuFile_' num2str(ifile) '_1']),'Label',h.MenuFile{ifile});
237         end
238     end
239     if isfield(h,'RootPath')
240         set(handles.RootPath,'UserData',h.RootPath); %store the previous campaign in the UserData of RootPath
241     end
242     if isfield(h,'transform_fct') && iscell(h.transform_fct) % load the menu of transform fct set by user
243         for ilist=1:length(h.transform_fct);
244             if exist(h.transform_fct{ilist},'file')
245                 [path,file]=fileparts(h.transform_fct{ilist});
246                 transform_menu=[transform_menu; {file}];
247                 path_list=[path_list; {path}];
248             end
249         end
250     end
251 end
252transform_menu=[transform_menu;{'more...'}];%append the option more.. to the menu
253set(handles.TransformName,'String',transform_menu)% display the menu of transform fcts
254set(handles.TransformName,'UserData',path_list)% store the corresponding list of path in UserData of uicontrol transform_fct
255set(handles.TransformPath,'String','')
256set(handles.TransformPath,'UserData',[])
257
258%% case of an input argument for uvmat
259testinputfield=0;
260inputfile=[];
261Field=[];
262if exist('input','var')
263    if ishandle(handles.UVMAT_title)
264        delete(handles.UVMAT_title)
265    end   
266    if isstruct(input)
267        if isfield(input,'InputFile')
268            inputfile=input.InputFile;
269        end
270        if isfield(input,'TimeIndex')
271            set(handles.i1,num2str(input.TimeIndex))
272        end
273        if isfield(input,'FieldsString')
274            UvData.FieldsString=input.FieldsString;
275        end
276    elseif ischar(input)% file name introduced as input
277           inputfile=input;
278    elseif isnumeric(input)%simple matrix introduced as input
279        sizinput=size(input);
280        if sizinput(1)<=1 || sizinput(2)<=1
281            msgbox_uvmat('ERROR','bad input for uvmat: file name, structure or numerical matrix accepted')
282            return
283        end
284        UvData.Field.ListVarName={'A','coord_y','coord_x'};
285        UvData.Field.VarDimName={{'coord_y','coord_x'},'cord_y','coord_x'};
286        UvData.Field.A=input;
287        UvData.Field.coord_x=[0.5 size(input,2)-0.5];
288        UvData.Field.coord_y=[size(input,1)-0.5 0.5];
289        testinputfield=1;
290    end
291else
292    %% check the path and date of modification of all functions in uvmat
293    path_to_uvmat=which ('uvmat');% check the path detected for source file uvmat
294    [infomsg,date_str,svn_info]=check_files;%check the path of the functions called by uvmat.m   
295    date_str=['last modification: ' date_str];
296    if ishandle(handles.UVMAT_title)
297        set(handles.UVMAT_title,'String',...
298            [{'Copyright  LEGI UMR 5519 /CNRS-UJF-Grenoble INP, 2010'};...
299            {'GNU General Public License'};...
300            {path_to_uvmat};...
301            {date_str};...
302            infomsg]);
303    end
304end
305set(handles.uvmat,'UserData',UvData)
306if ~isempty(inputfile)
307    %%%%% display the input field %%%%%%%
308    display_file_name(handles,inputfile)
309    %%%%%%%
310end
311
312set_vec_col_bar(handles) %update the display of color code for vectors
313
314%------------------------------------------------------------------------
315% --- Outputs from this function are returned to the command menuline.
316function varargout = uvmat_OutputFcn(hObject, eventdata, handles)
317varargout{1} = handles.output;% the only output argument is the handle to the GUI figure
318
319%------------------------------------------------------------------------
320% --- executed when closing uvmat: delete or desactivate the associated figures if exist
321function closefcn(gcbo,eventdata)
322%------------------------------------------------------------------------
323hh=findobj(allchild(0),'tag','view_field');
324if ~isempty(hh)
325    delete(hh)
326end
327hh=findobj(allchild(0),'tag','geometry_calib');
328if ~isempty(hh)
329    delete(hh)
330end
331hh=findobj(allchild(0),'tag','set_object');
332if ~isempty(hh)
333    hhh=findobj(hh,'tag','PLOT');
334    set(hhh,'enable','off')
335end
336
337%------------------------------------------------------------------------
338%------------------------------------------------------------------------
339%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
340% automatically sets the global properties when the rootfile name is introduced
341% then activate the view-field action if selected
342% it is activated either by clicking on the RootPath window or by the
343% browser
344%------------------------------------------------------------------------
345%------------------------------------------------------------------------
346% --- Executes on the menu Open/Browse...
347% search the files, recognize their type according to their name and fill the rootfile input windows
348function MenuBrowse_Callback(hObject, eventdata, handles)
349[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
350oldfile=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
351if isempty(oldfile) %loads the previously stored file name and set it as default in the file_input box
352    oldfile=get(handles.RootPath,'UserData');
353end
354fileinput=uigetfile_uvmat('select an input file:',oldfile);
355
356%% display the selected field and related information
357if ~isempty(fileinput)
358    display_file_name(handles,fileinput)
359end
360
361% -----------------------------------------------------------------------
362% --- Executes on the menu Open/Browse campaign...
363% search the file inside a campaign, using the GUI view_data
364function MenuBrowseCampaign_Callback(hObject, eventdata, handles)
365% -----------------------------------------------------------------------
366RootPath=get(handles.RootPath,'String');
367if isempty(RootPath)
368    RootPath=get(handles.RootPath,'UserData');%use Rootpath recored from the personal file at uvmat opening
369end
370CampaignPath=fileparts(fileparts(RootPath));
371DirFull = uigetdir(CampaignPath,'Select a Campaign dir, then press OK');
372if ~ischar(DirFull)|| ~exist(DirFull,'dir')
373    return
374end
375OutPut=browse_data(DirFull);% open the GUI browse_data to get select a campaign dir, experiment and device
376if ~isfield(OutPut,'Campaign')
377    return
378end
379DirName=fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.Device{1});
380hdir=dir(DirName); %list files and dirs
381for ilist=1:numel(hdir)
382    if ~isequal(hdir(ilist).isdir,1)%look for files, not dir
383        FileName=hdir(ilist).name;
384        FileType=get_file_type(fullfile(DirName,FileName));
385        switch FileType
386            case {'image','multimage','civx','civdata','netcdf'}
387            break
388        end
389    end
390end
391
392%% display the selected field and related information
393display_file_name( handles,fullfile(DirName,FileName))
394
395% -----------------------------------------------------------------------
396% --- Open again the file whose name has been recorded in MenuFile_1
397function MenuFile_1_Callback(hObject, eventdata, handles)
398%------------------------------------------------------------------------
399fileinput=get(handles.MenuFile_1,'Label');
400display_file_name( handles,fileinput)
401
402% -----------------------------------------------------------------------
403% --- Open again the file whose name has been recorded in MenuFile_2
404function MenuFile_2_Callback(hObject, eventdata, handles)
405%------------------------------------------------------------------------
406fileinput=get(handles.MenuFile_2,'Label');
407display_file_name(handles,fileinput)
408
409% -----------------------------------------------------------------------
410% --- Open again the file whose name has been recorded in MenuFile_3
411function MenuFile_3_Callback(hObject, eventdata, handles)
412%------------------------------------------------------------------------
413fileinput=get(handles.MenuFile_3,'Label');
414display_file_name(handles,fileinput)
415
416% -----------------------------------------------------------------------
417% --- Open again the file whose name has been recorded in MenuFile_4
418function MenuFile_4_Callback(hObject, eventdata, handles)
419%------------------------------------------------------------------------
420fileinput=get(handles.MenuFile_4,'Label');
421display_file_name(handles,fileinput)
422
423% -----------------------------------------------------------------------
424% --- Open again the file whose name has been recorded in MenuFile_5
425function MenuFile_5_Callback(hObject, eventdata, handles)
426%------------------------------------------------------------------------
427fileinput=get(handles.MenuFile_5,'Label');
428display_file_name(handles,fileinput)
429
430%------------------------------------------------------------------------
431% --- Executes on the menu Open/Browse_1 for the second input field,
432%     search the files, recognize their type according to their name and fill the rootfile input windows
433function MenuBrowse_1_Callback(hObject, eventdata, handles)
434%------------------------------------------------------------------------
435RootPath=get(handles.RootPath,'String');
436SubDir=get(handles.SubDir,'String');
437fileinput_1=uigetfile_uvmat('select a second input file:',fullfile(RootPath,SubDir));
438if ~isempty(fileinput_1)
439    % [FileName, PathName] = uigetfile({'*.*','All Files(*.*)'},'Pick a file',RootPath);
440    % if ~ischar(FileName),return,end %abandon if the browser is cancelled
441    % fileinput_1=[PathName FileName];%complete file name
442   
443    % refresh the current displayed field
444    set(handles.SubField,'Value',1)
445    display_file_name(handles,fileinput_1,2)
446   
447    %update list of recent files in the menubar
448    MenuFile_1=fileinput_1;
449    MenuFile_2=get(handles.MenuFile_1,'Label');
450    MenuFile_3=get(handles.MenuFile_2,'Label');
451    MenuFile_4=get(handles.MenuFile_3,'Label');
452    MenuFile_5=get(handles.MenuFile_4,'Label');
453    set(handles.MenuFile_1,'Label',MenuFile_1)
454    set(handles.MenuFile_2,'Label',MenuFile_2)
455    set(handles.MenuFile_3,'Label',MenuFile_3)
456    set(handles.MenuFile_4,'Label',MenuFile_4)
457    set(handles.MenuFile_5,'Label',MenuFile_5)
458    set(handles.MenuFile_1_1,'Label',MenuFile_1)
459    set(handles.MenuFile_2_1,'Label',MenuFile_2)
460    set(handles.MenuFile_3_1,'Label',MenuFile_3)
461    set(handles.MenuFile_4_1,'Label',MenuFile_4)
462    set(handles.MenuFile_5_1,'Label',MenuFile_5)
463end
464
465% --------------------------------------------------------------------
466function MenuBrowseCampaign_1_Callback(hObject, eventdata, handles)
467% -----------------------------------------------------------------------
468CampaignPath=fileparts(fileparts(get(handles.RootPath,'String')));
469DirFull = uigetdir(CampaignPath,'Select a Campaign dir, then press OK');
470if ~ischar(DirFull)|| ~exist(DirFull,'dir')
471    return
472end
473OutPut=browse_data(DirFull);% open the GUI browse_data to get select a campaign dir, experiment and device
474if ~isfield(OutPut,'Campaign')
475    return
476end
477DirName=fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.Device{1});
478hdir=dir(DirName); %list files and dirs
479for ilist=1:numel(hdir)
480    if ~isequal(hdir(ilist).isdir,1)%look for files, not dir
481        FileName=hdir(ilist).name;
482        FileType=get_file_type(fullfile(DirName,FileName));
483        switch FileType
484            case {'image','multimage','civx','civdata','netcdf'}
485            break
486        end
487    end
488end
489
490%% display the selected field and related information
491set(handles.SubField,'Value',1)
492display_file_name( handles,fullfile(DirName,FileName),2)
493
494% -----------------------------------------------------------------------
495% --- Open again as second field the file whose name has been recorded in MenuFile_1
496function MenuFile_1_1_Callback(hObject, eventdata, handles)
497% -----------------------------------------------------------------------
498fileinput_1=get(handles.MenuFile_1_1,'Label');
499set(handles.SubField,'Value',1)
500display_file_name(handles,fileinput_1,2)
501
502% -----------------------------------------------------------------------
503% --- Open again as second field the file whose name has been recorded in MenuFile_2
504function MenuFile_2_1_Callback(hObject, eventdata, handles)
505% -----------------------------------------------------------------------
506fileinput_1=get(handles.MenuFile_2_1,'Label');
507set(handles.SubField,'Value',1)
508display_file_name(handles,fileinput_1,2)
509
510% -----------------------------------------------------------------------
511% --- Open again as second field the file whose name has been recorded in MenuFile_3
512function MenuFile_3_1_Callback(hObject, eventdata, handles)
513% -----------------------------------------------------------------------
514fileinput_1=get(handles.MenuFile_3_1,'Label');
515set(handles.SubField,'Value',1)
516display_file_name(handles,fileinput_1,2)
517
518% -----------------------------------------------------------------------
519% --- Open again as second field the file whose name has been recorded in MenuFile_4
520function MenuFile_4_1_Callback(hObject, eventdata, handles)
521% -----------------------------------------------------------------------
522fileinput_1=get(handles.MenuFile_4_1,'Label');
523set(handles.SubField,'Value',1)
524display_file_name(handles,fileinput_1,2)
525
526% -----------------------------------------------------------------------
527% --- Open again as second field the file whose name has been recorded in MenuFile_5
528function MenuFile_5_1_Callback(hObject, eventdata, handles)
529% -----------------------------------------------------------------------
530fileinput_1=get(handles.MenuFile_5_1,'Label');
531set(handles.SubField,'Value',1)
532display_file_name(handles,fileinput_1,2)
533
534%------------------------------------------------------------------------
535% --- Called by action in RootPath edit box
536function RootPath_Callback(hObject,eventdata,handles)
537%------------------------------------------------------------------------
538% read the current input file name:
539[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
540if ~exist(fullfile(RootPath,SubDir),'dir')
541    msgbox_uvmat('ERROR',['directory ' fullfile(RootPath,SubDir) ' does not exist'])
542    return
543end
544% detect the file type, get the movie object if relevant, and look for the corresponding file series:
545[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,FileInfo,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
546% initiate the input file series and refresh the current field view:
547update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,1);
548
549%-----------------------------------------------------------------------
550% --- Called by action in RootPath_1 edit box
551function RootPath_1_Callback(hObject,eventdata,handles)
552% -----------------------------------------------------------------------
553% update_rootinfo_1(hObject,eventdata,handles)
554[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
555if ~exist(fullfile(RootPath,SubDir),'dir')
556    msgbox_uvmat('ERROR',['directory ' fullfile(RootPath,SubDir) ' does not exist'])
557    return
558end
559% detect the file type, get the movie object if relevant, and look for the corresponding file series:
560[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
561% initiate the input file series and refresh the current field view:
562update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,2);
563
564%------------------------------------------------------------------------
565% --- Called by action in RootFile edit box
566function SubDir_Callback(hObject, eventdata, handles)
567%------------------------------------------------------------------------
568%refresh the menu of input fieldname
569Fields_Callback(hObject, eventdata, handles);
570% refresh the current field view
571run0_Callback(hObject, eventdata, handles);
572
573%------------------------------------------------------------------------
574% --- Called by action in RootFile edit box
575function RootFile_Callback(hObject, eventdata, handles)
576%------------------------------------------------------------------------
577RootPath_Callback(hObject,eventdata,handles)
578
579%-----------------------------------------------------------------------
580% --- Called by action in RootFile_1 edit box
581function RootFile_1_Callback(hObject, eventdata, handles)
582% -----------------------------------------------------------------------
583RootPath_1_Callback(hObject,eventdata,handles)
584
585%------------------------------------------------------------------------
586% --- Called by action in FileIndex edit box
587function FileIndex_Callback(hObject, eventdata, handles)
588%------------------------------------------------------------------------
589[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
590set(handles.i1,'String',num2str(i1));
591set(handles.i2,'String',num2str(i2));
592set(handles.j1,'String',num2str(j1));
593set(handles.j2,'String',num2str(j2));
594
595% refresh the current field view
596run0_Callback(hObject, eventdata, handles)
597
598%------------------------------------------------------------------------
599% --- Called by action in FileIndex_1 edit box
600function FileIndex_1_Callback(hObject, eventdata, handles)
601%------------------------------------------------------------------------
602run0_Callback(hObject, eventdata, handles)
603
604%------------------------------------------------------------------------
605% --- Called by action in NomType edit box
606function NomType_Callback(hObject, eventdata, handles)
607%------------------------------------------------------------------------
608i1=str2num(get(handles.i1,'String'));
609i2=str2num(get(handles.i2,'String'));
610j1=str2num(get(handles.j1,'String'));
611j2=str2num(get(handles.j2,'String'));
612FileIndex=fullfile_uvmat('','','','',get(handles.NomType,'String'),i1,i2,j1,j2);
613set(handles.FileIndex,'String',FileIndex)
614% refresh the current settings and refresh the field view
615RootPath_Callback(hObject,eventdata,handles)
616
617%------------------------------------------------------------------------
618% --- Called by action in NomType edit box
619function NomType_1_Callback(hObject, eventdata, handles)
620%------------------------------------------------------------------------
621i1=str2num(get(handles.i1,'String'));
622i2=str2num(get(handles.i2,'String'));
623j1=str2num(get(handles.j1,'String'));
624j2=str2num(get(handles.j2,'String'));
625FileIndex=fullfile_uvmat('','','','',get(handles.NomType_1,'String'),i1,i2,j1,j2);
626set(handles.FileIndex_1,'String',FileIndex)
627% refresh the current settings and refresh the field view
628RootPath_1_Callback(hObject,eventdata,handles)
629
630%------------------------------------------------------------------------
631% --- Fills the edit boxes RootPath, RootFile,NomType...from an input file name 'fileinput'
632function display_file_name(handles,fileinput,index)
633%------------------------------------------------------------------------
634%% look for the input file existence
635if ~exist(fileinput,'file')
636    msgbox_uvmat('ERROR',['input file ' fileinput  ' does not exist'])
637    return
638end
639
640%% set the mouse pointer to 'watch'
641set(handles.uvmat,'Pointer','watch')
642set(handles.RootPath,'BackgroundColor',[1 1 0])
643drawnow
644
645%% define the relevant handles for the first field series (index=1) or the second file series (index=2)
646if ~exist('index','var')
647    index=1;
648end
649if index==1
650    handles_RootPath=handles.RootPath;
651    handles_SubDir=handles.SubDir;
652    handles_RootFile=handles.RootFile;
653    handles_FileIndex=handles.FileIndex;
654    handles_NomType=handles.NomType;
655    handles_FileExt=handles.FileExt;
656elseif index==2
657    handles_RootPath=handles.RootPath_1;
658    handles_SubDir=handles.SubDir_1;
659    handles_RootFile=handles.RootFile_1;
660    handles_FileIndex=handles.FileIndex_1;
661    handles_NomType=handles.NomType_1;
662    handles_FileExt=handles.FileExt_1;
663    set(handles.RootPath_1,'Visible','on')
664    set(handles.RootFile_1,'Visible','on')
665    set(handles.SubDir_1,'Visible','on');
666    set(handles.FileIndex_1,'Visible','on');
667    set(handles.FileExt_1,'Visible','on');
668    set(handles.NomType_1,'Visible','on');
669end
670
671%% detect root name, nomenclature and indices in the input file name:
672[FilePath,FileName,FileExt]=fileparts(fileinput);
673% detect the file type, get the movie object if relevant, and look for the corresponding file series:
674% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
675[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,FileInfo,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
676
677%% open the file or fill the GUI uvmat according to the detected file type
678switch FileType
679    case ''
680        msgbox_uvmat('ERROR','invalid input file type')
681    case 'txt'
682        edit(fileinput)
683    case 'figure'                           %display matlab figure
684        hfig=open(fileinput);
685        set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
686        set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
687        set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
688    case 'xml'                % edit xml files
689        t=xmltree(fileinput);
690        % the xml file marks a project or project link, open datatree_browser
691        if strcmp(get(t,1,'name'),'Project')&& exist(regexprep(fileinput,'.xml$',''),'dir')
692            datatree_browser(fileinput)
693        else % other xml file, open the xml editor
694            editxml(fileinput);
695        end
696    case 'xls'% Excel file opended by editxml
697        editxml(fileinput);
698    otherwise
699        set(handles_RootPath,'String',RootPath);
700        rootname=fullfile(RootPath,SubDir,RootFile);
701        set(handles_SubDir,'String',['/' SubDir]);
702        set(handles_RootFile,'String',['/' RootFile]); %display the separator
703        indices=fileinput(length(rootname)+1:end);
704        indices(end-length(FileExt)+1:end)=[]; %remove extension
705        set(handles_FileIndex,'String',indices);
706        set(handles_NomType,'String',NomType);
707        set(handles_FileExt,'String',FileExt);
708        if index==1
709            % fill file index counters if the first file series is opened
710            set(handles.i1,'String',num2str(i1));
711            set(handles.i2,'String',num2str(i2));
712            set(handles.j1,'String',num2stra(j1,NomType));
713            set(handles.j2,'String',num2stra(j2,NomType));
714        else %read the current field index to synchronise with the first series
715            i1_s=str2num(get(handles.i1,'String'));
716            i2_0=str2num(get(handles.i2,'String'));
717            if ~isempty(i2_0)
718                i2_s=i2_0;
719            else
720               i2_s=i2;
721            end
722            j1_0=stra2num(get(handles.j1,'String'));
723            if ~isempty(j1_0)
724                j1_s=j1_0;
725            else
726                j1_s=j1;
727            end
728            j2_0=stra2num(get(handles.j2,'String'));
729            if ~isempty(j2_0)
730                j2_s=j2_0;
731            else
732                j2_s=j2;
733            end
734        end
735       
736        % synchronise indices of the second  input file if it exists
737        if get(handles.SubField,'Value')==1% if the subfield button is activated, update the field numbers
738            Input=read_GUI(handles.InputFile);
739            if ~isfield(Input,'RootPath_1')||strcmp(Input.RootPath_1,'"')
740                Input.RootPath_1=Input.RootPath;
741            end
742            if ~isfield(Input,'SubDir_1')||strcmp(Input.SubDir_1,'"')
743                Input.SubDir_1=Input.SubDir;
744            end
745            if ~isfield(Input,'RootFile_1')||strcmp(Input.RootFile_1,'"')
746                Input.RootFile_1=Input.RootFile;
747            end
748            if ~isfield(Input,'FileExt_1')||strcmp(Input.FileExt_1,'"')
749                Input.FileExt_1=Input.FileExt;
750            end
751            if ~isfield(Input,'NomType_1')||strcmp(Input.NomType_1,'"')
752                Input.NomType_1=Input.NomType;
753            end
754            %updtate the indices of the second field series to correspond to the newly opened one
755            FileName_1=fullfile_uvmat(Input.RootPath_1,Input.SubDir_1,Input.RootFile_1,Input.FileExt_1,Input.NomType_1,i1_s,i2_s,j1_s,j2_s);
756            if exist(FileName_1,'file')
757                FileIndex_1=fullfile_uvmat('','','','',Input.NomType_1,i1_s,i2_s,j1_s,j2_s);
758            else
759                FileIndex_1=fullfile_uvmat('','','','',Input.NomType_1,i1,i2,j1,j2);
760                msgbox_uvmat('WARNING','unable to synchronise the indices of the two series')
761            end
762            set(handles.FileIndex_1,'String',FileIndex_1)
763        end
764       
765        %enable other menus
766        set(handles.MenuOpen_1,'Enable','on')
767        set(handles.MenuFile_1_1,'Enable','on')
768        set(handles.MenuFile_2_1,'Enable','on')
769        set(handles.MenuFile_3_1,'Enable','on')
770        set(handles.MenuFile_4_1,'Enable','on')
771        set(handles.MenuFile_5_1,'Enable','on')
772        set(handles.MenuExport,'Enable','on')
773        set(handles.MenuExportFigure,'Enable','on')
774        set(handles.MenuExportMovie,'Enable','on')
775        set(handles.MenuTools,'Enable','on')
776
777        % initiate input file series and refresh the current field view:     
778        update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,index);
779
780end
781
782%% update list of recent files in the menubar and save it for future opening
783MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
784    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
785str_find=strcmp(fileinput,MenuFile);
786if isempty(find(str_find,1))
787    MenuFile=[{fileinput};MenuFile];%insert the current file if not already in the list
788end
789for ifile=1:min(length(MenuFile),5)
790    set(handles.(['MenuFile_' num2str(ifile)]),'Label',MenuFile{ifile});
791    set(handles.(['MenuFile_' num2str(ifile) '_1']),'Label',MenuFile{ifile});
792end
793dir_perso=prefdir;
794profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
795if exist(profil_perso,'file')
796    save (profil_perso,'MenuFile','RootPath','-append'); %store the file names for future opening of uvmat
797else
798    save (profil_perso,'MenuFile','RootPath','-V6'); %store the file names for future opening of uvmat
799end
800
801%% set back the mouse pointer to arrow
802set(handles.uvmat,'Pointer','arrow')
803
804
805%------------------------------------------------------------------------
806% --- Update information about a new field series (indices to scan, timing,
807%     calibration from an xml file, then refresh current plots
808
809function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,VideoObject,index)
810%------------------------------------------------------------------------
811%% define the relevant handles depending on the index (1=first file series, 2= second file series)
812if ~exist('index','var')
813    index=1;
814end
815if index==1
816    handles_RootPath=handles.RootPath;
817    handles_Fields=handles.FieldName;
818elseif index==2
819    handles_RootPath=handles.RootPath_1;
820    handles_Fields=handles.FieldName_1;
821end
822
823set(handles_RootPath,'BackgroundColor',[1 1 0])
824drawnow
825set(handles.FieldName,'UserData',[])% reinialize data from uvmat opening
826UvData=get(handles.uvmat,'UserData');%huvmat=handles of the uvmat interface
827UvData.NewSeries=1; %flag for run0: begin a new series
828UvData.FileName_1='';% name of the current second field (used to detect a  constant field during file scanning)
829UvData.FileType{index}=FileType;
830UvData.i1_series{index}=i1_series;
831UvData.i2_series{index}=i2_series;
832UvData.j1_series{index}=j1_series;
833UvData.j2_series{index}=j2_series;
834set(handles.FixVelType,'Value',0); %desactivate fixed veltype
835if index==1
836    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
837else
838    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
839end
840FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
841FileBase=fullfile(RootPath,RootFile);
842if ~exist(FileName,'file')
843   msgbox_uvmat('ERROR',['input file ' FileName ' not found']);
844    return
845end
846
847%% read timing and total frame number from the current file (movie files) !! may be overrid by xml file
848XmlData.Time=[];%default
849XmlData.GeometryCalib=[];%default
850TimeUnit='';%default
851Time=[];
852imainfo=[];
853ColorType='falsecolor'; %default
854UvData.MovieObject{index}=VideoObject;
855if ~isempty(VideoObject)
856    imainfo=get(VideoObject);
857    TimeUnit='s';
858    if isempty(j1_series); %frame index along i
859        Time=zeros(imainfo.NumberOfFrames+1,2);
860        Time(:,2)=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)';
861    else
862        Time=[0;ones(size(i1_series,3)-1,1)]*(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate);
863    end
864    set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FrameRate) 'ms']);%display the elementary time interval in millisec
865    ColorType='truecolor';
866elseif ~isempty(FileExt(2:end))&&(~isempty(imformats(FileExt(2:end))) || isequal(FileExt,'.vol'))%&& isequal(NomType,'*')% multi-frame image
867%     testima=1;
868    if ~isequal(SubDir,'')
869        imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]);
870    else
871        imainfo=imfinfo([FileBase FileIndices FileExt]);
872    end
873    ColorType=imainfo.ColorType;%='truecolor' for color images
874end
875if isfield(imainfo,'Width') && isfield(imainfo,'Height')
876    if length(imainfo)>1
877        set(handles.num_Npx,'String',num2str(imainfo(1).Width));%fills nbre of pixels x box
878        set(handles.num_Npy,'String',num2str(imainfo(1).Height));%fills nbre of pixels x box
879    else
880        set(handles.num_Npx,'String',num2str(imainfo.Width));%fills nbre of pixels x box
881        set(handles.num_Npy,'String',num2str(imainfo.Height));%fills nbre of pixels x box
882    end
883else
884    set(handles.num_Npx,'String','');%fills nbre of pixels x box
885    set(handles.num_Npy,'String','');%fills nbre of pixels x box
886end
887set(handles.CheckBW,'Value',strcmp(ColorType,'grayscale'))% select handles.CheckBW if grayscale image
888
889%% read parameters (time, geometric calibration..) from a documentation file (.xml advised)
890XmlFileName=find_imadoc(RootPath,SubDir,RootFile,FileExt);
891[tild,tild,DocExt]=fileparts(XmlFileName);
892warntext='';%default warning message
893NbSlice=1;%default
894ImaDoc_str='';
895set(handles.RootPath,'BackgroundColor',[1 1 1])
896if ~isempty(XmlFileName)
897    set(handles.view_xml,'Visible','on')
898    set(handles.view_xml,'BackgroundColor',[1 1 0])% paint  to yellow color to indicate reading of the xml file
899    set(handles.view_xml,'String','view .xml')
900    drawnow
901    [XmlDataRead,warntext]=imadoc2struct(XmlFileName);
902    if ~isempty(warntext)
903        msgbox_uvmat('WARNING',warntext)
904    end
905    if ~isempty(XmlDataRead)
906        ImaDoc_str=['view ' DocExt];   
907        XmlData=XmlDataRead;
908        if isfield(XmlData,'TimeUnit')
909            if isfield(XmlData,'TimeUnit')&& ~isempty(XmlData.TimeUnit)
910                TimeUnit=XmlData.TimeUnit;
911            end
912        end
913        set(handles.view_xml,'BackgroundColor',[1 1 1])% paint black to white
914        drawnow
915        if isfield(XmlData, 'GeometryCalib') && ~isempty(XmlData.GeometryCalib)
916            if isfield(XmlData.GeometryCalib,'VolumeScan') && isequal(XmlData.GeometryCalib.VolumeScan,'y')
917                set (handles.slices,'String','volume')
918            end
919            hgeometry_calib=findobj('tag','geometry_calib');
920            if ~isempty(hgeometry_calib)
921                GUserData=get(hgeometry_calib,'UserData');
922                if ~(isfield(GUserData,'XmlInputFile') && strcmp(GUserData.XmlInputFile,XmlFileName))
923                    answer=msgbox_uvmat('INPUT_Y-N','replace the display of geometry_calib with the new input data?');
924                    if strcmp(answer,'Yes')
925                        geometry_calib(XmlFileName);%diplay the new calibration points and parameters in geometry_calib
926                    end
927                end
928            end
929        end
930    end
931end
932if ~(isfield(XmlData,'Time')&& ~isempty(XmlData.Time))
933    XmlData.Time=Time; %time set by video
934end
935if isempty(ImaDoc_str)
936    set(handles.view_xml,'Visible','off')
937else
938    set(handles.view_xml,'String',ImaDoc_str)
939end
940
941%% store last index in handles.lat_i and .last_j
942nbfield=max(max(max(i2_series)));
943if isempty(nbfield)
944    nbfield=max(max(max(i1_series)));
945end
946nbfield_j=max(max(max(j2_series)));
947if isempty(nbfield_j)
948    nbfield_j=max(max(max(j1_series)));
949end
950if ~isempty(XmlData.Time)
951    %transform .Time to a column vector if it is a line vector the nomenclature uses a single index
952    if isequal(size(XmlData.Time,1),1)
953        %NomType=get(handles.NomType,'String');
954        XmlData.Time=(XmlData.Time)';
955    end
956end
957last_i_cell=get(handles.last_i,'String');
958if isempty(nbfield)
959    last_i_cell{index}='';
960else
961    last_i_cell{index}=num2str(nbfield);
962end
963set(handles.last_i,'String',last_i_cell)
964last_j_cell=get(handles.last_j,'String');
965if isempty(nbfield_j)
966     last_j_cell{index}='';
967else
968     last_j_cell{index}=num2str(nbfield_j);
969end
970set(handles.last_j,'String',last_j_cell);
971
972%% store geometric calibration in UvData
973if isfield(XmlData,'GeometryCalib')
974    GeometryCalib=XmlData.GeometryCalib;
975    if isempty(GeometryCalib)
976        set(handles.pxcm,'String','')
977        set(handles.pycm,'String','')
978        set(handles.TransformName,'Value',1); %  no transform by default
979    else
980        if (isfield(GeometryCalib,'R')&& ~isequal(GeometryCalib.R(2,1),0) && ~isequal(GeometryCalib.R(1,2),0)) ||...
981            (isfield(GeometryCalib,'kappa1')&& ~isequal(GeometryCalib.kappa1,0))
982            set(handles.pxcm,'String','var')
983            set(handles.pycm,'String','var')
984        elseif isfield(GeometryCalib,'fx_fy')
985            pixcmx=GeometryCalib.fx_fy(1);%*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx);
986            pixcmy=GeometryCalib.fx_fy(2);%*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy);
987            set(handles.pxcm,'String',num2str(pixcmx))
988            set(handles.pycm,'String',num2str(pixcmy))
989        end
990        if ~get(handles.CheckFixLimits,'Value')
991            set(handles.TransformName,'Value',3); % phys transform by default if fixedLimits is off
992        end
993        if isfield(GeometryCalib,'SliceCoord')           
994           siz=size(GeometryCalib.SliceCoord);
995           if siz(1)>1
996               NbSlice=siz(1);
997               set(handles.slices,'Visible','on')
998               set(handles.slices,'Value',1)
999           end
1000           if isfield(GeometryCalib,'VolumeScan') && isequal(GeometryCalib.VolumeScan,'y')
1001               set(handles.num_NbSlice,'Visible','off')
1002           else
1003               set(handles.num_NbSlice,'Visible','on')
1004               set(handles.num_NbSlice,'String',num2str(NbSlice))
1005           end
1006           slices_Callback([],[], handles)
1007        end           
1008    end
1009end
1010
1011%% update the data attached to the uvmat interface
1012if ~isempty(TimeUnit)
1013    set(handles.time_txt,'String',['time (' TimeUnit ')'])
1014end
1015UvData.TimeUnit=TimeUnit;
1016UvData.XmlData{index}=XmlData;
1017UvData.NewSeries=1;
1018% UvData.MovieObject=MovieObject;
1019
1020%display warning message
1021if ~isequal(warntext,'')
1022    msgbox_uvmat('WARNING',warntext);
1023end
1024
1025%% set default options in menu 'FieldName'
1026switch FileType
1027    case {'civx','civdata'}
1028%         [FieldList,ColorList]=calc_field;
1029        [FieldList,ColorList]=set_field_list('U','V','C');
1030        set(handles_Fields,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data
1031        set(handles_Fields,'Value',2) % set menu to 'velocity
1032        if index==1
1033            set(handles.FieldName_1,'Value',1);
1034            set(handles.FieldName_1,'String',[{''};{'image'};FieldList;{'get_field...'}]);%standard menu for civx data reproduced for the second field
1035        end
1036        set(handles.ColorScalar,'Value',1)
1037        set(handles.ColorScalar,'String',ColorList)
1038        set(handles.Vectors,'Visible','on')
1039        set(handles.Coord_x,'Value',1);
1040        set(handles.Coord_x,'String',{'X'});
1041        set(handles.Coord_y,'Value',1);
1042        set(handles.Coord_y,'String',{'Y'});
1043    case 'netcdf'
1044        set(handles_Fields,'Value',1)
1045        set(handles_Fields,'String',{'get_field...'})
1046        FieldName_Callback([],[], handles)
1047%         hget_field=get_field(FileName);
1048%         hhget_field=guidata(hget_field);
1049%         get_field('RUN_Callback',hhget_field.RUN,[],hhget_field);
1050    otherwise
1051        set(handles_Fields,'Value',1) % set menu to 'image'
1052        set(handles_Fields,'String',{'image'})
1053        set(handles.Coord_x,'Value',1);
1054        set(handles.Coord_x,'String',{'AX'});
1055        set(handles.Coord_y,'Value',1);
1056        set(handles.Coord_y,'String',{'AY'});
1057end
1058set(handles.uvmat,'UserData',UvData)
1059
1060%% set index navigation options and refresh plots
1061scan_option='i';%default
1062state_j='off'; %default
1063if index==2
1064    if get(handles.scan_j,'Value')
1065        scan_option='j'; %keep the scan option for the second file series
1066    end
1067    if strcmp(get(handles.j1,'Visible'),'on')
1068        state_j='on';
1069    end
1070end
1071[ref_j,ref_i]=find(squeeze(i1_series(1,:,:)));
1072if ~isempty(j1_series)
1073        state_j='on';
1074        if index==1
1075            if isequal(ref_i,ref_i(1)*ones(size(ref_j)))% if ref_i is always equal to its first value
1076                scan_option='j'; %scan j indext               
1077            end
1078        end
1079end
1080if isequal(scan_option,'i')
1081    diff_ref_i=diff(ref_i,1);
1082    if isempty(diff_ref_i)
1083        diff_ref_i=1;
1084    end
1085    if isequal (diff_ref_i,diff_ref_i(1)*ones(size(diff_ref_i)))
1086        set(handles.num_IndexIncrement,'String',num2str(diff_ref_i(1)))
1087    end
1088     set(handles.scan_i,'Value',1)
1089     scan_i_Callback([],[], handles);
1090else
1091    diff_ref_j=diff(ref_j);
1092    if isempty(diff_ref_j)
1093        diff_ref_j=1;
1094    end
1095    if isequal (diff_ref_j,diff_ref_j(1)*ones(size(diff_ref_j)))
1096        set(handles.num_IndexIncrement,'String',num2str(diff_ref_j(1)))
1097    end
1098     set(handles.scan_j,'Value',1)
1099     scan_j_Callback([],[], handles);
1100end
1101set(handles.scan_j,'Visible',state_j)
1102set(handles.j1,'Visible',state_j)
1103set(handles.j2,'Visible',state_j)
1104set(handles.last_j,'Visible',state_j);
1105set(handles.frame_j,'Visible',state_j);
1106set(handles.j_text,'Visible',state_j);
1107if ~isempty(i2_series)||~isempty(j2_series)
1108    set(handles.CheckFixPair,'Visible','on')
1109elseif index==1
1110    set(handles.CheckFixPair,'Visible','off')
1111end
1112
1113%% apply the effect of the transform fct and view the field 
1114transform=get(handles.TransformPath,'UserData');
1115if index==2 && (~isa(transform,'function_handle')||nargin(transform)<3)
1116    set(handles.TransformName,'value',2); % set transform to sub_field if the current fct doe not accept two input fields
1117end
1118TransformName_Callback([],[],handles)
1119mask_test=get(handles.CheckMask,'value');
1120if mask_test
1121    MaskData=get(handles.CheckMask,'UserData');
1122    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1123          delete(MaskData.maskhandle)    %delete old mask
1124    end
1125    CheckMask_Callback([],[],handles)
1126end
1127
1128%------------------------------------------------------------------------
1129% --- switch file index scanning options scan_i and scan_j in an exclusive way
1130function scan_i_Callback(hObject, eventdata, handles)
1131%------------------------------------------------------------------------
1132if get(handles.scan_i,'Value')==1
1133%     set(handles.scan_i,'BackgroundColor',[1 1 0])
1134    set(handles.scan_j,'Value',0)
1135else
1136%     set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1137    set(handles.scan_j,'Value',1)
1138end
1139scan_j_Callback(hObject, eventdata, handles)
1140
1141%------------------------------------------------------------------------
1142% --- switch file index scanning options scan_i and scan_j in an exclusive way
1143function scan_j_Callback(hObject, eventdata, handles)
1144%------------------------------------------------------------------------
1145if get(handles.scan_j,'Value')==1
1146%     set(handles.scan_j,'BackgroundColor',[1 1 0])
1147    set(handles.scan_i,'Value',0)
1148%     set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1149%     NomType=get(handles.NomType,'String');
1150%     switch NomType
1151%     case {'_1_1-2','#_ab','%3dab'},% pair with j index
1152%         set(handles.CheckFixPair,'Visible','on')% option fixed pair on/off made visible (choice of avaible pair with buttons + and - if ='off')
1153%     otherwise
1154%         set(handles.CheckFixPair,'Visible','off')
1155%     end
1156else
1157%     set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
1158    set(handles.scan_i,'Value',1)
1159%     set(handles.scan_i,'BackgroundColor',[1 1 0])
1160    set(handles.CheckFixPair,'Visible','off')
1161end
1162
1163%------------------------------------------------------------------------
1164function i1_Callback(hObject, eventdata, handles)
1165%------------------------------------------------------------------------
1166update_ij(handles,1)
1167
1168%------------------------------------------------------------------------
1169function i2_Callback(hObject, eventdata, handles)
1170%------------------------------------------------------------------------
1171update_ij(handles,2)
1172
1173%------------------------------------------------------------------------
1174function j1_Callback(hObject, eventdata, handles)
1175%------------------------------------------------------------------------
1176update_ij(handles,3)
1177
1178%------------------------------------------------------------------------
1179function j2_Callback(hObject, eventdata, handles)
1180%------------------------------------------------------------------------
1181update_ij(handles,4)
1182
1183%------------------------------------------------------------------------
1184%--- update the index display after action on edit boxes i1, i2, j1 or j2
1185function update_ij(handles,index_rank)
1186NomType=get(handles.NomType,'String');
1187indices=get(handles.FileIndex,'String');
1188[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(indices);% the indices for the second series taken from FileIndex
1189switch index_rank
1190    case 1
1191        indices=fullfile_uvmat('','','','',NomType,stra2num(get(handles.i1,'String')),i2,j1,j2);
1192        set(handles.i1,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation
1193    case 2
1194        indices=fullfile_uvmat('','','','',NomType,i1,stra2num(get(handles.i2,'String')),j1,j2);
1195        set(handles.i2,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation
1196    case 3
1197        indices=fullfile_uvmat('','','','',NomType,i1,i2,stra2num(get(handles.j1,'String')),j2);
1198        set(handles.j1,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation
1199    case 4
1200        indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,stra2num(get(handles.j2,'String')));
1201        set(handles.j2,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation
1202end
1203set(handles.FileIndex,'String',indices)
1204set(handles.FileIndex,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation
1205% update the second index if relevant
1206if strcmp(get(handles.FileIndex_1,'Visible'),'on')
1207    NomType_1=get(handles.NomType_1,'String');
1208    indices_1=get(handles.FileIndex_1,'String');
1209    [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(indices_1);% the indices for the second series taken from FileIndex_1
1210    switch index_rank
1211        case 1
1212            indices_1=fullfile_uvmat('','','','',NomType_1,stra2num(get(handles.i1,'String')),i2_1,j1_1,j2_1);
1213        case 2
1214            indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,stra2num(get(handles.i2,'String')),j1_1,j2_1);
1215        case 3
1216            indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,i2_1,stra2num(get(handles.j1,'String')),j2_1);
1217        case 4
1218            indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,i2_1,j1_1,stra2num(get(handles.j2,'String')));
1219    end
1220    set(handles.FileIndex_1,'String',indices_1)
1221    set(handles.FileIndex_1,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation
1222end
1223   
1224%------------------------------------------------------------------------
1225
1226%------------------------------------------------------------------------
1227function slices_Callback(hObject, eventdata, handles)
1228%------------------------------------------------------------------------
1229if strcmp(get(handles.slices,'String'),'slices')
1230    if get(handles.slices,'Value')==1
1231        set(handles.num_NbSlice,'Visible','on')
1232        set(handles.z_text,'Visible','on')
1233        set(handles.z_index,'Visible','on')
1234        num_NbSlice_Callback(hObject, eventdata, handles)
1235    else
1236        set(handles.num_NbSlice,'Visible','off')
1237        set(handles.z_text,'Visible','off')
1238        set(handles.z_index,'Visible','off')
1239        set(handles.masklevel,'Value',1)
1240        set(handles.masklevel,'String',{'1'})
1241    end
1242end
1243
1244%------------------------------------------------------------------------
1245function num_NbSlice_Callback(hObject, eventdata, handles)
1246%------------------------------------------------------------------------
1247mode=get(handles.slices,'String');
1248nb_slice_str=get(handles.num_NbSlice,'String');
1249if strcmp(mode,'volume')
1250    z=stra2num(get(handles.j1,'String'));
1251else
1252    num=str2double(get(handles.i1,'String'));
1253    nbslice=str2double(get(handles.num_NbSlice,'String'));
1254    z=mod(num-1,nbslice)+1;
1255end
1256set(handles.z_index,'String',num2str(z))
1257for ilist=1:nbslice
1258    list_index{ilist,1}=num2str(ilist);
1259end   
1260set(handles.masklevel,'String',list_index)
1261set(handles.masklevel,'Value',z)
1262
1263%------------------------------------------------------------------------
1264% --- Executes on button press in view_xml.
1265function view_xml_Callback(hObject, eventdata, handles)
1266%------------------------------------------------------------------------
1267%[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles);
1268 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1269FileBase=fullfile(RootPath,RootFile);
1270option=get(handles.view_xml,'String');
1271if isequal(option,'view .xml')
1272    FileXml=fullfile(RootPath,[SubDir '.xml']);
1273    if ~exist(FileXml,'file')% case of civ files , removes the extension for subdir
1274        FileXml=fullfile(RootPath,[regexprep(SubDir,'\..+$','') '.xml']);
1275    end
1276    heditxml=editxml(FileXml);
1277end
1278
1279%------------------------------------------------------------------------
1280% --- Executes on button press in CheckMask.
1281function CheckMask_Callback(hObject, eventdata, handles)
1282%------------------------------------------------------------------------
1283%case of view mask selection
1284if isequal(get(handles.CheckMask,'Value'),1)
1285     [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1286     FileBase=fullfile(RootPath,RootFile);
1287    num_i1=stra2num(get(handles.i1,'String'));
1288    num_j1=stra2num(get(handles.j1,'String'));
1289    currentdir=pwd; 
1290    cd(RootPath);
1291    maskfiles=dir('*_*mask_*.png');%look for a mask file
1292    cd(currentdir);%come back to the working directory
1293    mdetect=0;
1294    if ~isempty(maskfiles)
1295        for ilist=1:length(maskfiles)
1296            maskname=maskfiles(ilist).name;% take the first mask file in the list
1297            [tild,tild,tild,tild,tild,tild,tild,MaskExt,Mask_NomType{ilist}]=fileparts_uvmat(maskname);
1298             [tild,Name]=fileparts(maskname);
1299            Namedouble=double(Name);
1300            val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1301            ind_mask=findstr('mask',Name);
1302            i=ind_mask-1;
1303            while val(i)==0 && i>0
1304                i=i-1;
1305            end
1306            nbmask_str=str2num(Name(i+1:ind_mask-1));
1307            if ~isempty(nbmask_str)
1308                nbslice(ilist)=nbmask_str; % number of different masks (slices)
1309            end
1310        end
1311        if isequal(min(nbslice),max(nbslice))
1312            nbslice=nbslice(1);
1313        else
1314            msgbox_uvmat('ERROR','several inconsistent mask sets coexist in the current image directory')
1315            return
1316        end
1317        if ~isempty(nbslice) && Name(i)=='_'
1318            Mask.Base=[FileBase Name(i:ind_mask+3)];
1319            Mask.NbSlice=nbslice;
1320            num_i1=mod(num_i1-1,nbslice)+1;
1321            Mask.NomType=regexprep(Mask_NomType{1},'0','');%remove '0' in nom type for masks
1322            [RootPath,RootFile]=fileparts(Mask.Base);
1323            maskname=fullfile_uvmat(RootPath,'',RootFile,'.png',Mask.NomType,num_i1,[],num_j1);
1324            %maskname=name_generator(Mask.Base,num_i1,num_j1,'.png',Mask.NomType);%
1325            mdetect=exist(maskname,'file');
1326            if mdetect
1327                set(handles.num_NbSlice,'String',Name(i+1:ind_mask-1));
1328                 set(handles.num_NbSlice,'BackgroundColor',[1 1 0])
1329                set(handles.CheckMask,'UserData',Mask);
1330                set(handles.CheckMask,'BackgroundColor',[1 1 0])
1331                if nbslice > 1
1332                    set(handles.slices,'value',1)
1333                    slices_Callback(hObject, eventdata, handles)
1334                end
1335            end
1336        end
1337    end
1338    errormsg=[];%default
1339    if mdetect==0
1340        [FileName, PathName, filterindex] = uigetfile( ...
1341            {'*.png', ' (*.png)';
1342            '*.png',  '.png files '; ...
1343            '*.*', 'All Files (*.*)'}, ...
1344            'Pick a mask file *.png',FileBase);
1345        if ~ischar(FileName),return,end %abandon if the browser is cancelled
1346        maskname=fullfile(PathName,FileName);
1347        [RootDir,SubDir,RootFile,tild,tild,tild,tild,tild,Mask.NomType]=fileparts_uvmat(maskname);
1348        Mask.Base=fullfile(RootDir,SubDir,RootFile);
1349        Mask.NbSlice=1;
1350        set(handles.CheckMask,'UserData',Mask);
1351        set(handles.CheckMask,'BackgroundColor',[1 1 0])
1352    end
1353    if isempty(errormsg)
1354        errormsg=update_mask(handles,num_i1,num_j1);
1355    end
1356    if ~isempty(errormsg)
1357            set(handles.CheckMask,'Value',0)
1358            set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1359     end
1360else % desactivate mask display
1361    MaskData=get(handles.CheckMask,'UserData');
1362    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1363          delete(MaskData.maskhandle)   
1364    end
1365    set(handles.CheckMask,'UserData',[])   
1366    UvData=get(handles.uvmat,'UserData');
1367    if isfield(UvData,'MaskName')
1368        UvData=rmfield(UvData,'MaskName');
1369        set(handles.uvmat,'UserData',UvData)
1370    end
1371    set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1372end
1373
1374%------------------------------------------------------------------------
1375function errormsg=update_mask(handles,num_i1,num_j1)
1376%------------------------------------------------------------------------
1377errormsg=[];%default
1378MaskData=get(handles.CheckMask,'UserData');
1379if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1380    uistack(MaskData.maskhandle,'top');
1381end
1382num_i1_mask=mod(num_i1-1,MaskData.NbSlice)+1;
1383[RootPath,RootFile]=fileparts(MaskData.Base);
1384MaskName=fullfile_uvmat(RootPath,'',RootFile,'.png',MaskData.NomType,num_i1_mask,[],num_j1);
1385UvData=get(handles.uvmat,'UserData');
1386%update mask image if the mask is new
1387if ~ (isfield(UvData,'MaskName') && isequal(UvData.MaskName,MaskName))
1388    UvData.MaskName=MaskName; %update the recorded name on UvData
1389    set(handles.uvmat,'UserData',UvData);
1390    if ~exist(MaskName,'file')
1391        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1392            delete(MaskData.maskhandle)   
1393        end
1394    else
1395        %read mask image
1396        [Mask,tild,errormsg] = read_field(MaskName,'image');
1397%         Mask.AName='image';
1398%         Mask.A=imread(MaskName);
1399        if ~isempty(errormsg)
1400            return
1401        end
1402        npxy=size(Mask.A);
1403        if length(npxy)>2
1404            errormsg=[MaskName ' is not a grey scale image'];
1405            return
1406        elseif ~isa(Mask.A,'uint8')
1407            errormsg=[MaskName ' is not a 8 bit grey level image'];
1408            return
1409        end
1410%         Mask.AX=[0.5 npxy(2)-0.5];
1411%         Mask.AY=[npxy(1)-0.5 0.5 ];
1412%         Mask.CoordUnit='pixel';
1413        if isequal(get(handles.slices,'Value'),1)
1414           NbSlice=str2num(get(handles.num_NbSlice,'String'));
1415           num_i1=str2num(get(handles.i1,'String'));
1416           Mask.ZIndex=mod(num_i1-1,NbSlice)+1;
1417        end
1418        %px to phys or other transform on field
1419         menu_transform=get(handles.TransformName,'String');
1420        choice_value=get(handles.TransformName,'Value');
1421        transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1422        transform=get(handles.TransformPath,'UserData');
1423        if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
1424            if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
1425                Calib=UvData.XmlData{1}.GeometryCalib;
1426                Mask=transform(Mask,UvData.XmlData{1});
1427            end
1428        end
1429        flagmask=Mask.A < 200;
1430       
1431        %make brown color image
1432        imflag(:,:,1)=0.9*flagmask;
1433        imflag(:,:,2)=0.7*flagmask;
1434        imflag(:,:,3)=zeros(size(flagmask));
1435       
1436        %update mask image
1437        hmask=[]; %default
1438        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1439            hmask=MaskData.maskhandle;
1440        end
1441        if ~isempty(hmask)
1442            set(hmask,'CData',imflag)   
1443            set(hmask,'AlphaData',flagmask*0.6)
1444            set(hmask,'XData',Mask.AX);
1445            set(hmask,'YData',Mask.AY);
1446%             uistack(hmask,'top')
1447        else
1448            axes(handles.PlotAxes)
1449            hold on   
1450            MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*ones(size(flagmask)));
1451            set(handles.CheckMask,'UserData',MaskData)
1452        end
1453    end
1454end
1455
1456%------------------------------------------------------------------------
1457%------------------------------------------------------------------------
1458% III - MAIN REFRESH FUNCTIONS : 'FRAME PLOT'
1459%------------------------------------------------------------------------
1460
1461%------------------------------------------------------------------------
1462% --- Executes on button press in runplus: make one step forward and call
1463% --- run0. The step forward is along the fieldname series 1 or 2 depending on
1464% --- the scan_i and scan_j check box (exclusive each other)
1465function runplus_Callback(hObject, eventdata, handles)
1466%------------------------------------------------------------------------
1467
1468set(handles.runplus,'BackgroundColor',[1 1 0])%paint the command button in yellow
1469drawnow
1470increment=str2double(get(handles.num_IndexIncrement,'String')); %get the field increment d
1471if isnan(increment)% case of free increment: move to next available field index
1472    increment='+';
1473end
1474errormsg=runpm(hObject,eventdata,handles,increment);
1475if ~isempty(errormsg)
1476    msgbox_uvmat('ERROR',errormsg);
1477end
1478set(handles.runplus,'BackgroundColor',[1 0 0])%paint the command button back to red
1479
1480%------------------------------------------------------------------------
1481% --- Executes on button press in runmin: make one step backward and call
1482% --- run0. The step backward is along the fieldname series 1 or 2 depending on
1483% --- the scan_i and scan_j check box (exclusive each other)
1484function runmin_Callback(hObject, eventdata, handles)
1485%------------------------------------------------------------------------
1486
1487set(handles.runmin,'BackgroundColor',[1 1 0])%paint the command button in yellow
1488drawnow
1489increment=-str2double(get(handles.num_IndexIncrement,'String')); %get the field increment d
1490if isnan(increment)% case of free increment: move to previous available field index
1491    increment='-';
1492end
1493errormsg=runpm(hObject,eventdata,handles,increment);
1494if ~isempty(errormsg)
1495    msgbox_uvmat('ERROR',errormsg);
1496end
1497set(handles.runmin,'BackgroundColor',[1 0 0])%paint the command button back to red
1498
1499%------------------------------------------------------------------------
1500% -- Executes on button press in Movie: make a series of +> steps
1501function Movie_Callback(hObject, eventdata, handles)
1502%------------------------------------------------------------------------
1503
1504set(handles.Movie,'BackgroundColor',[1 1 0])%paint the command button in yellow
1505drawnow
1506increment=str2double(get(handles.num_IndexIncrement,'String')); %get the field increment d
1507if isnan(increment)% case of free increment: move to next available field index
1508    increment='+';
1509end
1510set(handles.STOP,'Visible','on')
1511set(handles.speed,'Visible','on')
1512set(handles.speed_txt,'Visible','on')
1513set(handles.Movie,'BusyAction','queue')
1514UvData=get(handles.uvmat,'UserData');
1515
1516while get(handles.Movie,'Value')==1 && get(handles.speed,'Value')~=0 && isequal(get(handles.Movie,'BusyAction'),'queue') % enable STOP command
1517        errormsg=runpm(hObject,eventdata,handles,increment);
1518        if ~isempty(errormsg)
1519            set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1520            return
1521        end
1522        pause(1.02-get(handles.speed,'Value'))% wait for next image
1523end
1524if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1525    UvData.aviobj=close(UvData.aviobj);
1526   set(handles.uvmat,'UserData',UvData);
1527end
1528set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1529
1530%------------------------------------------------------------------------
1531% -- Executes on button press in Movie: make a series of <- steps
1532function MovieBackward_Callback(hObject, eventdata, handles)
1533%------------------------------------------------------------------------
1534set(handles.MovieBackward,'BackgroundColor',[1 1 0])%paint the command button in yellow
1535drawnow
1536increment=-str2double(get(handles.num_IndexIncrement,'String')); %get the field increment d
1537if isnan(increment)% case of free increment: move to next available field index
1538    increment='-';
1539end
1540set(handles.STOP,'Visible','on')
1541set(handles.speed,'Visible','on')
1542set(handles.speed_txt,'Visible','on')
1543set(handles.MovieBackward,'BusyAction','queue')
1544UvData=get(handles.uvmat,'UserData');
1545
1546while get(handles.MovieBackward,'Value')==1 && get(handles.speed,'Value')~=0 && isequal(get(handles.MovieBackward,'BusyAction'),'queue') % enable STOP command
1547        errormsg=runpm(hObject,eventdata,handles,increment);
1548        if ~isempty(errormsg)
1549            set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1550            return
1551        end
1552        pause(1.02-get(handles.speed,'Value'))% wait for next image
1553end
1554if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1555    UvData.aviobj=close(UvData.aviobj);
1556   set(handles.uvmat,'UserData',UvData);
1557end
1558set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1559
1560%------------------------------------------------------------------------
1561function STOP_Callback(hObject, eventdata, handles)
1562%------------------------------------------------------------------------
1563set(handles.movie_pair,'BusyAction','Cancel')
1564set(handles.movie_pair,'value',0)
1565set(handles.Movie,'BusyAction','Cancel')
1566set(handles.MovieBackward,'BusyAction','Cancel')
1567set(handles.MenuExportMovie,'BusyAction','Cancel')
1568set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1569set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1570set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1571
1572%------------------------------------------------------------------------
1573% --- function activated by runplus and run minus
1574function errormsg=runpm(hObject,eventdata,handles,increment)
1575%------------------------------------------------------------------------
1576errormsg='';%default
1577%% check for movie pair status
1578movie_status=get(handles.movie_pair,'Value');
1579if isequal(movie_status,1)
1580    STOP_Callback(hObject, eventdata, handles)%interrupt movie pair if active
1581end
1582
1583%% read the current input file name(s) and field indices
1584InputFile=read_GUI(handles.InputFile);
1585InputFile.RootFile=regexprep(InputFile.RootFile,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1586InputFile.SubDir=regexprep(InputFile.SubDir,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1587FileExt=InputFile.FileExt;
1588NomType=get(handles.NomType,'String');
1589i1=str2num(get(handles.i1,'String'));%read the field indices (for movie, it is not given by the file name)
1590i2=[];%default
1591if strcmp(get(handles.i2,'Visible'),'on')
1592    i2=str2num(get(handles.i2,'String'));
1593end
1594j1=[];
1595if strcmp(get(handles.j1,'Visible'),'on')
1596    j1=stra2num(get(handles.j1,'String'));
1597end
1598j2=j1;
1599if strcmp(get(handles.j2,'Visible'),'on')
1600    j2=stra2num(get(handles.j2,'String'));
1601end
1602sub_value= get(handles.SubField,'Value');
1603if sub_value % a second input file has been entered
1604     [InputFile.RootPath_1,InputFile.SubDir_1,InputFile.RootFile_1,InputFile.FileIndex_1,InputFile.FileExt_1,InputFile.NomType_1]=read_file_boxes_1(handles);   
1605    [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
1606else
1607    filename_1=[];
1608end   
1609
1610%% increment (or decrement) the field indices and update the input filename(s)
1611if ~isnumeric(increment)% undefined increment value
1612    set(handles.CheckFixPair,'Value',0)
1613end
1614CheckFixPair=get(handles.CheckFixPair,'Value')||(isempty(i2)&&isempty(j2));
1615
1616% the pair i1-i2 or j1-j2 is imposed (check box CheckFixPair selected)
1617        i1_1=i1;
1618        i2_1=i2;
1619        j1_1=j1;
1620        j2_1=j2;
1621if CheckFixPair && isnumeric(increment)
1622    if get(handles.scan_i,'Value')==1% case of scanning along index i
1623        i1=i1+increment;
1624        i2=i2+increment;
1625        if sub_value
1626            i1_1=i1_1+increment;
1627            i2_1=i2_1+increment;
1628        end       
1629    else % case of scanning along index j (burst numbers)
1630        j1=j1+increment;
1631        j2=j2+increment;
1632        if sub_value
1633            j1_1=j1_1+increment;
1634            j2_1=j2_1+increment;
1635        end
1636    end
1637   
1638% the pair i1-i2 or j1-j2 is free (check box CheckFixPair not selected): the list of existing indices recorded in UvData is used
1639else
1640    UvData=get(handles.uvmat,'UserData');
1641    ref_i=i1;
1642    if ~isempty(i2)
1643        ref_i=floor((i1+i2)/2);% current reference index i
1644    end
1645    ref_j=1;
1646    if ~isempty(j1)
1647        ref_j=j1;
1648        if ~isempty(j2)
1649            ref_j=floor((j1+j2)/2);% current reference index j
1650        end
1651    end
1652    if isnumeric(increment)
1653        if get(handles.scan_i,'Value')==1% case of scanning along index i
1654            ref_i=ref_i+increment;% increment the current reference index i
1655        else % case of scanning along index j (burst numbers)
1656            ref_j=ref_j+increment;% increment the current reference index j if scan_j option is used
1657        end
1658    else % free increment
1659        runaction=get(gcbo,'tag');
1660        if strcmp(increment,'+')% if runplus or movie is activated
1661            step=1;
1662        else
1663            step=-1;
1664        end
1665        if get(handles.scan_i,'Value')==1% case of scanning along index i
1666            ref_i=ref_i+step;
1667            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
1668                ref_i=ref_i+step;
1669            end
1670        else % case of scanning along index j (burst numbers)
1671            ref_j=ref_j+step;
1672            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
1673                ref_j=ref_j+step;
1674            end
1675        end
1676    end
1677    if ref_i<0
1678        errormsg='minimum i index reached';
1679    elseif ref_j<0
1680        errormsg='minimum j index reached';
1681    elseif ref_i+1>size(UvData.i1_series{1},3)
1682        errormsg='maximum i index reached (reload the input file to update the index bound)';
1683    elseif ref_j+1>size(UvData.i1_series{1},2)
1684        errormsg='maximum j index reached (reload the input file to update the index bound)';
1685    end
1686    if ~isempty(errormsg),return,end
1687    siz=size(UvData.i1_series{1});
1688    ref_indices=ref_i*siz(1)*siz(2)+ref_j*siz(1)+1:ref_i*siz(1)*siz(2)+(ref_j+1)*siz(1);
1689    i1_subseries=UvData.i1_series{1}(ref_indices);
1690    ref_indices=ref_indices(i1_subseries>0);
1691    if isempty(ref_indices)% case of pairs (free index i)
1692        ref_indices=ref_i*siz(1)*siz(2)+1:(ref_i+1)*siz(1)*siz(2);
1693        i1_subseries=UvData.i1_series{1}(ref_indices);
1694        ref_indices=ref_indices(i1_subseries>0);
1695    end
1696    if isempty(ref_indices),errormsg='no next frame: set num_IndexIncrement =''*'' to reach the next existing file';return
1697    end
1698    i1=UvData.i1_series{1}(ref_indices(end));
1699    if ~isempty(UvData.i2_series{1})
1700        i2=UvData.i2_series{1}(ref_indices(end));
1701    end
1702    if ~isempty(UvData.j1_series{1})
1703        j1=UvData.j1_series{1}(ref_indices(end));
1704    end
1705    if ~isempty(UvData.j2_series{1})
1706        j2=UvData.j2_series{1}(ref_indices(end));
1707    end
1708   
1709    % case of a second file series
1710    if sub_value
1711        ref_i_1=i1_1;
1712        if ~isempty(i2_1)
1713            ref_i_1=floor((i1_1+i2_1)/2);% current reference index i
1714        end
1715        ref_j_1=1;
1716        if ~isempty(j1_1)
1717            ref_j_1=j1_1;
1718            if ~isempty(j2_1)
1719                ref_j_1=floor((j1_1+j2_1)/2);% current reference index j
1720            end
1721        end
1722        if isnumeric(increment)
1723            if get(handles.scan_i,'Value')==1% case of scanning along index i
1724                ref_i_1=ref_i_1+increment;% increment the current reference index i
1725            else % case of scanning along index j (burst numbers)
1726                ref_j_1=ref_j_1+increment;% increment the current reference index j if scan_j option is used
1727            end
1728        else % free increment, synchronise the ref indices with the first series
1729            ref_i_1=ref_i;
1730            ref_j_1=ref_j;
1731        end
1732        if numel(UvData.i1_series)==1
1733            UvData.i1_series{2}=UvData.i1_series{1};
1734            UvData.j1_series{2}=UvData.j1_series{1};
1735            UvData.i2_series{2}=UvData.i2_series{1};
1736            UvData.j2_series{2}=UvData.j2_series{1};
1737        end
1738        if ref_i_1<0
1739            errormsg='minimum i index reached';
1740        elseif ref_j_1<0
1741            errormsg='minimum j index reached';
1742        elseif ref_i_1+1>size(UvData.i1_series{2},3)
1743            errormsg='maximum i index reached for the second series (reload the input file to update the index bound)';
1744        elseif ref_j_1+1>size(UvData.i1_series{2},2)
1745            errormsg='maximum j index reached for the second series(reload the input file to update the index bound)';
1746        end
1747        if ~isempty(errormsg),return,end
1748        siz=size(UvData.i1_series{2});
1749        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);
1750        i1_subseries=UvData.i1_series{2}(ref_indices);
1751        ref_indices=ref_indices(i1_subseries>0);
1752        if isempty(ref_indices)% case of pairs (free index i)
1753            ref_indices=ref_i_1*siz(1)*siz(2)+1:(ref_i_1+1)*siz(1)*siz(2);
1754            i1_subseries=UvData.i1_series{2}(ref_indices);
1755            ref_indices=ref_indices(i1_subseries>0);
1756        end
1757        i1_1=UvData.i1_series{2}(ref_indices(end));
1758        if ~isempty(UvData.i2_series{2})
1759            i2_1=UvData.i2_series{2}(ref_indices(end));
1760        end
1761        if ~isempty(UvData.j1_series{2})
1762            j1_1=UvData.j1_series{2}(ref_indices(end));
1763        end
1764        if ~isempty(UvData.j2_series{2})
1765            j2_1=UvData.j2_series{1}(ref_indices(end));
1766        end   
1767    else% the second series (if needed) is the same file as the first
1768        i1_1=i1;
1769        i2_1=i2;
1770        j1_1=j1;
1771        j2_1=j2;
1772    end
1773end
1774filename=fullfile_uvmat(InputFile.RootPath,InputFile.SubDir,InputFile.RootFile,FileExt,NomType,i1,i2,j1,j2);
1775if sub_value
1776    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);
1777end
1778
1779%% refresh plots
1780errormsg=refresh_field(handles,filename,filename_1,i1,i2,j1,j2,i1_1,i2_1,j1_1,j2_1);
1781
1782%% update the index counters if the index move is successfull
1783if isempty(errormsg)
1784    set(handles.i1,'String',num2stra(i1,NomType,1));
1785    if isequal(i2,i1)
1786        set(handles.i2,'String','');
1787    else
1788        set(handles.i2,'String',num2stra(i2,NomType,1));
1789    end
1790    set(handles.j1,'String',num2stra(j1,NomType,2));
1791    if isequal(j2,j1)
1792        set(handles.j2,'String','');
1793    else
1794        set(handles.j2,'String',num2stra(j2,NomType,2));
1795    end
1796    indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1797    set(handles.FileIndex,'String',indices);
1798    if ~isempty(filename_1)
1799        indices_1=fullfile_uvmat('','','','',InputFile.NomType_1,i1_1,i2_1,j1_1,j2_1);
1800        set(handles.FileIndex_1,'String',indices_1);
1801    end
1802    if isequal(movie_status,1)
1803        set(handles.movie_pair,'Value',1)
1804        movie_pair_Callback(hObject, eventdata, handles); %reactivate moviepair if it was activated
1805    end
1806end
1807
1808%------------------------------------------------------------------------
1809% --- Executes on button press in movie_pair: create an alternating movie with two view
1810function movie_pair_Callback(hObject, eventdata, handles)
1811%------------------------------------------------------------------------
1812
1813%% stop movie action if the movie_pair button is off
1814if ~get(handles.movie_pair,'value')
1815    set(handles.movie_pair,'BusyAction','Cancel')%stop movie pair if button is 'off'
1816    set(handles.i2,'String','')
1817    set(handles.j2,'String','')
1818    return
1819else
1820    set(handles.movie_pair,'BusyAction','queue')
1821end
1822
1823%% initialisation
1824set(handles.movie_pair,'BackgroundColor',[1 1 0])%paint the command button in yellow
1825drawnow
1826list_fields=get(handles.FieldName,'String');% list menu fields
1827index_fields=get(handles.FieldName,'Value');% selected string index
1828FieldName=list_fields{index_fields}; % selected field
1829UvData=get(handles.uvmat,'UserData');
1830if isequal(FieldName,'image')
1831    index=1;
1832    [RootPath,SubDir,RootFile,FileIndices,Ext]=read_file_boxes(handles);
1833    NomType=get(handles.NomType,'String');
1834else
1835    list_fields=get(handles.FieldName_1,'String');% list menu fields
1836    index_fields=get(handles.FieldName_1,'Value');% selected string index
1837    FieldName=list_fields{index_fields}; % selected field
1838    if isequal(FieldName,'image')
1839        index=2;
1840        [RootPath,tild,RootFile,FileIndex_1,Ext,NomType]=read_file_boxes_1(handles);
1841    else
1842        msgbox_uvmat('ERROR','an image or movie must be first introduced as input')
1843        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1844        set(handles.movie_pair,'Value',0)
1845        return
1846    end
1847end
1848num_i1=str2num(get(handles.i1,'String'));
1849num_j1=stra2num(get(handles.j1,'String'));
1850num_i2=str2num(get(handles.i2,'String'));
1851num_j2=stra2num(get(handles.j2,'String'));
1852imaname_1='';
1853if isempty(num_j2)
1854    if isempty(num_i2)
1855        if strcmp(get(handles.j2,'Visible'),'on') %if the j box is visible
1856            imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,Ext,NomType,num_i1,[],num_j1+1);
1857        end
1858        if exist(imaname_1,'file')
1859            num_j2=num_j1+1;% look by default for the next j index as the second file
1860            set(handles.j2,'String',num2stra(num_j2,NomType));
1861        else
1862            imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,Ext,NomType,num_i1+1,[],num_j1);
1863            if exist(imaname_1,'file')
1864                num_i2=num_i1+1;
1865                set(handles.i2,'String',num2str(num_i2));
1866            else
1867                msgbox_uvmat('ERROR', 'a second image index i2 or j2 is needed to show the pair as a movie')
1868                set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1869                set(handles.movie_pair,'Value',0)
1870                return
1871            end
1872        end
1873    else
1874        num_j2=num_j1;%repeat the index i1 by default
1875    end
1876end
1877if isempty(num_i2)
1878    num_i2=num_i1;%repeat the index i1 by default
1879end
1880imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,Ext,NomType,num_i2,[],num_j2);
1881if strcmp(NomType,'*')
1882    num_frame=num_i2;
1883else
1884    num_frame=num_j2;
1885end
1886if ~exist(imaname_1,'file')
1887      msgbox_uvmat('ERROR',['second input open (-)  ' imaname_1 ' not found']);
1888      set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1889       set(handles.movie_pair,'Value',0)
1890      return
1891end
1892
1893%% get the first image
1894%Field.AName='image';
1895if index==1
1896    Field_a=UvData.Field;% movie on the second field
1897else
1898    Field_a=UvData.Field_1;% movie on the first field
1899end
1900
1901%% read the second image
1902MovieObject=[];
1903if numel(UvData.MovieObject)>=index
1904    MovieObject=UvData.MovieObject{index};
1905end
1906[Field_b,ParamOut,errormsg] = read_field(imaname_1,UvData.FileType{index},MovieObject,num_frame);
1907% Field_b.AX=Field_a.AX;
1908% Field_b.AY=Field_a.AY;
1909% % z index
1910% nbslice=str2double(get(handles.num_NbSlice,'String'));
1911% if ~isempty(nbslice)
1912%     Field_b.ZIndex=mod(num_i2-1,nbslice)+1;
1913% end
1914% Field_b.CoordUnit='pixel';
1915%
1916% %% determine the input file type
1917% if (test_1 && isfield(UvData,'MovieObject')&& numel(UvData.MovieObject>=2))||(~test_1 && ~isempty(UvData.MovieObject{1}))
1918%     FileType='movie';
1919% elseif isequal(lower(Ext),'.avi')
1920%     FileType='avi';
1921% elseif isequal(lower(Ext),'.vol')
1922%     FileType='vol';
1923% else
1924%    form=imformats(Ext(2:end));
1925%    if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
1926%        if isequal(NomType,'*');
1927%            FileType='multimage';
1928%        else
1929%            FileType='image';
1930%        end
1931%    end
1932% end
1933% switch FileType
1934%         case 'movie'
1935%             if test_1
1936%                 Field_b.A=read(UvData.MovieObject{2},num_i2);
1937%             else
1938%                 Field_b.A=read(UvData.MovieObject{1},num_i2);
1939%             end
1940%         case 'avi'
1941%             mov=aviread(imaname_1,num_i2);
1942%             Field_b.A=frame2im(mov(1));
1943%         case 'vol'
1944%             Field_b.A=imread(imaname_1);
1945%         case 'multimage'
1946%             Field_b.A=imread(imaname_1,num_i2);
1947%         case 'image'
1948%             Field_b.A=imread(imaname_1);
1949% end
1950% if get(handles.slices,'Value')
1951%     Field.ZIndex=str2double(get(handles.z_index,'String'));
1952% end
1953
1954%px to phys or other transform on field
1955transform=get(handles.TransformPath,'UserData');
1956if  ~isempty(transform)
1957    if isfield(UvData,'XmlData') && numel(UvData.XmlData)>=index %use geometry calib recorded from the ImaDoc xml file as first priority
1958        if index==2
1959        Field_a=transform(Field_a,UvData.XmlData{index});%the first field has been stored without transform
1960        end
1961        Field_b=transform(Field_b,UvData.XmlData{index});
1962    end
1963end
1964
1965 % make movie until movie speed is set to 0 or STOP is activated
1966hima=findobj(handles.PlotAxes,'Tag','ima');% %handles.PlotAxes =main plotting window (A GENERALISER)
1967set(handles.STOP,'Visible','on')
1968set(handles.speed,'Visible','on')
1969set(handles.speed_txt,'Visible','on')
1970while get(handles.speed,'Value')~=0 && isequal(get(handles.movie_pair,'BusyAction'),'queue')%isequal(get(handles.run0,'BusyAction'),'queue'); % enable STOP command
1971    % read and plot the series of images in non erase mode
1972    set(hima,'CData',Field_b.A);
1973    pause(1.02-get(handles.speed,'Value'));% wait for next image
1974    set(hima,'CData',Field_a.A);
1975    pause(1.02-get(handles.speed,'Value'));% wait for next image
1976end
1977set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1978 set(handles.movie_pair,'Value',0)
1979
1980%------------------------------------------------------------------------
1981% --- Executes on button press in run0.
1982function run0_Callback(hObject, eventdata, handles)
1983%------------------------------------------------------------------------
1984set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
1985drawnow
1986[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
1987filename=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
1988filename_1='';%default
1989FileIndex_1='';
1990if get(handles.SubField,'Value')
1991    [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
1992    filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
1993end
1994num_i1=stra2num(get(handles.i1,'String'));
1995num_i2=stra2num(get(handles.i2,'String'));
1996num_j1=stra2num(get(handles.j1,'String'));
1997num_j2=stra2num(get(handles.j2,'String'));
1998[tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(FileIndex_1);% get the indices of the second series from the string FileIndex_1
1999if isempty(j1_1)% case of movies, the index is not given by file index
2000    j1_1=num_j1;
2001end
2002
2003errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1);
2004
2005if ~isempty(errormsg)
2006      msgbox_uvmat('ERROR',errormsg);
2007else
2008    set(handles.i1,'BackgroundColor',[1 1 1])
2009    set(handles.i2,'BackgroundColor',[1 1 1])
2010    set(handles.j1,'BackgroundColor',[1 1 1])
2011    set(handles.j2,'BackgroundColor',[1 1 1])
2012    set(handles.FileIndex,'BackgroundColor',[1 1 1])
2013    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
2014end   
2015set(handles.run0,'BackgroundColor',[1 0 0])
2016
2017
2018%------------------------------------------------------------------------
2019% --- read the input files and refresh all the plots, including projection.
2020% OUTPUT:
2021%  errormsg: error message char string  =[] by default
2022% INPUT:
2023% filename: first input file (=[] in the absence of input file)
2024% filename_1: second input file (=[] in the asbsenc of secodn input file)
2025% num_i1,num_i2,num_j1,num_j2; frame indices
2026% Field: structure describing an optional input field (then replace the input file)
2027
2028function errormsg=refresh_field(handles,FileName,FileName_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1)
2029%------------------------------------------------------------------------
2030
2031%% initialisation
2032if ~exist('Field','var')
2033    Field={};
2034end
2035UvData=get(handles.uvmat,'UserData');
2036if ishandle(handles.UVMAT_title) %remove title panel on uvmat
2037    delete(handles.UVMAT_title)
2038end
2039
2040%% determine the main input file information for action
2041if ~exist(FileName,'file')
2042    errormsg=['input file ' FileName ' does not exist'];
2043    return
2044end
2045NomType=get(handles.NomType,'String');
2046NomType_1='';
2047if strcmp(get(handles.NomType_1,'Visible'),'on')
2048    NomType_1=get(handles.NomType_1,'String');
2049end
2050%update the z position index
2051mode_slice=get(handles.slices,'String');
2052if strcmp(mode_slice,'volume')
2053    z_index=num_j1;
2054    set(handles.z_index,'String',num2str(z_index))
2055else
2056    nbslice=str2num(get(handles.num_NbSlice,'String'));
2057    z_index=mod(num_i1-1,nbslice)+1;
2058    set(handles.z_index,'String',num2str(z_index))
2059end
2060% refresh menu for save_mask if relevant
2061masknumber=get(handles.masklevel,'String');
2062if length(masknumber)>=z_index
2063    set(handles.masklevel,'Value',z_index)
2064end
2065
2066%% test for need of tps
2067check_proj_tps=0;
2068if  (strcmp(UvData.FileType{1},'civdata')||strcmp(UvData.FileType{1},'civx'))
2069    for iobj=1:numel(UvData.ProjObject)
2070        if isfield(UvData.ProjObject{iobj},'ProjMode')&& strcmp(UvData.ProjObject{iobj}.ProjMode,'interp_tps')
2071            check_proj_tps=1;
2072            break
2073        end
2074    end
2075end
2076
2077%% read the first input field
2078ParamIn.ColorVar='';%default variable name for vector color
2079frame_index=1;%default
2080FieldName='';%default
2081VelType='';%default
2082switch UvData.FileType{1}
2083    case {'civx','civdata','netcdf'};
2084        list_fields=get(handles.FieldName,'String');% list menu fields
2085        FieldName= list_fields{get(handles.FieldName,'Value')}; % selected field
2086        % if get_field... is selected, the GUI get_field will be used to enter fields
2087        if ~strcmp(FieldName,'get_field...')
2088            if get(handles.FixVelType,'Value')
2089                VelTypeList=get(handles.VelType,'String');
2090                VelType=VelTypeList{get(handles.VelType,'Value')};
2091            end
2092        end
2093        % case of input vector field, get the scalar used for vector color
2094        if ~isempty(regexp(FieldName,'^vec('))
2095            list_code=get(handles.ColorCode,'String');% list menu fields
2096            index_code=get(handles.ColorCode,'Value');% selected string index
2097            if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2098                list_code=get(handles.ColorScalar,'String');% list menu fields
2099                index_code=get(handles.ColorScalar,'Value');% selected string index
2100                ParamIn.ColorVar= list_code{index_code}; % selected field
2101            end
2102        end
2103    case {'video','mmreader'}
2104        ParamIn=UvData.MovieObject{1};     
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 'multimage'
2111        if ~strcmp(NomType,'*')
2112            frame_index=num_j1;%frame index for movies or multimage
2113        else
2114            frame_index=num_i1;
2115        end
2116    case 'vol' %TODO: update
2117        if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2118            ParamIn.Npy=UvData.XmlData.Npy;
2119            ParamIn.Npx=UvData.XmlData.Npx;
2120        else           
2121            errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2122            return
2123        end
2124end
2125if isstruct (ParamIn)
2126    ParamIn.FieldName=FieldName;
2127    ParamIn.VelType=VelType;
2128    XNameMenu=get(handles.Coord_x,'String');
2129    if ~isempty(XNameMenu)
2130        ParamIn.Coord_x=XNameMenu(get(handles.Coord_x,'Value'));
2131    end
2132    YNameMenu=get(handles.Coord_y,'String');
2133    if ~isempty(YNameMenu)
2134        ParamIn.Coord_y=YNameMenu(get(handles.Coord_y,'Value'));
2135    end
2136end
2137check_tps = 0;         
2138if strcmp(UvData.FileType{1},'civdata')&&~strcmp(ParamIn.FieldName,'velocity')&&~strcmp(ParamIn.FieldName,'get_field...')
2139       check_tps=1;%tps needed to get the requested field
2140end
2141[Field{1},ParamOut,errormsg] = read_field(FileName,UvData.FileType{1},ParamIn,frame_index);
2142if ~isempty(errormsg)
2143    errormsg=['uvmat / refresh_field / read_field( ' FileName ') / ' errormsg];
2144    return
2145end 
2146if isfield(ParamOut,'Npx')&& isfield(ParamOut,'Npy')
2147    set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2148    set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2149end
2150if isfield(ParamOut,'TimeIndex')% case of time obtained from get_field
2151    set(handles.i1,'String',num2str(ParamOut.TimeIndex))
2152end
2153if isfield(ParamOut,'TimeValue')
2154    Field{1}.Time=ParamOut.TimeValue;% case of time obtained from get_field
2155end
2156Field{1}.ZIndex=z_index; %used for multiplane 3D calibration
2157
2158
2159%% choose and read a second field FileName_1 if defined
2160VelType_1=[];%default
2161FieldName_1=[];
2162ParamIn_1=[];
2163ParamOut_1=[];
2164frame_index_1=1;
2165if ~isempty(FileName_1)
2166    if ~exist(FileName_1,'file')
2167        errormsg=['second file ' FileName_1 ' does not exist'];
2168        return
2169    end
2170   % Name=FileName_1;
2171    switch UvData.FileType{2}
2172        case {'civx','civdata','netcdf'};
2173            list_fields=get(handles.FieldName_1,'String');% list menu fields
2174            if ischar(list_fields),list_fields={list_fields};end
2175            FieldName_1= list_fields{get(handles.FieldName_1,'Value')}; % selected field
2176            if ~strcmp(FieldName,'get_field...')
2177                if get(handles.FixVelType,'Value')
2178                    VelTypeList=get(handles.VelType_1,'String');
2179                    VelType_1=VelTypeList{get(handles.VelType_1,'Value')};% read the velocity type.
2180                end
2181            end
2182            if strcmp(FieldName_1,'velocity')&& strcmp(get(handles.ColorCode,'Visible'),'on')
2183                list_code=get(handles.ColorCode,'String');% list menu fields
2184                index_code=get(handles.ColorCode,'Value');% selected string index
2185                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2186                    list_code=get(handles.ColorScalar,'String');% list menu fields
2187                    index_code=get(handles.ColorScalar,'Value');% selected string index
2188                    ParamIn_1.ColorVar= list_code{index_code}; % selected field for vector color display                 
2189                end
2190            end
2191        case {'video','mmreader'}
2192            ParamIn_1=UvData.MovieObject{2};
2193                        if ~strcmp(NomType_1,'*')
2194                frame_index_1=j1_1;%frame index for movies or multimage
2195            else
2196                frame_index_1=i1_1;
2197            end 
2198         case 'multimage'
2199            if strcmp(NomType_1,'*')%frame index for movies or multimage
2200                frame_index_1=i1_1;
2201            else
2202                frame_index_1=j1_1;
2203            end   
2204        case 'vol' %TODO: update
2205            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2206                ParamIn_1.Npy=UvData.XmlData.Npy;
2207                ParamIn_1.Npx=UvData.XmlData.Npx;
2208            else
2209                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2210                return
2211            end
2212    end
2213    if isequal(get(handles.NomType_1,'Visible'),'on')
2214    NomType_1=get(handles.NomType_1,'String');
2215    else
2216        NomType_1=get(handles.NomType,'String');
2217    end
2218    test_keepdata_1=0;% test for keeping the previous stored data if the input files are unchanged
2219    if ~isequal(NomType_1,'*')&& isfield(UvData,'FileName_1')
2220           test_keepdata_1= strcmp(FileName_1,UvData.FileName_1) ;
2221    end
2222    if test_keepdata_1
2223        Field{2}=UvData.Field_1;% keep the stored field
2224        ParamOut_1=UvData.ParamOut_1;
2225    else
2226        if isempty(ParamIn_1) || isstruct(ParamIn_1)
2227        ParamIn_1.FieldName=FieldName_1;
2228        ParamIn_1.VelType=VelType_1;
2229        ParamIn_1.GUIName='get_field_1';
2230        end 
2231        [Field{2},ParamOut_1,errormsg] = read_field(FileName_1,UvData.FileType{2},ParamIn_1,frame_index_1);
2232        if ~isempty(errormsg)
2233            errormsg=['error in reading ' FieldName_1 ' in ' FileName_1 ': ' errormsg];
2234            return
2235        end
2236        if isstruct(ParamOut_1)&&~strcmp(ParamOut_1.FieldName,'get_field...')&& (strcmp(UvData.FileType{2},'civdata')||strcmp(UvData.FileType{2},'civx'))...
2237                &&~strcmp(ParamOut_1.FieldName,'velocity') && ~strcmp(ParamOut_1.FieldName,'get_field...')
2238            if ~check_proj_tps
2239             %   Field{2}=calc_field([{ParamOut_1.FieldName} {ParamOut_1.ColorVar}],Field{2});
2240            end
2241        end
2242    end
2243    Field{2}.ZIndex=z_index;%used for multi-plane 3D calibration
2244end
2245
2246%% update uvmat interface
2247if isfield(ParamOut,'Npx')
2248    set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2249    set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2250elseif isfield(ParamOut_1,'Npx')
2251    set(handles.num_Npx,'String',num2str(ParamOut_1.Npx));% display image size on the interface
2252    set(handles.num_Npy,'String',num2str(ParamOut_1.Npy));
2253end
2254
2255%% update the display menu for the first velocity type (first menuline)
2256test_veltype=0;
2257% if ~isequal(FileType,'netcdf')|| isequal(FieldName,'get_field...')
2258if (strcmp(UvData.FileType{1},'civx')||strcmp(UvData.FileType{1},'civdata'))&& ~strcmp(FieldName,'get_field...')
2259    test_veltype=1;
2260    set(handles.VelType,'Visible','on')
2261    set(handles.VelType_1,'Visible','on')
2262    set(handles.FixVelType,'Visible','on')
2263    menu=set_veltype_display(ParamOut.CivStage,UvData.FileType{1});
2264    index_menu=strcmp(ParamOut.VelType,menu);%look for VelType in  the menu
2265    index_val=find(index_menu,1);
2266    if isempty(index_val)
2267        index_val=1;
2268    end
2269    set(handles.VelType,'Value',index_val)
2270    if ~get(handles.SubField,'value')
2271        set(handles.VelType,'String',menu)
2272        set(handles.VelType_1,'Value',1)
2273        set(handles.VelType_1,'String',[{''};menu])
2274    end
2275else
2276    set(handles.VelType,'Visible','off')
2277end
2278% display the FieldName menu from the input file and pick the selected one:
2279% if isstruct(ParamOut)
2280%     field_index=strcmp(ParamOut.FieldName,ParamOut.FieldList);
2281%     set(handles.FieldName,'String',ParamOut.FieldList); %update the field menu
2282%     set(handles.FieldName,'Value',find(field_index,1))
2283% end
2284
2285%% update the display menu for the second velocity type (second menuline)
2286test_veltype_1=0;
2287if isempty(FileName_1)
2288    %     set(handles.FieldName_1,'Value',1); %update the field menu
2289    %     if isstruct(ParamOut)
2290    %     set(handles.FieldName_1,'String',[{''};ParamOut.FieldList]); %update the field menu
2291    %     end
2292elseif ~test_keepdata_1
2293    if (~strcmp(UvData.FileType{2},'netcdf')&&~strcmp(UvData.FileType{2},'civdata')&&~strcmp(UvData.FileType{2},'civx'))|| isequal(FieldName_1,'get_field...')
2294        set(handles.VelType_1,'Visible','off')
2295    else
2296        test_veltype_1=1;
2297        set(handles.VelType_1,'Visible','on')
2298        menu=set_veltype_display(ParamOut_1.CivStage,UvData.FileType{2});
2299        index_menu=strcmp(ParamOut_1.VelType,menu);
2300        set(handles.VelType_1,'Value',1+find(index_menu,1))
2301        set(handles.VelType_1,'String',[{''};menu])
2302    end
2303    % update the second field menu: the same quantity
2304    if isstruct(ParamOut_1)
2305%        set(handles.FieldName_1,'String',[{''};ParamOut_1.FieldList]); %update the field menu
2306        % display the FieldName menu from the input file and pick the selected one:
2307        FieldList=get(handles.FieldName_1,'String');
2308        field_index=strcmp(ParamOut_1.FieldName,FieldList);
2309        if ~isempty(field_index)
2310            set(handles.FieldName_1,'Value',find(field_index,1))
2311        end
2312    end
2313end
2314if test_veltype||test_veltype_1
2315    set(handles.FixVelType,'Visible','on')
2316else
2317    set(handles.FixVelType,'Visible','off')
2318end
2319
2320% field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
2321% set(handles.FieldName,'String',ParamOut.FieldList); %update the field menu
2322% set(handles.FieldName,'Value',find(field_index,1))
2323   
2324%% introduce w as background image by default for a new series (only for nbdim=2)
2325if ~isfield(UvData,'NewSeries')
2326    UvData.NewSeries=1;
2327end
2328%put W as background image by default if NbDim=2:
2329if  UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W) && ~isequal(Field{1}.NbDim,3);
2330        set(handles.SubField,'Value',1);
2331        set(handles.RootPath_1,'String','"')
2332        set(handles.RootFile_1,'String','"')
2333        set(handles.SubDir_1,'String','"');
2334         indices=fullfile_uvmat('','','','',NomType,num_i1,num_i2,num_j1,num_j2);
2335        set(handles.FileIndex_1,'String',indices)
2336        set(handles.FileExt_1,'String','"');
2337        set(handles.FieldName_1,'Visible','on');
2338        set(handles.FieldName_1,'Visible','on');
2339        set(handles.RootPath_1,'Visible','on')
2340        set(handles.RootFile_1,'Visible','on')
2341        set(handles.SubDir_1,'Visible','on');
2342        set(handles.FileIndex_1,'Visible','on');
2343        set(handles.FileExt_1,'Visible','on');
2344        set(handles.FieldName_1,'Visible','on');
2345        Field{1}.AName='w';
2346end           
2347
2348%% display time
2349abstime=[];%default inputs
2350abstime_1=[];
2351dt=[];
2352TimeUnit='';
2353% time from xml file or video movie
2354if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'Time')
2355    if isempty(num_i2)||isnan(num_i2)
2356        num_i2=num_i1;
2357    end
2358    if isempty(num_j1)||isnan(num_j1)
2359        num_j1=1;
2360    end
2361    if isempty(num_j2)||isnan(num_j2)
2362        num_j2=num_j1;
2363    end
2364    siz=size(UvData.XmlData{1}.Time);
2365    if ~isempty(num_i1)&& ~isempty(num_i2) && num_i1>=0 &&siz(1)>=max(num_i1+1,num_i2+1) && siz(2)>=max(num_j1+1,num_j2+1)
2366        abstime=(UvData.XmlData{1}.Time(num_i1+1,num_j1+1)+UvData.XmlData{1}.Time(num_i2+1,num_j2+1))/2;%overset the time read from files
2367        dt=(UvData.XmlData{1}.Time(num_i2+1,num_j2+1)-UvData.XmlData{1}.Time(num_i1+1,num_j1+1));
2368        Field{1}.Dt=dt;
2369        if isfield(UvData.XmlData{1},'TimeUnit')
2370            TimeUnit=UvData.XmlData{1}.TimeUnit;
2371        end
2372    end
2373    if numel(UvData.XmlData)==2
2374        if isempty(i2_1)
2375            i2_1=num_i1;
2376        end
2377        if isempty(j1_1)
2378            j1_1=1;
2379        end
2380        if isempty(j2_1)
2381            j2_1=j1_1;
2382        end
2383        siz=size(UvData.XmlData{2}.Time);
2384        if ~isempty(i1_1) && siz(1)>=max(i1_1+1,i2_1+1) && siz(2)>=max(j1_1+1,j2_1+1)
2385            abstime_1=(UvData.XmlData{2}.Time(i1_1+1,j1_1+1)+UvData.XmlData{2}.Time(i2_1+1,j2_1+1))/2;%overset the time read from files
2386            Field{2}.Dt=(UvData.XmlData{2}.Time(i2_1+1,j2_1+1)-UvData.XmlData{2}.Time(i1_1+1,j1_1+1));
2387        end
2388    end
2389end
2390% if isfield(Field{1},'Time')
2391%     abstime=Field{1}.Time;%time read from the netcdf input file
2392% end
2393% if numel(Field)==2 && isfield(Field{2},'Time')
2394%     abstime_1=Field{2}.Time;%time read from the netcdf input file
2395% end
2396
2397% look for timing in the input file if not defined in a xml file or movie
2398if isempty(abstime)
2399if isfield(Field{1},'Dt')
2400    dt=Field{1}.Dt;%dt read from the netcdf input file
2401    if isfield(Field{1},'TimeUnit')
2402       TimeUnit=Field{1}.TimeUnit;
2403    end
2404elseif numel(Field)==2 && isfield(Field{2},'Dt')%dt obtained from the second field if not defined in the first
2405    dt=Field{2}.Dt;%dt read from the netcdf input file
2406    if isfield(Field{2},'TimeUnit')
2407       TimeUnit=Field{2}.TimeUnit;
2408    end
2409end
2410end
2411% if ~isequal(numel(abstime),1)
2412%     abstime=[];
2413% end
2414% if ~isequal(numel(abstime_1),1)
2415%       abstime_1=[];
2416% end 
2417set(handles.abs_time,'String',num2str(abstime,5))
2418set(handles.abs_time_1,'String',num2str(abstime_1,5))
2419if isempty(dt)||isequal(dt,0)
2420    set(handles.Dt_txt,'String','')
2421else
2422    if  isempty(TimeUnit)
2423        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  10^(-3)'] )
2424    else
2425        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  m' TimeUnit] )
2426    end
2427end
2428
2429
2430%% store the current open names, fieldname and vel types in uvmat interface
2431UvData.FileName_1=FileName_1;
2432UvData.ParamOut_1=ParamOut_1;
2433if numel(Field)==2
2434UvData.Field_1=Field{2}; %store the second field for possible use at next RUN
2435end
2436
2437%% apply coordinate transform or other user fct
2438transform=get(handles.TransformPath,'UserData');
2439if isempty(transform)
2440    UvData.Field=Field{1};
2441else
2442    XmlData=[];%default
2443    XmlData_1=[];%default
2444    if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority
2445        XmlData=UvData.XmlData{1};
2446        if numel(UvData.XmlData)==2
2447            XmlData_1=UvData.XmlData{2};
2448        end
2449    end
2450    transform=get(handles.TransformPath,'UserData');
2451    switch nargin(transform)
2452        case 4
2453            if length(Field)==2
2454                UvData.Field=transform(Field{1},XmlData,Field{2},XmlData_1);
2455            else
2456                UvData.Field=transform(Field{1},XmlData);
2457            end
2458        case 3
2459            if length(Field)==2
2460                UvData.Field=transform(Field{1},XmlData,Field{2});
2461            else
2462                UvData.Field=transform(Field{1},XmlData);
2463            end
2464        case 2
2465            UvData.Field=transform(Field{1},XmlData);
2466        case 1
2467            UvData.Field=transform(Field{1});
2468    end
2469end
2470
2471%% calculate tps coefficients if needed
2472UvData.Field=tps_coeff_field(UvData.Field,check_proj_tps);
2473
2474%% analyse input field
2475%test_x=0;
2476%test_z=0;% test for unstructured z coordinate
2477%[errormsg,ListDimName,DimValue,VarDimIndex]=check_field_structure(UvData.Field);% check the input field structure
2478% if ~isempty(errormsg)
2479%     errormsg=['error in uvmat/refresh_field/check_field_structure: ' errormsg];% display error
2480%     return
2481% end
2482[CellInfo,NbDimArray,errormsg]=find_field_cells(UvData.Field);% analyse  the input field structure
2483if ~isempty(errormsg)
2484    errormsg=['uvmat /refresh_field / find_field_cells / ' errormsg];% display error
2485    return
2486end
2487
2488NbDim=max(NbDimArray);% spatial dimension of the input field
2489imax=find(NbDimArray==NbDim);% indices of field cells to consider
2490if isfield(UvData.Field,'NbDim')
2491    NbDim=double(UvData.Field.NbDim);% deal with plane fields containing z coordinates
2492end
2493
2494%UvData.Field=get_bounds(UvData.Field);
2495
2496%% get bounds and mesh (needed  to propose default options for projection objects)
2497if NbDim>1
2498    CoordMax=zeros(numel(imax),NbDim);
2499    CoordMin=zeros(numel(imax),NbDim);
2500    Mesh=zeros(1,numel(imax));
2501    for ind=1:numel(imax)
2502        if strcmp(CellInfo{imax(ind)}.CoordType,'tps')
2503            CoordName=UvData.Field.ListVarName{CellInfo{imax(ind)}.CoordIndex};% X,Y coordinates in a single variable
2504            CoordMax(ind,NbDim)=max(max(UvData.Field.(CoordName)(1:end-3,1,:),[],1),[],3);% max of x component (2D case)
2505            CoordMax(ind,NbDim-1)=max(max(UvData.Field.(CoordName)(1:end-3,2,:),[],1),[],3);% max of y component (2D case)
2506            CoordMin(ind,NbDim)=min(min(UvData.Field.(CoordName)(1:end-3,1,:),[],1),[],3);
2507            CoordMin(ind,NbDim-1)=min(min(UvData.Field.(CoordName)(1:end-3,2,:),[],1),[],3);% min of y component (2D case)
2508        else
2509            XName=UvData.Field.ListVarName{CellInfo{imax(ind)}.CoordIndex(end)};
2510            YName=UvData.Field.ListVarName{CellInfo{imax(ind)}.CoordIndex(end-1)};
2511            CoordMax(ind,NbDim)=max(max(UvData.Field.(XName)));
2512            CoordMin(ind,NbDim)=min(min(UvData.Field.(XName)));
2513            CoordMax(ind,NbDim-1)=max(max(UvData.Field.(YName)));
2514            CoordMin(ind,NbDim-1)=min(min(UvData.Field.(YName)));
2515            %         test_x=1;%test for unstructured coordinates
2516            if NbDim==3
2517                ZName=UvData.Field.ListVarName{CellInfo{imax(ind)}.CoordIndex(1)};
2518                CoordMax(imax(ind),1)=max(max(UvData.Field.(ZName)));
2519                CoordMin(ind,1)=min(min(UvData.Field.(ZName)));
2520            end
2521        end
2522        switch CellInfo{imax(ind)}.CoordType
2523           
2524            case {'scattered','tps'} %unstructured coordinates
2525                NbPoints=CellInfo{imax(ind)}.CoordSize;% total nbre of points
2526                Mesh(ind)=(prod(CoordMax(ind,:)-CoordMin(ind,:))/NbPoints)^(1/NbDim); %(volume or area per point)^(1/NbDim)
2527            case 'grid'%structured coordinate
2528                NbPoints=CellInfo{imax(ind)}.CoordSize;% nbre of points in each direction
2529                Mesh(ind)=min((CoordMax(ind,:)-CoordMin(ind,:))./(NbPoints-1));               
2530        end
2531    end
2532    UvData.Field.CoordMesh=min(Mesh);
2533    UvData.Field.XMax=max(CoordMax(ind,end));
2534    UvData.Field.XMin=min(CoordMin(ind,end));
2535    UvData.Field.YMax=max(CoordMax(ind,end-1));
2536    UvData.Field.YMin=max(CoordMin(ind,end-1));
2537    if NbDim==3
2538        UvData.Field.ZMax=max(CoordMax(ind,1));
2539        UvData.Field.ZMin=max(CoordMin(ind,1));
2540    end
2541    % adjust the mesh to a value 1, 2 , 5 *10^n
2542    ord=10^(floor(log10(UvData.Field.CoordMesh)));%order of magnitude
2543    if UvData.Field.CoordMesh/ord>=5
2544        UvData.Field.CoordMesh=5*ord;
2545    elseif UvData.Field.CoordMesh/ord>=2
2546        UvData.Field.CoordMesh=2*ord;
2547    else
2548        UvData.Field.CoordMesh=ord;
2549    end
2550    % default projection plane
2551    if isempty(UvData.ProjObject{1})
2552        UvData.ProjObject{1}.Type='plane';%main plotting plane
2553        UvData.ProjObject{1}.ProjMode='projection';%main plotting plane
2554       % UvData.ProjObject{1}.Coord=[0 0 0];
2555        UvData.ProjObject{1}.DisplayHandle.uvmat=[]; %plane not visible in uvmat
2556        UvData.ProjObject{1}.DisplayHandle.view_field=[]; %plane not visible in uvmat
2557    end
2558    %% 3D case (menuvolume)
2559    if NbDim==3% && UvData.NewSeries
2560        test_set_object=1;
2561        hset_object=findobj(allchild(0),'tag','set_object');% look for the set_object GUI
2562        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
2563        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
2564        if ~isempty(hset_object) %if set_object is detected
2565            delete(hset_object);% delete the GUI set_object if it does not fit
2566        end
2567        if test_set_object% reinitiate the GUI set_object
2568            delete_object(1);% delete the current projection object in the list UvData.ProjObject, delete its graphic representations and update the list displayed in handles.ListObject and 2
2569            UvData.ProjObject{1}.NbDim=NbDim;%test for 3D objects
2570            UvData.ProjObject{1}.RangeZ=UvData.Field.CoordMesh;%main plotting plane
2571            UvData.ProjObject{1}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen
2572            UvData.ProjObject{1}.Angle=[0 0 0];
2573            UvData.ProjObject{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR
2574            UvData.ProjObject{1}.Name='1-PLANE';
2575            UvData.ProjObject{1}.enable_plot=1;
2576            set_object(UvData.ProjObject{1},handles,ZBounds);
2577            set(handles.ListObject,'Value',1);
2578            set(handles.ListObject,'String',{'1-PLANE'});
2579            set(handles.edit_object,'Value',1)% put the plane in edit mode to enable the z cursor
2580            edit_object_Callback([],[], handles)
2581        end
2582        %multilevel case (single menuplane in a 3D space)
2583    elseif isfield(UvData,'Z')
2584        if isfield(UvData,'CoordType')&& isequal(UvData.CoordType,'phys') && isfield(UvData,'XmlData')
2585            XmlData=UvData.XmlData{1};
2586            if isfield(XmlData,'PlanePos')
2587                UvData.ProjObject{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:);
2588            end
2589            if isfield(XmlData,'PlaneAngle')
2590                siz=size(XmlData.PlaneAngle);
2591                indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning)
2592                UvData.ProjObject{1}.PlaneAngle=XmlData.PlaneAngle(indangle,:);
2593            end
2594        elseif isfield(UvData,'ZIndex')
2595            UvData.ProjObject{1}.ZObject=UvData.ZIndex;
2596        end
2597    end
2598end
2599
2600testnewseries=UvData.NewSeries;
2601UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback)
2602set(handles.uvmat,'UserData',UvData)
2603
2604%% reset the min and max of scalar if only the mask is displayed(TODO: check the need)
2605% if isfield(UvData,'Mask')&& ~isfield(UvData,'A')
2606%     set(handles.num_MinA,'String','0')
2607%     set(handles.num_MaxA,'String','255')
2608% end
2609
2610%% usual 1D (x,y) plots
2611if NbDim<=1
2612    set(handles.Objects,'Visible','off')
2613    set(handles.ListObject_1_title,'Visible','off')
2614    set(handles.ListObject_1,'Visible','off')
2615    [PlotType,PlotParamOut]=plot_field(UvData.Field,handles.PlotAxes,read_GUI(handles.uvmat));
2616    errormsg=fill_GUI(PlotParamOut,handles.uvmat);
2617    for list={'Scalar','Vectors'}
2618        if ~isfield(PlotParamOut,list{1})
2619            set(handles.(list{1}),'Visible','off')
2620        end
2621    end
2622   
2623%% 2D or 3D fieldname are generally projected
2624else
2625    set(handles.Objects,'Visible','on')
2626    set(handles.ListObject_1_title,'Visible','on')
2627    set(handles.ListObject_1,'Visible','on')
2628   
2629    %% Plot the projections on the selected  projection objects
2630    % main projection object (uvmat display)
2631    list_object=get(handles.ListObject_1,'String');
2632    if isequal(list_object,{''})||isequal(list_object,' ')%refresh list of objects if the menu is empty
2633        set(handles.ListObject,'Value',1)
2634        set(handles.ListObject,'String',{'plane'})
2635        UvData.ProjObject{1}.Type='plane';%main plotting plane
2636        UvData.ProjObject{1}.ProjMode='projection';%main plotting plane
2637        UvData.ProjObject{1}.DisplayHandle.uvmat=[]; %plane not visible in uvmat
2638        UvData.ProjObject{1}.DisplayHandle.view_field=[]; %plane not visible in uvmat
2639        set(handles.ListObject_1,'Value',1)
2640        set(handles.ListObject_1,'String',{'plane'})
2641    end
2642    IndexObj(1)=get(handles.ListObject_1,'Value');%selected projection object for main view
2643    if IndexObj(1)> numel(UvData.ProjObject)
2644        IndexObj(1)=1;%select the first object if the selected one does not exist
2645        set(handles.ListObject_1,'Value',1)
2646    end
2647    IndexObj(2)=get(handles.ListObject,'Value');%selected projection object for main view
2648    if isequal(IndexObj(2),IndexObj(1))
2649        IndexObj(2)=[];
2650    end
2651    plot_handles{1}=handles;
2652    if isfield(UvData,'plotaxes')%case of movies
2653        haxes(1)=UvData.plotaxes;
2654    else
2655        haxes(1)=handles.PlotAxes;
2656    end
2657    PlotParam{1}=read_GUI(handles.uvmat);
2658    %default settings if vectors not visible
2659    if ~isfield(PlotParam{1},'Vectors')
2660        PlotParam{1}.Vectors.MaxVec=1;
2661        PlotParam{1}.Vectors.MinVec=0;
2662        PlotParam{1}.Vectors.CheckFixVecColor=1;
2663        PlotParam{1}.Vectors.ColCode1=0.33;
2664        PlotParam{1}.Vectors.ColCode2=0.66;
2665        PlotParam{1}.Vectors.ColorScalar={''};
2666        PlotParam{1}.Vectors.ColorCode= {'rgb'};
2667    end
2668    PosColorbar{1}=UvData.OpenParam.PosColorbar;%prescribe the colorbar position on the uvmat interface
2669   
2670    %% second projection object (view_field display)
2671    if length( IndexObj)>=2
2672        view_field_handle=findobj(allchild(0),'tag','view_field');%handles of the view_field GUI
2673        if ~isempty(view_field_handle)
2674            plot_handles{2}=guidata(view_field_handle);
2675            haxes(2)=plot_handles{2}.PlotAxes;
2676            PlotParam{2}=read_GUI(view_field_handle);
2677           % PlotParam{2}=read_GUI(handles.uvmat);%read plotting parameters on the uvmat interface
2678            PosColorbar{2}='*'; %TODO: deal with colorbar position on view_field
2679        end
2680    end
2681   
2682    %% loop on the projection objects: one or two
2683   
2684    for imap=1:numel(IndexObj)
2685        iobj=IndexObj(imap);
2686        if numel(UvData.ProjObject)<iobj
2687            break
2688        end
2689        [ObjectData,errormsg]=proj_field(UvData.Field,UvData.ProjObject{iobj});% project field on the object
2690        if ~isempty(errormsg)
2691            return
2692        end
2693        if testnewseries
2694            PlotParam{imap}.Scalar.CheckBW=[]; %B/W option depends on the input field (image or scalar)
2695            if isfield(ObjectData,'CoordUnit')
2696                PlotParam{imap}.Coordinates.CheckFixAspectRatio=1;% set x and y scaling equal if CoordUnit is defined (common unit for x and y)
2697                PlotParam{imap}.Coordinates.AspectRatio=1; %set aspect ratio to 1
2698            end
2699        end
2700        %use of mask (TODO: check)
2701        if isfield(ObjectData,'NbDim') && isequal(ObjectData.NbDim,2) && isfield(ObjectData,'Mask') && isfield(ObjectData,'A')
2702            flag_mask=double(ObjectData.Mask>200);%=0 for masked regions
2703            AX=ObjectData.AX;%x coordiantes for the scalar field
2704            AY=ObjectData.AY;%y coordinates for the scalar field
2705            MaskX=ObjectData.MaskX;%x coordiantes for the mask
2706            MaskY=ObjectData.MaskY;%y coordiantes for the mask
2707            if ~isequal(MaskX,AX)||~isequal(MaskY,AY)
2708                nxy=size(flag_mask);
2709                sizpx=(ObjectData.MaskX(end)-ObjectData.MaskX(1))/(nxy(2)-1);%size of a mask pixel
2710                sizpy=(ObjectData.MaskY(1)-ObjectData.MaskY(end))/(nxy(1)-1);
2711                x_mask=ObjectData.MaskX(1):sizpx:ObjectData.MaskX(end); % pixel x coordinates for image display
2712                y_mask=ObjectData.MaskY(1):-sizpy:ObjectData.MaskY(end);% pixel x coordinates for image display
2713                %project on the positions of the scalar
2714                npxy=size(ObjectData.A);
2715                dxy(1)=(ObjectData.AY(end)-ObjectData.AY(1))/(npxy(1)-1);%grid mesh in y
2716                dxy(2)=(ObjectData.AX(end)-ObjectData.AX(1))/(npxy(2)-1);%grid mesh in x
2717                xi=ObjectData.AX(1):dxy(2):ObjectData.AX(end);
2718                yi=ObjectData.AY(1):dxy(1):ObjectData.AY(end);
2719                [XI,YI]=meshgrid(xi,yi);% creates the matrix of regular coordinates
2720                flag_mask = interp2(x_mask,y_mask,flag_mask,XI,YI);
2721            end
2722            AClass=class(ObjectData.A);
2723            ObjectData.A=flag_mask.*double(ObjectData.A);
2724            ObjectData.A=feval(AClass,ObjectData.A);
2725        end
2726        if ~isempty(ObjectData)
2727            %PlotType='none'; %default
2728            if imap==2 && isempty(view_field_handle)
2729                view_field(ObjectData)
2730            else
2731                [PlotType,PlotParamOut]=plot_field(ObjectData,haxes(imap),PlotParam{imap},PosColorbar{imap});
2732                if imap==1
2733                    errormsg=fill_GUI(PlotParamOut,handles.uvmat);
2734                else
2735                    errormsg=fill_GUI(PlotParamOut,view_field_handle);
2736                end
2737                for list={'Scalar','Vectors'}
2738                    if ~isfield(PlotParamOut,list{1})
2739                        set(plot_handles{imap}.(list{1}),'Visible','off')
2740                    end
2741                end
2742                if isfield(Field,'CoordMesh')&&~isempty(Field.CoordMesh)
2743                    ObjectData.CoordMesh=Field.CoordMesh; % gives an estimated mesh size (useful for mouse action on the plot)
2744                end
2745            end
2746        end
2747    end
2748   
2749    %% update the mask
2750    if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
2751        update_mask(handles,num_i1,num_i2);
2752    end
2753   
2754    %% prepare the menus of histograms and plot them (histogram of the whole volume in 3D case)
2755    menu_histo=(UvData.Field.ListVarName)';%list of field variables to be displayed for the menu of histogram display
2756    ind_skip=[];
2757    % nb_histo=1;
2758    Ustring='';
2759    Vstring='';
2760    % suppress coordinates from the histogram menu
2761    for ivar=1:numel(menu_histo)%l loop on field variables:
2762        if isfield(UvData.Field,'VarAttribute') && numel(UvData.Field.VarAttribute)>=ivar && isfield(UvData.Field.VarAttribute{ivar},'Role')
2763            Role=UvData.Field.VarAttribute{ivar}.Role;
2764            switch Role
2765                case {'coord_x','coord_y','coord_z','dimvar'}
2766                    ind_skip=[ind_skip ivar];
2767                case {'vector_x'}
2768                    Ustring=UvData.Field.ListVarName{ivar};
2769                    ind_skip=[ind_skip ivar];
2770                case {'vector_y'}
2771                    Vstring=UvData.Field.ListVarName{ivar};
2772                    ind_skip=[ind_skip ivar];
2773            end
2774        end
2775        DimCell=UvData.Field.VarDimName{ivar};
2776        DimName='';
2777        if ischar(DimCell)
2778            DimName=DimCell;
2779        elseif iscell(DimCell)&& numel(DimCell)==1
2780            DimName=DimCell{1};
2781        end
2782        if strcmp(DimName,menu_histo{ivar})
2783            ind_skip=[ind_skip ivar];
2784        end
2785    end
2786    menu_histo(ind_skip)=[];% remove skipped items
2787    if ~isempty(Ustring)
2788        menu_histo=[{[Ustring ',' Vstring]};menu_histo];% add U, V at the beginning if they exist
2789    end
2790   
2791    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2792    % display menus and plot histograms
2793    test_v=0;
2794    if ~isempty(menu_histo)
2795        set(handles.histo1_menu,'Value',1)
2796        set(handles.histo1_menu,'String',menu_histo)
2797        histo1_menu_Callback(handles.histo1_menu, [], handles)% plot first histogram
2798    end
2799end
2800
2801%------------------------------------------------------------------------
2802function histo1_menu_Callback(hObject, eventdata, handles)
2803%--------------------------------------------
2804histo_menu=get(handles.histo1_menu,'String');
2805histo_value=get(handles.histo1_menu,'Value');
2806FieldName=histo_menu{histo_value};
2807
2808UvData=get(handles.uvmat,'UserData');
2809Field=UvData.Field;
2810r=regexp(FieldName,'(?<var1>.*)(?<sep>,)(?<var2>.*)','names');
2811FieldName_2='';
2812if ~isempty(r)
2813    FieldName=r.var1;
2814    FieldName_2=r.var2;
2815end
2816if ~isfield(UvData.Field,FieldName)
2817    msgbox_uvmat('ERROR',['no field  ' FieldName ' for histogram'])
2818    return
2819end
2820FieldHisto=Field.(FieldName);
2821if isfield(Field,'FF') && ~isempty(Field.FF) && isequal(size(Field.FF),size(FieldHisto))
2822    indsel=find(Field.FF==0);%find values marked as false
2823    if ~isempty(indsel)
2824        FieldHisto=FieldHisto(indsel);
2825        if ~isempty(FieldName_2)
2826            FieldHisto(:,:,2)=Field.(FieldName_2)(indsel);
2827        end
2828    end
2829end
2830if isempty(Field)
2831    msgbox_uvmat('ERROR',['empty field ' FieldName])
2832else
2833    nxy=size(FieldHisto);
2834    Amin=double(min(min(min(FieldHisto))));%min of field value
2835    Amax=double(max(max(max(FieldHisto))));%max of field value
2836    if isequal(Amin,Amax)
2837        cla(handles.HistoAxes)
2838    else
2839        Histo.ListVarName={FieldName,'histo'};
2840        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
2841            Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
2842        else
2843            if numel(nxy)==2
2844                Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
2845            else
2846                Histo.VarDimName={FieldName,{FieldName,'component'}}; %dimensions for the histogram
2847            end
2848        end
2849        %unit
2850        units=[]; %default
2851        for ivar=1:numel(Field.ListVarName)
2852            if strcmp(Field.ListVarName{ivar},FieldName)
2853                if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'units')
2854                    units=Field.VarAttribute{ivar}.units;
2855                    break
2856                end
2857            end
2858        end
2859        if ~isempty(units)
2860            Histo.VarAttribute{1}.units=units;
2861        end
2862        eval(['Histo.' FieldName '=linspace(Amin,Amax,50);'])%absissa values for histo
2863        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
2864            C=reshape(double(FieldHisto),1,[]);% reshape in a vector
2865            Histo.histo(:,1)=hist(C, Histo.(FieldName));  %calculate histogram
2866        else
2867            for col=1:size(FieldHisto,3)
2868                B=FieldHisto(:,:,col);
2869                C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector
2870                Histo.histo(:,col)=hist(C, Histo.(FieldName));  %calculate histogram
2871            end
2872        end
2873        plot_field(Histo,handles.HistoAxes);
2874        hlegend=legend;
2875        if isempty(FieldName_2)
2876        set(hlegend,'String',FieldName)
2877        else
2878            set(hlegend,'String',{FieldName;FieldName_2})
2879        end
2880    end
2881end
2882
2883%------------------------------------------------------------------------
2884% --- translate coordinate to matrix index
2885%------------------------------------------------------------------------
2886function [indx,indy]=pos2ind(x0,rangx0,nxy)
2887indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel 
2888indy=1+round((nxy(1)-1)*(y12-rangy0(1))/(rangy0(2)-rangy0(1)));% index y of pixel
2889
2890%------------------------------------------------------------------------
2891% --- Executes on button press in 'CheckZoom'.
2892%------------------------------------------------------------------------
2893function CheckZoom_Callback(hObject, eventdata, handles)
2894
2895if get(handles.CheckZoom,'Value')
2896    set(handles.CheckFixLimits,'Value',1)% propose by default fixed limits for the plotting axes
2897    set(handles.CheckZoomFig,'Value',0)%desactivate zoom fig
2898end
2899
2900%------------------------------------------------------------------------
2901% --- Executes on button press in CheckZoomFig.
2902%------------------------------------------------------------------------
2903function CheckZoomFig_Callback(hObject, eventdata, handles)
2904
2905if get(handles.CheckZoomFig,'Value')
2906    set(handles.CheckZoom,'value',0)
2907end
2908
2909%------------------------------------------------------------------------
2910% --- Executes on button press in 'CheckFixLimits'.
2911%------------------------------------------------------------------------
2912function CheckFixLimits_Callback(hObject, eventdata, handles)
2913
2914if ~get(handles.CheckFixLimits,'Value')
2915    update_plot(handles);
2916end
2917
2918%------------------------------------------------------------------------
2919% --- Executes on button press in CheckFixAspectRatio.
2920function CheckFixAspectRatio_Callback(hObject, eventdata, handles)
2921%------------------------------------------------------------------------
2922
2923if get(handles.CheckFixAspectRatio,'Value')
2924    update_plot(handles);
2925else
2926    update_plot(handles);
2927end
2928
2929%------------------------------------------------------------------------
2930function num_AspectRatio_Callback(hObject, eventdata, handles)
2931%------------------------------------------------------------------------
2932set(handles.CheckFixAspectRatio,'Value',1)% select the fixed aspect ratio button
2933update_plot(handles);
2934
2935%------------------------------------------------------------------------
2936%----Executes on button press in 'record': records the current flags of manual correction.
2937%------------------------------------------------------------------------
2938function record_Callback(hObject, eventdata, handles)
2939
2940[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
2941FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
2942[erread,message]=fileattrib(FileName);
2943if ~isempty(message) && ~isequal(message.UserWrite,1)
2944     msgbox_uvmat('ERROR',['no writting access to ' FileName])
2945     return
2946end
2947MenuVelType=get(handles.VelType,'String');
2948test_civ2=strcmp(MenuVelType{get(handles.VelType,'Value')},'civ2');
2949test_civ1=strcmp(MenuVelType{get(handles.VelType,'Value')},'civ1');
2950if ~test_civ2 && ~test_civ1
2951    msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
2952end
2953if test_civ2
2954    nbname='nb_vec_2';
2955   flagname='Civ2_FF';
2956   CivStage=5;
2957end
2958if test_civ1
2959    nbname='nb_vec_1';
2960   flagname='Civ1_FF';
2961    CivStage=2;
2962end
2963%write fix flags in the netcdf file
2964UvData=get(handles.uvmat,'UserData');
2965hhh=which('netcdf.open');% look for built-in matlab netcdf library
2966if ~isequal(hhh,'')% case of  builtin Matlab netcdf library
2967    nc=netcdf.open(FileName,'NC_WRITE');
2968    netcdf.reDef(nc);
2969    netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),'CivStage',CivStage);
2970    dimid = netcdf.inqDimID(nc,nbname);
2971    try
2972        varid = netcdf.inqVarID(nc,flagname);% look for already existing fixflag variable
2973    catch
2974        varid=netcdf.defVar(nc,flagname,'double',dimid);%create fixflag variable if it does not exist
2975    end
2976    netcdf.endDef(nc);
2977    netcdf.putVar(nc,varid,UvData.PlotAxes.FF);
2978    netcdf.close(nc); 
2979else %old netcdf library
2980    netcdf_toolbox(FileName,AxeData,attrname,nbname,flagname)
2981end
2982
2983%-------------------------------------------------------------------
2984%----Correct the netcdf file, using toolbox (old versions of Matlab).
2985%-------------------------------------------------------------------
2986function netcdf_toolbox(FileName,AxeData,attrname,nbname,flagname)
2987nc=netcdf(FileName,'write'); %open netcdf file
2988result=redef(nc);
2989eval(['nc.' attrname '=1;']);
2990theDim=nc(nbname) ;% get the number of velocity vectors
2991nb_vectors=size(theDim);
2992var_FixFlag=ncvar(flagname,nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag
2993var_FixFlag(1:nb_vectors)=AxeData.FF;%
2994fin=close(nc);
2995
2996%-------------------------------------------------------------------
2997% --- Executes on button press in SubField
2998function SubField_Callback(hObject, eventdata, handles)
2999%-------------------------------------------------------------------
3000UvData=get(handles.uvmat,'UserData');
3001if get(handles.SubField,'Value')==0% if the subfield button is desactivated   
3002    set(handles.RootPath_1,'String','')
3003    set(handles.RootFile_1,'String','')
3004    set(handles.SubDir_1,'String','');
3005    set(handles.FileIndex_1,'String','');
3006    set(handles.FileExt_1,'String','');
3007    set(handles.RootPath_1,'Visible','off')
3008    set(handles.RootFile_1,'Visible','off')
3009    set(handles.SubDir_1,'Visible','off');
3010    set(handles.NomType_1,'Visible','off');
3011    set(handles.abs_time_1,'Visible','off')
3012    set(handles.FileIndex_1,'Visible','off');
3013    set(handles.FileExt_1,'Visible','off');
3014    set(handles.FieldName_1,'Value',1);%set to blank state
3015    set(handles.VelType_1,'Value',1);%set to blank state
3016    set(handles.num_Opacity,'String','')% desactivate opacity setting
3017    FieldList=get(handles.FieldName,'String');
3018    if numel(FieldList)>1   % if a choice of fields exists
3019        set(handles.FieldName_1,'Value',1)% set second field choice to blank
3020        set(handles.FieldName_1,'String',[{''};FieldList])% reproduce the menu FieldName plus a blank option
3021    else
3022        set(handles.FieldName_1,'String',{''})% set second field choice to blank
3023    end
3024    if ~strcmp(get(handles.VelType,'Visible'),'on')
3025        set(handles.VelType_1,'Visible','off')
3026    end
3027    if isfield(UvData,'XmlData_1')
3028        UvData=rmfield(UvData,'XmlData_1');
3029    end
3030    set(handles.uvmat,'UserData',UvData);
3031    transform_fct_list=get(handles.TransformName,'String');
3032    transform_fct=transform_fct_list(get(handles.TransformName,'Value'));
3033    if strcmp(transform_fct,'sub_field')
3034        set(handles.TransformName,'Value',1)%suppress the sub_field transform
3035        transform_fct_Callback(hObject, eventdata, handles);
3036    else
3037        run0_Callback(hObject, eventdata, handles)
3038    end 
3039else
3040    MenuBrowse_1_Callback(hObject, eventdata, handles)
3041end
3042
3043%------------------------------------------------------------------------
3044% --- read the data displayed for the input rootfile windows (new): TODO use read_GUI
3045
3046function [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles)
3047%------------------------------------------------------------------------
3048InputFile=read_GUI(handles.InputFile);
3049RootPath=InputFile.RootPath;
3050SubDir=regexprep(InputFile.SubDir,'/|\','');
3051RootFile=regexprep(InputFile.RootFile,'/|\','');
3052FileIndices=InputFile.FileIndex;
3053FileExt=InputFile.FileExt;
3054
3055
3056%------------------------------------------------------------------------
3057% ---- read the data displayed for the second input rootfile windows
3058function [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1,NomType_1]=read_file_boxes_1(handles)
3059%------------------------------------------------------------------------
3060RootPath_1=get(handles.RootPath_1,'String'); % read the data from the file1_input window
3061if isequal(get(handles.RootPath_1,'Visible'),'off') || isequal(RootPath_1,'"')
3062    RootPath_1=get(handles.RootPath,'String');
3063end;
3064SubDir_1=get(handles.SubDir_1,'String');
3065if isequal(get(handles.SubDir_1,'Visible'),'off')|| isequal(SubDir_1,'"')
3066    SubDir_1=get(handles.SubDir,'String');
3067end
3068SubDir_1=regexprep(SubDir_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3069RootFile_1=get(handles.RootFile_1,'String');
3070if isequal(get(handles.RootFile_1,'Visible'),'off') || isequal(RootFile_1,'"')
3071    RootFile_1=get(handles.RootFile,'String');
3072end
3073RootFile_1=regexprep(RootFile_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3074FileIndex_1=get(handles.FileIndex_1,'String');
3075if isequal(get(handles.FileIndex_1,'Visible'),'off')|| isequal(FileIndex_1,'"')
3076    FileIndex_1=get(handles.FileIndex,'String');
3077end
3078FileExt_1=get(handles.FileExt_1,'String');
3079if isequal(get(handles.FileExt_1,'Visible'),'off') || isequal(FileExt_1,'"')
3080    FileExt_1=get(handles.FileExt,'String');%read FileExt by default
3081end
3082NomType_1=get(handles.NomType_1,'String');
3083if isequal(get(handles.NomType_1,'Visible'),'off') || isequal(NomType_1,'"')
3084    NomType_1=get(handles.NomType,'String');%read FileExt by default
3085end
3086%------------------------------------------------------------------------
3087% --- Executes on menu selection FieldName
3088function FieldName_Callback(hObject, eventdata, handles)
3089%------------------------------------------------------------------------
3090UvData=get(handles.uvmat,'UserData');
3091list_fields=get(handles.FieldName,'String');% list menu fields
3092index_fields=get(handles.FieldName,'Value');% selected string index
3093field= list_fields{index_fields(1)}; % selected string
3094
3095%% fill the coordinates and variables from selections in get_field
3096if isequal(field,'get_field...')
3097    ParamIn=[];
3098    if strcmp(get(handles.VelType,'Visible'),'on')
3099        % we use the civ choice as default input
3100        ParamIn.SwitchVarIndexTime='attribute';
3101        ListVelType=get(handles.VelType,'String');
3102        VelType=ListVelType{get(handles.VelType,'Value')};
3103        switch VelType
3104            case 'civ1'
3105                 ParamIn.TimeVarName='Civ1_Time';
3106                 ParamIn.vector_x='Civ1_U';
3107                 ParamIn.vector_y='Civ1_V';
3108                 ParamIn.vec_color='Civ1_C';               
3109            case 'filter1'
3110                 ParamIn.TimeVarName='Civ1_Time';
3111                 ParamIn.vector_x='Civ1_U_smooth';
3112                 ParamIn.vector_y='Civ1_V_smooth';
3113            case 'civ2'
3114                 ParamIn.TimeVarName='Civ2_Time';
3115                 ParamIn.vector_x='Civ2_U';
3116                 ParamIn.vector_y='Civ2_V';
3117            case 'filter2'
3118                 ParamIn.TimeVarName='Civ2_Time';
3119                 ParamIn.vector_x='Civ2_U_smooth';
3120                 ParamIn.vector_y='Civ2_V_smooth';
3121                 ParamIn.vec_color='Civ2_C';
3122        end
3123    end
3124    set(handles.FixVelType,'visible','off')
3125    set(handles.VelType,'Visible','off')
3126    set(handles.VelType_1,'Visible','off')
3127    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3128    FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3129%     hget_field=findobj(allchild(0),'name','get_field');
3130%     if ~isempty(hget_field)
3131%         delete(hget_field)
3132%     end
3133    GetFieldData=get_field(FileName,ParamIn);
3134    FieldList={};
3135    VecColorList={};
3136    XName=GetFieldData.XVarName;
3137    if GetFieldData.CheckVector
3138        UName=GetFieldData.PanelVectors.vector_x;
3139        VName=GetFieldData.PanelVectors.vector_y;
3140        XName=GetFieldData.XVarName;
3141        YName=GetFieldData.YVarName;
3142        CName=GetFieldData.PanelVectors.vec_color;
3143        [FieldList,VecColorList]=set_field_list(UName,VName,CName);
3144    elseif GetFieldData.CheckScalar
3145        AName=GetFieldData.PanelScalar.scalar;
3146        XName=GetFieldData.XVarName;
3147        YName=GetFieldData.YVarName;
3148        FieldList={AName};
3149    elseif GetFieldData.CheckPlot1D;
3150        YName=GetFieldData.CheckPlot1D.ordinate;
3151    end
3152    set(handles.Coord_x,'String',{XName})
3153    set(handles.Coord_y,'String',{YName})
3154    set(handles.FieldName,'Value',1)
3155    set(handles.FieldName,'String',[FieldList; {'get_field...'}]);
3156    set(handles.ColorScalar,'Value',1)
3157    set(handles.ColorScalar,'String',VecColorList);
3158    UvData.FileType{1}='netcdf';
3159    set(handles.uvmat,'UserData',UvData)
3160    run0_Callback(hObject, eventdata, handles)
3161    return %no further action
3162end
3163
3164
3165
3166%read the rootfile input display
3167[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3168FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3169[tild,tild,tild,i1,i2,j1,j2,tild,NomType]=fileparts_uvmat(['xxx' get(handles.FileIndex,'String') FileExt]);
3170if isequal(field,'image')
3171    if  isfield(UvData.Field,'Civ2_ImageA')%get the corresponding input image in the netcdf file
3172        imagename=UvData.Field.Civ2_ImageA;
3173    elseif isfield(UvData.Field,'Civ1_ImageA')%
3174        imagename=UvData.Field.Civ1_ImageA;
3175    else
3176        SubDirBase=regexprep(SubDir,'\..*','');%take the root part of SubDir, before the first dot '.'
3177        imagename=fullfile_uvmat(RootPath,SubDirBase,RootFile,'.png',NomType,i1,[],j1,[]);
3178    end
3179    if ~exist(imagename,'file')
3180        [FileName,PathName] = uigetfile( ...
3181            {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3182            '*.jpg',' jpeg image files'; ...
3183            '*.png','.png image files'; ...
3184            '*.tif','.tif image files'; ...
3185            '*.avi;*.AVI','.avi movie files'; ...
3186            '*.vol','.volume images (png)'; ...
3187            '*.*',  'All Files (*.*)'}, ...
3188            'Pick an image',imagename);
3189        if ~ischar(FileName),return,end %abandon if the browser is cancelled
3190        imagename=[PathName FileName];
3191    end
3192     % display the selected field and related information
3193    display_file_name(handles,imagename)%display the image
3194    return
3195else
3196    ext=get(handles.FileExt,'String');
3197    if ~isequal(ext,'.nc') %find the new NomType if the previous display was not already a netcdf file
3198        [FileName,PathName] = uigetfile( ...
3199            {'*.nc', ' (*.nc)';
3200            '*.nc',' netcdf files'; ...
3201            '*.*',  'All Files (*.*)'}, ...
3202            'Pick a netcdf file',FileBase);
3203        if ~ischar(FileName),return,end %abandon if the browser is cancelled
3204        FullFileName=[PathName FileName];
3205        % display the selected field and related information
3206        display_file_name( handles,FullFileName)
3207        return
3208    end
3209end
3210indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
3211set(handles.FileIndex,'String',indices)
3212
3213%common to Fields_1_Callback
3214list_fields_1=get(handles.FieldName_1,'String');% list menu fields
3215field_1='';
3216if ~isempty(list_fields_1)
3217field_1= list_fields_1{get(handles.FieldName_1,'Value')}; % selected string
3218end
3219if isequal(field,'image')||isequal(field_1,'image')
3220    set(handles.TitleNpxy,'Visible','on')% visible npx,pxcm... buttons
3221    set(handles.num_Npx,'Visible','on')
3222    set(handles.num_Npy,'Visible','on')
3223else
3224    set(handles.TitleNpxy,'Visible','off')% visible npx,pxcm... buttons
3225    set(handles.num_Npx,'Visible','off')
3226    set(handles.num_Npy,'Visible','off')
3227end
3228if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3229    run0_Callback(hObject, eventdata, handles)
3230end
3231
3232%----------------------------------------------------------------
3233% --- Executes on menu selection FieldName
3234function FieldName_1_Callback(hObject, eventdata, handles)
3235%-------------------------------------------------
3236%% read input data
3237check_new=~get(handles.SubField,'Value'); %check_new=1 if a second field was not previously entered
3238UvData=get(handles.uvmat,'UserData');
3239if check_new && isfield(UvData,'XmlData')
3240    UvData.XmlData{2}=UvData.XmlData{1};
3241end
3242if isfield(UvData,'Field_1')
3243    UvData=rmfield(UvData,'Field_1');% remove the stored second field (a new one needs to be read)
3244end
3245UvData.FileName_1='';% desactivate the use of a constant second file
3246list_fields=get(handles.FieldName,'String');% list menu fields
3247field= list_fields{get(handles.FieldName,'Value')}; % selected string
3248list_fields=get(handles.FieldName_1,'String');% list menu fields
3249field_1= list_fields{get(handles.FieldName_1,'Value')}; % selected string for the second field
3250if isempty(field_1)%||(numel(UvData.FileType)>=2 && strcmp(UvData.FileType{2},'image'))
3251    set(handles.SubField,'Value',0)
3252    SubField_Callback(hObject, eventdata, handles)
3253    return
3254else
3255    set(handles.SubField,'Value',1)%state that a second field is now entered
3256end
3257
3258%% read the rootfile input display
3259[RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
3260FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
3261[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
3262switch field_1
3263    case 'get_field...'
3264        set_veltype_display(0) % no veltype display
3265        hget_field=findobj(allchild(0),'name','get_field_1');
3266        if ~isempty(hget_field)
3267            delete(hget_field)
3268        end
3269        hget_field=get_field(FileName_1);
3270        set(hget_field,'name','get_field_1')
3271        hhget_field=guidata(hget_field);
3272        set(hhget_field.list_fig,'Value',1)
3273        set(hhget_field.list_fig,'String',{'uvmat'})
3274        if check_new
3275            UvData.FileType{2}=UvData.FileType{1};
3276            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3277              set(handles.uvmat,'UserData',UvData)
3278        end
3279    case 'image'
3280        % get the image name corresponding to the current netcdf name (no unique correspondance)
3281        if  isfield(UvData.Field,'Civ2_ImageA')%get the corresponding input image in the netcdf file
3282            imagename=UvData.Field.Civ2_ImageA;
3283        elseif isfield(UvData.Field,'Civ1_ImageA')%
3284            imagename=UvData.Field.Civ1_ImageA;
3285        else
3286            SubDirBase=regexprep(SubDir_1,'\..*','');%take the root part of SubDir, before the first dot '.'
3287            imagename=fullfile_uvmat(RootPath_1,SubDirBase,RootFile_1,'.png',get(handles.NomType,'String'),i1,[],j1);
3288        end
3289        if ~exist(imagename,'file') % browse for images if it is not found
3290            [FileName,PathName] = uigetfile( ...
3291                {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3292                '*.jpg',' jpeg image files'; ...
3293                '*.png','.png image files'; ...
3294                '*.tif','.tif image files'; ...
3295                '*.avi;*.AVI','.avi movie files'; ...
3296                '*.vol','.volume images (png)'; ...
3297                '*.*',  'All Files (*.*)'}, ...
3298                'Pick an image',imagename);
3299            if ~ischar(FileName),return,end %abandon if the browser is cancelled
3300            imagename=[PathName FileName];
3301        end
3302        if ~ischar(imagename)% quit if the browser has  been closed
3303            set(handles.SubField,'Value',0)
3304        else %valid browser input:  display the selected image
3305            set(handles.TitleNpxy,'Visible','on')% visible npx,pxcm... buttons
3306            set(handles.num_Npx,'Visible','on')
3307            set(handles.num_Npy,'Visible','on')
3308            display_file_name(handles,imagename,2)%display the imag
3309        end
3310    otherwise
3311        check_refresh=1;
3312        if check_new% if a second field was not previously entered, we just read another field in the first input file
3313            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3314            set(handles.FileExt_1,'String',get(handles.FileExt,'String'))
3315           
3316            UvData.FileType{2}=UvData.FileType{1};
3317            UvData.XmlData{2}= UvData.XmlData{1};
3318            transform=get(handles.TransformPath,'UserData');
3319             if (~isa(transform,'function_handle')||nargin(transform)<3)
3320                set(handles.uvmat,'UserData',UvData)
3321                set(handles.TransformName,'value',2); % set transform fct to 'sub_field' if the current fct does not accept two input fields
3322                transform_fct_Callback(hObject, eventdata, handles)% activate transform_fct_Callback and refresh current plot
3323                 check_refresh=0;
3324             end             
3325        end
3326        if ~isequal(field,'image')
3327            set(handles.TitleNpxy,'Visible','off')% visible npx,pxcm... buttons
3328            set(handles.num_Npx,'Visible','off')
3329            set(handles.num_Npy,'Visible','off')
3330        end
3331        set(handles.uvmat,'UserData',UvData)
3332 
3333        if check_refresh && ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3334            run0_Callback(hObject, eventdata, handles)
3335        end
3336end
3337
3338%------------------------------------------------------------------------
3339% --- set the visibility of relevant velocity type menus:
3340function menu=set_veltype_display(Civ,FileType)
3341%------------------------------------------------------------------------
3342if ~exist('FileType','var')
3343    FileType='civx';
3344end
3345switch FileType
3346    case 'civx'
3347        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3348        if isequal(Civ,0)
3349            imax=0;
3350        elseif isequal(Civ,1) || isequal(Civ,2)
3351            imax=1;
3352        elseif isequal(Civ,3)
3353            imax=3;
3354        elseif isequal(Civ,4) || isequal(Civ,5)
3355            imax=4;
3356        elseif isequal(Civ,6) %patch2
3357            imax=6;
3358        end
3359    case 'civdata'
3360        menu={'civ1';'filter1';'civ2';'filter2'};
3361        if isequal(Civ,0)
3362            imax=0;
3363        elseif isequal(Civ,1) || isequal(Civ,2)
3364            imax=1;
3365        elseif isequal(Civ,3)
3366            imax=2;
3367        elseif isequal(Civ,4) || isequal(Civ,5)
3368            imax=3;
3369        elseif isequal(Civ,6) %patch2
3370            imax=4;
3371        end
3372end
3373menu=menu(1:imax);
3374
3375%------------------------------------------------------------------------
3376% --- Executes on button press in FixVelType.
3377function FixVelType_Callback(hObject, eventdata, handles)
3378%------------------------------------------------------------------------
3379% refresh the current plot if the fixed  veltype is unselected
3380if ~get(handles.FixVelType,'Value')
3381    run0_Callback(hObject, eventdata, handles)
3382end
3383
3384%------------------------------------------------------------------------
3385% --- Executes on button press in VelType.
3386function VelType_Callback(hObject, eventdata, handles)
3387%------------------------------------------------------------------------
3388set(handles.FixVelType,'Value',1)
3389run0_Callback(hObject, eventdata, handles)
3390
3391%------------------------------------------------------------------------
3392% --- Executes on choice selection in VelType_1.
3393function VelType_1_Callback(hObject, eventdata, handles)
3394%------------------------------------------------------------------------
3395set(handles.FixVelType,'Value',1)% the velocity type is now imposed by the GUI (not automatic)
3396UvData=get(handles.uvmat,'UserData');
3397set(handles.run0,'BackgroundColor',[1 1 0])%paint run0 button in yellow to indicate its activation
3398drawnow   
3399InputFile=read_GUI(handles.InputFile);% read the input file parameters
3400[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
3401[RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
3402FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];% name of the first input file
3403
3404check_refresh=0;
3405if isempty(InputFile.VelType_1)
3406        FileName_1='';% we plot the first input field without the second field
3407        set(handles.SubField,'Value',0)
3408        SubField_Callback(hObject, eventdata, handles)% activate SubField_Callback and refresh current plot, removing the second field
3409elseif get(handles.SubField,'Value')% if subfield is already 'on'
3410     FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];% name of the second input file
3411     check_refresh=1;%will refresh the current plot
3412else% we introduce the same file (with a different field) for the second series
3413     FileName_1=FileName;% we compare two fields in the same file
3414     UvData.FileType{2}=UvData.FileType{1};
3415     UvData.XmlData{2}= UvData.XmlData{1};
3416     set(handles.SubField,'Value',1)
3417     transform=get(handles.TransformPath,'UserData');
3418     if (~isa(transform,'function_handle')||nargin(transform)<3)
3419        set(handles.uvmat,'UserData',UvData)
3420        set(handles.TransformName,'value',2); % set transform fct to 'sub_field' if the current fct does not accept two input fields
3421        transform_fct_Callback(hObject, eventdata, handles)% activate transform_fct_Callback and refresh current plot
3422     else
3423         check_refresh=1;
3424     end 
3425end
3426
3427% refresh the current plot if it has not been done previously
3428if check_refresh
3429    UvData.FileName_1='';% desactivate the use of a constant second file
3430    set(handles.uvmat,'UserData',UvData)
3431    num_i1=stra2num(get(handles.i1,'String'));
3432    num_i2=stra2num(get(handles.i2,'String'));
3433    num_j1=stra2num(get(handles.j1,'String'));
3434    num_j2=stra2num(get(handles.j2,'String'));
3435    [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(['xx' FileIndex_1]);
3436    errormsg=refresh_field(handles,FileName,FileName_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1);
3437    if ~isempty(errormsg)
3438        msgbox_uvmat('ERROR',errormsg);
3439    else
3440        set(handles.i1,'BackgroundColor',[1 1 1])
3441        set(handles.i2,'BackgroundColor',[1 1 1])
3442        set(handles.j1,'BackgroundColor',[1 1 1])
3443        set(handles.j2,'BackgroundColor',[1 1 1])
3444        set(handles.FileIndex,'BackgroundColor',[1 1 1])
3445        set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
3446    end
3447    set(handles.run0,'BackgroundColor',[1 0 0])
3448end
3449
3450
3451%------------------------------------------------------------------------
3452% --- reset civ buttons
3453function reset_vel_type(handles_civ0,handle1)
3454%------------------------------------------------------------------------
3455for ibutton=1:length(handles_civ0)
3456    set(handles_civ0(ibutton),'BackgroundColor',[0.831 0.816 0.784])
3457    set(handles_civ0(ibutton),'Value',0)
3458end
3459if exist('handle1','var')%handles of selected button
3460        set(handle1,'BackgroundColor',[1 1 0]) 
3461end
3462
3463%-----------------------------------------------------------------------
3464% --- Executes on button press in MENUVOLUME.
3465function VOLUME_Callback(hObject, eventdata, handles)
3466%-----------------------------------------------------------------------
3467%errordlg('command VOL not implemented yet')
3468if ishandle(handles.UVMAT_title)
3469    delete(handles.UVMAT_title)
3470end
3471UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3472if isequal(get(handles.VOLUME,'Value'),1)
3473    set(handles.CheckZoom,'Value',0)
3474%     set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3475    set(handles.edit_vect,'Value',0)
3476    edit_vect_Callback(hObject, eventdata, handles)
3477    set(handles.edit_object,'Value',0)
3478%     set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3479%     set(handles.cal,'Value',0)
3480%     set(handles.cal,'BackgroundColor',[0 1 0])
3481    set(handles.edit_vect,'Value',0)
3482    edit_vect_Callback(hObject, eventdata, handles)
3483    %initiate set_object GUI
3484    data.Name='VOLUME';
3485    if isfield(UvData,'CoordType')
3486        data.CoordType=UvData.CoordType;
3487    end
3488    if isfield(UvData.Field,'CoordMesh')&~isempty(UvData.Field.CoordMesh)
3489        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
3490        data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
3491        data.DX=UvData.Field.CoordMesh;
3492        data.DY=UvData.Field.CoordMesh;
3493    elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3494        np=size(UvData.Field.A);
3495        meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
3496        meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
3497        data.RangeY=max(meshx,meshy);
3498        data.RangeX=max(meshx,meshy);
3499        data.DX=max(meshx,meshy);
3500    end
3501    data.ParentButton=handles.VOLUME;
3502    PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
3503    [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes,
3504                                                      % associate the set_object interface handle to the plotting axes
3505    %set(hset_object,'Position',get(handles.uvmat,'Position')+UvData.OpenParam.PosSetObject)
3506    UvData.MouseAction='create_object';
3507else
3508    set(handles.VOLUME,'BackgroundColor',[0 1 0])
3509end
3510set(handles.uvmat,'UserData',UvData)
3511
3512%-------------------------------------------------------
3513function edit_vect_Callback(hObject, eventdata, handles)
3514%-------------------------------------------------------
3515%
3516if isequal(get(handles.edit_vect,'Value'),1)
3517    VelTypeMenu=get(handles.VelType,'String');
3518    VelType=VelTypeMenu{get(handles.VelType,'Value')};
3519    if ~strcmp(VelType,'civ2') && ~strcmp(VelType,'civ1')
3520        msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
3521    end
3522    set(handles.record,'Visible','on')
3523    set(handles.edit_vect,'BackgroundColor',[1 1 0])
3524    set(handles.edit_object,'Value',0)
3525    set(handles.CheckZoom,'Value',0)
3526%     set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3527%     set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3528    set(gcf,'Pointer','arrow')
3529else
3530    set(handles.record,'Visible','off')
3531    set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7])
3532end
3533
3534%----------------------------------------------
3535function save_mask_Callback(hObject, eventdata, handles)
3536%-----------------------------------------------------------------------
3537UvData=get(handles.uvmat,'UserData');
3538
3539flag=1;
3540npx=size(UvData.Field.A,2);
3541npy=size(UvData.Field.A,1);
3542xi=0.5:npx-0.5;
3543yi=0.5:npy-0.5;
3544[Xi,Yi]=meshgrid(xi,yi);
3545if isfield(UvData,'ProjObject')
3546    for iobj=1:length(UvData.ProjObject)
3547        ObjectData=UvData.ProjObject{iobj};
3548        if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
3549            flagobj=1;
3550            testphys=0; %coordinates in pixels by default
3551            if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys')
3552                if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
3553                    Calib=UvData.XmlData{1}.GeometryCalib;
3554                    testphys=1;
3555                end
3556            end
3557            if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style')
3558                if isequal(ObjectData.Type,'polygon')
3559                    X=ObjectData.Coord(:,1);
3560                    Y=ObjectData.Coord(:,2);
3561                    if testphys
3562                        [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
3563                    end
3564                    flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside                 
3565                elseif isequal(ObjectData.Type,'ellipse')
3566                    if testphys
3567                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3568                    end
3569                    RangeX=max(ObjectData.RangeX);
3570                    RangeY=max(ObjectData.RangeY);
3571                    X2Max=RangeX*RangeX;
3572                    Y2Max=RangeY*RangeY;
3573                    distX=(Xi-ObjectData.Coord(1,1));
3574                    distY=(Yi-ObjectData.Coord(1,2));
3575                    flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
3576                elseif isequal(ObjectData.Type,'rectangle')
3577                    if testphys
3578                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3579                    end
3580                    distX=abs(Xi-ObjectData.Coord(1,1));
3581                    distY=abs(Yi-ObjectData.Coord(1,2));
3582                    flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
3583                end
3584                if isequal(ObjectData.ProjMode,'mask_outside')
3585                    flagobj=~flagobj;
3586                end
3587                flag=flag & flagobj;
3588            end
3589        end
3590    end
3591end
3592% flag=~flag;
3593%mask name
3594RootPath=get(handles.RootPath,'String');
3595RootFile=get(handles.RootFile,'String');
3596RootFile=regexprep(RootFile,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3597filebase=fullfile(RootPath,RootFile);
3598list=get(handles.masklevel,'String');
3599masknumber=num2str(length(list));
3600maskindex=get(handles.masklevel,'Value');
3601mask_name=fullfile_uvmat(RootPath,SubDir,[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
3602%mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
3603imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
3604imflag=flipdim(imflag,1);
3605% imflag=uint8(255*flag);% =0 for flag=0 (vectors=0 when 20<imflag<200)
3606msgbox_uvmat('CONFIRMATION',[mask_name ' saved'])
3607imwrite(imflag,mask_name,'BitDepth',8);
3608
3609%display the mask
3610figure;
3611vec=linspace(0,1,256);%define a linear greyscale colormap
3612map=[vec' vec' vec'];
3613colormap(map)
3614
3615image(imflag);
3616
3617%------------------------------------------------------------------------
3618%------------------------------------------------------------------------
3619%  - FUNCTIONS FOR SETTING PLOTTING PARAMETERS
3620
3621%------------------------------------------------------------------------
3622%------------------------------------------------------------------------
3623% --- Executes on selection change in TransformName.
3624
3625function TransformName_Callback(hObject, eventdata, handles)
3626%------------------------------------------------------------------------
3627UvData=get(handles.uvmat,'UserData');
3628menu=get(handles.TransformName,'String');refresh
3629ichoice=get(handles.TransformName,'Value');%item number in the menu
3630transform_name=menu{ichoice};% choice of the transform fct
3631list_path=get(handles.TransformName,'UserData');
3632
3633%% add a new item to the menu if the option 'more...' has been selected
3634prev_path=fullfile(get(handles.TransformPath,'String'));
3635if ~exist(prev_path,'dir')
3636    prev_path=fullfile(fileparts(which('uvmat')),'transform_field');
3637end
3638if strcmp(transform_name,'more...');
3639    [FileName, PathName] = uigetfile( ...
3640        {'*.m', ' (*.m)';
3641        '*.m',  '.m files '; ...
3642        '*.*', 'All Files (*.*)'}, ...
3643        'Pick the transform function', prev_path);
3644    if ~ischar(FileName),return,end %abandon if the browser is cancelled
3645    path_transform_fct =fullfile(PathName,FileName);
3646    if isempty(regexp(FileName,'\.m$'))% detect file extension .m
3647        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3648        return
3649    else
3650        transform_name=regexprep(FileName,'\.m','');
3651    end
3652    ichoice=find(strcmp(transform_name,menu),1);%look for the selected fct in the existing menu
3653    if isempty(ichoice)% if the item is not found, add it to the menu (before 'more...' and select it)
3654        menu=[menu(1:end-1);{transform_name};{'more...'}];
3655        ichoice=numel(menu)-1;   
3656    end
3657    list_path{ichoice}=PathName;%update the list fo fct paths
3658    set(handles.TransformName,'String',menu)
3659    set(handles.TransformName,'Value',ichoice)
3660   
3661    % save the new menu in the personal file 'uvmat_perso.mat'
3662    dir_perso=prefdir;%personal Matalb directory
3663    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3664    if exist(profil_perso,'file')
3665        nb_builtin=UvData.OpenParam.NbBuiltin;% number of 'builtin' (basic) transform fcts in uvmat
3666        if nb_builtin<numel(list_path)
3667        for ilist=nb_builtin+1:numel(list_path)
3668            transform_fct{ilist-nb_builtin}=[fullfile(list_path{ilist},menu{ilist}) '.m'];
3669        end
3670        save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
3671        end
3672    end
3673end
3674
3675%% create the function handle of the selected fct
3676
3677if isempty(list_path{ichoice})% case of no selected fct
3678    transform_handle=[];
3679else
3680    if ~exist(list_path{ichoice},'dir')
3681        msgbox_uvmat('ERROR','invalid fct path: select the transform fct again with the option more...')
3682        return
3683    end
3684    current_dir=pwd;%current working dir
3685    cd(list_path{ichoice})
3686    transform_handle=str2func(transform_name);
3687    cd(current_dir)
3688end
3689set(handles.TransformPath,'String',list_path{ichoice})
3690set(handles.TransformPath,'UserData',transform_handle)
3691set(handles.TransformName,'UserData',list_path)
3692
3693%% update the ToolTip string of the menu TransformName with the first line of the selected fct file
3694if isempty(list_path{ichoice})% case of no selected fct
3695    set(handles.TransformName,'ToolTipString','transform_fct:choose a transform function')
3696else
3697    try
3698        [fid,errormsg] =fopen([fullfile(list_path{ichoice},transform_name) '.m']);
3699        InputText=textscan(fid,'%s',1,'delimiter','\n');
3700        fclose(fid)
3701        set(handles.TransformName,'ToolTipString',['transform_fct: ' InputText{1}{1}])% put the first line of the selected function as tooltip help
3702    end
3703end
3704
3705%% adapt the GUI to the input/output conditions of the selected transform fct
3706DataOut=[];
3707CoordUnit='';
3708CoordUnitPrev='';
3709if isfield(UvData,'Field')&&isfield(UvData.Field,'CoordUnit')
3710    CoordUnitPrev=UvData.Field.CoordUnit;
3711end
3712if ~isempty(list_path{ichoice})
3713    if nargin(transform_handle)>1 && isfield(UvData,'XmlData')&&~isempty(UvData.XmlData)
3714        XmlData=UvData.XmlData{1};
3715        DataOut=feval(transform_handle,'*',XmlData);
3716        if isfield(DataOut,'CoordUnit')
3717            CoordUnit=DataOut.CoordUnit;
3718        end
3719        if isfield(DataOut,'InputFieldType')
3720            UvData.InputFieldType=DataOut.InputFieldType;
3721        end
3722    else
3723        DataOut=feval(transform_handle,'*');
3724    end
3725end
3726
3727
3728%% delete drawn objects if the output CooordUnit is different from the previous one
3729if ~strcmp(CoordUnit,CoordUnitPrev)
3730    set(handles.CheckFixLimits,'Value',0)
3731% set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
3732    hother=findobj('Tag','proj_object');%find all the proj objects
3733    for iobj=1:length(hother)
3734        delete_object(hother(iobj))
3735    end
3736    hother=findobj('Tag','DeformPoint');%find all the proj objects
3737    for iobj=1:length(hother)
3738        delete_object(hother(iobj))
3739    end
3740    hh=findobj('Tag','calib_points');
3741    if ~isempty(hh)
3742        delete(hh)
3743    end
3744    hhh=findobj('Tag','calib_marker');
3745    if ~isempty(hhh)
3746        delete(hhh)
3747    end
3748    set(handles.ListObject,'Value',1)
3749    set(handles.ListObject,'String',{''})
3750    set(handles.ListObject_1,'Value',1)
3751    set(handles.ListObject_1,'String',{''})
3752    set(handles.ViewObject,'value',0)
3753    ViewObject_Callback(hObject, eventdata, handles)
3754    set(handles.ViewField,'value',0)
3755    ViewField_Callback(hObject, eventdata, handles)
3756    set(handles.edit_object,'Value',0)
3757    edit_object_Callback(hObject, eventdata, handles)
3758    UvData.ProjObject={[]};
3759end
3760set(handles.uvmat,'UserData',UvData)
3761
3762%% refresh the current plot
3763if isempty(list_path{ichoice}) || nargin(transform_handle)<3
3764    set(handles.SubField,'Value',0)
3765    SubField_Callback(hObject, eventdata, handles)
3766else
3767    run0_Callback(hObject, eventdata, handles)
3768end
3769
3770%------------------------------------------------
3771%CALLBACKS FOR PLOTTING PARAMETERS
3772%-------------------------------------------------
3773%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3774% Plot coordinates
3775%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3776%------------------------------------------------------------------------
3777function num_MinX_Callback(hObject, eventdata, handles)
3778%------------------------------------------------------------------------
3779set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3780% set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3781update_plot(handles);
3782
3783%------------------------------------------------------------------------
3784function num_MaxX_Callback(hObject, eventdata, handles)
3785%------------------------------------------------------------------------
3786set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3787% set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3788update_plot(handles);
3789
3790%------------------------------------------------------------------------
3791function num_MinY_Callback(hObject, eventdata, handles)
3792%------------------------------------------
3793set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3794% set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3795update_plot(handles);
3796
3797%------------------------------------------------------------------------
3798function num_MaxY_Callback(hObject, eventdata, handles)
3799%------------------------------------------------------------------------
3800set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3801% set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3802update_plot(handles);
3803
3804%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3805% Scalar or image representation
3806%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3807%------------------------------------------------------------------------
3808function num_MinA_Callback(hObject, eventdata, handles)
3809%------------------------------------------
3810set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3811% set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3812MinA=str2double(get(handles.num_MinA,'String'));
3813MaxA=str2double(get(handles.num_MaxA,'String'));
3814if MinA>MaxA% switch minA and maxA in case of error
3815    MinA_old=MinA;
3816    MinA=MaxA;
3817    MaxA=MinA_old;
3818    set(handles.num_MinA,'String',num2str(MinA,5));
3819    set(handles.num_MaxA,'String',num2str(MaxA,5));
3820end
3821update_plot(handles);
3822
3823%------------------------------------------------------------------------
3824function num_MaxA_Callback(hObject, eventdata, handles)
3825%------------------------------------------------------------------------
3826set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3827% set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3828MinA=str2double(get(handles.num_MinA,'String'));
3829MaxA=str2double(get(handles.num_MaxA,'String'));
3830if MinA>MaxA% switch minA and maxA in case of error
3831        MinA_old=MinA;
3832    MinA=MaxA;
3833    MaxA=MinA_old;
3834    set(handles.num_MinA,'String',num2str(MinA,5));
3835    set(handles.num_MaxA,'String',num2str(MaxA,5));
3836end
3837update_plot(handles);
3838
3839%------------------------------------------------------------------------
3840function CheckFixScalar_Callback(hObject, eventdata, handles)
3841%------------------------------------------------------------------------
3842test=get(handles.CheckFixScalar,'Value');
3843if test
3844%     set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3845else
3846%     set(handles.CheckFixScalar,'BackgroundColor',[0.7 0.7 0.7])
3847    update_plot(handles);
3848end
3849
3850%-------------------------------------------------------------------
3851function CheckBW_Callback(hObject, eventdata, handles)
3852%-------------------------------------------------------------------
3853update_plot(handles);
3854
3855%-------------------------------------------------------------------
3856function num_Opacity_Callback(hObject, eventdata, handles)
3857update_plot(handles);
3858%-------------------------------------------------------------------
3859
3860%-------------------------------------------------------------------
3861function ListContour_Callback(hObject, eventdata, handles)
3862%-------------------------------------------------------------------
3863val=get(handles.ListContour,'Value');
3864if val==2
3865    set(handles.interval_txt,'Visible','on')
3866    set(handles.num_IncrA,'Visible','on')
3867else
3868    set(handles.interval_txt,'Visible','off')
3869    set(handles.num_IncrA,'Visible','off')
3870end
3871update_plot(handles);
3872
3873%-------------------------------------------------------------------
3874function num_IncrA_Callback(hObject, eventdata, handles)
3875%-------------------------------------------------------------------
3876update_plot(handles);
3877
3878
3879%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3880% Vector representation
3881%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3882%-------------------------------------------------------------------
3883function CheckHideWarning_Callback(hObject, eventdata, handles)
3884%-------------------------------------------------------------------
3885update_plot(handles);
3886
3887%-------------------------------------------------------------------
3888function CheckHideFalse_Callback(hObject, eventdata, handles)
3889%-------------------------------------------------------------------
3890update_plot(handles);
3891
3892%-------------------------------------------------------------------
3893function num_VecScale_Callback(hObject, eventdata, handles)
3894%-------------------------------------------------------------------
3895set(handles.CheckFixVectors,'Value',1);
3896set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3897update_plot(handles);
3898
3899%-------------------------------------------------------------------
3900function CheckFixVectors_Callback(hObject, eventdata, handles)
3901%-------------------------------------------------------------------
3902test=get(handles.CheckFixVectors,'Value');
3903if test
3904%     set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3905else
3906    update_plot(handles);
3907    %set(handles.num_VecScale,'String',num2str(ScalOut.num_VecScale,3))
3908%     set(handles.CheckFixVectors,'BackgroundColor',[0.7 0.7 0.7])
3909end
3910
3911%------------------------------------------------------------------------
3912% --- Executes on selection change in CheckDecimate4 (nb_vec/4).
3913%------------------------------------------------------------------------
3914function CheckDecimate4_Callback(hObject, eventdata, handles)
3915
3916if isequal(get(handles.CheckDecimate4,'Value'),1)
3917    set(handles.CheckDecimate16,'Value',0)
3918end
3919update_plot(handles);
3920
3921%------------------------------------------------------------------------
3922% --- Executes on selection change in CheckDecimate16 (nb_vec/16).
3923%------------------------------------------------------------------------
3924function CheckDecimate16_Callback(hObject, eventdata, handles)
3925
3926if isequal(get(handles.CheckDecimate16,'Value'),1)
3927    set(handles.CheckDecimate4,'Value',0)
3928end
3929update_plot(handles);
3930
3931%------------------------------------------------------------------------
3932% --- Executes on selection change in ColorCode menu
3933function ColorCode_Callback(hObject, eventdata, handles)
3934%------------------------------------------------------------------------
3935% edit the choice for color code
3936update_color_code_boxes(handles);
3937update_plot(handles);
3938
3939%------------------------------------------------------------------------
3940function update_color_code_boxes(handles)
3941%------------------------------------------------------------------------
3942list_code=get(handles.ColorCode,'String');% list menu fields
3943colcode= list_code{get(handles.ColorCode,'Value')}; % selected field
3944enable_slider='off';%default
3945enable_bounds='off';%default
3946enable_scalar='off';%default
3947switch colcode
3948    case {'rgb','bgr'}
3949        enable_slider='on';
3950        enable_bounds='on';
3951        enable_scalar='on';
3952    case '64 colors'
3953        enable_bounds='on';
3954        enable_scalar='on';
3955end
3956set(handles.Slider1,'Visible',enable_slider)
3957set(handles.Slider2,'Visible', enable_slider)
3958set(handles.num_ColCode1,'Visible',enable_slider)
3959set(handles.num_ColCode2,'Visible',enable_slider)
3960set(handles.TitleColCode1,'Visible',enable_slider)
3961set(handles.TitleColCode2,'Visible',enable_slider)
3962set(handles.CheckFixVecColor,'Visible',enable_bounds)
3963set(handles.num_MinVec,'Visible',enable_bounds)
3964set(handles.num_MaxVec,'Visible',enable_bounds)
3965set(handles.ColorScalar,'Visible',enable_scalar)
3966set_vec_col_bar(handles)
3967
3968%------------------------------------------------------------------
3969% --- Executes on selection change in ColorScalar: choice of the color code.
3970function ColorScalar_Callback(hObject, eventdata, handles)
3971%------------------------------------------------------------------
3972% edit the choice for color code
3973list_scalar=get(handles.ColorScalar,'String');% list menu fields
3974col_scalar= list_scalar{get(handles.ColorScalar,'Value')}; % selected field
3975if isequal(col_scalar,'ima_cor')
3976    set(handles.CheckFixVecColor,'Value',1)%fixed scale by default
3977    ColorCode='rgb';
3978    set(handles.num_MinVec,'String','0')
3979    set(handles.num_MaxVec,'String','1')
3980    set(handles.num_ColCode1,'String','0.333')
3981    set(handles.num_ColCode2,'String','0.666')
3982else
3983    set(handles.CheckFixVecColor,'Value',0)%auto scale between min,max by default
3984    ColorCode='64 colors';
3985end
3986ColorCodeList=get(handles.ColorCode,'String');
3987ichoice=find(strcmp(ColorCode,ColorCodeList),1);
3988set(handles.ColorCode,'Value',ichoice)% set color code in the menu
3989
3990update_color_code_boxes(handles);
3991%replot the current graph
3992run0_Callback(hObject, eventdata, handles)
3993
3994%----------------------------------------------------------------
3995% -- Executes on slider movement to set the color code
3996%
3997function Slider1_Callback(hObject, eventdata, handles)
3998%------------------------------------------------------------------
3999slider1=get(handles.Slider1,'Value');
4000min_val=str2num(get(handles.num_MinVec,'String'));
4001max_val=str2num(get(handles.num_MaxVec,'String'));
4002col=min_val+(max_val-min_val)*slider1;
4003set(handles.num_ColCode1,'String',num2str(col))
4004if(get(handles.Slider2,'Value') < col)%move also the second slider at the same value if needed
4005    set(handles.Slider2,'Value',col)
4006    set(handles.num_ColCode2,'String',num2str(col))
4007end
4008set_vec_col_bar(handles)
4009update_plot(handles);
4010
4011%----------------------------------------------------------------
4012% Executes on slider movement to set the color code
4013%----------------------------------------------------------------
4014function Slider2_Callback(hObject, eventdata, handles)
4015slider2=get(handles.Slider2,'Value');
4016min_val=str2num(get(handles.num_MinVec,'String'));
4017max_val=str2num(get(handles.num_MaxVec,'String'));
4018col=min_val+(max_val-min_val)*slider2;
4019set(handles.num_ColCode2,'String',num2str(col))
4020if(get(handles.Slider1,'Value') > col)%move also the first slider at the same value if needed
4021    set(handles.Slider1,'Value',col)
4022    set(handles.num_ColCode1,'String',num2str(col))
4023end
4024set_vec_col_bar(handles)
4025update_plot(handles);
4026
4027%----------------------------------------------------------------
4028% --- Execute on return carriage on the edit box corresponding to slider 1
4029%----------------------------------------------------------------
4030function num_ColCode1_Callback(hObject, eventdata, handles)
4031set_vec_col_bar(handles)
4032update_plot(handles);
4033
4034%----------------------------------------------------------------
4035% --- Execute on return carriage on the edit box corresponding to slider 2
4036%----------------------------------------------------------------
4037function num_ColCode2_Callback(hObject, eventdata, handles)
4038set_vec_col_bar(handles)
4039update_plot(handles);
4040%------------------------------------------------------------------------
4041%-------------------------------------------------------
4042% --- Executes on button press in CheckFixVecColor.
4043%-------------------------------------------------------
4044function VecColBar_Callback(hObject, eventdata, handles)
4045set_vec_col_bar(handles)
4046
4047%------------------------------------------------------------------------
4048% --- Executes on button press in CheckFixVecColor.
4049function CheckFixVecColor_Callback(hObject, eventdata, handles)
4050%------------------------------------------------------------------------
4051if ~get(handles.CheckFixVecColor,'Value')
4052    update_plot(handles);
4053end
4054
4055%------------------------------------------------------------------------
4056% --- Executes on selection change in num_MaxVec.
4057function num_MinVec_Callback(hObject, eventdata, handles)
4058%------------------------------------------------------------------------
4059max_vec_Callback(hObject, eventdata, handles)
4060
4061%------------------------------------------------------------------------
4062% --- Executes on selection change in num_MaxVec.
4063function num_MaxVec_Callback(hObject, eventdata, handles)
4064%------------------------------------------------------------------------
4065set(handles.CheckFixVecColor,'Value',1)
4066CheckFixVecColor_Callback(hObject, eventdata, handles)
4067min_val=str2num(get(handles.num_MinVec,'String'));
4068max_val=str2num(get(handles.num_MaxVec,'String'));
4069slider1=get(handles.Slider1,'Value');
4070slider2=get(handles.Slider2,'Value');
4071colcode1=min_val+(max_val-min_val)*slider1;
4072colcode2=min_val+(max_val-min_val)*slider2;
4073set(handles.num_ColCode1,'String',num2str(colcode1))
4074set(handles.num_ColCode2,'String',num2str(colcode2))
4075update_plot(handles);
4076
4077%------------------------------------------------------------------------
4078% --- update the display of color code for vectors (on vecColBar)
4079function set_vec_col_bar(handles)
4080%------------------------------------------------------------------------
4081%get the image of the color display button 'VecColBar' in pixels
4082set(handles.VecColBar,'Unit','pixel');
4083pos_vert=get(handles.VecColBar,'Position');
4084set(handles.VecColBar,'Unit','Normalized');
4085width=ceil(pos_vert(3));
4086height=ceil(pos_vert(4));
4087
4088%get slider indications
4089list=get(handles.ColorCode,'String');
4090ichoice=get(handles.ColorCode,'Value');
4091colcode.ColorCode=list{ichoice};
4092colcode.MinVec=str2num(get(handles.num_MinVec,'String'));
4093colcode.MaxVec=str2num(get(handles.num_MaxVec,'String'));
4094test3color=strcmp(colcode.ColorCode,'rgb') || strcmp(colcode.ColorCode,'bgr');
4095if test3color
4096    colcode.ColCode1=str2num(get(handles.num_ColCode1,'String'));
4097    colcode.ColCode2=str2num(get(handles.num_ColCode2,'String'));
4098end
4099vec_C=colcode.MinVec+(colcode.MaxVec-colcode.MinVec)*(0.5:width-0.5)/width;%sample of vec_C values from min to max
4100[colorlist,col_vec]=set_col_vec(colcode,vec_C);
4101oneheight=ones(1,height);
4102A1=colorlist(col_vec,1)*oneheight;
4103A2=colorlist(col_vec,2)*oneheight;
4104A3=colorlist(col_vec,3)*oneheight;
4105A(:,:,1)=A1';
4106A(:,:,2)=A2';
4107A(:,:,3)=A3';
4108set(handles.VecColBar,'Cdata',A)
4109
4110%-------------------------------------------------------------------
4111function update_plot(handles)
4112%-------------------------------------------------------------------
4113UvData=get(handles.uvmat,'UserData');
4114AxeData=UvData.PlotAxes;% retrieve the current plotted data
4115PlotParam=read_GUI(handles.uvmat);
4116[tild,PlotParamOut]= plot_field(AxeData,handles.PlotAxes,PlotParam);
4117errormsg=fill_GUI(PlotParamOut,handles.uvmat);
4118%write_plot_param(handles,PlotParamOut); %update the auto plot parameters
4119
4120%------------------------------------------------------------------------
4121%------------------------------------------------------------------------
4122%   SELECTION AND EDITION OF PROJECTION OBJECTS
4123%------------------------------------------------------------------------
4124%------------------------------------------------------------------------
4125
4126% --- Executes on selection change in ListObject_1.
4127function ListObject_1_Callback(hObject, eventdata, handles)
4128list_str=get(handles.ListObject,'String');
4129UvData=get(handles.uvmat,'UserData');
4130ObjectData=UvData.ProjObject{get(handles.ListObject_1,'Value')};
4131
4132%% update the projection plot on uvmat
4133ProjData= proj_field(UvData.Field,ObjectData);%project the current input field on object ObjectData
4134plot_field(ProjData,handles.PlotAxes,read_GUI(handles.uvmat));% plot the projected field;
4135%replot all the objects within the new projected field
4136for IndexObj=1:numel(list_str)
4137        hobject=UvData.ProjObject{IndexObj}.DisplayHandle.uvmat;
4138        if isempty(hobject) || ~ishandle(hobject)
4139            hobject=handles.PlotAxes;
4140        end
4141        if isequal(IndexObj,get(handles.ListObject,'Value'))
4142            objectcolor='m'; %paint in magenta the currently selected object in ListObject
4143        else
4144            objectcolor='b';
4145        end
4146        UvData.ProjObject{IndexObj}.DisplayHandle.uvmat=plot_object(UvData.ProjObject{IndexObj},ObjectData,hobject,objectcolor);%draw the object in uvmat     
4147end
4148set(handles.uvmat,'UserData',UvData)
4149
4150%% display the object parameters if the GUI set_object is already opened
4151if ~get(handles.ViewObject,'Value')
4152    ZBounds=0; % default
4153    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4154        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4155        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4156    end
4157    ObjectData.Name=list_str{get(handles.ListObject_1,'Value')};
4158    set_object(ObjectData,[],ZBounds);
4159    set(handles.ViewObject,'Value',1)% show that the selected object in ListObject_1 is currently visualised
4160end
4161
4162%  desactivate the edit object mode
4163set(handles.edit_object,'Value',0)
4164% set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])
4165
4166%------------------------------------------------------------------------
4167% --- Executes on selection change in ListObject.
4168function ListObject_Callback(hObject, eventdata, handles)
4169%------------------------------------------------------------------------
4170list_str=get(handles.ListObject,'String');
4171IndexObj=get(handles.ListObject,'Value');%present object selection
4172UvData=get(handles.uvmat,'UserData');
4173ObjectData=UvData.ProjObject{IndexObj};
4174    ZBounds=0; % default
4175    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4176        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4177        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4178    end
4179
4180%% show object features if view_object isselected
4181if get(handles.ViewObject,'value')
4182    set_object(ObjectData,[],ZBounds);
4183end
4184
4185%% The object  is displayed in set_object if this GUI is already opened
4186%
4187% hset_object=findobj(allchild(0),'tag','set_object');
4188% if ~isempty(hset_object)
4189%
4190%     ObjectData.Name=list_str{IndexObj};
4191%     set_object(ObjectData,[],ZBounds);
4192%     set(handles.ViewField,'Value',1)% show that the selected object in ListObject is currently visualised
4193% end
4194
4195%%  desactivate the edit object mode for security
4196set(handles.edit_object,'Value',0)
4197
4198% set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])
4199
4200%% update the  plot on view_field if view_field is already openened
4201hview_field=findobj(allchild(0),'tag','view_field');
4202if isempty(hview_field)
4203    hhview_field.PlotAxes=[];
4204else
4205    Data=get(hview_field,'UserData');
4206    hhview_field=guidata(hview_field);
4207    ProjData= proj_field(UvData.Field,ObjectData);%project the current interface field on ObjectData
4208    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.PlotAxes,read_GUI(hview_field));%read plotting parameters on the uvmat interface
4209   
4210    %write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
4211    haxes=findobj(hview_field,'tag','axes3');
4212    pos=get(hview_field,'Position'); 
4213    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
4214        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
4215        pos_table=get(h_TableDisplay,'Position');
4216        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
4217        drawnow% needed to change position before the next command
4218        set(hview_field,'UserData',Data);% restore the previously stored GUI position after GUI resizing
4219    else
4220        set(hview_field,'Position',Data.GUISize)% return to the previously stored GUI position and size
4221    end
4222end
4223
4224%% update the color of the graphic object representation: the selected object in magenta, others in blue
4225update_object_color(handles.PlotAxes,hhview_field.PlotAxes,UvData.ProjObject{IndexObj}.DisplayHandle.uvmat)
4226
4227%------------------------------------------------------------------------
4228%--- update the color representation of objects (indicating the selected ones)
4229function update_object_color(axes_uvmat,axes_view_field,DisplayHandle)
4230%------------------------------------------------------------------------
4231if isempty(axes_view_field)% case with no view_field plot
4232hother=[findobj(axes_uvmat,'Tag','proj_object');findobj(axes_uvmat,'Tag','DeformPoint')];%find all the proj object and deform point representations
4233else
4234hother=[findobj(axes_uvmat,'Tag','proj_object') ;findobj(axes_view_field,'Tag','proj_object');... %find all the proj object representations
4235findobj(axes_uvmat,'Tag','DeformPoint'); findobj(axes_view_field,'Tag','DeformPoint')];%find all the deform point representations
4236end
4237for iobj=1:length(hother)
4238    if isequal(get(hother(iobj),'Type'),'rectangle')||isequal(get(hother(iobj),'Type'),'patch')
4239        set(hother(iobj),'EdgeColor','b')
4240        if isequal(get(hother(iobj),'FaceColor'),'m')
4241            set(hother(iobj),'FaceColor','b')
4242        end
4243    elseif isequal(get(hother(iobj),'Type'),'image')
4244        Acolor=get(hother(iobj),'CData');
4245        Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2));
4246        set(hother(iobj),'CData',Acolor);
4247    else
4248        set(hother(iobj),'Color','b')
4249    end
4250    set(hother(iobj),'Selected','off')
4251end
4252if ishandle(DisplayHandle)
4253    linetype=get(DisplayHandle,'Type');
4254    if isequal(linetype,'line')
4255        set(DisplayHandle,'Color','m'); %set the selected object to magenta color
4256    elseif isequal(linetype,'rectangle')
4257        set(DisplayHandle,'EdgeColor','m'); %set the selected object to magenta color
4258    elseif isequal(linetype,'patch')
4259        set(DisplayHandle,'FaceColor','m'); %set the selected object to magenta color
4260    end
4261    SubObjectData=get(DisplayHandle,'UserData');
4262    if isfield(SubObjectData,'SubObject') & ishandle(SubObjectData.SubObject)
4263        for iobj=1:length(SubObjectData.SubObject)
4264            hsub=SubObjectData.SubObject(iobj);
4265            if isequal(get(hsub,'Type'),'rectangle')
4266                set(hsub,'EdgeColor','m'); %set the selected object to magenta color
4267            elseif isequal(get(hsub,'Type'),'image')
4268                Acolor=get(hsub,'CData');
4269                Acolor(:,:,1)=Acolor(:,:,3);
4270                set(hsub,'CData',Acolor);
4271            else
4272                set(hsub,'Color','m')
4273            end
4274        end
4275    end
4276    if isfield(SubObjectData,'DeformPoint') & ishandle(SubObjectData.DeformPoint)
4277        set(SubObjectData.DeformPoint,'Color','m')
4278    end
4279end
4280
4281%-------------------------------------------------------------------
4282% --- Executes on selection change in edit_object.
4283function edit_object_Callback(hObject, eventdata, handles)
4284%-------------------------------------------------------------------
4285hset_object=findobj(allchild(0),'Tag','set_object');
4286if get(handles.edit_object,'Value')
4287    %suppress the other options
4288    set(handles.CheckZoom,'Value',0)
4289    CheckZoom_Callback(hObject, eventdata, handles)
4290    hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4291    if ishandle(hgeometry_calib)
4292        hhgeometry_calib=guidata(hgeometry_calib);
4293        set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4294    end
4295    set(handles.ViewObject,'value',1)
4296    ViewObject_Callback(hObject, eventdata, handles)
4297else % desactivate object edit mode
4298    if ~isempty(hset_object)% open the
4299        set(get(hset_object,'children'),'Enable','off')
4300        hSAVE=findobj(hset_object,'Tag','SAVE');
4301        set(hSAVE,'Enable','on')
4302    end
4303end
4304
4305
4306%------------------------------------------------------------------------
4307% --- Executes on button press in ViewObject.
4308function ViewObject_Callback(hObject, eventdata, handles)
4309%------------------------------------------------------------------------
4310check_view=get(handles.ViewObject,'Value');
4311
4312if check_view %activate set_object   
4313    IndexObj=get(handles.ListObject,'Value');
4314    list_object=get(handles.ListObject,'String');
4315    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4316    UvData.ProjObject{IndexObj}.Name=list_object{IndexObj};
4317    if numel(UvData.ProjObject)<IndexObj;% error in UvData
4318        msgbox_uvmat('ERROR','invalid object list')
4319        return
4320    end
4321    ZBounds=0; % default
4322    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4323        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4324        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4325    end
4326    data=UvData.ProjObject{IndexObj};
4327    if ~isfield(data,'Type')% default plane
4328        data.Type='plane';
4329    end
4330    hset_object=set_object(data,[],ZBounds);
4331    hhset_object=guidata(hset_object);
4332    if get(handles.edit_object,'Value')% edit mode
4333        set(get(hset_object,'children'),'Enable','on')
4334    else
4335        set(get(hset_object,'children'),'Enable','off')% deactivate the GUI except SAVE
4336        set(hhset_object.SAVE,'Enable','on')
4337    end
4338else
4339    hset_object=findobj(allchild(0),'tag','set_object');
4340    if ~isempty(hset_object)
4341        delete(hset_object)% delete existing version of set_object
4342    end
4343end
4344 
4345
4346%------------------------------------------------------------------------
4347% --- Executes on button press in ViewField.
4348function ViewField_Callback(hObject, eventdata, handles)
4349%------------------------------------------------------------------------
4350check_view=get(handles.ViewField,'Value');
4351
4352if check_view
4353    IndexObj=get(handles.ListObject,'Value');
4354    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4355    if numel(UvData.ProjObject)<IndexObj(end);% error in UvData
4356        msgbox_uvmat('ERROR','invalid object list')
4357        return
4358    end
4359    ZBounds=0; % default
4360    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4361        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4362        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4363    end
4364    set(handles.ListObject,'Value',IndexObj);%restore ListObject selection after set_object deletion
4365    if ~isfield(UvData.ProjObject{IndexObj(1)},'Type')% default plane
4366        UvData.ProjObject{IndexObj(1)}.Type='plane';
4367    end
4368    list_object=get(handles.ListObject,'String');
4369    UvData.ProjObject{IndexObj(end)}.Name=list_object{IndexObj(end)};
4370   
4371    %% show the projection of the selected object on view_field
4372    ProjData= proj_field(UvData.Field,UvData.ProjObject{IndexObj});%project the current field on ObjectData
4373    hview_field=findobj(allchild(0),'tag','view_field');
4374    if isempty(hview_field)
4375        hview_field=view_field;
4376    end
4377    hhview_field=guidata(hview_field);
4378    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.PlotAxes,read_GUI(hview_field));%read plotting parameters on the GUI view_field);
4379    errormsg=fill_GUI(PlotParam,hview_field);
4380    for list={'Scalar','Vectors'}
4381        if ~isfield(PlotParam,list{1})
4382            set(hhview_field.(list{1}),'Visible','off')
4383        end
4384    end
4385    %write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
4386    haxes=findobj(hview_field,'tag','axes3');
4387    pos=get(hview_field,'Position');
4388    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
4389        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
4390        pos_table=get(h_TableDisplay,'Position');
4391        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
4392    else
4393        Data=get(hview_field,'UserData');
4394        set(hview_field,'Position',Data.GUISize)% restore the size of view_field for plots
4395    end
4396else
4397    hview_field=findobj(allchild(0),'tag','view_field');
4398    if ~isempty(hview_field)
4399        delete(hview_field)% delete existing version of set_object
4400    end
4401end
4402
4403
4404%------------------------------------------------------------------------
4405% --- Executes on button press in delete_object.
4406%------------------------------------------------------------------------
4407function delete_object_Callback(hObject, eventdata, handles)
4408
4409IndexObj=get(handles.ListObject,'Value');%projection object selected for view_field
4410IndexObj_1=get(handles.ListObject_1,'Value');%projection object selected for uvmat plot
4411if IndexObj>1 && ~isequal(IndexObj,IndexObj_1) % do not delete the object used for the uvmat plot
4412    delete_object(IndexObj)
4413end
4414
4415%'delete_object': delete a projection object, defined by its index in the Uvmat list or by its graphic handle
4416%------------------------------------------------------------------------
4417% function delete_object(hObject)
4418%
4419% INPUT:
4420% hObject: object index (if integer) or handle of the graphic object. If
4421%          hObject is a subobject, the parent object is detected and deleted.
4422
4423function delete_object(IndexObj)
4424
4425huvmat=findobj('tag','uvmat');%handles of the uvmat interface
4426UvData=get(huvmat,'UserData');
4427hlist_object=findobj(huvmat,'Tag','ListObject');%handles of the object list in the uvmat interface
4428list_str=get(hlist_object,'String');%objet list
4429% if isequal(floor(hObject),hObject) %case of an index
4430    if  ~isempty(UvData) && isfield(UvData, 'ProjObject') && length(UvData.ProjObject)>=IndexObj
4431        if isfield(UvData.ProjObject{IndexObj},'DisplayHandle') && isfield(UvData.ProjObject{IndexObj}.DisplayHandle,'uvmat')
4432            hdisplay=UvData.ProjObject{IndexObj}.DisplayHandle.uvmat;
4433            for iview=1:length(hdisplay)
4434                if ishandle(hdisplay(iview)) && ~isequal(hdisplay(iview),0)
4435                    ObjectData=get(hdisplay(iview),'UserData');
4436                    if isfield(ObjectData,'SubObject') & ishandle(ObjectData.SubObject)
4437                        delete(ObjectData.SubObject);
4438                    end
4439                    if isfield(ObjectData,'DeformPoint') & ishandle(ObjectData.DeformPoint)
4440                        delete(ObjectData.DeformPoint);
4441                    end
4442                    delete(hdisplay(iview))
4443                end
4444                ishandle(hdisplay(iview))
4445            end
4446            for iobj=IndexObj+1:length(UvData.ProjObject)
4447                hdisplay=UvData.ProjObject{iobj}.DisplayHandle.uvmat;
4448                for iview=1:length(hdisplay)
4449                    if ishandle(hdisplay(iview)) && ~isequal(hdisplay(iview),0)
4450                        PlotData=get(hdisplay(iview),'UserData');
4451                        PlotData.IndexObj=iobj-1;
4452                        set(hdisplay(iview),'UserData',PlotData);
4453                    end
4454                end
4455            end
4456        end
4457        UvData.ProjObject(IndexObj)=[]; 
4458        if ~isempty(list_str)
4459            list_str(IndexObj)=[];
4460        end
4461    end
4462% elseif ishandle(hObject)%object handle
4463%     userdata=get(hObject,'UserData');
4464%     if ishandle(userdata)%the selected line depends on a parent line
4465%         hdisplay=userdata;% the parent object becomes the current one
4466%     else
4467%         hdisplay=hObject;% the selected object becomes the current one
4468%     end
4469%     PlotData=get(hdisplay,'UserData');
4470%     if isfield(PlotData,'SubObject') & ishandle(PlotData.SubObject)
4471%             delete(PlotData.SubObject);
4472%     end
4473%     if isfield(PlotData,'DeformPoint') & ishandle(PlotData.DeformPoint)
4474%            delete(PlotData.DeformPoint);
4475%     end
4476%     delete(hdisplay);
4477%     if isfield(PlotData,'IndexObj')
4478%         IndexObj=PlotData.IndexObj;
4479%         if  isequal(round(IndexObj),IndexObj) & IndexObj>=1 & length(list_str) > IndexObj
4480%             if isfield(UvData,'ProjObject')& length(UvData.ProjObject) > IndexObj
4481%                UvData.ProjObject(IndexObj)=[];
4482%             end
4483%             list_str(IndexObj)=[];
4484%         end
4485%     end
4486% end
4487set(huvmat,'UserData',UvData);
4488set(hlist_object,'String',list_str)
4489set(hlist_object,'Value',length(list_str))
4490hlist_object_1=findobj(huvmat,'Tag','ListObject_1');%handles of the first object list in the uvmat interface
4491old_index=get(hlist_object_1,'Value');
4492set(hlist_object_1,'String',list_str)
4493if IndexObj<=old_index
4494    set(hlist_object_1,'Value',old_index-1)
4495end
4496
4497%------------------------------------------------------------------------
4498%------------------------------------------------------------------------
4499%  II - TOOLS FROM THE UPPER MENU BAR
4500%------------------------------------------------------------------------
4501%------------------------------------------------------------------------
4502
4503%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4504% Export  Menu Callbacks
4505%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4506%------------------------------------------------------------------------
4507% --- Executes on button press in Menu/Export/field in workspace.
4508function MenuExportField_Callback(hObject, eventdata, handles)
4509%------------------------------------------------------------------------
4510global Data_uvmat
4511Data_uvmat=get(handles.uvmat,'UserData');
4512evalin('base','global Data_uvmat')%make CurData global in the workspace
4513display('current field :')
4514evalin('base','Data_uvmat') %display CurData in the workspace
4515commandwindow; %brings the Matlab command window to the front
4516
4517%------------------------------------------------------------------------
4518% --- Executes on button press in Menu/Export/extract figure.
4519function MenuExportFigure_Callback(hObject, eventdata, handles)
4520%------------------------------------------------------------------------
4521% huvmat=get(handles.MenuExport,'parent');
4522hfig=figure;
4523copyobj(handles.PlotAxes,hfig);
4524map=colormap(handles.PlotAxes);
4525colormap(map);%transmit the current colormap to the zoom fig
4526colorbar
4527
4528% --------------------------------------------------------------------
4529function MenuExportAxis_Callback(hObject, eventdata, handles)
4530ListFig=findobj(allchild(0),'Type','figure');
4531nb_option=0;
4532menu={};
4533for ilist=1:numel(ListFig)
4534    FigName=get(ListFig(ilist),'name');
4535    if isempty(FigName)
4536        FigName=['figure ' num2str(ListFig(ilist))];
4537    end
4538    if ~strcmp(FigName,'uvmat')
4539        ListAxes=findobj(ListFig(ilist),'Type','axes');
4540        ListTags=get(ListAxes,'Tag');
4541        if ~isempty(ListTags) && ~isempty(find(~strcmp('Colorbar',ListTags), 1))
4542            ListAxes=ListAxes(~strcmp('Colorbar',ListTags));
4543            if numel(ListAxes)==1
4544                nb_option=nb_option+1;
4545                menu{nb_option}=FigName ;
4546                AxesHandle(nb_option)=ListAxes;
4547            else
4548                nb_axis=0;
4549                for iaxes=1:numel(ListAxes)
4550                    nb_axis=nb_axis+1;
4551                    nb_option=nb_option+1;
4552                    menu{nb_option}=[FigName '_' num2str(nb_axis)];
4553                    AxesHandle(nb_option)=ListAxes(nb_axis);
4554                end
4555            end
4556        end
4557    end
4558end
4559if isempty(menu)
4560    answer=msgbox_uvmat('INPUT_Y-N','no existing plotting axes available, create new figure?');
4561    if strcmp(answer,'Yes')
4562        hfig=figure;
4563        copyobj(handles.PlotAxes,hfig);
4564    else
4565        return
4566    end
4567    map=colormap(handles.PlotAxes);
4568    colormap(map);%transmit the current colormap to the zoom fig
4569    colorbar
4570else
4571    answer=msgbox_uvmat('INPUT_MENU','select a figure/axis on which the current uvmat plot will be exported',menu);
4572    if isempty(answer)
4573        return
4574    else
4575        axes(AxesHandle(answer))
4576        hold on
4577        hchild=get(handles.PlotAxes,'children');
4578        copyobj(hchild,gca);
4579    end
4580end
4581
4582
4583%------------------------------------------------------------------------
4584% --------------------------------------------------------------------
4585function MenuExportMovie_Callback(hObject, eventdata, handles)
4586% --------------------------------------------------------------------
4587set(handles.MenuExportMovie,'BusyAction','queue')% activate the button
4588huvmat=get(handles.run0,'parent');
4589UvData=get(huvmat,'UserData');
4590%[xx,xx,FileBase]=read_file_boxes(handles);
4591[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
4592FileBase=fullfile(RootPath,RootFile);
4593 %read the current input file name
4594prompt = {'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)'};
4595dlg_title = 'select properties of the output avi movie';
4596num_lines= 1;
4597def     = {[FileBase '_out.avi'];'10';'1';'[0.03 0.05 0.95 0.92]';'10'};
4598answer = inputdlg(prompt,dlg_title,num_lines,def,'on');
4599aviname=answer{1};
4600fps=str2double(answer{2});
4601% check for existing file with output name aviname
4602if exist(aviname,'file')
4603    backup=aviname;
4604    testexist=2;
4605    while testexist==2
4606        backup=[backup '~'];
4607        testexist=exist(backup,'file');     
4608    end
4609    [success,message]=copyfile(aviname,backup);%make backup of the existing file
4610    if isequal(success,1)
4611        delete(aviname)%delete existing file
4612    else
4613        msgbox_uvmat('ERROR',message)
4614        return
4615    end
4616end
4617%create avi open
4618aviobj=avifile(aviname,'Compression','None','fps',fps);
4619
4620%display first view for tests
4621newfig=figure;
4622newaxes=copyobj(handles.PlotAxes,newfig);%new plotting axes in the new figure
4623set(newaxes,'Tag','movieaxes')
4624nbpix=[512 384]*str2double(answer{3});
4625set(gcf,'Position',[1 1 nbpix])% resolution XVGA
4626set(newaxes,'Position',eval(answer{4}));
4627map=colormap(handles.PlotAxes);
4628colormap(map);%transmit the current colormap to the zoom fig
4629msgbox_uvmat('INPUT_Y-N',{['adjust figure ' num2str(newfig) ' with its matlab edit menu '] ;...
4630        ['then press OK to get the avi movie as a copy of figure ' num2str(newfig) ' display']});
4631UvData.plotaxes=newaxes;% the axis in the new figure becomes the current main plotting axes
4632set(huvmat,'UserData',UvData);
4633increment=str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d
4634set(handles.STOP,'Visible','on')
4635set(handles.speed,'Visible','on')
4636set(handles.speed_txt,'Visible','on')
4637set(handles.Movie,'BusyAction','queue')
4638
4639%imin=str2double(get(handles.i1,'String'));
4640imax=str2double(answer{5});
4641% if isfield(UvData,'Time')
4642htitle=get(newaxes,'Title');
4643xlim=get(newaxes,'XLim');
4644ylim=get(newaxes,'YLim');
4645set(htitle,'Position',[xlim(2)+0.07*(xlim(2)-xlim(1)) ylim(2)-0.05*(ylim(2)-ylim(1)) 0])
4646time_str=get(handles.abs_time,'String');
4647set(htitle,'String',['t=' time_str])
4648set(handles.speed,'Value',1)
4649for i=1:imax
4650    if get(handles.speed,'Value')~=0 && isequal(get(handles.MenuExportMovie,'BusyAction'),'queue') % enable STOP command
4651            runpm(hObject,eventdata,handles,increment)% run plus
4652            drawnow
4653            time_str=get(handles.abs_time,'String');
4654            if ishandle(htitle)
4655             set(htitle,'String',['t=' time_str])
4656            end
4657            mov=getframe(newfig);
4658            aviobj=addframe(aviobj,mov);
4659    end
4660end
4661aviobj=close(aviobj);
4662UvData=rmfield(UvData,'plotaxes');
4663set(huvmat,'UserData',UvData);
4664msgbox_uvmat('CONFIRMATION',{['movie ' aviname ' created '];['with ' num2str(imax) ' frames']})
4665
4666
4667%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4668% Projection Objects Menu Callbacks
4669%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4670
4671% -----------------------------------------------------------------------
4672function Menupoints_Callback(hObject, eventdata, handles)
4673%------------------------------------------------------------------------
4674data.Type='points';
4675data.ProjMode='projection';%default
4676data.ProjModeMenu={};% do not restrict ProjMode menus
4677create_object(data,handles)
4678
4679% -----------------------------------------------------------------------
4680function Menuline_Callback(hObject, eventdata, handles)
4681%------------------------------------------------------------------------
4682data.Type='line';
4683data.ProjMode='projection';%default
4684data.ProjModeMenu={};% do not restrict ProjMode menus
4685create_object(data,handles)
4686
4687%------------------------------------------------------------------------
4688function Menupolyline_Callback(hObject, eventdata, handles)
4689%------------------------------------------------------------------------
4690data.Type='polyline';
4691data.ProjMode='projection';%default
4692data.ProjModeMenu={};% do not restrict ProjMode menus
4693create_object(data,handles)
4694
4695%------------------------------------------------------------------------
4696function Menupolygon_Callback(hObject, eventdata, handles)
4697%------------------------------------------------------------------------
4698data.Type='polygon';
4699data.ProjMode='inside';%default
4700data.ProjModeMenu={};% do not restrict ProjMode menus
4701create_object(data,handles)
4702
4703%------------------------------------------------------------------------
4704function Menurectangle_Callback(hObject, eventdata, handles)
4705%------------------------------------------------------------------------
4706data.Type='rectangle';
4707data.ProjMode='inside';%default
4708data.ProjModeMenu={};% do not restrict ProjMode menus
4709create_object(data,handles)
4710
4711%------------------------------------------------------------------------
4712function Menuellipse_Callback(hObject, eventdata, handles)
4713%------------------------------------------------------------------------
4714data.Type='ellipse';
4715data.ProjMode='inside';%default
4716data.ProjModeMenu={};% do not restrict ProjMode menus
4717create_object(data,handles)
4718
4719%------------------------------------------------------------------------
4720function MenuMaskObject_Callback(hObject, eventdata, handles)
4721%------------------------------------------------------------------------
4722data.Type='polygon';
4723data.TypeMenu={'polygon'};
4724data.ProjMode='mask_inside';%default
4725data.ProjModeMenu={'mask_inside';'mask_outside'};
4726create_object(data,handles)
4727
4728%------------------------------------------------------------------------
4729function Menuplane_Callback(hObject, eventdata, handles)
4730%------------------------------------------------------------------------
4731data.Type='plane';
4732data.ProjMode='projection';%default
4733data.ProjModeMenu={};% do not restrict ProjMode menus
4734create_object(data,handles)
4735
4736%------------------------------------------------------------------------
4737function Menuvolume_Callback(hObject, eventdata, handles)
4738%------------------------------------------------------------------------
4739data.Type='volume';
4740data.ProjMode='interp_lin';%default
4741data.ProjModeMenu={};
4742% set(handles.create,'Visible','on')
4743% set(handles.create,'Value',1)
4744% VOLUME_Callback(hObject,eventdata,handles)data.ProjModeMenu={};
4745create_object(data,handles)
4746
4747%------------------------------------------------------------------------
4748% --- generic function used for the creation of a projection object
4749function create_object(data,handles)
4750%------------------------------------------------------------------------
4751%% desactivate concurrent tools
4752hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');% search the GUI geometric calibration
4753if ishandle(hgeometry_calib)
4754    hhgeometry_calib=guidata(hgeometry_calib);
4755    set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4756end
4757set(handles.edit_object,'Value',0)  %desactivate the object edit mode
4758edit_object_Callback([],[],handles)
4759set(handles.ViewObject,'Value',0) % desactivate view_object (new object created)
4760set(handles.CheckZoomFig,'Value',0) %desactivate zoom sub fig
4761set(handles.CheckZoom,'Value',0)    %desactivate the zoom action
4762if ishandle(handles.UVMAT_title)
4763    delete(handles.UVMAT_title)     %delete the initial display of uvmat if no field has been entered yet
4764end
4765
4766%% append a new line to the list of projection objects A METTRE PLUS TARD
4767% ListObject=get(handles.ListObject,'String');
4768% if isempty(ListObject)
4769%     ListObject={''};
4770% end
4771% if ~strcmp(ListObject{end},'')
4772%     ListObject=[ListObject;{''}]; %append a blank to the list (if nort already done) to indicate the creation of a new object
4773%     set(handles.ListObject,'String',ListObject)
4774% end
4775% IndexObj=length(ListObject);
4776% set(handles.ListObject,'Value',IndexObj)
4777UvData=get(handles.uvmat,'UserData');
4778% UvData.ProjObject{IndexObj}=[]; %create a new empty object
4779% UvData.ProjObject{IndexObj}.DisplayHandle.uvmat=handles.PlotAxes; % axes for plot_object
4780% UvData.ProjObject{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation
4781% set(handles.uvmat,'UserData',UvData)
4782
4783%% initiate the new projection object
4784data.Name=data.Type;% default name=type
4785data.Coord=[0 0]; %default
4786if isfield(UvData,'Field')
4787    Field=UvData.Field;
4788    if isfield(UvData.Field,'CoordMesh')&&~isempty(UvData.Field.CoordMesh)
4789        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
4790        if strcmp(data.Type,'line')||strcmp(data.Type,'polyline')||strcmp(data.Type,'points')
4791            data.RangeY=UvData.Field.CoordMesh;
4792        else
4793            data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
4794        end
4795        data.DX=UvData.Field.CoordMesh;
4796        data.DY=UvData.Field.CoordMesh;
4797        if strcmp(data.Type,'rectangle')||strcmp(data.Type,'ellipse')
4798            data.RangeX=UvData.Field.CoordMesh;
4799            data.RangeY=UvData.Field.CoordMesh;
4800        end
4801    end
4802    if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
4803         data.Coord=[0 0 0]; %default
4804    end
4805    if isfield(Field,'CoordUnit')
4806        data.CoordUnit=Field.CoordUnit;
4807    end
4808end
4809hset_object=set_object(data,handles);% call the GUI set_object
4810hchild=get(hset_object,'children');
4811set(hchild,'enable','on')
4812
4813
4814set(handles.delete_object,'Visible','on')
4815
4816%------------------------------------------------------------------------
4817function MenuBrowseObject_Callback(hObject, eventdata, handles)
4818%------------------------------------------------------------------------
4819%get the object file
4820[FileName, PathName, filterindex] = uigetfile( ...
4821       {'*.xml;*.mat', ' (*.xml,*.mat)';
4822       '*.xml',  '.xml files '; ...
4823        '*.mat',  '.mat matlab files '}, ...
4824        'Pick an xml Object file',get(handles.RootPath,'String'));
4825fileinput=[PathName FileName];%complete file name
4826sizf=size(fileinput);
4827if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
4828
4829%read the file
4830[data,heading]=xml2struct(fileinput);
4831if ~strcmp(heading,'ProjObject')
4832    msgbox_uvmat('WARNING','The xml file does not have the heading ProjObject for projection objects')
4833end
4834[tild,data.Name]=fileparts(FileName);% object name set as file name
4835ListObject=get(handles.ListObject,'String');
4836if ~strcmp(ListObject{end},'')
4837    ListObject=[ListObject;{''}]; %append a blank to the list (if not already done) to indicate the creation of a new object
4838    set(handles.ListObject,'String',ListObject)
4839end
4840IndexObj=length(ListObject);
4841
4842UvData=get(handles.uvmat,'UserData');
4843UvData.ProjObject{IndexObj}=[]; %create a new empty object
4844UvData.ProjObject{IndexObj}.DisplayHandle.uvmat=[]; %no plot handle before plot_field operation
4845UvData.ProjObject{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation
4846set(handles.uvmat,'UserData',UvData)
4847set(handles.ListObject,'Value',IndexObj)
4848hset_object=set_object(data);% call the set_object interface
4849set(get(hset_object,'children'),'enable','on')% enable edit action on elements on GUI set_object
4850set(handles.edit_object,'Value',0); %suppress the object edit mode
4851edit_object_Callback([],[],handles)
4852% set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4853set(handles.delete_object,'Visible','on')
4854
4855
4856% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4857% % MenuEdit Callbacks
4858% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4859% %------------------------------------------------------------------------
4860% function MenuEditObject_Callback(hObject, eventdata, handles)
4861% %------------------------------------------------------------------------
4862% set(handles.edit_object,'Value',1)
4863% edit_Callback(hObject, eventdata, handles)
4864%
4865% %------------------------------------------------------------------------
4866% function MenuEditVectors_Callback(hObject, eventdata, handles)
4867% %------------------------------------------------------------------------
4868% set(handles.edit_vect,'Visible','on')
4869% set(handles.edit_vect,'Value',1)
4870% edit_vect_Callback(hObject, eventdata, handles)
4871
4872%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4873% MenuTools Callbacks
4874%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4875%------------------------------------------------------------------------
4876function MenuCalib_Callback(hObject, eventdata, handles)
4877%------------------------------------------------------------------------
4878
4879UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4880
4881%suppress competing options
4882set(handles.CheckZoom,'Value',0)
4883set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
4884set(handles.ListObject,'Value',1)     
4885% initiate display of GUI geometry_calib
4886data=[]; %default
4887if isfield(UvData,'CoordType')
4888    data.CoordType=UvData.CoordType;
4889end
4890[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
4891FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
4892set(handles.view_xml,'Backgroundcolor',[1 1 0])%indicate the reading of the current xml file by geometry_calib
4893pos_uvmat=get(handles.uvmat,'Position');
4894pos_cal(1)=pos_uvmat(1)+UvData.OpenParam.PosGeometryCalib(1)*pos_uvmat(3);
4895pos_cal(2)=pos_uvmat(2)+UvData.OpenParam.PosGeometryCalib(2)*pos_uvmat(4);
4896pos_cal(3:4)=UvData.OpenParam.PosGeometryCalib(3:4).* pos_uvmat(3:4);
4897geometry_calib(FileName,pos_cal);% call the geometry_calib interface   
4898set(handles.view_xml,'Backgroundcolor',[1 1 1])%indicate the end of reading of the current xml file by geometry_calib
4899set(handles.MenuCalib,'checked','on')% indicate that MenuCalib is activated, test used by mouse action
4900
4901
4902%-----------------------------------------------------------------------
4903function MenuLIFCalib_Callback(hObject, eventdata, handles)
4904%------------------------------------------------------------------------
4905%% read UvData properties stored on the uvmat interface
4906UvData=get(handles.uvmat,'UserData');
4907if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
4908    XmlData=UvData.XmlData{1};
4909else
4910    msgbox_uvmat('ERROR','geometric calibration needed: use Tools/geometric calibration in the menu bar');
4911    return
4912end
4913
4914%% read lines currently drawn
4915ListObj=UvData.ProjObject;
4916select=zeros(1,numel(ListObj));
4917for iobj=1:numel(ListObj);
4918    if isfield(ListObj{iobj},'Type') && strcmp(ListObj{iobj}.Type,'line')
4919        select(iobj)=1;
4920    end
4921end
4922val=find(select);
4923if numel(val)<2
4924    msgbox_uvmat('ERROR','light rays must be defined by at least two lines created by Projection object/line in the menu bar');
4925    return
4926else
4927    set(handles.ListObject,'Value',val);% show the selected lines on the list
4928    ObjectData=UvData.ProjObject(val);
4929    for iobj=1:length(ObjectData)
4930%         if isfield(ObjectData{iobj},'Coord')
4931            xA(iobj)=ObjectData{iobj}.Coord(1,1);
4932            yA(iobj)=ObjectData{iobj}.Coord(1,2);
4933            xB(iobj)=ObjectData{iobj}.Coord(2,1);
4934            yB(iobj)=ObjectData{iobj}.Coord(2,2);
4935%         end
4936    end
4937end
4938
4939%% find the origin as intersection of the two first lines (see http://www.ahristov.com/tutorial/geometry-games/intersection-lines.html )
4940x1=xA(1);x2=xB(1);
4941x3=xA(2);x4=xB(2);
4942y1=yA(1);y2=yB(1);
4943y3=yA(2);y4=yB(2);
4944D = (x1-x2)*(y3-y4) -(y1-y2)*(x3-x4);
4945if D==0
4946    msgbox_uvmat('ERROR','the two lines are parallel');
4947    return
4948end
4949x0=((x3-x4)*(x1*y2-y1*x2)-(x1-x2)*(x3*y4-y3*x4))/D;
4950y0=((y3-y4)*(x1*y2-y1*x2)-(y1-y2)*(x3*y4-y3*x4))/D;
4951XmlData.Illumination.Origin=[x0 y0];
4952XmlData.PolarCentre=[x0 y0];
4953
4954%% display the current image in polar coordinates with origin at the  illumination source
4955currentdir=pwd; 
4956uvmatpath=fileparts(which('uvmat'));
4957cd(fullfile(uvmatpath,'transform_field'));
4958phys_polar=str2func('phys_polar');
4959cd(currentdir)
4960DataOut=phys_polar(UvData.Field,XmlData);
4961view_field(DataOut);
4962
4963%% use the third line for reference luminosity
4964if numel(val)==3
4965    x_ref=linspace(ObjectData{3}.Coord(1,1),ObjectData{3}.Coord(2,1),10);
4966    y_ref=linspace(ObjectData{3}.Coord(1,2),ObjectData{3}.Coord(2,2),10);
4967    x_ref=x_ref-x0;
4968    y_ref=y_ref-y0;
4969    [theta_ref,r_ref] = cart2pol(x_ref,y_ref);%theta_ref  and r_ref are the polar coordinates of the points on the line
4970    theta_ref=theta_ref*180/pi;
4971    figure
4972    plot(theta_ref,r_ref)
4973    azimuth_ima=linspace(DataOut.AY(1),DataOut.AY(2),size(DataOut.A,1));%profile of x index on the transformed image
4974    dist_source = interp1(theta_ref,r_ref,azimuth_ima);
4975    dist_source_pixel=round(size(DataOut.A,2)*(dist_source-DataOut.AX(1))/(DataOut.AX(2)-DataOut.AX(1)));
4976    line_nan= isnan(dist_source_pixel);
4977    dist_source_pixel(line_nan)=1;
4978    width=20; %number of pixels used for reference
4979    DataOut.A=double(DataOut.A);
4980    Anorm=zeros(size(DataOut.A));
4981    Aval=mean(mean(DataOut.A));
4982    for iline=1:size(DataOut.A,1)
4983        lum(iline)=mean(DataOut.A(iline,dist_source_pixel(iline):dist_source_pixel(iline)+width));
4984        Anorm(iline,:)=uint16(Aval*DataOut.A(iline,:)/lum(iline));
4985    end
4986    lum(line_nan)=NaN;
4987    figure
4988    plot(1:size(DataOut.A,1),lum)
4989end
4990ImaName=regexprep([get(handles.RootFile,'String') get(handles.FileIndex,'String')],'//','');
4991NewImageName=fullfile(get(handles.RootPath,'String'),'polar',[ImaName get(handles.FileExt,'String')]);
4992imwrite(Anorm,NewImageName,'BitDepth',16)
4993
4994%% record the origin in the xml file
4995XmlFileName=find_imadoc(get(handles.RootPath,'String'),get(handles.SubDir,'String'),get(handles.RootFile,'String'),get(handles.FileExt,'String'));
4996answer=msgbox_uvmat('INPUT_Y-N','save the illumination origin in the current xml file?');
4997if strcmp(answer,'Yes')
4998    t=xmltree(XmlFileName); %read the file
4999    title=get(t,1,'name');
5000    if ~strcmp(title,'ImaDoc')
5001        msgbox_uvmat('ERROR','wrong xml file');
5002        return
5003    end
5004    % backup the output file if it already exist, and read it
5005    backupfile=XmlFileName;
5006    testexist=2;
5007    while testexist==2
5008        backupfile=[backupfile '~'];
5009        testexist=exist(backupfile,'file');
5010    end
5011    [success,message]=copyfile(XmlFileName,backupfile);%make backup
5012    if success~=1
5013        errormsg=['errror in xml file backup: ' message];
5014        return
5015    end
5016    uid_illumination=find(t,'ImaDoc/Illumination');
5017    if isempty(uid_illumination)  %if GeometryCalib does not already exists, create it
5018        [t,uid_illumination]=add(t,1,'element','Illumination');
5019    end
5020    uid_origin=find(t,'ImaDoc/Illumination/Origin');
5021    if ~isempty(uid_origin)  %if GeometryCalib does not already exists, create it
5022         t=delete(t,uid_origin);
5023    end
5024    % save the illumination origin
5025    t=struct2xml(XmlData.Illumination,t,uid_illumination);
5026    save(t,XmlFileName);
5027end
5028   
5029
5030
5031%------------------------------------------------------------------------
5032function MenuMask_Callback(hObject, eventdata, handles)
5033%------------------------------------------------------------------------
5034UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
5035ListObj=UvData.ProjObject;
5036select=zeros(1,numel(ListObj));
5037for iobj=1:numel(ListObj);
5038    if strcmp(ListObj{iobj}.ProjMode,'mask_inside')||strcmp(ListObj{iobj}.ProjMode,'mask_outside')
5039        select(iobj)=1;
5040    end
5041end
5042val=find(select);
5043if isempty(val)
5044    msgbox_uvmat('ERROR','polygons must be first created by Projection object/mask polygon in the menu bar');
5045    return
5046else
5047    set(handles.ListObject,'Value',val);
5048    flag=1;
5049    if ~isfield(UvData.Field,'A')
5050            msgbox_uvmat('ERROR','an image needs to be opened to set the mask size');
5051    return
5052    end
5053    npx=size(UvData.Field.A,2);
5054    npy=size(UvData.Field.A,1);
5055    xi=0.5:npx-0.5;
5056    yi=0.5:npy-0.5;
5057    [Xi,Yi]=meshgrid(xi,yi);
5058        for iobj=1:length(UvData.ProjObject)
5059            ObjectData=UvData.ProjObject{iobj};
5060            if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
5061                flagobj=1;
5062                testphys=0; %coordinates in pixels by default
5063                if isfield(ObjectData,'CoordUnit') && ~isequal(ObjectData.CoordUnit,'pixel')
5064                    if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
5065                        Calib=UvData.XmlData{1}.GeometryCalib;
5066                        testphys=1;
5067                    end
5068                end
5069                if isfield(ObjectData,'Coord')&& isfield(ObjectData,'Type')
5070                    if isequal(ObjectData.Type,'polygon')
5071                        X=ObjectData.Coord(:,1);
5072                        Y=ObjectData.Coord(:,2);
5073                        if testphys
5074                            pos=[X Y zeros(size(X))];
5075                            if isfield(Calib,'SliceCoord') && length(Calib.SliceCoord)>=3
5076                                if isfield(Calib,'SliceAngle')&&~isequal(Calib.SliceAngle,[0 0 0])
5077                                    om=norm(Calib.SliceAngle);%norm of rotation angle in radians
5078                                    OmAxis=Calib.SliceAngle/om; %unit vector marking the rotation axis
5079                                    cos_om=cos(pi*om/180);
5080                                    sin_om=sin(pi*om/180);
5081                                    pos=cos_om*pos+sin_om*cross(OmAxis,pos)+(1-cos_om)*(OmAxis*pos')*OmAxis;
5082                                end
5083                                pos(:,1)=pos(:,1)+Calib.SliceCoord(1);
5084                                pos(:,2)=pos(:,2)+Calib.SliceCoord(2);
5085                                pos(:,3)=pos(:,3)+Calib.SliceCoord(3);
5086                            end                           
5087                            [X,Y]=px_XYZ(Calib,pos(:,1),pos(:,2),pos(:,3));
5088                        end
5089                        flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside
5090                    elseif isequal(ObjectData.Type,'ellipse')
5091                        if testphys
5092                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
5093                        end
5094                        RangeX=max(ObjectData.RangeX);
5095                        RangeY=max(ObjectData.RangeY);
5096                        X2Max=RangeX*RangeX;
5097                        Y2Max=RangeY*RangeY;
5098                        distX=(Xi-ObjectData.Coord(1,1));
5099                        distY=(Yi-ObjectData.Coord(1,2));
5100                        flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
5101                    elseif isequal(ObjectData.Type,'rectangle')
5102                        if testphys
5103                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
5104                        end
5105                        distX=abs(Xi-ObjectData.Coord(1,1));
5106                        distY=abs(Yi-ObjectData.Coord(1,2));
5107                        flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
5108                    end
5109                    if isequal(ObjectData.ProjMode,'mask_outside')
5110                        flagobj=~flagobj;
5111                    end
5112                    flag=flag & flagobj;
5113                end
5114            end
5115        end
5116%     end
5117    %mask name
5118    RootPath=get(handles.RootPath,'String');
5119    SubDir=get(handles.SubDir,'String');
5120    RootFile=get(handles.RootFile,'String');
5121    if ~isempty(RootFile)&&(isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
5122        RootFile(1)=[];
5123    end
5124    list=get(handles.masklevel,'String');
5125    masknumber=num2str(length(list));
5126    maskindex=get(handles.masklevel,'Value');
5127   % mask_name=fullfile_uvmat(RootPath,'',[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
5128    mask_name=fullfile_uvmat(RootPath,[SubDir '.mask'],'mask','.png','_1',maskindex);
5129    imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
5130    imflag=flipdim(imflag,1);
5131
5132    %display the mask
5133    hfigmask=figure;
5134    set(hfigmask,'Name','mask image')
5135    vec=linspace(0,1,256);%define a linear greyscale colormap
5136    map=[vec' vec' vec'];
5137    colormap(map)
5138    image(imflag);
5139    answer=msgbox_uvmat('INPUT_TXT','mask file name:', mask_name);
5140    if ~strcmp(answer,'Cancel')
5141        mask_dir=fileparts(answer);
5142        if ~exist(mask_dir,'dir')
5143            [xx,msg1]=mkdir(mask_dir);
5144            if ~strcmp(msg1,'')
5145                errormsg=['cannot create ' mask_dir ': ' msg1];%error message for directory creation
5146                return
5147            end
5148        end
5149        imwrite(imflag,answer,'BitDepth',8);
5150    end
5151    set(handles.ListObject,'Value',1)
5152end
5153
5154%------------------------------------------------------------------------
5155%-- open the GUI set_grid.fig to create grid
5156function MenuGrid_Callback(hObject, eventdata, handles)
5157%------------------------------------------------------------------------
5158%suppress the other options if grid is chosen
5159set(handles.edit_vect,'Value',0)
5160edit_vect_Callback(hObject, eventdata, handles)
5161% set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
5162set(handles.ListObject,'Value',1)     
5163
5164%prepare display of the set_grid GUI
5165[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
5166FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
5167UvData=get(handles.uvmat,'UserData');
5168% CoordList=get(handles.TransformName,'String');
5169% val=get(handles.TransformName,'Value');
5170set_grid(FileName,UvData.Field);% call the set_object interface
5171
5172
5173%------------------------------------------------------------------------
5174function MenuRuler_Callback(hObject, eventdata, handles)
5175%------------------------------------------------------------------------
5176set(handles.CheckZoom,'Value',0)
5177CheckZoom_Callback(handles.uvmat, [], handles)
5178set(handles.MenuRuler,'checked','on')
5179UvData=get(handles.uvmat,'UserData');
5180UvData.MouseAction='ruler';
5181set(handles.uvmat,'UserData',UvData);
5182
5183%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
5184% MenuRun Callbacks
5185%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
5186
5187%------------------------------------------------------------------------
5188% open the GUI 'series'
5189function MenuSeries_Callback(hObject, eventdata, handles)
5190%------------------------------------------------------------------------
5191[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
5192Param.FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];%first input file name
5193if isequal(get(handles.SubField,'Value'),1)
5194    [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
5195    FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
5196    if ~isequal(FileName_1,Param.FileName)
5197        Param.FileName_1=FileName_1;%second input file name if relevant
5198    end
5199end
5200Param.NomType=get(handles.NomType,'String');
5201Param.NomType_1=get(handles.NomType_1,'String');
5202Param.CheckFixPair=get(handles.CheckFixPair,'Value');
5203UvData=get(handles.uvmat,'UserData');
5204if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'Time')
5205    Param.Time=UvData.XmlData{1}.Time;
5206end
5207if isequal(get(handles.scan_i,'Value'),1)
5208    Param.incr_i=str2num(get(handles.num_IndexIncrement,'String'));
5209elseif isequal(get(handles.scan_j,'Value'),1)
5210    Param.incr_j=str2num(get(handles.num_IndexIncrement,'String'));
5211end
5212
5213%% transfer fields and coordinate names
5214Param.list_fields=get(handles.FieldName,'String');% list menu fields
5215FieldName=Param.list_fields{get(handles.FieldName,'Value')};
5216ind_image=find(strcmp('image',Param.list_fields));
5217if ~isempty(ind_image) && numel(Param.list_fields)>1
5218    Param.list_fields(ind_image)=[]; %suppress  'image' option
5219end
5220Param.index_fields=find(strcmp(FieldName,Param.list_fields));% selected string index
5221Param.list_fields_1=get(handles.FieldName_1,'String');% list menu fields
5222if ischar(Param.list_fields_1),Param.list_fields_1={Param.list_fields_1};end
5223FieldName_1=Param.list_fields_1{get(handles.FieldName_1,'Value')};
5224ind_image=find(strcmp('image',Param.list_fields_1));
5225if ~isempty(ind_image) && numel(Param.list_fields_1)>1
5226    Param.list_fields_1(ind_image)=[]; %suppress  'image' option
5227end
5228Param.index_fields_1=find(strcmp(FieldName_1,Param.list_fields_1));% selected string index
5229TransformList=get(handles.TransformName,'String');
5230Param.TransformName=TransformList{get(handles.TransformName,'Value')};
5231Param.Coord_x_str=get(handles.Coord_x,'String');
5232Param.Coord_x_val=get(handles.Coord_x,'Value');
5233Param.Coord_y_str=get(handles.Coord_y,'String');
5234Param.Coord_y_val=get(handles.Coord_y,'Value');
5235series(Param); %run the series interface
5236
5237%------------------------------------------------------------------------
5238% -- open the GUI civ.fig for PIV
5239function MenuPIV_Callback(hObject, eventdata, handles)
5240%------------------------------------------------------------------------
5241 [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
5242 FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
5243civ(FileName);% interface de civ(not in the uvmat file)
5244
5245% --------------------------------------------------------------------
5246function MenuHelp_Callback(hObject, eventdata, handles)
5247% --------------------------------------------------------------------
5248path_to_uvmat=which ('uvmat');% check the path of uvmat
5249pathelp=fileparts(path_to_uvmat);
5250helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
5251if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
5252else
5253    addpath (fullfile(pathelp,'uvmat_doc'))
5254    web(helpfile);
5255end
5256
5257% --- Executes on selection change in Coord_y.
5258function Coord_y_Callback(hObject, eventdata, handles)
5259
5260% --- Executes on selection change in Coord_x.
5261function Coord_x_Callback(hObject, eventdata, handles)
5262
5263
5264% --- Executes on button press in CheckColorBar.
5265function CheckColorBar_Callback(hObject, eventdata, handles)
5266
5267
5268
5269function TransformPath_Callback(hObject, eventdata, handles)
5270% hObject    handle to TransformPath (see GCBO)
5271% eventdata  reserved - to be defined in a future version of MATLAB
5272% handles    structure with handles and user data (see GUIDATA)
5273
5274% Hints: get(hObject,'String') returns contents of TransformPath as text
5275%        str2double(get(hObject,'String')) returns contents of TransformPath as a double
5276
5277
5278%TODO: use to modify fill_GUI
5279%'write_plot_param': update the plotting parameters on the uvmat or view_field interface after a plotting operation
5280function write_plot_param(handles,PlotParam)
5281%% coordinates
5282if isempty(PlotParam.Coordinates)
5283    set(handles.Coordinates,'Visible','off')
5284    set(handles.PlotAxes,'Visible','off')
5285    set(handles.text_display,'Visible','off')
5286    set(handles.TableDisplay,'Visible','on')
5287else
5288    set(handles.Coordinates,'Visible','on')
5289    set(handles.PlotAxes,'Visible','on')
5290    set(handles.text_display,'Visible','on')
5291    if isfield(handles,'TableDisplay')
5292    set(handles.TableDisplay,'Visible','off')
5293    end
5294    Coordinates=PlotParam.Coordinates;
5295    if isfield(Coordinates,'CheckFixAspectRatio')
5296        if Coordinates.CheckFixAspectRatio
5297            set(handles.CheckFixAspectRatio,'Value',1)
5298        else
5299            set(handles.CheckFixAspectRatio,'Value',0)
5300 
5301        end
5302    end
5303    if isfield(Coordinates,'AspectRatio')
5304        set(handles.num_AspectRatio,'String',num2str(Coordinates.AspectRatio))
5305    end
5306    if isfield(Coordinates,'MinX')
5307        set(handles.num_MinX,'String',num2str(Coordinates.MinX,4));
5308        set(handles.num_MaxX,'String',num2str(Coordinates.MaxX,4));
5309        set(handles.num_MinY,'String',num2str(Coordinates.MinY,4));
5310        set(handles.num_MaxY,'String',num2str(Coordinates.MaxY,4));
5311    else
5312        set(handles.num_MinX,'String','');
5313        set(handles.num_MaxX,'String','');
5314        set(handles.num_MinY,'String','');
5315        set(handles.num_MaxY,'String','');
5316    end
5317end
5318
5319%% scalar or image parameters
5320if isfield(PlotParam,'Scalar')
5321    set(handles.Scalar,'Visible','on')
5322    if isfield(PlotParam.Scalar,'MaxA')
5323        set(handles.num_MaxA,'String',num2str(PlotParam.Scalar.MaxA,3));
5324    end
5325    if isfield(PlotParam.Scalar,'MinA')
5326        set(handles.num_MinA,'String',num2str(PlotParam.Scalar.MinA,3));
5327    end   
5328    if isfield(PlotParam.Scalar,'IncrA')
5329        set(handles.num_IncrA,'String',num2str(PlotParam.Scalar.IncrA,3))
5330    end
5331    set(handles.CheckBW,'Value',PlotParam.Scalar.CheckBW)
5332    if isfield(PlotParam.Scalar,'Opacity')&&isfield(handles,'num_Opacity')
5333        set(handles.num_Opacity,'String',num2str(PlotParam.Scalar.Opacity))
5334    end
5335else
5336    set(handles.Scalar,'Visible','off')
5337end
5338
5339%% parameter for vector field
5340if isfield(PlotParam,'Vectors')
5341    set(handles.Vectors,'Visible','on')
5342    if isfield(PlotParam.Vectors,'VecScale')
5343        set(handles.num_VecScale,'String',num2str(PlotParam.Vectors.VecScale,3))
5344    end
5345    if isfield(PlotParam.Vectors,'MinC')&& isfield(PlotParam.Vectors,'MaxC')
5346        MinC=PlotParam.Vectors.MinC;
5347        MaxC=PlotParam.Vectors.MaxC;
5348        set(handles.num_MinVec,'String', num2str(MinC,3));
5349        set(handles.num_MaxVec,'String',num2str(MaxC,3));
5350        list=get(handles.ColorCode,'String');
5351        ichoice=get(handles.ColorCode,'Value');
5352        color_option=list{ichoice};
5353        test3color=strcmp(color_option,'rgb')||strcmp(color_option,'bgr');
5354        if test3color% need to update color thresholds
5355            set(handles.num_ColCode1,'Visible','on')
5356            set(handles.num_ColCode2,'Visible','on')
5357            set(handles.Slider1,'Visible','on')
5358            set(handles.Slider2,'Visible','on')
5359            %ColCode1=MinC+(MaxC-MinC)*PlotParam.Vectors.ColCode1;
5360            %ColCode2=MinC+(MaxC-MinC)*PlotParam.Vectors.ColCode2;
5361%             ColCode1=MinC+(MaxC-MinC)*PlotParam.Vectors.ColCode1;
5362            %ColCode2=MinC+(MaxC-MinC)*PlotParam.Vectors.ColCode2;
5363            set(handles.num_ColCode1,'String',num2str(PlotParam.Vectors.ColCode1,3))
5364            set(handles.num_ColCode2,'String',num2str(PlotParam.Vectors.ColCode2,3))
5365            set(handles.Slider1,'Value',(PlotParam.Vectors.ColCode1-MinC)/(MaxC-MinC))
5366            set(handles.Slider2,'Value',(PlotParam.Vectors.ColCode2-MinC)/(MaxC-MinC))
5367        else
5368            set(handles.num_ColCode1,'Visible','off')
5369            set(handles.num_ColCode2,'Visible','off')
5370            set(handles.Slider1,'Visible','off')
5371            set(handles.Slider2,'Visible','off')
5372        end
5373    end
5374else
5375    set(handles.Vectors,'Visible','off')
5376    if isfield(handles,'edit_vect')
5377        set(handles.edit_vect,'Visible','off')
5378        set(handles.record,'Visible','off')
5379    end
5380end
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