source: trunk/src/uvmat.m @ 623

Last change on this file since 623 was 623, checked in by sommeria, 8 years ago

waitbar system for series improved to aloow use as stand alone fcts.

to add at the head of series fcts:
hseries=findobj(allchild(0),'Tag','series');
RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
WaitbarHandle?=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series

call to waitbar:

update_waitbar(WaitbarHandle?,index/nbfield)
if ishandle(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction?'),'queue')

disp('program stopped by user')
break

end

File size: 230.1 KB
Line 
1%'uvmat': function associated with the GUI 'uvmat.fig' for images and data field visualization
2%------------------------------------------------------------------------
3% function huvmat=uvmat(input)
4%
5%OUTPUT
6% huvmat=current handles of the GUI uvmat.fig
7%%
8%
9%INPUT:
10% input: input file name (if character chain), or input image matrix to
11% visualize, or Matlab structure representing  netcdf fieldname (with fieldname
12% ListVarName....)
13%
14%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
15%  Copyright Joel Sommeria,  2008, LEGI / CNRS-UJF-INPG, joel.sommeria@legi.grenoble-inp.fr.
16%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17%     This open is part of the toolbox UVMAT.
18%
19%     UVMAT is free software; you can redistribute it and/or modify
20%     it under the terms of the GNU General Public License as published by
21%     the Free Software Foundation; either version 2 of the License, or
22%     (at your option) any later version.
23%
24%     UVMAT is distributed in the hope that it will be useful,
25%     but WITHOUT ANY WARRANTY; without even the implied warranty of
26%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
27%     GNU General Public License (open UVMAT/COPYING.txt) for more details.
28%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
29%
30% Information stored on the interface:(use 'Export/field in workspace' in
31% the menu bar of uvmat to retrieve it)
32%          .OpenParam: structure containing parameters defined when uvmat is opened
33%                       .PosColorbar: position (1x4 vector)of the colorbar (relative to the fig uvmat)
34%                       .PosGeometryCalib: size of set_object
35%                       .NbBuiltin: nbre of functions always displayed in TransformName menu
36%          .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%------------------------------------------------------------------------
1467set(handles.runplus,'BackgroundColor',[1 1 0])%paint the command button in yellow
1468drawnow
1469%TODO: introduce the option: increment ='*' to move to the next available view
1470increment=str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d
1471% if isnan(increment)
1472%     set(handles.num_IndexIncrement,'String','1')%default value
1473%     increment=1;
1474% end
1475errormsg=runpm(hObject,eventdata,handles,increment);
1476if ~isempty(errormsg)
1477    msgbox_uvmat('ERROR',errormsg);
1478end
1479set(handles.runplus,'BackgroundColor',[1 0 0])%paint the command button back to red
1480
1481%------------------------------------------------------------------------
1482% --- Executes on button press in runmin: make one step backward and call
1483% --- run0. The step backward is along the fieldname series 1 or 2 depending on
1484% --- the scan_i and scan_j check box (exclusive each other)
1485function runmin_Callback(hObject, eventdata, handles)
1486%------------------------------------------------------------------------
1487set(handles.runmin,'BackgroundColor',[1 1 0])%paint the command button in yellow
1488drawnow
1489increment=-str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d
1490% if isnan(increment)
1491%     set(handles.num_IndexIncrement,'String','1')%default value
1492%     increment=1;
1493% end
1494errormsg=runpm(hObject,eventdata,handles,increment);
1495if ~isempty(errormsg)
1496    msgbox_uvmat('ERROR',errormsg);
1497end
1498set(handles.runmin,'BackgroundColor',[1 0 0])%paint the command button back to red
1499
1500%------------------------------------------------------------------------
1501% -- Executes on button press in Movie: make a series of +> steps
1502function Movie_Callback(hObject, eventdata, handles)
1503%------------------------------------------------------------------------
1504set(handles.Movie,'BackgroundColor',[1 1 0])%paint the command button in yellow
1505drawnow
1506increment=str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d
1507% if isnan(increment)
1508%     set(handles.num_IndexIncrement,'String','1')%default value
1509%     increment=1;
1510% end
1511set(handles.STOP,'Visible','on')
1512set(handles.speed,'Visible','on')
1513set(handles.speed_txt,'Visible','on')
1514set(handles.Movie,'BusyAction','queue')
1515UvData=get(handles.uvmat,'UserData');
1516
1517while get(handles.Movie,'Value')==1 && get(handles.speed,'Value')~=0 && isequal(get(handles.Movie,'BusyAction'),'queue') % enable STOP command
1518        errormsg=runpm(hObject,eventdata,handles,increment);
1519        if ~isempty(errormsg)
1520            set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1521            return
1522        end
1523        pause(1.02-get(handles.speed,'Value'))% wait for next image
1524end
1525if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1526    UvData.aviobj=close(UvData.aviobj);
1527   set(handles.uvmat,'UserData',UvData);
1528end
1529set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1530
1531%------------------------------------------------------------------------
1532% -- Executes on button press in Movie: make a series of <- steps
1533function MovieBackward_Callback(hObject, eventdata, handles)
1534%------------------------------------------------------------------------
1535set(handles.MovieBackward,'BackgroundColor',[1 1 0])%paint the command button in yellow
1536drawnow
1537increment=-str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d
1538set(handles.STOP,'Visible','on')
1539set(handles.speed,'Visible','on')
1540set(handles.speed_txt,'Visible','on')
1541set(handles.MovieBackward,'BusyAction','queue')
1542UvData=get(handles.uvmat,'UserData');
1543
1544while get(handles.MovieBackward,'Value')==1 && get(handles.speed,'Value')~=0 && isequal(get(handles.MovieBackward,'BusyAction'),'queue') % enable STOP command
1545        errormsg=runpm(hObject,eventdata,handles,increment);
1546        if ~isempty(errormsg)
1547            set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1548            return
1549        end
1550        pause(1.02-get(handles.speed,'Value'))% wait for next image
1551end
1552if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1553    UvData.aviobj=close(UvData.aviobj);
1554   set(handles.uvmat,'UserData',UvData);
1555end
1556set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1557
1558%------------------------------------------------------------------------
1559function STOP_Callback(hObject, eventdata, handles)
1560%------------------------------------------------------------------------
1561set(handles.movie_pair,'BusyAction','Cancel')
1562set(handles.movie_pair,'value',0)
1563set(handles.Movie,'BusyAction','Cancel')
1564set(handles.MovieBackward,'BusyAction','Cancel')
1565set(handles.MenuExportMovie,'BusyAction','Cancel')
1566set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1567set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1568set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1569
1570%------------------------------------------------------------------------
1571% --- function activated by runplus and run minus
1572function errormsg=runpm(hObject,eventdata,handles,increment)
1573%------------------------------------------------------------------------
1574errormsg='';%default
1575%% check for movie pair status
1576movie_status=get(handles.movie_pair,'Value');
1577if isequal(movie_status,1)
1578    STOP_Callback(hObject, eventdata, handles)%interrupt movie pair if active
1579end
1580
1581%% read the current input file name(s) and field indices
1582InputFile=read_GUI(handles.InputFile);
1583InputFile.RootFile=regexprep(InputFile.RootFile,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1584InputFile.SubDir=regexprep(InputFile.SubDir,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1585FileExt=InputFile.FileExt;
1586NomType=get(handles.NomType,'String');
1587i1=str2num(get(handles.i1,'String'));%read the field indices (for movie, it is not given by the file name)
1588i2=[];%default
1589if strcmp(get(handles.i2,'Visible'),'on')
1590    i2=str2num(get(handles.i2,'String'));
1591end
1592j1=[];
1593if strcmp(get(handles.j1,'Visible'),'on')
1594    j1=stra2num(get(handles.j1,'String'));
1595end
1596j2=j1;
1597if strcmp(get(handles.j2,'Visible'),'on')
1598    j2=stra2num(get(handles.j2,'String'));
1599end
1600sub_value= get(handles.SubField,'Value');
1601if sub_value % a second input file has been entered
1602     [InputFile.RootPath_1,InputFile.SubDir_1,InputFile.RootFile_1,InputFile.FileIndex_1,InputFile.FileExt_1,InputFile.NomType_1]=read_file_boxes_1(handles);   
1603    [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(InputFile.FileIndex_1);% the indices for the second series taken from FileIndex_1
1604else
1605    filename_1=[];
1606end   
1607
1608%% increment (or decrement) the field indices and update the input filename(s)
1609if isempty(increment)
1610    set(handles.CheckFixPair,'Value',0)
1611end
1612CheckFixPair=get(handles.CheckFixPair,'Value')||(isempty(i2)&&isempty(j2));
1613
1614% the pair i1-i2 or j1-j2 is imposed (check box CheckFixPair selected)
1615        i1_1=i1;
1616        i2_1=i2;
1617        j1_1=j1;
1618        j2_1=j2;
1619if CheckFixPair
1620    if get(handles.scan_i,'Value')==1% case of scanning along index i
1621        i1=i1+increment;
1622        i2=i2+increment;
1623        if sub_value
1624            i1_1=i1_1+increment;
1625            i2_1=i2_1+increment;
1626        end
1627       
1628    else % case of scanning along index j (burst numbers)
1629        j1=j1+increment;
1630        j2=j2+increment;
1631        if sub_value
1632            j1_1=j1_1+increment;
1633            j2_1=j2_1+increment;
1634        end
1635    end
1636   
1637% the pair i1-i2 or j1-j2 is free (check box CheckFixPair not selected): the list of existing indices recorded in UvData is used
1638else
1639    UvData=get(handles.uvmat,'UserData');
1640    ref_i=i1;
1641    if ~isempty(i2)
1642        ref_i=floor((i1+i2)/2);% current reference index i
1643    end
1644    ref_j=1;
1645    if ~isempty(j1)
1646        ref_j=j1;
1647        if ~isempty(j2)
1648            ref_j=floor((j1+j2)/2);% current reference index j
1649        end
1650    end
1651    if ~isempty(increment)
1652        if get(handles.scan_i,'Value')==1% case of scanning along index i
1653            ref_i=ref_i+increment;% increment the current reference index i
1654        else % case of scanning along index j (burst numbers)
1655            ref_j=ref_j+increment;% increment the current reference index j if scan_j option is used
1656        end
1657    else % free increment
1658        runaction=get(gcbo,'tag');
1659        if strcmp(runaction,'runplus')||strcmp(runaction,'Movie')% if runplus or movie is activated
1660            step=1;
1661        else
1662            step=-1;
1663        end
1664        if get(handles.scan_i,'Value')==1% case of scanning along index i
1665            ref_i=ref_i+step;
1666            while ref_i>=0  && size(UvData.i1_series{1},3)>=ref_i+1 && UvData.i1_series{1}(1,ref_j+1,ref_i+1)==0
1667                ref_i=ref_i+step;
1668            end
1669        else % case of scanning along index j (burst numbers)
1670            ref_j=ref_j+step;
1671            while ref_j>=0  && size(UvData.i1_series{1},2)>=ref_j+1 && UvData.i1_series{1}(1,ref_j+1,ref_i+1)==0
1672                ref_j=ref_j+step;
1673            end
1674        end
1675    end
1676    if ref_i<0
1677        errormsg='minimum i index reached';
1678    elseif ref_j<0
1679        errormsg='minimum j index reached';
1680    elseif ref_i+1>size(UvData.i1_series{1},3)
1681        errormsg='maximum i index reached (reload the input file to update the index bound)';
1682    elseif ref_j+1>size(UvData.i1_series{1},2)
1683        errormsg='maximum j index reached (reload the input file to update the index bound)';
1684    end
1685    if ~isempty(errormsg),return,end
1686    siz=size(UvData.i1_series{1});
1687    ref_indices=ref_i*siz(1)*siz(2)+ref_j*siz(1)+1:ref_i*siz(1)*siz(2)+(ref_j+1)*siz(1);
1688    i1_subseries=UvData.i1_series{1}(ref_indices);
1689    ref_indices=ref_indices(i1_subseries>0);
1690    if isempty(ref_indices)% case of pairs (free index i)
1691        ref_indices=ref_i*siz(1)*siz(2)+1:(ref_i+1)*siz(1)*siz(2);
1692        i1_subseries=UvData.i1_series{1}(ref_indices);
1693        ref_indices=ref_indices(i1_subseries>0);
1694    end
1695    if isempty(ref_indices),errormsg='no next frame: set num_IndexIncrement =''*'' to reach the next existing file';return
1696    end
1697    i1=UvData.i1_series{1}(ref_indices(end));
1698    if ~isempty(UvData.i2_series{1})
1699        i2=UvData.i2_series{1}(ref_indices(end));
1700    end
1701    if ~isempty(UvData.j1_series{1})
1702        j1=UvData.j1_series{1}(ref_indices(end));
1703    end
1704    if ~isempty(UvData.j2_series{1})
1705        j2=UvData.j2_series{1}(ref_indices(end));
1706    end
1707   
1708    % case of a second file series
1709    if sub_value
1710        ref_i_1=i1_1;
1711        if ~isempty(i2_1)
1712            ref_i_1=floor((i1_1+i2_1)/2);% current reference index i
1713        end
1714        ref_j_1=1;
1715        if ~isempty(j1_1)
1716            ref_j_1=j1_1;
1717            if ~isempty(j2_1)
1718                ref_j_1=floor((j1_1+j2_1)/2);% current reference index j
1719            end
1720        end
1721        if ~isempty(increment)
1722            if get(handles.scan_i,'Value')==1% case of scanning along index i
1723                ref_i_1=ref_i_1+increment;% increment the current reference index i
1724            else % case of scanning along index j (burst numbers)
1725                ref_j_1=ref_j_1+increment;% increment the current reference index j if scan_j option is used
1726            end
1727        else % free increment, synchronise the ref indices with the first series
1728            ref_i_1=ref_i;
1729            ref_j_1=ref_j;
1730        end
1731        if numel(UvData.i1_series)==1
1732            UvData.i1_series{2}=UvData.i1_series{1};
1733            UvData.j1_series{2}=UvData.j1_series{1};
1734            UvData.i2_series{2}=UvData.i2_series{1};
1735            UvData.j2_series{2}=UvData.j2_series{1};
1736        end
1737        if ref_i_1<0
1738            errormsg='minimum i index reached';
1739        elseif ref_j_1<0
1740            errormsg='minimum j index reached';
1741        elseif ref_i_1+1>size(UvData.i1_series{2},3)
1742            errormsg='maximum i index reached for the second series (reload the input file to update the index bound)';
1743        elseif ref_j_1+1>size(UvData.i1_series{2},2)
1744            errormsg='maximum j index reached for the second series(reload the input file to update the index bound)';
1745        end
1746        if ~isempty(errormsg),return,end
1747        siz=size(UvData.i1_series{2});
1748        ref_indices=ref_i_1*siz(1)*siz(2)+ref_j_1*siz(1)+1:ref_i_1*siz(1)*siz(2)+(ref_j_1+1)*siz(1);
1749        i1_subseries=UvData.i1_series{2}(ref_indices);
1750        ref_indices=ref_indices(i1_subseries>0);
1751        if isempty(ref_indices)% case of pairs (free index i)
1752            ref_indices=ref_i_1*siz(1)*siz(2)+1:(ref_i_1+1)*siz(1)*siz(2);
1753            i1_subseries=UvData.i1_series{2}(ref_indices);
1754            ref_indices=ref_indices(i1_subseries>0);
1755        end
1756        i1_1=UvData.i1_series{2}(ref_indices(end));
1757        if ~isempty(UvData.i2_series{2})
1758            i2_1=UvData.i2_series{2}(ref_indices(end));
1759        end
1760        if ~isempty(UvData.j1_series{2})
1761            j1_1=UvData.j1_series{2}(ref_indices(end));
1762        end
1763        if ~isempty(UvData.j2_series{2})
1764            j2_1=UvData.j2_series{1}(ref_indices(end));
1765        end   
1766    else% the second series (if needed) is the same file as the first
1767        i1_1=i1;
1768        i2_1=i2;
1769        j1_1=j1;
1770        j2_1=j2;
1771    end
1772end
1773filename=fullfile_uvmat(InputFile.RootPath,InputFile.SubDir,InputFile.RootFile,FileExt,NomType,i1,i2,j1,j2);
1774if sub_value
1775    filename_1=fullfile_uvmat(InputFile.RootPath_1,InputFile.SubDir_1,InputFile.RootFile_1,InputFile.FileExt_1,InputFile.NomType_1,i1_1,i2_1,j1_1,j2_1);
1776end
1777
1778%% refresh plots
1779errormsg=refresh_field(handles,filename,filename_1,i1,i2,j1,j2,i1_1,i2_1,j1_1,j2_1);
1780
1781%% update the index counters if the index move is successfull
1782if isempty(errormsg)
1783    set(handles.i1,'String',num2stra(i1,NomType,1));
1784    if isequal(i2,i1)
1785        set(handles.i2,'String','');
1786    else
1787        set(handles.i2,'String',num2stra(i2,NomType,1));
1788    end
1789    set(handles.j1,'String',num2stra(j1,NomType,2));
1790    if isequal(j2,j1)
1791        set(handles.j2,'String','');
1792    else
1793        set(handles.j2,'String',num2stra(j2,NomType,2));
1794    end
1795    indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1796    set(handles.FileIndex,'String',indices);
1797    if ~isempty(filename_1)
1798        indices_1=fullfile_uvmat('','','','',InputFile.NomType_1,i1_1,i2_1,j1_1,j2_1);
1799        set(handles.FileIndex_1,'String',indices_1);
1800    end
1801    if isequal(movie_status,1)
1802        set(handles.movie_pair,'Value',1)
1803        movie_pair_Callback(hObject, eventdata, handles); %reactivate moviepair if it was activated
1804    end
1805end
1806
1807%------------------------------------------------------------------------
1808% --- Executes on button press in movie_pair: create an alternating movie with two view
1809function movie_pair_Callback(hObject, eventdata, handles)
1810%------------------------------------------------------------------------
1811
1812%% stop movie action if the movie_pair button is off
1813if ~get(handles.movie_pair,'value')
1814    set(handles.movie_pair,'BusyAction','Cancel')%stop movie pair if button is 'off'
1815    set(handles.i2,'String','')
1816    set(handles.j2,'String','')
1817    return
1818else
1819    set(handles.movie_pair,'BusyAction','queue')
1820end
1821
1822%% initialisation
1823set(handles.movie_pair,'BackgroundColor',[1 1 0])%paint the command button in yellow
1824drawnow
1825list_fields=get(handles.FieldName,'String');% list menu fields
1826index_fields=get(handles.FieldName,'Value');% selected string index
1827FieldName=list_fields{index_fields}; % selected field
1828UvData=get(handles.uvmat,'UserData');
1829if isequal(FieldName,'image')
1830    index=1;
1831    [RootPath,SubDir,RootFile,FileIndices,Ext]=read_file_boxes(handles);
1832    NomType=get(handles.NomType,'String');
1833else
1834    list_fields=get(handles.FieldName_1,'String');% list menu fields
1835    index_fields=get(handles.FieldName_1,'Value');% selected string index
1836    FieldName=list_fields{index_fields}; % selected field
1837    if isequal(FieldName,'image')
1838        index=2;
1839        [RootPath,tild,RootFile,FileIndex_1,Ext,NomType]=read_file_boxes_1(handles);
1840    else
1841        msgbox_uvmat('ERROR','an image or movie must be first introduced as input')
1842        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1843        set(handles.movie_pair,'Value',0)
1844        return
1845    end
1846end
1847num_i1=str2num(get(handles.i1,'String'));
1848num_j1=stra2num(get(handles.j1,'String'));
1849num_i2=str2num(get(handles.i2,'String'));
1850num_j2=stra2num(get(handles.j2,'String'));
1851imaname_1='';
1852if isempty(num_j2)
1853    if isempty(num_i2)
1854        if strcmp(get(handles.j2,'Visible'),'on') %if the j box is visible
1855            imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,Ext,NomType,num_i1,[],num_j1+1);
1856        end
1857        if exist(imaname_1,'file')
1858            num_j2=num_j1+1;% look by default for the next j index as the second file
1859            set(handles.j2,'String',num2stra(num_j2,NomType));
1860        else
1861            imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,Ext,NomType,num_i1+1,[],num_j1);
1862            if exist(imaname_1,'file')
1863                num_i2=num_i1+1;
1864                set(handles.i2,'String',num2str(num_i2));
1865            else
1866                msgbox_uvmat('ERROR', 'a second image index i2 or j2 is needed to show the pair as a movie')
1867                set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1868                set(handles.movie_pair,'Value',0)
1869                return
1870            end
1871        end
1872    else
1873        num_j2=num_j1;%repeat the index i1 by default
1874    end
1875end
1876if isempty(num_i2)
1877    num_i2=num_i1;%repeat the index i1 by default
1878end
1879imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,Ext,NomType,num_i2,[],num_j2);
1880if strcmp(NomType,'*')
1881    num_frame=num_i2;
1882else
1883    num_frame=num_j2;
1884end
1885if ~exist(imaname_1,'file')
1886      msgbox_uvmat('ERROR',['second input open (-)  ' imaname_1 ' not found']);
1887      set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1888       set(handles.movie_pair,'Value',0)
1889      return
1890end
1891
1892%% get the first image
1893%Field.AName='image';
1894if index==1
1895    Field_a=UvData.Field;% movie on the second field
1896else
1897    Field_a=UvData.Field_1;% movie on the first field
1898end
1899
1900%% read the second image
1901MovieObject=[];
1902if numel(UvData.MovieObject)>=index
1903    MovieObject=UvData.MovieObject{index};
1904end
1905[Field_b,ParamOut,errormsg] = read_field(imaname_1,UvData.FileType{index},MovieObject,num_frame);
1906% Field_b.AX=Field_a.AX;
1907% Field_b.AY=Field_a.AY;
1908% % z index
1909% nbslice=str2double(get(handles.num_NbSlice,'String'));
1910% if ~isempty(nbslice)
1911%     Field_b.ZIndex=mod(num_i2-1,nbslice)+1;
1912% end
1913% Field_b.CoordUnit='pixel';
1914%
1915% %% determine the input file type
1916% if (test_1 && isfield(UvData,'MovieObject')&& numel(UvData.MovieObject>=2))||(~test_1 && ~isempty(UvData.MovieObject{1}))
1917%     FileType='movie';
1918% elseif isequal(lower(Ext),'.avi')
1919%     FileType='avi';
1920% elseif isequal(lower(Ext),'.vol')
1921%     FileType='vol';
1922% else
1923%    form=imformats(Ext(2:end));
1924%    if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
1925%        if isequal(NomType,'*');
1926%            FileType='multimage';
1927%        else
1928%            FileType='image';
1929%        end
1930%    end
1931% end
1932% switch FileType
1933%         case 'movie'
1934%             if test_1
1935%                 Field_b.A=read(UvData.MovieObject{2},num_i2);
1936%             else
1937%                 Field_b.A=read(UvData.MovieObject{1},num_i2);
1938%             end
1939%         case 'avi'
1940%             mov=aviread(imaname_1,num_i2);
1941%             Field_b.A=frame2im(mov(1));
1942%         case 'vol'
1943%             Field_b.A=imread(imaname_1);
1944%         case 'multimage'
1945%             Field_b.A=imread(imaname_1,num_i2);
1946%         case 'image'
1947%             Field_b.A=imread(imaname_1);
1948% end
1949% if get(handles.slices,'Value')
1950%     Field.ZIndex=str2double(get(handles.z_index,'String'));
1951% end
1952
1953%px to phys or other transform on field
1954transform=get(handles.TransformPath,'UserData');
1955if  ~isempty(transform)
1956    if isfield(UvData,'XmlData') && numel(UvData.XmlData)>=index %use geometry calib recorded from the ImaDoc xml file as first priority
1957        if index==2
1958        Field_a=transform(Field_a,UvData.XmlData{index});%the first field has been stored without transform
1959        end
1960        Field_b=transform(Field_b,UvData.XmlData{index});
1961    end
1962end
1963
1964 % make movie until movie speed is set to 0 or STOP is activated
1965hima=findobj(handles.PlotAxes,'Tag','ima');% %handles.PlotAxes =main plotting window (A GENERALISER)
1966set(handles.STOP,'Visible','on')
1967set(handles.speed,'Visible','on')
1968set(handles.speed_txt,'Visible','on')
1969while get(handles.speed,'Value')~=0 && isequal(get(handles.movie_pair,'BusyAction'),'queue')%isequal(get(handles.run0,'BusyAction'),'queue'); % enable STOP command
1970    % read and plot the series of images in non erase mode
1971    set(hima,'CData',Field_b.A);
1972    pause(1.02-get(handles.speed,'Value'));% wait for next image
1973    set(hima,'CData',Field_a.A);
1974    pause(1.02-get(handles.speed,'Value'));% wait for next image
1975end
1976set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1977 set(handles.movie_pair,'Value',0)
1978
1979%------------------------------------------------------------------------
1980% --- Executes on button press in run0.
1981function run0_Callback(hObject, eventdata, handles)
1982%------------------------------------------------------------------------
1983set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
1984drawnow
1985[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
1986filename=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
1987filename_1='';%default
1988FileIndex_1='';
1989if get(handles.SubField,'Value')
1990    [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
1991    filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
1992end
1993num_i1=stra2num(get(handles.i1,'String'));
1994num_i2=stra2num(get(handles.i2,'String'));
1995num_j1=stra2num(get(handles.j1,'String'));
1996num_j2=stra2num(get(handles.j2,'String'));
1997[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
1998if isempty(j1_1)% case of movies, the index is not given by file index
1999    j1_1=num_j1;
2000end
2001
2002errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1);
2003
2004if ~isempty(errormsg)
2005      msgbox_uvmat('ERROR',errormsg);
2006else
2007    set(handles.i1,'BackgroundColor',[1 1 1])
2008    set(handles.i2,'BackgroundColor',[1 1 1])
2009    set(handles.j1,'BackgroundColor',[1 1 1])
2010    set(handles.j2,'BackgroundColor',[1 1 1])
2011    set(handles.FileIndex,'BackgroundColor',[1 1 1])
2012    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
2013end   
2014set(handles.run0,'BackgroundColor',[1 0 0])
2015
2016
2017%------------------------------------------------------------------------
2018% --- read the input files and refresh all the plots, including projection.
2019% OUTPUT:
2020%  errormsg: error message char string  =[] by default
2021% INPUT:
2022% filename: first input file (=[] in the absence of input file)
2023% filename_1: second input file (=[] in the asbsenc of secodn input file)
2024% num_i1,num_i2,num_j1,num_j2; frame indices
2025% Field: structure describing an optional input field (then replace the input file)
2026
2027function errormsg=refresh_field(handles,FileName,FileName_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1)
2028%------------------------------------------------------------------------
2029
2030%% initialisation
2031if ~exist('Field','var')
2032    Field={};
2033end
2034UvData=get(handles.uvmat,'UserData');
2035if ishandle(handles.UVMAT_title) %remove title panel on uvmat
2036    delete(handles.UVMAT_title)
2037end
2038
2039%% determine the main input file information for action
2040if ~exist(FileName,'file')
2041    errormsg=['input file ' FileName ' does not exist'];
2042    return
2043end
2044NomType=get(handles.NomType,'String');
2045NomType_1='';
2046if strcmp(get(handles.NomType_1,'Visible'),'on')
2047    NomType_1=get(handles.NomType_1,'String');
2048end
2049%update the z position index
2050mode_slice=get(handles.slices,'String');
2051if strcmp(mode_slice,'volume')
2052    z_index=num_j1;
2053    set(handles.z_index,'String',num2str(z_index))
2054else
2055    nbslice=str2num(get(handles.num_NbSlice,'String'));
2056    z_index=mod(num_i1-1,nbslice)+1;
2057    set(handles.z_index,'String',num2str(z_index))
2058end
2059% refresh menu for save_mask if relevant
2060masknumber=get(handles.masklevel,'String');
2061if length(masknumber)>=z_index
2062    set(handles.masklevel,'Value',z_index)
2063end
2064
2065%% test for need of tps
2066check_proj_tps=0;
2067if  (strcmp(UvData.FileType{1},'civdata')||strcmp(UvData.FileType{1},'civx'))
2068    for iobj=1:numel(UvData.ProjObject)
2069        if isfield(UvData.ProjObject{iobj},'ProjMode')&& strcmp(UvData.ProjObject{iobj}.ProjMode,'interp_tps')
2070            check_proj_tps=1;
2071            break
2072        end
2073    end
2074end
2075
2076%% read the first input field
2077ParamIn.ColorVar='';%default variable name for vector color
2078frame_index=1;%default
2079FieldName='';%default
2080VelType='';%default
2081switch UvData.FileType{1}
2082    case {'civx','civdata','netcdf'};
2083        list_fields=get(handles.FieldName,'String');% list menu fields
2084        FieldName= list_fields{get(handles.FieldName,'Value')}; % selected field
2085        % if get_field... is selected, the GUI get_field will be used to enter fields
2086        if ~strcmp(FieldName,'get_field...')
2087            if get(handles.FixVelType,'Value')
2088                VelTypeList=get(handles.VelType,'String');
2089                VelType=VelTypeList{get(handles.VelType,'Value')};
2090            end
2091        end
2092        % case of input vector field, get the scalar used for vector color
2093        if ~isempty(regexp(FieldName,'^vec('))
2094            list_code=get(handles.ColorCode,'String');% list menu fields
2095            index_code=get(handles.ColorCode,'Value');% selected string index
2096            if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2097                list_code=get(handles.ColorScalar,'String');% list menu fields
2098                index_code=get(handles.ColorScalar,'Value');% selected string index
2099                ParamIn.ColorVar= list_code{index_code}; % selected field
2100            end
2101        end
2102    case {'video','mmreader'}
2103        ParamIn=UvData.MovieObject{1};     
2104        if ~strcmp(NomType,'*')
2105            frame_index=num_j1;%frame index for movies or multimage
2106        else
2107            frame_index=num_i1;
2108        end
2109    case 'multimage'
2110        if ~strcmp(NomType,'*')
2111            frame_index=num_j1;%frame index for movies or multimage
2112        else
2113            frame_index=num_i1;
2114        end
2115    case 'vol' %TODO: update
2116        if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2117            ParamIn.Npy=UvData.XmlData.Npy;
2118            ParamIn.Npx=UvData.XmlData.Npx;
2119        else           
2120            errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2121            return
2122        end
2123end
2124if isstruct (ParamIn)
2125    ParamIn.FieldName=FieldName;
2126    ParamIn.VelType=VelType;
2127    XNameMenu=get(handles.Coord_x,'String');
2128    if ~isempty(XNameMenu)
2129        ParamIn.Coord_x=XNameMenu(get(handles.Coord_x,'Value'));
2130    end
2131    YNameMenu=get(handles.Coord_y,'String');
2132    if ~isempty(YNameMenu)
2133        ParamIn.Coord_y=YNameMenu(get(handles.Coord_y,'Value'));
2134    end
2135end
2136check_tps = 0;         
2137if strcmp(UvData.FileType{1},'civdata')&&~strcmp(ParamIn.FieldName,'velocity')&&~strcmp(ParamIn.FieldName,'get_field...')
2138       check_tps=1;%tps needed to get the requested field
2139end
2140[Field{1},ParamOut,errormsg] = read_field(FileName,UvData.FileType{1},ParamIn,frame_index);
2141if ~isempty(errormsg)
2142    errormsg=['uvmat / refresh_field / read_field( ' FileName ') / ' errormsg];
2143    return
2144end 
2145if isfield(ParamOut,'Npx')&& isfield(ParamOut,'Npy')
2146    set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2147    set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2148end
2149if isfield(ParamOut,'TimeIndex')% case of time obtained from get_field
2150    set(handles.i1,'String',num2str(ParamOut.TimeIndex))
2151end
2152if isfield(ParamOut,'TimeValue')
2153    Field{1}.Time=ParamOut.TimeValue;% case of time obtained from get_field
2154end
2155Field{1}.ZIndex=z_index; %used for multiplane 3D calibration
2156
2157
2158%% choose and read a second field FileName_1 if defined
2159VelType_1=[];%default
2160FieldName_1=[];
2161ParamIn_1=[];
2162ParamOut_1=[];
2163frame_index_1=1;
2164if ~isempty(FileName_1)
2165    if ~exist(FileName_1,'file')
2166        errormsg=['second file ' FileName_1 ' does not exist'];
2167        return
2168    end
2169   % Name=FileName_1;
2170    switch UvData.FileType{2}
2171        case {'civx','civdata','netcdf'};
2172            list_fields=get(handles.FieldName_1,'String');% list menu fields
2173            if ischar(list_fields),list_fields={list_fields};end
2174            FieldName_1= list_fields{get(handles.FieldName_1,'Value')}; % selected field
2175            if ~strcmp(FieldName,'get_field...')
2176                if get(handles.FixVelType,'Value')
2177                    VelTypeList=get(handles.VelType_1,'String');
2178                    VelType_1=VelTypeList{get(handles.VelType_1,'Value')};% read the velocity type.
2179                end
2180            end
2181            if strcmp(FieldName_1,'velocity')&& strcmp(get(handles.ColorCode,'Visible'),'on')
2182                list_code=get(handles.ColorCode,'String');% list menu fields
2183                index_code=get(handles.ColorCode,'Value');% selected string index
2184                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2185                    list_code=get(handles.ColorScalar,'String');% list menu fields
2186                    index_code=get(handles.ColorScalar,'Value');% selected string index
2187                    ParamIn_1.ColorVar= list_code{index_code}; % selected field for vector color display                 
2188                end
2189            end
2190        case {'video','mmreader'}
2191            ParamIn_1=UvData.MovieObject{2};
2192                        if ~strcmp(NomType_1,'*')
2193                frame_index_1=j1_1;%frame index for movies or multimage
2194            else
2195                frame_index_1=i1_1;
2196            end 
2197         case 'multimage'
2198            if strcmp(NomType_1,'*')%frame index for movies or multimage
2199                frame_index_1=i1_1;
2200            else
2201                frame_index_1=j1_1;
2202            end   
2203        case 'vol' %TODO: update
2204            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2205                ParamIn_1.Npy=UvData.XmlData.Npy;
2206                ParamIn_1.Npx=UvData.XmlData.Npx;
2207            else
2208                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2209                return
2210            end
2211    end
2212    if isequal(get(handles.NomType_1,'Visible'),'on')
2213    NomType_1=get(handles.NomType_1,'String');
2214    else
2215        NomType_1=get(handles.NomType,'String');
2216    end
2217    test_keepdata_1=0;% test for keeping the previous stored data if the input files are unchanged
2218    if ~isequal(NomType_1,'*')&& isfield(UvData,'FileName_1')
2219           test_keepdata_1= strcmp(FileName_1,UvData.FileName_1) ;
2220    end
2221    if test_keepdata_1
2222        Field{2}=UvData.Field_1;% keep the stored field
2223        ParamOut_1=UvData.ParamOut_1;
2224    else
2225        if isempty(ParamIn_1) || isstruct(ParamIn_1)
2226        ParamIn_1.FieldName=FieldName_1;
2227        ParamIn_1.VelType=VelType_1;
2228        ParamIn_1.GUIName='get_field_1';
2229        end 
2230        [Field{2},ParamOut_1,errormsg] = read_field(FileName_1,UvData.FileType{2},ParamIn_1,frame_index_1);
2231        if ~isempty(errormsg)
2232            errormsg=['error in reading ' FieldName_1 ' in ' FileName_1 ': ' errormsg];
2233            return
2234        end
2235        if isstruct(ParamOut_1)&&~strcmp(ParamOut_1.FieldName,'get_field...')&& (strcmp(UvData.FileType{2},'civdata')||strcmp(UvData.FileType{2},'civx'))...
2236                &&~strcmp(ParamOut_1.FieldName,'velocity') && ~strcmp(ParamOut_1.FieldName,'get_field...')
2237            if ~check_proj_tps
2238             %   Field{2}=calc_field([{ParamOut_1.FieldName} {ParamOut_1.ColorVar}],Field{2});
2239            end
2240        end
2241    end
2242    Field{2}.ZIndex=z_index;%used for multi-plane 3D calibration
2243end
2244
2245%% update uvmat interface
2246if isfield(ParamOut,'Npx')
2247    set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2248    set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2249elseif isfield(ParamOut_1,'Npx')
2250    set(handles.num_Npx,'String',num2str(ParamOut_1.Npx));% display image size on the interface
2251    set(handles.num_Npy,'String',num2str(ParamOut_1.Npy));
2252end
2253
2254%% update the display menu for the first velocity type (first menuline)
2255test_veltype=0;
2256% if ~isequal(FileType,'netcdf')|| isequal(FieldName,'get_field...')
2257if (strcmp(UvData.FileType{1},'civx')||strcmp(UvData.FileType{1},'civdata'))&& ~strcmp(FieldName,'get_field...')
2258    test_veltype=1;
2259    set(handles.VelType,'Visible','on')
2260    set(handles.VelType_1,'Visible','on')
2261    set(handles.FixVelType,'Visible','on')
2262    menu=set_veltype_display(ParamOut.CivStage,UvData.FileType{1});
2263    index_menu=strcmp(ParamOut.VelType,menu);%look for VelType in  the menu
2264    index_val=find(index_menu,1);
2265    if isempty(index_val)
2266        index_val=1;
2267    end
2268    set(handles.VelType,'Value',index_val)
2269    if ~get(handles.SubField,'value')
2270        set(handles.VelType,'String',menu)
2271        set(handles.VelType_1,'Value',1)
2272        set(handles.VelType_1,'String',[{''};menu])
2273    end
2274else
2275    set(handles.VelType,'Visible','off')
2276end
2277% display the FieldName menu from the input file and pick the selected one:
2278% if isstruct(ParamOut)
2279%     field_index=strcmp(ParamOut.FieldName,ParamOut.FieldList);
2280%     set(handles.FieldName,'String',ParamOut.FieldList); %update the field menu
2281%     set(handles.FieldName,'Value',find(field_index,1))
2282% end
2283
2284%% update the display menu for the second velocity type (second menuline)
2285test_veltype_1=0;
2286if isempty(FileName_1)
2287    %     set(handles.FieldName_1,'Value',1); %update the field menu
2288    %     if isstruct(ParamOut)
2289    %     set(handles.FieldName_1,'String',[{''};ParamOut.FieldList]); %update the field menu
2290    %     end
2291elseif ~test_keepdata_1
2292    if (~strcmp(UvData.FileType{2},'netcdf')&&~strcmp(UvData.FileType{2},'civdata')&&~strcmp(UvData.FileType{2},'civx'))|| isequal(FieldName_1,'get_field...')
2293        set(handles.VelType_1,'Visible','off')
2294    else
2295        test_veltype_1=1;
2296        set(handles.VelType_1,'Visible','on')
2297        menu=set_veltype_display(ParamOut_1.CivStage,UvData.FileType{2});
2298        index_menu=strcmp(ParamOut_1.VelType,menu);
2299        set(handles.VelType_1,'Value',1+find(index_menu,1))
2300        set(handles.VelType_1,'String',[{''};menu])
2301    end
2302    % update the second field menu: the same quantity
2303    if isstruct(ParamOut_1)
2304%        set(handles.FieldName_1,'String',[{''};ParamOut_1.FieldList]); %update the field menu
2305        % display the FieldName menu from the input file and pick the selected one:
2306        FieldList=get(handles.FieldName_1,'String');
2307        field_index=strcmp(ParamOut_1.FieldName,FieldList);
2308        if ~isempty(field_index)
2309            set(handles.FieldName_1,'Value',find(field_index,1))
2310        end
2311    end
2312end
2313if test_veltype||test_veltype_1
2314    set(handles.FixVelType,'Visible','on')
2315else
2316    set(handles.FixVelType,'Visible','off')
2317end
2318
2319% field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
2320% set(handles.FieldName,'String',ParamOut.FieldList); %update the field menu
2321% set(handles.FieldName,'Value',find(field_index,1))
2322   
2323%% introduce w as background image by default for a new series (only for nbdim=2)
2324if ~isfield(UvData,'NewSeries')
2325    UvData.NewSeries=1;
2326end
2327%put W as background image by default if NbDim=2:
2328if  UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W) && ~isequal(Field{1}.NbDim,3);
2329        set(handles.SubField,'Value',1);
2330        set(handles.RootPath_1,'String','"')
2331        set(handles.RootFile_1,'String','"')
2332        set(handles.SubDir_1,'String','"');
2333         indices=fullfile_uvmat('','','','',NomType,num_i1,num_i2,num_j1,num_j2);
2334        set(handles.FileIndex_1,'String',indices)
2335        set(handles.FileExt_1,'String','"');
2336        set(handles.FieldName_1,'Visible','on');
2337        set(handles.FieldName_1,'Visible','on');
2338        set(handles.RootPath_1,'Visible','on')
2339        set(handles.RootFile_1,'Visible','on')
2340        set(handles.SubDir_1,'Visible','on');
2341        set(handles.FileIndex_1,'Visible','on');
2342        set(handles.FileExt_1,'Visible','on');
2343        set(handles.FieldName_1,'Visible','on');
2344        Field{1}.AName='w';
2345end           
2346
2347%% display time
2348abstime=[];%default inputs
2349abstime_1=[];
2350dt=[];
2351TimeUnit='';
2352% time from xml file or video movie
2353if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'Time')
2354    if isempty(num_i2)||isnan(num_i2)
2355        num_i2=num_i1;
2356    end
2357    if isempty(num_j1)||isnan(num_j1)
2358        num_j1=1;
2359    end
2360    if isempty(num_j2)||isnan(num_j2)
2361        num_j2=num_j1;
2362    end
2363    siz=size(UvData.XmlData{1}.Time);
2364    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)
2365        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
2366        dt=(UvData.XmlData{1}.Time(num_i2+1,num_j2+1)-UvData.XmlData{1}.Time(num_i1+1,num_j1+1));
2367        Field{1}.Dt=dt;
2368        if isfield(UvData.XmlData{1},'TimeUnit')
2369            TimeUnit=UvData.XmlData{1}.TimeUnit;
2370        end
2371    end
2372    if numel(UvData.XmlData)==2
2373        if isempty(i2_1)
2374            i2_1=num_i1;
2375        end
2376        if isempty(j1_1)
2377            j1_1=1;
2378        end
2379        if isempty(j2_1)
2380            j2_1=j1_1;
2381        end
2382        siz=size(UvData.XmlData{2}.Time);
2383        if ~isempty(i1_1) && siz(1)>=max(i1_1+1,i2_1+1) && siz(2)>=max(j1_1+1,j2_1+1)
2384            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
2385            Field{2}.Dt=(UvData.XmlData{2}.Time(i2_1+1,j2_1+1)-UvData.XmlData{2}.Time(i1_1+1,j1_1+1));
2386        end
2387    end
2388end
2389% if isfield(Field{1},'Time')
2390%     abstime=Field{1}.Time;%time read from the netcdf input file
2391% end
2392% if numel(Field)==2 && isfield(Field{2},'Time')
2393%     abstime_1=Field{2}.Time;%time read from the netcdf input file
2394% end
2395
2396% look for timing in the input file if not defined in a xml file or movie
2397if isempty(abstime)
2398if isfield(Field{1},'Dt')
2399    dt=Field{1}.Dt;%dt read from the netcdf input file
2400    if isfield(Field{1},'TimeUnit')
2401       TimeUnit=Field{1}.TimeUnit;
2402    end
2403elseif numel(Field)==2 && isfield(Field{2},'Dt')%dt obtained from the second field if not defined in the first
2404    dt=Field{2}.Dt;%dt read from the netcdf input file
2405    if isfield(Field{2},'TimeUnit')
2406       TimeUnit=Field{2}.TimeUnit;
2407    end
2408end
2409end
2410% if ~isequal(numel(abstime),1)
2411%     abstime=[];
2412% end
2413% if ~isequal(numel(abstime_1),1)
2414%       abstime_1=[];
2415% end 
2416set(handles.abs_time,'String',num2str(abstime,5))
2417set(handles.abs_time_1,'String',num2str(abstime_1,5))
2418if isempty(dt)||isequal(dt,0)
2419    set(handles.Dt_txt,'String','')
2420else
2421    if  isempty(TimeUnit)
2422        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  10^(-3)'] )
2423    else
2424        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  m' TimeUnit] )
2425    end
2426end
2427
2428
2429%% store the current open names, fieldname and vel types in uvmat interface
2430UvData.FileName_1=FileName_1;
2431UvData.ParamOut_1=ParamOut_1;
2432if numel(Field)==2
2433UvData.Field_1=Field{2}; %store the second field for possible use at next RUN
2434end
2435
2436%% apply coordinate transform or other user fct
2437transform=get(handles.TransformPath,'UserData');
2438if isempty(transform)
2439    UvData.Field=Field{1};
2440else
2441    XmlData=[];%default
2442    XmlData_1=[];%default
2443    if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority
2444        XmlData=UvData.XmlData{1};
2445        if numel(UvData.XmlData)==2
2446            XmlData_1=UvData.XmlData{2};
2447        end
2448    end
2449    transform=get(handles.TransformPath,'UserData');
2450    switch nargin(transform)
2451        case 4
2452            if length(Field)==2
2453                UvData.Field=transform(Field{1},XmlData,Field{2},XmlData_1);
2454            else
2455                UvData.Field=transform(Field{1},XmlData);
2456            end
2457        case 3
2458            if length(Field)==2
2459                UvData.Field=transform(Field{1},XmlData,Field{2});
2460            else
2461                UvData.Field=transform(Field{1},XmlData);
2462            end
2463        case 2
2464            UvData.Field=transform(Field{1},XmlData);
2465        case 1
2466            UvData.Field=transform(Field{1});
2467    end
2468end
2469
2470%% calculate tps coefficients if needed
2471UvData.Field=tps_coeff_field(UvData.Field,check_proj_tps);
2472
2473%% analyse input field
2474%test_x=0;
2475%test_z=0;% test for unstructured z coordinate
2476%[errormsg,ListDimName,DimValue,VarDimIndex]=check_field_structure(UvData.Field);% check the input field structure
2477% if ~isempty(errormsg)
2478%     errormsg=['error in uvmat/refresh_field/check_field_structure: ' errormsg];% display error
2479%     return
2480% end
2481[CellInfo,NbDimArray,errormsg]=find_field_cells(UvData.Field);% analyse  the input field structure
2482if ~isempty(errormsg)
2483    errormsg=['uvmat /refresh_field / find_field_cells / ' errormsg];% display error
2484    return
2485end
2486
2487NbDim=max(NbDimArray);% spatial dimension of the input field
2488imax=find(NbDimArray==NbDim);% indices of field cells to consider
2489if isfield(UvData.Field,'NbDim')
2490    NbDim=double(UvData.Field.NbDim);% deal with plane fields containing z coordinates
2491end
2492
2493%UvData.Field=get_bounds(UvData.Field);
2494
2495%% get bounds and mesh (needed  to propose default options for projection objects)
2496if NbDim>1
2497    CoordMax=zeros(numel(imax),NbDim);
2498    CoordMin=zeros(numel(imax),NbDim);
2499    Mesh=zeros(1,numel(imax));
2500    for ind=1:numel(imax)
2501        if strcmp(CellInfo{imax(ind)}.CoordType,'tps')
2502            CoordName=UvData.Field.ListVarName{CellInfo{imax(ind)}.CoordIndex};% X,Y coordinates in a single variable
2503            CoordMax(ind,NbDim)=max(max(UvData.Field.(CoordName)(1:end-3,1,:),[],1),[],3);% max of x component (2D case)
2504            CoordMax(ind,NbDim-1)=max(max(UvData.Field.(CoordName)(1:end-3,2,:),[],1),[],3);% max of y component (2D case)
2505            CoordMin(ind,NbDim)=min(min(UvData.Field.(CoordName)(1:end-3,1,:),[],1),[],3);
2506            CoordMin(ind,NbDim-1)=min(min(UvData.Field.(CoordName)(1:end-3,2,:),[],1),[],3);% min of y component (2D case)
2507        else
2508            XName=UvData.Field.ListVarName{CellInfo{imax(ind)}.CoordIndex(end)};
2509            YName=UvData.Field.ListVarName{CellInfo{imax(ind)}.CoordIndex(end-1)};
2510            CoordMax(ind,NbDim)=max(max(UvData.Field.(XName)));
2511            CoordMin(ind,NbDim)=min(min(UvData.Field.(XName)));
2512            CoordMax(ind,NbDim-1)=max(max(UvData.Field.(YName)));
2513            CoordMin(ind,NbDim-1)=min(min(UvData.Field.(YName)));
2514            %         test_x=1;%test for unstructured coordinates
2515            if NbDim==3
2516                ZName=UvData.Field.ListVarName{CellInfo{imax(ind)}.CoordIndex(1)};
2517                CoordMax(imax(ind),1)=max(max(UvData.Field.(ZName)));
2518                CoordMin(ind,1)=min(min(UvData.Field.(ZName)));
2519            end
2520        end
2521        switch CellInfo{imax(ind)}.CoordType
2522           
2523            case {'scattered','tps'} %unstructured coordinates
2524                NbPoints=CellInfo{imax(ind)}.CoordSize;% total nbre of points
2525                Mesh(ind)=(prod(CoordMax(ind,:)-CoordMin(ind,:))/NbPoints)^(1/NbDim); %(volume or area per point)^(1/NbDim)
2526            case 'grid'%structured coordinate
2527                NbPoints=CellInfo{imax(ind)}.CoordSize;% nbre of points in each direction
2528                Mesh(ind)=min((CoordMax(ind,:)-CoordMin(ind,:))./(NbPoints-1));               
2529        end
2530    end
2531    UvData.Field.CoordMesh=min(Mesh);
2532    UvData.Field.XMax=max(CoordMax(ind,end));
2533    UvData.Field.XMin=min(CoordMin(ind,end));
2534    UvData.Field.YMax=max(CoordMax(ind,end-1));
2535    UvData.Field.YMin=max(CoordMin(ind,end-1));
2536    if NbDim==3
2537        UvData.Field.ZMax=max(CoordMax(ind,1));
2538        UvData.Field.ZMin=max(CoordMin(ind,1));
2539    end
2540    % adjust the mesh to a value 1, 2 , 5 *10^n
2541    ord=10^(floor(log10(UvData.Field.CoordMesh)));%order of magnitude
2542    if UvData.Field.CoordMesh/ord>=5
2543        UvData.Field.CoordMesh=5*ord;
2544    elseif UvData.Field.CoordMesh/ord>=2
2545        UvData.Field.CoordMesh=2*ord;
2546    else
2547        UvData.Field.CoordMesh=ord;
2548    end
2549    % default projection plane
2550    if isempty(UvData.ProjObject{1})
2551        UvData.ProjObject{1}.Type='plane';%main plotting plane
2552        UvData.ProjObject{1}.ProjMode='projection';%main plotting plane
2553        UvData.ProjObject{1}.DisplayHandle.uvmat=[]; %plane not visible in uvmat
2554        UvData.ProjObject{1}.DisplayHandle.view_field=[]; %plane not visible in uvmat
2555    end
2556    %% 3D case (menuvolume)
2557    if NbDim==3% && UvData.NewSeries
2558        test_set_object=1;
2559        hset_object=findobj(allchild(0),'tag','set_object');% look for the set_object GUI
2560        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
2561        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
2562        if ~isempty(hset_object) %if set_object is detected
2563            delete(hset_object);% delete the GUI set_object if it does not fit
2564        end
2565        if test_set_object% reinitiate the GUI set_object
2566            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
2567            UvData.ProjObject{1}.NbDim=NbDim;%test for 3D objects
2568            UvData.ProjObject{1}.RangeZ=UvData.Field.CoordMesh;%main plotting plane
2569            UvData.ProjObject{1}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen
2570            UvData.ProjObject{1}.Angle=[0 0 0];
2571            UvData.ProjObject{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR
2572            UvData.ProjObject{1}.Name='1-PLANE';
2573            UvData.ProjObject{1}.enable_plot=1;
2574            set_object(UvData.ProjObject{1},handles,ZBounds);
2575            set(handles.ListObject,'Value',1);
2576            set(handles.ListObject,'String',{'1-PLANE'});
2577            set(handles.edit_object,'Value',1)% put the plane in edit mode to enable the z cursor
2578            edit_object_Callback([],[], handles)
2579        end
2580        %multilevel case (single menuplane in a 3D space)
2581    elseif isfield(UvData,'Z')
2582        if isfield(UvData,'CoordType')&& isequal(UvData.CoordType,'phys') && isfield(UvData,'XmlData')
2583            XmlData=UvData.XmlData{1};
2584            if isfield(XmlData,'PlanePos')
2585                UvData.ProjObject{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:);
2586            end
2587            if isfield(XmlData,'PlaneAngle')
2588                siz=size(XmlData.PlaneAngle);
2589                indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning)
2590                UvData.ProjObject{1}.PlaneAngle=XmlData.PlaneAngle(indangle,:);
2591            end
2592        elseif isfield(UvData,'ZIndex')
2593            UvData.ProjObject{1}.ZObject=UvData.ZIndex;
2594        end
2595    end
2596end
2597
2598testnewseries=UvData.NewSeries;
2599UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback)
2600set(handles.uvmat,'UserData',UvData)
2601
2602%% reset the min and max of scalar if only the mask is displayed(TODO: check the need)
2603% if isfield(UvData,'Mask')&& ~isfield(UvData,'A')
2604%     set(handles.num_MinA,'String','0')
2605%     set(handles.num_MaxA,'String','255')
2606% end
2607
2608%% usual 1D (x,y) plots
2609if NbDim<=1
2610    set(handles.Objects,'Visible','off')
2611    set(handles.ListObject_1_title,'Visible','off')
2612    set(handles.ListObject_1,'Visible','off')
2613    [PlotType,PlotParamOut]=plot_field(UvData.Field,handles.PlotAxes,read_GUI(handles.uvmat));
2614    errormsg=fill_GUI(PlotParamOut,handles.uvmat);
2615    for list={'Scalar','Vectors'}
2616        if ~isfield(PlotParamOut,list{1})
2617            set(handles.(list{1}),'Visible','off')
2618        end
2619    end
2620    %write_plot_param(handles,PlotParamOut) %update the auto plot parameters
2621   
2622%% 2D or 3D fieldname are generally projected
2623else
2624    set(handles.Objects,'Visible','on')
2625    set(handles.ListObject_1_title,'Visible','on')
2626    set(handles.ListObject_1,'Visible','on')
2627   
2628    %% Plot the projections on the selected  projection objects
2629    % main projection object (uvmat display)
2630    list_object=get(handles.ListObject_1,'String');
2631    if isequal(list_object,{''})||isequal(list_object,' ')%refresh list of objects if the menu is empty
2632        set(handles.ListObject,'Value',1)
2633        set(handles.ListObject,'String',{'plane'})
2634        UvData.ProjObject{1}.Type='plane';%main plotting plane
2635        UvData.ProjObject{1}.ProjMode='projection';%main plotting plane
2636        UvData.ProjObject{1}.DisplayHandle.uvmat=[]; %plane not visible in uvmat
2637        UvData.ProjObject{1}.DisplayHandle.view_field=[]; %plane not visible in uvmat
2638        set(handles.ListObject_1,'Value',1)
2639        set(handles.ListObject_1,'String',{'plane'})
2640    end
2641    IndexObj(1)=get(handles.ListObject_1,'Value');%selected projection object for main view
2642    if IndexObj(1)> numel(UvData.ProjObject)
2643        IndexObj(1)=1;%select the first object if the selected one does not exist
2644        set(handles.ListObject_1,'Value',1)
2645    end
2646    IndexObj(2)=get(handles.ListObject,'Value');%selected projection object for main view
2647    if isequal(IndexObj(2),IndexObj(1))
2648        IndexObj(2)=[];
2649    end
2650    plot_handles{1}=handles;
2651    if isfield(UvData,'plotaxes')%case of movies
2652        haxes(1)=UvData.plotaxes;
2653    else
2654        haxes(1)=handles.PlotAxes;
2655    end
2656    PlotParam{1}=read_GUI(handles.uvmat);
2657    %default settings if vectors not visible
2658    if ~isfield(PlotParam{1},'Vectors')
2659        PlotParam{1}.Vectors.MaxVec=1;
2660        PlotParam{1}.Vectors.MinVec=0;
2661        PlotParam{1}.Vectors.CheckFixVecColor=1;
2662        PlotParam{1}.Vectors.ColCode1=0.33;
2663        PlotParam{1}.Vectors.ColCode2=0.66;
2664        PlotParam{1}.Vectors.ColorScalar={''};
2665        PlotParam{1}.Vectors.ColorCode= {'rgb'};
2666    end
2667    PosColorbar{1}=UvData.OpenParam.PosColorbar;%prescribe the colorbar position on the uvmat interface
2668   
2669    %% second projection object (view_field display)
2670    if length( IndexObj)>=2
2671        view_field_handle=findobj(allchild(0),'tag','view_field');%handles of the view_field GUI
2672        if ~isempty(view_field_handle)
2673            plot_handles{2}=guidata(view_field_handle);
2674            haxes(2)=plot_handles{2}.PlotAxes;
2675            PlotParam{2}=read_GUI(view_field_handle);
2676           % PlotParam{2}=read_GUI(handles.uvmat);%read plotting parameters on the uvmat interface
2677            PosColorbar{2}='*'; %TODO: deal with colorbar position on view_field
2678        end
2679    end
2680   
2681    %% loop on the projection objects: one or two
2682   
2683    for imap=1:numel(IndexObj)
2684        iobj=IndexObj(imap);
2685        if numel(UvData.ProjObject)<iobj
2686            break
2687        end
2688        [ObjectData,errormsg]=proj_field(UvData.Field,UvData.ProjObject{iobj});% project field on the object
2689        if ~isempty(errormsg)
2690            return
2691        end
2692        if testnewseries
2693            PlotParam{imap}.Scalar.CheckBW=[]; %B/W option depends on the input field (image or scalar)
2694            if isfield(ObjectData,'CoordUnit')
2695                PlotParam{imap}.Coordinates.CheckFixAspectRatio=1;% set x and y scaling equal if CoordUnit is defined (common unit for x and y)
2696                PlotParam{imap}.Coordinates.AspectRatio=1; %set aspect ratio to 1
2697            end
2698        end
2699        %use of mask (TODO: check)
2700        if isfield(ObjectData,'NbDim') && isequal(ObjectData.NbDim,2) && isfield(ObjectData,'Mask') && isfield(ObjectData,'A')
2701            flag_mask=double(ObjectData.Mask>200);%=0 for masked regions
2702            AX=ObjectData.AX;%x coordiantes for the scalar field
2703            AY=ObjectData.AY;%y coordinates for the scalar field
2704            MaskX=ObjectData.MaskX;%x coordiantes for the mask
2705            MaskY=ObjectData.MaskY;%y coordiantes for the mask
2706            if ~isequal(MaskX,AX)||~isequal(MaskY,AY)
2707                nxy=size(flag_mask);
2708                sizpx=(ObjectData.MaskX(end)-ObjectData.MaskX(1))/(nxy(2)-1);%size of a mask pixel
2709                sizpy=(ObjectData.MaskY(1)-ObjectData.MaskY(end))/(nxy(1)-1);
2710                x_mask=ObjectData.MaskX(1):sizpx:ObjectData.MaskX(end); % pixel x coordinates for image display
2711                y_mask=ObjectData.MaskY(1):-sizpy:ObjectData.MaskY(end);% pixel x coordinates for image display
2712                %project on the positions of the scalar
2713                npxy=size(ObjectData.A);
2714                dxy(1)=(ObjectData.AY(end)-ObjectData.AY(1))/(npxy(1)-1);%grid mesh in y
2715                dxy(2)=(ObjectData.AX(end)-ObjectData.AX(1))/(npxy(2)-1);%grid mesh in x
2716                xi=ObjectData.AX(1):dxy(2):ObjectData.AX(end);
2717                yi=ObjectData.AY(1):dxy(1):ObjectData.AY(end);
2718                [XI,YI]=meshgrid(xi,yi);% creates the matrix of regular coordinates
2719                flag_mask = interp2(x_mask,y_mask,flag_mask,XI,YI);
2720            end
2721            AClass=class(ObjectData.A);
2722            ObjectData.A=flag_mask.*double(ObjectData.A);
2723            ObjectData.A=feval(AClass,ObjectData.A);
2724        end
2725        if ~isempty(ObjectData)
2726            %PlotType='none'; %default
2727            if imap==2 && isempty(view_field_handle)
2728                view_field(ObjectData)
2729            else
2730                [PlotType,PlotParamOut]=plot_field(ObjectData,haxes(imap),PlotParam{imap},PosColorbar{imap});
2731                if imap==1
2732                    errormsg=fill_GUI(PlotParamOut,handles.uvmat);
2733                else
2734                    errormsg=fill_GUI(PlotParamOut,view_field_handle);
2735                end
2736                for list={'Scalar','Vectors'}
2737                    if ~isfield(PlotParamOut,list{1})
2738                        set(plot_handles{imap}.(list{1}),'Visible','off')
2739                    end
2740                end
2741                if isfield(Field,'CoordMesh')&&~isempty(Field.CoordMesh)
2742                    ObjectData.CoordMesh=Field.CoordMesh; % gives an estimated mesh size (useful for mouse action on the plot)
2743                end
2744            end
2745        end
2746    end
2747   
2748    %% update the mask
2749    if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
2750        update_mask(handles,num_i1,num_i2);
2751    end
2752   
2753    %% prepare the menus of histograms and plot them (histogram of the whole volume in 3D case)
2754    menu_histo=(UvData.Field.ListVarName)';%list of field variables to be displayed for the menu of histogram display
2755    ind_skip=[];
2756    % nb_histo=1;
2757    Ustring='';
2758    Vstring='';
2759    % suppress coordinates from the histogram menu
2760    for ivar=1:numel(menu_histo)%l loop on field variables:
2761        if isfield(UvData.Field,'VarAttribute') && numel(UvData.Field.VarAttribute)>=ivar && isfield(UvData.Field.VarAttribute{ivar},'Role')
2762            Role=UvData.Field.VarAttribute{ivar}.Role;
2763            switch Role
2764                case {'coord_x','coord_y','coord_z','dimvar'}
2765                    ind_skip=[ind_skip ivar];
2766                case {'vector_x'}
2767                    Ustring=UvData.Field.ListVarName{ivar};
2768                    ind_skip=[ind_skip ivar];
2769                case {'vector_y'}
2770                    Vstring=UvData.Field.ListVarName{ivar};
2771                    ind_skip=[ind_skip ivar];
2772            end
2773        end
2774        DimCell=UvData.Field.VarDimName{ivar};
2775        DimName='';
2776        if ischar(DimCell)
2777            DimName=DimCell;
2778        elseif iscell(DimCell)&& numel(DimCell)==1
2779            DimName=DimCell{1};
2780        end
2781        if strcmp(DimName,menu_histo{ivar})
2782            ind_skip=[ind_skip ivar];
2783        end
2784    end
2785    menu_histo(ind_skip)=[];% remove skipped items
2786    if ~isempty(Ustring)
2787        menu_histo=[{[Ustring ',' Vstring]};menu_histo];% add U, V at the beginning if they exist
2788    end
2789   
2790    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2791    % display menus and plot histograms
2792    test_v=0;
2793    if ~isempty(menu_histo)
2794        set(handles.histo1_menu,'Value',1)
2795        set(handles.histo1_menu,'String',menu_histo)
2796        histo1_menu_Callback(handles.histo1_menu, [], handles)% plot first histogram
2797    end
2798end
2799
2800%------------------------------------------------------------------------
2801function histo1_menu_Callback(hObject, eventdata, handles)
2802%--------------------------------------------
2803histo_menu=get(handles.histo1_menu,'String');
2804histo_value=get(handles.histo1_menu,'Value');
2805FieldName=histo_menu{histo_value};
2806
2807UvData=get(handles.uvmat,'UserData');
2808Field=UvData.Field;
2809r=regexp(FieldName,'(?<var1>.*)(?<sep>,)(?<var2>.*)','names');
2810FieldName_2='';
2811if ~isempty(r)
2812    FieldName=r.var1;
2813    FieldName_2=r.var2;
2814end
2815if ~isfield(UvData.Field,FieldName)
2816    msgbox_uvmat('ERROR',['no field  ' FieldName ' for histogram'])
2817    return
2818end
2819FieldHisto=Field.(FieldName);
2820if isfield(Field,'FF') && ~isempty(Field.FF) && isequal(size(Field.FF),size(FieldHisto))
2821    indsel=find(Field.FF==0);%find values marked as false
2822    if ~isempty(indsel)
2823        FieldHisto=FieldHisto(indsel);
2824        if ~isempty(FieldName_2)
2825            FieldHisto(:,:,2)=Field.(FieldName_2)(indsel);
2826        end
2827    end
2828end
2829if isempty(Field)
2830    msgbox_uvmat('ERROR',['empty field ' FieldName])
2831else
2832    nxy=size(FieldHisto);
2833    Amin=double(min(min(min(FieldHisto))));%min of field value
2834    Amax=double(max(max(max(FieldHisto))));%max of field value
2835    if isequal(Amin,Amax)
2836        cla(handles.HistoAxes)
2837    else
2838        Histo.ListVarName={FieldName,'histo'};
2839        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
2840            Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
2841        else
2842            if numel(nxy)==2
2843                Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
2844            else
2845                Histo.VarDimName={FieldName,{FieldName,'component'}}; %dimensions for the histogram
2846            end
2847        end
2848        %unit
2849        units=[]; %default
2850        for ivar=1:numel(Field.ListVarName)
2851            if strcmp(Field.ListVarName{ivar},FieldName)
2852                if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'units')
2853                    units=Field.VarAttribute{ivar}.units;
2854                    break
2855                end
2856            end
2857        end
2858        if ~isempty(units)
2859            Histo.VarAttribute{1}.units=units;
2860        end
2861        eval(['Histo.' FieldName '=linspace(Amin,Amax,50);'])%absissa values for histo
2862        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
2863            C=reshape(double(FieldHisto),1,[]);% reshape in a vector
2864            Histo.histo(:,1)=hist(C, Histo.(FieldName));  %calculate histogram
2865        else
2866            for col=1:size(FieldHisto,3)
2867                B=FieldHisto(:,:,col);
2868                C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector
2869                Histo.histo(:,col)=hist(C, Histo.(FieldName));  %calculate histogram
2870            end
2871        end
2872        plot_field(Histo,handles.HistoAxes);
2873        hlegend=legend;
2874        if isempty(FieldName_2)
2875        set(hlegend,'String',FieldName)
2876        else
2877            set(hlegend,'String',{FieldName;FieldName_2})
2878        end
2879    end
2880end
2881
2882%------------------------------------------------------------------------
2883% --- translate coordinate to matrix index
2884%------------------------------------------------------------------------
2885function [indx,indy]=pos2ind(x0,rangx0,nxy)
2886indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel 
2887indy=1+round((nxy(1)-1)*(y12-rangy0(1))/(rangy0(2)-rangy0(1)));% index y of pixel
2888
2889%------------------------------------------------------------------------
2890% --- Executes on button press in 'CheckZoom'.
2891%------------------------------------------------------------------------
2892function CheckZoom_Callback(hObject, eventdata, handles)
2893
2894if get(handles.CheckZoom,'Value')
2895    set(handles.CheckFixLimits,'Value',1)% propose by default fixed limits for the plotting axes
2896    set(handles.CheckZoomFig,'Value',0)%desactivate zoom fig
2897end
2898
2899%------------------------------------------------------------------------
2900% --- Executes on button press in CheckZoomFig.
2901%------------------------------------------------------------------------
2902function CheckZoomFig_Callback(hObject, eventdata, handles)
2903
2904if get(handles.CheckZoomFig,'Value')
2905    set(handles.CheckZoom,'value',0)
2906end
2907
2908%------------------------------------------------------------------------
2909% --- Executes on button press in 'CheckFixLimits'.
2910%------------------------------------------------------------------------
2911function CheckFixLimits_Callback(hObject, eventdata, handles)
2912
2913if ~get(handles.CheckFixLimits,'Value')
2914    update_plot(handles);
2915end
2916
2917%------------------------------------------------------------------------
2918% --- Executes on button press in CheckFixAspectRatio.
2919function CheckFixAspectRatio_Callback(hObject, eventdata, handles)
2920%------------------------------------------------------------------------
2921
2922if get(handles.CheckFixAspectRatio,'Value')
2923    update_plot(handles);
2924else
2925    update_plot(handles);
2926end
2927
2928%------------------------------------------------------------------------
2929function num_AspectRatio_Callback(hObject, eventdata, handles)
2930%------------------------------------------------------------------------
2931set(handles.CheckFixAspectRatio,'Value',1)% select the fixed aspect ratio button
2932update_plot(handles);
2933
2934%------------------------------------------------------------------------
2935%----Executes on button press in 'record': records the current flags of manual correction.
2936%------------------------------------------------------------------------
2937function record_Callback(hObject, eventdata, handles)
2938
2939[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
2940FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
2941[erread,message]=fileattrib(FileName);
2942if ~isempty(message) && ~isequal(message.UserWrite,1)
2943     msgbox_uvmat('ERROR',['no writting access to ' FileName])
2944     return
2945end
2946test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
2947test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
2948if ~test_civ2 && ~test_civ1
2949    msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
2950end
2951if test_civ2
2952    nbname='nb_vectors2';
2953   flagname='vec2_FixFlag';
2954   attrname='fix2';
2955end
2956if test_civ1
2957    nbname='nb_vectors';
2958   flagname='vec_FixFlag';
2959   attrname='fix';
2960end
2961%write fix flags in the netcdf file
2962UvData=get(handles.uvmat,'UserData');
2963hhh=which('netcdf.open');% look for built-in matlab netcdf library
2964if ~isequal(hhh,'')% case of new builtin Matlab netcdf library
2965    nc=netcdf.open(FileName,'NC_WRITE');
2966    netcdf.reDef(nc);
2967    netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),attrname,1);
2968    dimid = netcdf.inqDimID(nc,nbname);
2969    try
2970        varid = netcdf.inqVarID(nc,flagname);% look for already existing fixflag variable
2971    catch
2972        varid=netcdf.defVar(nc,flagname,'double',dimid);%create fixflag variable if it does not exist
2973    end
2974    netcdf.endDef(nc);
2975    netcdf.putVar(nc,varid,UvData.PlotAxes.FF);
2976    netcdf.close(nc); 
2977else %old netcdf library
2978    netcdf_toolbox(FileName,AxeData,attrname,nbname,flagname)
2979end
2980
2981%-------------------------------------------------------------------
2982%----Correct the netcdf file, using toolbox (old versions of Matlab).
2983%-------------------------------------------------------------------
2984function netcdf_toolbox(FileName,AxeData,attrname,nbname,flagname)
2985nc=netcdf(FileName,'write'); %open netcdf file
2986result=redef(nc);
2987eval(['nc.' attrname '=1;']);
2988theDim=nc(nbname) ;% get the number of velocity vectors
2989nb_vectors=size(theDim);
2990var_FixFlag=ncvar(flagname,nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag
2991var_FixFlag(1:nb_vectors)=AxeData.FF;%
2992fin=close(nc);
2993
2994%-------------------------------------------------------------------
2995% --- Executes on button press in SubField
2996function SubField_Callback(hObject, eventdata, handles)
2997%-------------------------------------------------------------------
2998UvData=get(handles.uvmat,'UserData');
2999if get(handles.SubField,'Value')==0% if the subfield button is desactivated   
3000    set(handles.RootPath_1,'String','')
3001    set(handles.RootFile_1,'String','')
3002    set(handles.SubDir_1,'String','');
3003    set(handles.FileIndex_1,'String','');
3004    set(handles.FileExt_1,'String','');
3005    set(handles.RootPath_1,'Visible','off')
3006    set(handles.RootFile_1,'Visible','off')
3007    set(handles.SubDir_1,'Visible','off');
3008    set(handles.NomType_1,'Visible','off');
3009    set(handles.abs_time_1,'Visible','off')
3010    set(handles.FileIndex_1,'Visible','off');
3011    set(handles.FileExt_1,'Visible','off');
3012    set(handles.FieldName_1,'Value',1);%set to blank state
3013    set(handles.VelType_1,'Value',1);%set to blank state
3014    set(handles.num_Opacity,'String','')% desactivate opacity setting
3015    FieldList=get(handles.FieldName,'String');
3016    if numel(FieldList)>1   % if a choice of fields exists
3017        set(handles.FieldName_1,'Value',1)% set second field choice to blank
3018        set(handles.FieldName_1,'String',[{''};FieldList])% reproduce the menu FieldName plus a blank option
3019    else
3020        set(handles.FieldName_1,'String',{''})% set second field choice to blank
3021    end
3022    if ~strcmp(get(handles.VelType,'Visible'),'on')
3023        set(handles.VelType_1,'Visible','off')
3024    end
3025    if isfield(UvData,'XmlData_1')
3026        UvData=rmfield(UvData,'XmlData_1');
3027    end
3028    set(handles.uvmat,'UserData',UvData);
3029    transform_fct_list=get(handles.TransformName,'String');
3030    transform_fct=transform_fct_list(get(handles.TransformName,'Value'));
3031    if strcmp(transform_fct,'sub_field')
3032        set(handles.TransformName,'Value',1)%suppress the sub_field transform
3033        transform_fct_Callback(hObject, eventdata, handles);
3034    else
3035        run0_Callback(hObject, eventdata, handles)
3036    end 
3037else
3038    MenuBrowse_1_Callback(hObject, eventdata, handles)
3039end
3040
3041%------------------------------------------------------------------------
3042% --- read the data displayed for the input rootfile windows (new): TODO use read_GUI
3043
3044function [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles)
3045%------------------------------------------------------------------------
3046InputFile=read_GUI(handles.InputFile);
3047RootPath=InputFile.RootPath;
3048SubDir=regexprep(InputFile.SubDir,'/|\','');
3049RootFile=regexprep(InputFile.RootFile,'/|\','');
3050FileIndices=InputFile.FileIndex;
3051FileExt=InputFile.FileExt;
3052
3053
3054%------------------------------------------------------------------------
3055% ---- read the data displayed for the second input rootfile windows
3056function [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1,NomType_1]=read_file_boxes_1(handles)
3057%------------------------------------------------------------------------
3058RootPath_1=get(handles.RootPath_1,'String'); % read the data from the file1_input window
3059if isequal(get(handles.RootPath_1,'Visible'),'off') || isequal(RootPath_1,'"')
3060    RootPath_1=get(handles.RootPath,'String');
3061end;
3062SubDir_1=get(handles.SubDir_1,'String');
3063if isequal(get(handles.SubDir_1,'Visible'),'off')|| isequal(SubDir_1,'"')
3064    SubDir_1=get(handles.SubDir,'String');
3065end
3066SubDir_1=regexprep(SubDir_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3067RootFile_1=get(handles.RootFile_1,'String');
3068if isequal(get(handles.RootFile_1,'Visible'),'off') || isequal(RootFile_1,'"')
3069    RootFile_1=get(handles.RootFile,'String');
3070end
3071RootFile_1=regexprep(RootFile_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3072FileIndex_1=get(handles.FileIndex_1,'String');
3073if isequal(get(handles.FileIndex_1,'Visible'),'off')|| isequal(FileIndex_1,'"')
3074    FileIndex_1=get(handles.FileIndex,'String');
3075end
3076FileExt_1=get(handles.FileExt_1,'String');
3077if isequal(get(handles.FileExt_1,'Visible'),'off') || isequal(FileExt_1,'"')
3078    FileExt_1=get(handles.FileExt,'String');%read FileExt by default
3079end
3080NomType_1=get(handles.NomType_1,'String');
3081if isequal(get(handles.NomType_1,'Visible'),'off') || isequal(NomType_1,'"')
3082    NomType_1=get(handles.NomType,'String');%read FileExt by default
3083end
3084%------------------------------------------------------------------------
3085% --- Executes on menu selection FieldName
3086function FieldName_Callback(hObject, eventdata, handles)
3087%------------------------------------------------------------------------
3088UvData=get(handles.uvmat,'UserData');
3089list_fields=get(handles.FieldName,'String');% list menu fields
3090index_fields=get(handles.FieldName,'Value');% selected string index
3091field= list_fields{index_fields(1)}; % selected string
3092
3093%% fill the coordinates and variables from selections in get_field
3094if isequal(field,'get_field...')
3095    ParamIn=[];
3096    if strcmp(get(handles.VelType,'Visible'),'on')
3097        % we use the civ choice as default input
3098        ParamIn.SwitchVarIndexTime='attribute';
3099        ListVelType=get(handles.VelType,'String');
3100        VelType=ListVelType{get(handles.VelType,'Value')};
3101        switch VelType
3102            case 'civ1'
3103                 ParamIn.TimeVarName='Civ1_Time';
3104                 ParamIn.vector_x='Civ1_U';
3105                 ParamIn.vector_y='Civ1_V';
3106                 ParamIn.vec_color='Civ1_C';               
3107            case 'filter1'
3108                 ParamIn.TimeVarName='Civ1_Time';
3109                 ParamIn.vector_x='Civ1_U_smooth';
3110                 ParamIn.vector_y='Civ1_V_smooth';
3111            case 'civ2'
3112                 ParamIn.TimeVarName='Civ2_Time';
3113                 ParamIn.vector_x='Civ2_U';
3114                 ParamIn.vector_y='Civ2_V';
3115            case 'filter2'
3116                 ParamIn.TimeVarName='Civ2_Time';
3117                 ParamIn.vector_x='Civ2_U_smooth';
3118                 ParamIn.vector_y='Civ2_V_smooth';
3119                 ParamIn.vec_color='Civ2_C';
3120        end
3121    end
3122    set(handles.FixVelType,'visible','off')
3123    set(handles.VelType,'Visible','off')
3124    set(handles.VelType_1,'Visible','off')
3125    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3126    FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3127%     hget_field=findobj(allchild(0),'name','get_field');
3128%     if ~isempty(hget_field)
3129%         delete(hget_field)
3130%     end
3131    GetFieldData=get_field(FileName,ParamIn);
3132    FieldList={};
3133    VecColorList={};
3134    XName=GetFieldData.XVarName;
3135    if GetFieldData.CheckVector
3136        UName=GetFieldData.PanelVectors.vector_x;
3137        VName=GetFieldData.PanelVectors.vector_y;
3138        XName=GetFieldData.XVarName;
3139        YName=GetFieldData.YVarName;
3140        CName=GetFieldData.PanelVectors.vec_color;
3141        [FieldList,VecColorList]=set_field_list(UName,VName,CName);
3142    elseif GetFieldData.CheckScalar
3143        AName=GetFieldData.PanelScalar.scalar;
3144        XName=GetFieldData.XVarName;
3145        YName=GetFieldData.YVarName;
3146        FieldList={AName};
3147    elseif GetFieldData.CheckPlot1D;
3148        YName=GetFieldData.CheckPlot1D.ordinate;
3149    end
3150    set(handles.Coord_x,'String',{XName})
3151    set(handles.Coord_y,'String',{YName})
3152    set(handles.FieldName,'Value',1)
3153    set(handles.FieldName,'String',[FieldList; {'get_field...'}]);
3154    set(handles.ColorScalar,'Value',1)
3155    set(handles.ColorScalar,'String',VecColorList);
3156    UvData.FileType{1}='netcdf';
3157    set(handles.uvmat,'UserData',UvData)
3158    run0_Callback(hObject, eventdata, handles)
3159    return %no further action
3160end
3161
3162
3163
3164%read the rootfile input display
3165[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3166FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3167[tild,tild,tild,i1,i2,j1,j2,tild,NomType]=fileparts_uvmat(['xxx' get(handles.FileIndex,'String') FileExt]);
3168if isequal(field,'image')
3169    if  isfield(UvData.Field,'Civ2_ImageA')%get the corresponding input image in the netcdf file
3170        imagename=UvData.Field.Civ2_ImageA;
3171    elseif isfield(UvData.Field,'Civ1_ImageA')%
3172        imagename=UvData.Field.Civ1_ImageA;
3173    else
3174        SubDirBase=regexprep(SubDir,'\..*','');%take the root part of SubDir, before the first dot '.'
3175        imagename=fullfile_uvmat(RootPath,SubDirBase,RootFile,'.png',NomType,i1,[],j1,[]);
3176    end
3177    if ~exist(imagename,'file')
3178        [FileName,PathName] = uigetfile( ...
3179            {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3180            '*.jpg',' jpeg image files'; ...
3181            '*.png','.png image files'; ...
3182            '*.tif','.tif image files'; ...
3183            '*.avi;*.AVI','.avi movie files'; ...
3184            '*.vol','.volume images (png)'; ...
3185            '*.*',  'All Files (*.*)'}, ...
3186            'Pick an image',imagename);
3187        if ~ischar(FileName),return,end %abandon if the browser is cancelled
3188        imagename=[PathName FileName];
3189    end
3190     % display the selected field and related information
3191    display_file_name(handles,imagename)%display the image
3192    return
3193else
3194    ext=get(handles.FileExt,'String');
3195    if ~isequal(ext,'.nc') %find the new NomType if the previous display was not already a netcdf file
3196        [FileName,PathName] = uigetfile( ...
3197            {'*.nc', ' (*.nc)';
3198            '*.nc',' netcdf files'; ...
3199            '*.*',  'All Files (*.*)'}, ...
3200            'Pick a netcdf file',FileBase);
3201        if ~ischar(FileName),return,end %abandon if the browser is cancelled
3202        FullFileName=[PathName FileName];
3203        % display the selected field and related information
3204        display_file_name( handles,FullFileName)
3205        return
3206    end
3207end
3208indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
3209set(handles.FileIndex,'String',indices)
3210
3211%common to Fields_1_Callback
3212list_fields_1=get(handles.FieldName_1,'String');% list menu fields
3213field_1='';
3214if ~isempty(list_fields_1)
3215field_1= list_fields_1{get(handles.FieldName_1,'Value')}; % selected string
3216end
3217if isequal(field,'image')||isequal(field_1,'image')
3218    set(handles.TitleNpxy,'Visible','on')% visible npx,pxcm... buttons
3219    set(handles.num_Npx,'Visible','on')
3220    set(handles.num_Npy,'Visible','on')
3221else
3222    set(handles.TitleNpxy,'Visible','off')% visible npx,pxcm... buttons
3223    set(handles.num_Npx,'Visible','off')
3224    set(handles.num_Npy,'Visible','off')
3225end
3226if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3227    run0_Callback(hObject, eventdata, handles)
3228end
3229
3230%----------------------------------------------------------------
3231% --- Executes on menu selection FieldName
3232function FieldName_1_Callback(hObject, eventdata, handles)
3233%-------------------------------------------------
3234%% read input data
3235check_new=~get(handles.SubField,'Value'); %check_new=1 if a second field was not previously entered
3236UvData=get(handles.uvmat,'UserData');
3237if check_new && isfield(UvData,'XmlData')
3238    UvData.XmlData{2}=UvData.XmlData{1};
3239end
3240if isfield(UvData,'Field_1')
3241    UvData=rmfield(UvData,'Field_1');% remove the stored second field (a new one needs to be read)
3242end
3243UvData.FileName_1='';% desactivate the use of a constant second file
3244list_fields=get(handles.FieldName,'String');% list menu fields
3245field= list_fields{get(handles.FieldName,'Value')}; % selected string
3246list_fields=get(handles.FieldName_1,'String');% list menu fields
3247field_1= list_fields{get(handles.FieldName_1,'Value')}; % selected string for the second field
3248if isempty(field_1)%||(numel(UvData.FileType)>=2 && strcmp(UvData.FileType{2},'image'))
3249    set(handles.SubField,'Value',0)
3250    SubField_Callback(hObject, eventdata, handles)
3251    return
3252else
3253    set(handles.SubField,'Value',1)%state that a second field is now entered
3254end
3255
3256%% read the rootfile input display
3257[RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
3258FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
3259[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
3260switch field_1
3261    case 'get_field...'
3262        set_veltype_display(0) % no veltype display
3263        hget_field=findobj(allchild(0),'name','get_field_1');
3264        if ~isempty(hget_field)
3265            delete(hget_field)
3266        end
3267        hget_field=get_field(FileName_1);
3268        set(hget_field,'name','get_field_1')
3269        hhget_field=guidata(hget_field);
3270        set(hhget_field.list_fig,'Value',1)
3271        set(hhget_field.list_fig,'String',{'uvmat'})
3272        if check_new
3273            UvData.FileType{2}=UvData.FileType{1};
3274            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3275              set(handles.uvmat,'UserData',UvData)
3276        end
3277    case 'image'
3278        % get the image name corresponding to the current netcdf name (no unique correspondance)
3279        if  isfield(UvData.Field,'Civ2_ImageA')%get the corresponding input image in the netcdf file
3280            imagename=UvData.Field.Civ2_ImageA;
3281        elseif isfield(UvData.Field,'Civ1_ImageA')%
3282            imagename=UvData.Field.Civ1_ImageA;
3283        else
3284            SubDirBase=regexprep(SubDir_1,'\..*','');%take the root part of SubDir, before the first dot '.'
3285            imagename=fullfile_uvmat(RootPath_1,SubDirBase,RootFile_1,'.png',get(handles.NomType,'String'),i1,[],j1);
3286        end
3287        if ~exist(imagename,'file') % browse for images if it is not found
3288            [FileName,PathName] = uigetfile( ...
3289                {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3290                '*.jpg',' jpeg image files'; ...
3291                '*.png','.png image files'; ...
3292                '*.tif','.tif image files'; ...
3293                '*.avi;*.AVI','.avi movie files'; ...
3294                '*.vol','.volume images (png)'; ...
3295                '*.*',  'All Files (*.*)'}, ...
3296                'Pick an image',imagename);
3297            if ~ischar(FileName),return,end %abandon if the browser is cancelled
3298            imagename=[PathName FileName];
3299        end
3300        if ~ischar(imagename)% quit if the browser has  been closed
3301            set(handles.SubField,'Value',0)
3302        else %valid browser input:  display the selected image
3303            set(handles.TitleNpxy,'Visible','on')% visible npx,pxcm... buttons
3304            set(handles.num_Npx,'Visible','on')
3305            set(handles.num_Npy,'Visible','on')
3306            display_file_name(handles,imagename,2)%display the imag
3307        end
3308    otherwise
3309        check_refresh=1;
3310        if check_new% if a second field was not previously entered, we just read another field in the first input file
3311            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3312            set(handles.FileExt_1,'String',get(handles.FileExt,'String'))
3313           
3314            UvData.FileType{2}=UvData.FileType{1};
3315            UvData.XmlData{2}= UvData.XmlData{1};
3316            transform=get(handles.TransformPath,'UserData');
3317             if (~isa(transform,'function_handle')||nargin(transform)<3)
3318                set(handles.uvmat,'UserData',UvData)
3319                set(handles.TransformName,'value',2); % set transform fct to 'sub_field' if the current fct does not accept two input fields
3320                transform_fct_Callback(hObject, eventdata, handles)% activate transform_fct_Callback and refresh current plot
3321                 check_refresh=0;
3322             end             
3323        end
3324        if ~isequal(field,'image')
3325            set(handles.TitleNpxy,'Visible','off')% visible npx,pxcm... buttons
3326            set(handles.num_Npx,'Visible','off')
3327            set(handles.num_Npy,'Visible','off')
3328        end
3329        set(handles.uvmat,'UserData',UvData)
3330 
3331        if check_refresh && ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3332            run0_Callback(hObject, eventdata, handles)
3333        end
3334end
3335
3336%------------------------------------------------------------------------
3337% --- set the visibility of relevant velocity type menus:
3338function menu=set_veltype_display(Civ,FileType)
3339%------------------------------------------------------------------------
3340if ~exist('FileType','var')
3341    FileType='civx';
3342end
3343switch FileType
3344    case 'civx'
3345        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3346        if isequal(Civ,0)
3347            imax=0;
3348        elseif isequal(Civ,1) || isequal(Civ,2)
3349            imax=1;
3350        elseif isequal(Civ,3)
3351            imax=3;
3352        elseif isequal(Civ,4) || isequal(Civ,5)
3353            imax=4;
3354        elseif isequal(Civ,6) %patch2
3355            imax=6;
3356        end
3357    case 'civdata'
3358        menu={'civ1';'filter1';'civ2';'filter2'};
3359        if isequal(Civ,0)
3360            imax=0;
3361        elseif isequal(Civ,1) || isequal(Civ,2)
3362            imax=1;
3363        elseif isequal(Civ,3)
3364            imax=2;
3365        elseif isequal(Civ,4) || isequal(Civ,5)
3366            imax=3;
3367        elseif isequal(Civ,6) %patch2
3368            imax=4;
3369        end
3370end
3371menu=menu(1:imax);
3372
3373%------------------------------------------------------------------------
3374% --- Executes on button press in FixVelType.
3375function FixVelType_Callback(hObject, eventdata, handles)
3376%------------------------------------------------------------------------
3377% refresh the current plot if the fixed  veltype is unselected
3378if ~get(handles.FixVelType,'Value')
3379    run0_Callback(hObject, eventdata, handles)
3380end
3381
3382%------------------------------------------------------------------------
3383% --- Executes on button press in VelType.
3384function VelType_Callback(hObject, eventdata, handles)
3385%------------------------------------------------------------------------
3386set(handles.FixVelType,'Value',1)
3387run0_Callback(hObject, eventdata, handles)
3388
3389%------------------------------------------------------------------------
3390% --- Executes on choice selection in VelType_1.
3391function VelType_1_Callback(hObject, eventdata, handles)
3392%------------------------------------------------------------------------
3393set(handles.FixVelType,'Value',1)% the velocity type is now imposed by the GUI (not automatic)
3394UvData=get(handles.uvmat,'UserData');
3395set(handles.run0,'BackgroundColor',[1 1 0])%paint run0 button in yellow to indicate its activation
3396drawnow   
3397InputFile=read_GUI(handles.InputFile);% read the input file parameters
3398[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
3399[RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
3400FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];% name of the first input file
3401
3402check_refresh=0;
3403if isempty(InputFile.VelType_1)
3404        FileName_1='';% we plot the first input field without the second field
3405        set(handles.SubField,'Value',0)
3406        SubField_Callback(hObject, eventdata, handles)% activate SubField_Callback and refresh current plot, removing the second field
3407elseif get(handles.SubField,'Value')% if subfield is already 'on'
3408     FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];% name of the second input file
3409     check_refresh=1;%will refresh the current plot
3410else% we introduce the same file (with a different field) for the second series
3411     FileName_1=FileName;% we compare two fields in the same file
3412     UvData.FileType{2}=UvData.FileType{1};
3413     UvData.XmlData{2}= UvData.XmlData{1};
3414     set(handles.SubField,'Value',1)
3415     transform=get(handles.TransformPath,'UserData');
3416     if (~isa(transform,'function_handle')||nargin(transform)<3)
3417        set(handles.uvmat,'UserData',UvData)
3418        set(handles.TransformName,'value',2); % set transform fct to 'sub_field' if the current fct does not accept two input fields
3419        transform_fct_Callback(hObject, eventdata, handles)% activate transform_fct_Callback and refresh current plot
3420     else
3421         check_refresh=1;
3422     end 
3423end
3424
3425% refresh the current plot if it has not been done previously
3426if check_refresh
3427    UvData.FileName_1='';% desactivate the use of a constant second file
3428    set(handles.uvmat,'UserData',UvData)
3429    num_i1=stra2num(get(handles.i1,'String'));
3430    num_i2=stra2num(get(handles.i2,'String'));
3431    num_j1=stra2num(get(handles.j1,'String'));
3432    num_j2=stra2num(get(handles.j2,'String'));
3433    [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(['xx' FileIndex_1]);
3434    errormsg=refresh_field(handles,FileName,FileName_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1);
3435    if ~isempty(errormsg)
3436        msgbox_uvmat('ERROR',errormsg);
3437    else
3438        set(handles.i1,'BackgroundColor',[1 1 1])
3439        set(handles.i2,'BackgroundColor',[1 1 1])
3440        set(handles.j1,'BackgroundColor',[1 1 1])
3441        set(handles.j2,'BackgroundColor',[1 1 1])
3442        set(handles.FileIndex,'BackgroundColor',[1 1 1])
3443        set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
3444    end
3445    set(handles.run0,'BackgroundColor',[1 0 0])
3446end
3447
3448
3449%------------------------------------------------------------------------
3450% --- reset civ buttons
3451function reset_vel_type(handles_civ0,handle1)
3452%------------------------------------------------------------------------
3453for ibutton=1:length(handles_civ0)
3454    set(handles_civ0(ibutton),'BackgroundColor',[0.831 0.816 0.784])
3455    set(handles_civ0(ibutton),'Value',0)
3456end
3457if exist('handle1','var')%handles of selected button
3458        set(handle1,'BackgroundColor',[1 1 0]) 
3459end
3460
3461%-----------------------------------------------------------------------
3462% --- Executes on button press in MENUVOLUME.
3463function VOLUME_Callback(hObject, eventdata, handles)
3464%-----------------------------------------------------------------------
3465%errordlg('command VOL not implemented yet')
3466if ishandle(handles.UVMAT_title)
3467    delete(handles.UVMAT_title)
3468end
3469UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3470if isequal(get(handles.VOLUME,'Value'),1)
3471    set(handles.CheckZoom,'Value',0)
3472%     set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3473    set(handles.edit_vect,'Value',0)
3474    edit_vect_Callback(hObject, eventdata, handles)
3475    set(handles.edit_object,'Value',0)
3476%     set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3477%     set(handles.cal,'Value',0)
3478%     set(handles.cal,'BackgroundColor',[0 1 0])
3479    set(handles.edit_vect,'Value',0)
3480    edit_vect_Callback(hObject, eventdata, handles)
3481    %initiate set_object GUI
3482    data.Name='VOLUME';
3483    if isfield(UvData,'CoordType')
3484        data.CoordType=UvData.CoordType;
3485    end
3486    if isfield(UvData.Field,'CoordMesh')&~isempty(UvData.Field.CoordMesh)
3487        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
3488        data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
3489        data.DX=UvData.Field.CoordMesh;
3490        data.DY=UvData.Field.CoordMesh;
3491    elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3492        np=size(UvData.Field.A);
3493        meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
3494        meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
3495        data.RangeY=max(meshx,meshy);
3496        data.RangeX=max(meshx,meshy);
3497        data.DX=max(meshx,meshy);
3498    end
3499    data.ParentButton=handles.VOLUME;
3500    PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
3501    [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes,
3502                                                      % associate the set_object interface handle to the plotting axes
3503    %set(hset_object,'Position',get(handles.uvmat,'Position')+UvData.OpenParam.PosSetObject)
3504    UvData.MouseAction='create_object';
3505else
3506    set(handles.VOLUME,'BackgroundColor',[0 1 0])
3507end
3508set(handles.uvmat,'UserData',UvData)
3509
3510%-------------------------------------------------------
3511function edit_vect_Callback(hObject, eventdata, handles)
3512%-------------------------------------------------------
3513%
3514if isequal(get(handles.edit_vect,'Value'),1)
3515    VelTypeMenu=get(handles.VelType,'String');
3516    VelType=VelTypeMenu{get(handles.VelType,'Value')};
3517    if ~strcmp(VelType,'civ2') && ~strcmp(VelType,'civ1')
3518        msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
3519    end
3520    set(handles.record,'Visible','on')
3521    set(handles.edit_vect,'BackgroundColor',[1 1 0])
3522    set(handles.edit_object,'Value',0)
3523    set(handles.CheckZoom,'Value',0)
3524%     set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3525%     set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3526    set(gcf,'Pointer','arrow')
3527else
3528    set(handles.record,'Visible','off')
3529    set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7])
3530end
3531
3532%----------------------------------------------
3533function save_mask_Callback(hObject, eventdata, handles)
3534%-----------------------------------------------------------------------
3535UvData=get(handles.uvmat,'UserData');
3536
3537flag=1;
3538npx=size(UvData.Field.A,2);
3539npy=size(UvData.Field.A,1);
3540xi=0.5:npx-0.5;
3541yi=0.5:npy-0.5;
3542[Xi,Yi]=meshgrid(xi,yi);
3543if isfield(UvData,'ProjObject')
3544    for iobj=1:length(UvData.ProjObject)
3545        ObjectData=UvData.ProjObject{iobj};
3546        if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
3547            flagobj=1;
3548            testphys=0; %coordinates in pixels by default
3549            if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys')
3550                if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
3551                    Calib=UvData.XmlData{1}.GeometryCalib;
3552                    testphys=1;
3553                end
3554            end
3555            if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style')
3556                if isequal(ObjectData.Type,'polygon')
3557                    X=ObjectData.Coord(:,1);
3558                    Y=ObjectData.Coord(:,2);
3559                    if testphys
3560                        [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
3561                    end
3562                    flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside                 
3563                elseif isequal(ObjectData.Type,'ellipse')
3564                    if testphys
3565                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3566                    end
3567                    RangeX=max(ObjectData.RangeX);
3568                    RangeY=max(ObjectData.RangeY);
3569                    X2Max=RangeX*RangeX;
3570                    Y2Max=RangeY*RangeY;
3571                    distX=(Xi-ObjectData.Coord(1,1));
3572                    distY=(Yi-ObjectData.Coord(1,2));
3573                    flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
3574                elseif isequal(ObjectData.Type,'rectangle')
3575                    if testphys
3576                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3577                    end
3578                    distX=abs(Xi-ObjectData.Coord(1,1));
3579                    distY=abs(Yi-ObjectData.Coord(1,2));
3580                    flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
3581                end
3582                if isequal(ObjectData.ProjMode,'mask_outside')
3583                    flagobj=~flagobj;
3584                end
3585                flag=flag & flagobj;
3586            end
3587        end
3588    end
3589end
3590% flag=~flag;
3591%mask name
3592RootPath=get(handles.RootPath,'String');
3593RootFile=get(handles.RootFile,'String');
3594RootFile=regexprep(RootFile,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3595filebase=fullfile(RootPath,RootFile);
3596list=get(handles.masklevel,'String');
3597masknumber=num2str(length(list));
3598maskindex=get(handles.masklevel,'Value');
3599mask_name=fullfile_uvmat(RootPath,SubDir,[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
3600%mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
3601imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
3602imflag=flipdim(imflag,1);
3603% imflag=uint8(255*flag);% =0 for flag=0 (vectors=0 when 20<imflag<200)
3604msgbox_uvmat('CONFIRMATION',[mask_name ' saved'])
3605imwrite(imflag,mask_name,'BitDepth',8);
3606
3607%display the mask
3608figure;
3609vec=linspace(0,1,256);%define a linear greyscale colormap
3610map=[vec' vec' vec'];
3611colormap(map)
3612
3613image(imflag);
3614
3615%------------------------------------------------------------------------
3616%------------------------------------------------------------------------
3617%  - FUNCTIONS FOR SETTING PLOTTING PARAMETERS
3618
3619%------------------------------------------------------------------------
3620%------------------------------------------------------------------------
3621% --- Executes on selection change in TransformName.
3622
3623function TransformName_Callback(hObject, eventdata, handles)
3624%------------------------------------------------------------------------
3625UvData=get(handles.uvmat,'UserData');
3626menu=get(handles.TransformName,'String');refresh
3627ichoice=get(handles.TransformName,'Value');%item number in the menu
3628transform_name=menu{ichoice};% choice of the transform fct
3629list_path=get(handles.TransformName,'UserData');
3630
3631%% add a new item to the menu if the option 'more...' has been selected
3632prev_path=fullfile(get(handles.TransformPath,'String'));
3633if ~exist(prev_path,'dir')
3634    prev_path=fullfile(fileparts(which('uvmat')),'transform_field');
3635end
3636if strcmp(transform_name,'more...');
3637    [FileName, PathName] = uigetfile( ...
3638        {'*.m', ' (*.m)';
3639        '*.m',  '.m files '; ...
3640        '*.*', 'All Files (*.*)'}, ...
3641        'Pick the transform function', prev_path);
3642    if ~ischar(FileName),return,end %abandon if the browser is cancelled
3643    path_transform_fct =fullfile(PathName,FileName);
3644    if isempty(regexp(FileName,'\.m$'))% detect file extension .m
3645        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3646        return
3647    else
3648        transform_name=regexprep(FileName,'\.m','');
3649    end
3650    ichoice=find(strcmp(transform_name,menu),1);%look for the selected fct in the existing menu
3651    if isempty(ichoice)% if the item is not found, add it to the menu (before 'more...' and select it)
3652        menu=[menu(1:end-1);{transform_name};{'more...'}];
3653        ichoice=numel(menu)-1;   
3654    end
3655    list_path{ichoice}=PathName;%update the list fo fct paths
3656    set(handles.TransformName,'String',menu)
3657    set(handles.TransformName,'Value',ichoice)
3658   
3659    % save the new menu in the personal file 'uvmat_perso.mat'
3660    dir_perso=prefdir;%personal Matalb directory
3661    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3662    if exist(profil_perso,'file')
3663        nb_builtin=UvData.OpenParam.NbBuiltin;% number of 'builtin' (basic) transform fcts in uvmat
3664        if nb_builtin<numel(list_path)
3665        for ilist=nb_builtin+1:numel(list_path)
3666            transform_fct{ilist-nb_builtin}=[fullfile(list_path{ilist},menu{ilist}) '.m'];
3667        end
3668        save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
3669        end
3670    end
3671end
3672
3673%% create the function handle of the selected fct
3674
3675if isempty(list_path{ichoice})% case of no selected fct
3676    transform_handle=[];
3677else
3678    if ~exist(list_path{ichoice},'dir')
3679        msgbox_uvmat('ERROR','invalid fct path: select the transform fct again with the option more...')
3680        return
3681    end
3682    current_dir=pwd;%current working dir
3683    cd(list_path{ichoice})
3684    transform_handle=str2func(transform_name);
3685    cd(current_dir)
3686end
3687set(handles.TransformPath,'String',list_path{ichoice})
3688set(handles.TransformPath,'UserData',transform_handle)
3689set(handles.TransformName,'UserData',list_path)
3690
3691%% update the ToolTip string of the menu TransformName with the first line of the selected fct file
3692if isempty(list_path{ichoice})% case of no selected fct
3693    set(handles.TransformName,'ToolTipString','transform_fct:choose a transform function')
3694else
3695    try
3696        [fid,errormsg] =fopen([fullfile(list_path{ichoice},transform_name) '.m']);
3697        InputText=textscan(fid,'%s',1,'delimiter','\n');
3698        fclose(fid)
3699        set(handles.TransformName,'ToolTipString',['transform_fct: ' InputText{1}{1}])% put the first line of the selected function as tooltip help
3700    end
3701end
3702
3703%% adapt the GUI to the input/output conditions of the selected transform fct
3704DataOut=[];
3705CoordUnit='';
3706CoordUnitPrev='';
3707if isfield(UvData,'Field')&&isfield(UvData.Field,'CoordUnit')
3708    CoordUnitPrev=UvData.Field.CoordUnit;
3709end
3710if ~isempty(list_path{ichoice})
3711    if nargin(transform_handle)>1 && isfield(UvData,'XmlData')&&~isempty(UvData.XmlData)
3712        XmlData=UvData.XmlData{1};
3713        DataOut=feval(transform_handle,'*',XmlData);
3714        if isfield(DataOut,'CoordUnit')
3715            CoordUnit=DataOut.CoordUnit;
3716        end
3717        if isfield(DataOut,'InputFieldType')
3718            UvData.InputFieldType=DataOut.InputFieldType;
3719        end
3720    else
3721        DataOut=feval(transform_handle,'*');
3722    end
3723end
3724
3725
3726%% delete drawn objects if the output CooordUnit is different from the previous one
3727if ~strcmp(CoordUnit,CoordUnitPrev)
3728    set(handles.CheckFixLimits,'Value',0)
3729set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
3730    hother=findobj('Tag','proj_object');%find all the proj objects
3731    for iobj=1:length(hother)
3732        delete_object(hother(iobj))
3733    end
3734    hother=findobj('Tag','DeformPoint');%find all the proj objects
3735    for iobj=1:length(hother)
3736        delete_object(hother(iobj))
3737    end
3738    hh=findobj('Tag','calib_points');
3739    if ~isempty(hh)
3740        delete(hh)
3741    end
3742    hhh=findobj('Tag','calib_marker');
3743    if ~isempty(hhh)
3744        delete(hhh)
3745    end
3746    set(handles.ListObject,'Value',1)
3747    set(handles.ListObject,'String',{''})
3748    set(handles.ListObject_1,'Value',1)
3749    set(handles.ListObject_1,'String',{''})
3750    set(handles.ViewObject,'value',0)
3751    ViewObject_Callback(hObject, eventdata, handles)
3752    set(handles.ViewField,'value',0)
3753    ViewField_Callback(hObject, eventdata, handles)
3754    set(handles.edit_object,'Value',0)
3755    edit_object_Callback(hObject, eventdata, handles)
3756    UvData.ProjObject={[]};
3757end
3758set(handles.uvmat,'UserData',UvData)
3759
3760%% refresh the current plot
3761if isempty(list_path{ichoice}) || nargin(transform_handle)<3
3762    set(handles.SubField,'Value',0)
3763    SubField_Callback(hObject, eventdata, handles)
3764else
3765    run0_Callback(hObject, eventdata, handles)
3766end
3767
3768%------------------------------------------------
3769%CALLBACKS FOR PLOTTING PARAMETERS
3770%-------------------------------------------------
3771%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3772% Plot coordinates
3773%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3774%------------------------------------------------------------------------
3775function num_MinX_Callback(hObject, eventdata, handles)
3776%------------------------------------------------------------------------
3777set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3778set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3779update_plot(handles);
3780
3781%------------------------------------------------------------------------
3782function num_MaxX_Callback(hObject, eventdata, handles)
3783%------------------------------------------------------------------------
3784set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3785set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3786update_plot(handles);
3787
3788%------------------------------------------------------------------------
3789function num_MinY_Callback(hObject, eventdata, handles)
3790%------------------------------------------
3791set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3792set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3793update_plot(handles);
3794
3795%------------------------------------------------------------------------
3796function num_MaxY_Callback(hObject, eventdata, handles)
3797%------------------------------------------------------------------------
3798set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3799set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3800update_plot(handles);
3801
3802%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3803% Scalar or image representation
3804%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3805%------------------------------------------------------------------------
3806function num_MinA_Callback(hObject, eventdata, handles)
3807%------------------------------------------
3808set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3809set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3810MinA=str2double(get(handles.num_MinA,'String'));
3811MaxA=str2double(get(handles.num_MaxA,'String'));
3812if MinA>MaxA% switch minA and maxA in case of error
3813    MinA_old=MinA;
3814    MinA=MaxA;
3815    MaxA=MinA_old;
3816    set(handles.num_MinA,'String',num2str(MinA,5));
3817    set(handles.num_MaxA,'String',num2str(MaxA,5));
3818end
3819update_plot(handles);
3820
3821%------------------------------------------------------------------------
3822function num_MaxA_Callback(hObject, eventdata, handles)
3823%------------------------------------------------------------------------
3824set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3825set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3826MinA=str2double(get(handles.num_MinA,'String'));
3827MaxA=str2double(get(handles.num_MaxA,'String'));
3828if MinA>MaxA% switch minA and maxA in case of error
3829        MinA_old=MinA;
3830    MinA=MaxA;
3831    MaxA=MinA_old;
3832    set(handles.num_MinA,'String',num2str(MinA,5));
3833    set(handles.num_MaxA,'String',num2str(MaxA,5));
3834end
3835update_plot(handles);
3836
3837%------------------------------------------------------------------------
3838function CheckFixScalar_Callback(hObject, eventdata, handles)
3839%------------------------------------------------------------------------
3840test=get(handles.CheckFixScalar,'Value');
3841if test
3842    set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3843else
3844    set(handles.CheckFixScalar,'BackgroundColor',[0.7 0.7 0.7])
3845    update_plot(handles);
3846end
3847
3848%-------------------------------------------------------------------
3849function CheckBW_Callback(hObject, eventdata, handles)
3850%-------------------------------------------------------------------
3851update_plot(handles);
3852
3853%-------------------------------------------------------------------
3854function num_Opacity_Callback(hObject, eventdata, handles)
3855update_plot(handles);
3856%-------------------------------------------------------------------
3857
3858%-------------------------------------------------------------------
3859function ListContour_Callback(hObject, eventdata, handles)
3860%-------------------------------------------------------------------
3861val=get(handles.ListContour,'Value');
3862if val==2
3863    set(handles.interval_txt,'Visible','on')
3864    set(handles.num_IncrA,'Visible','on')
3865else
3866    set(handles.interval_txt,'Visible','off')
3867    set(handles.num_IncrA,'Visible','off')
3868end
3869update_plot(handles);
3870
3871%-------------------------------------------------------------------
3872function num_IncrA_Callback(hObject, eventdata, handles)
3873%-------------------------------------------------------------------
3874update_plot(handles);
3875
3876
3877%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3878% Vector representation
3879%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3880%-------------------------------------------------------------------
3881function CheckHideWarning_Callback(hObject, eventdata, handles)
3882%-------------------------------------------------------------------
3883update_plot(handles);
3884
3885%-------------------------------------------------------------------
3886function CheckHideFalse_Callback(hObject, eventdata, handles)
3887%-------------------------------------------------------------------
3888update_plot(handles);
3889
3890%-------------------------------------------------------------------
3891function num_VecScale_Callback(hObject, eventdata, handles)
3892%-------------------------------------------------------------------
3893set(handles.CheckFixVectors,'Value',1);
3894set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3895update_plot(handles);
3896
3897%-------------------------------------------------------------------
3898function CheckFixVectors_Callback(hObject, eventdata, handles)
3899%-------------------------------------------------------------------
3900test=get(handles.CheckFixVectors,'Value');
3901if test
3902    set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3903else
3904    update_plot(handles);
3905    %set(handles.num_VecScale,'String',num2str(ScalOut.num_VecScale,3))
3906    set(handles.CheckFixVectors,'BackgroundColor',[0.7 0.7 0.7])
3907end
3908
3909%------------------------------------------------------------------------
3910% --- Executes on selection change in CheckDecimate4 (nb_vec/4).
3911%------------------------------------------------------------------------
3912function CheckDecimate4_Callback(hObject, eventdata, handles)
3913
3914if isequal(get(handles.CheckDecimate4,'Value'),1)
3915    set(handles.CheckDecimate16,'Value',0)
3916end
3917update_plot(handles);
3918
3919%------------------------------------------------------------------------
3920% --- Executes on selection change in CheckDecimate16 (nb_vec/16).
3921%------------------------------------------------------------------------
3922function CheckDecimate16_Callback(hObject, eventdata, handles)
3923
3924if isequal(get(handles.CheckDecimate16,'Value'),1)
3925    set(handles.CheckDecimate4,'Value',0)
3926end
3927update_plot(handles);
3928
3929%------------------------------------------------------------------------
3930% --- Executes on selection change in ColorCode menu
3931function ColorCode_Callback(hObject, eventdata, handles)
3932%------------------------------------------------------------------------
3933% edit the choice for color code
3934update_color_code_boxes(handles);
3935update_plot(handles);
3936
3937%------------------------------------------------------------------------
3938function update_color_code_boxes(handles)
3939%------------------------------------------------------------------------
3940list_code=get(handles.ColorCode,'String');% list menu fields
3941colcode= list_code{get(handles.ColorCode,'Value')}; % selected field
3942enable_slider='off';%default
3943enable_bounds='off';%default
3944enable_scalar='off';%default
3945switch colcode
3946    case {'rgb','bgr'}
3947        enable_slider='on';
3948        enable_bounds='on';
3949        enable_scalar='on';
3950    case '64 colors'
3951        enable_bounds='on';
3952        enable_scalar='on';
3953end
3954set(handles.Slider1,'Visible',enable_slider)
3955set(handles.Slider2,'Visible', enable_slider)
3956set(handles.num_ColCode1,'Visible',enable_slider)
3957set(handles.num_ColCode2,'Visible',enable_slider)
3958set(handles.TitleColCode1,'Visible',enable_slider)
3959set(handles.TitleColCode2,'Visible',enable_slider)
3960set(handles.CheckFixVecColor,'Visible',enable_bounds)
3961set(handles.num_MinVec,'Visible',enable_bounds)
3962set(handles.num_MaxVec,'Visible',enable_bounds)
3963set(handles.ColorScalar,'Visible',enable_scalar)
3964set_vec_col_bar(handles)
3965
3966%------------------------------------------------------------------
3967% --- Executes on selection change in ColorScalar: choice of the color code.
3968function ColorScalar_Callback(hObject, eventdata, handles)
3969%------------------------------------------------------------------
3970% edit the choice for color code
3971list_scalar=get(handles.ColorScalar,'String');% list menu fields
3972col_scalar= list_scalar{get(handles.ColorScalar,'Value')}; % selected field
3973if isequal(col_scalar,'ima_cor')
3974    set(handles.CheckFixVecColor,'Value',1)%fixed scale by default
3975    ColorCode='rgb';
3976    set(handles.num_MinVec,'String','0')
3977    set(handles.num_MaxVec,'String','1')
3978    set(handles.num_ColCode1,'String','0.333')
3979    set(handles.num_ColCode2,'String','0.666')
3980else
3981    set(handles.CheckFixVecColor,'Value',0)%auto scale between min,max by default
3982    ColorCode='64 colors';
3983end
3984ColorCodeList=get(handles.ColorCode,'String');
3985ichoice=find(strcmp(ColorCode,ColorCodeList),1);
3986set(handles.ColorCode,'Value',ichoice)% set color code in the menu
3987
3988update_color_code_boxes(handles);
3989%replot the current graph
3990run0_Callback(hObject, eventdata, handles)
3991
3992%----------------------------------------------------------------
3993% -- Executes on slider movement to set the color code
3994%
3995function Slider1_Callback(hObject, eventdata, handles)
3996%------------------------------------------------------------------
3997slider1=get(handles.Slider1,'Value');
3998min_val=str2num(get(handles.num_MinVec,'String'));
3999max_val=str2num(get(handles.num_MaxVec,'String'));
4000col=min_val+(max_val-min_val)*slider1;
4001set(handles.num_ColCode1,'String',num2str(col))
4002if(get(handles.Slider2,'Value') < col)%move also the second slider at the same value if needed
4003    set(handles.Slider2,'Value',col)
4004    set(handles.num_ColCode2,'String',num2str(col))
4005end
4006set_vec_col_bar(handles)
4007update_plot(handles);
4008
4009%----------------------------------------------------------------
4010% Executes on slider movement to set the color code
4011%----------------------------------------------------------------
4012function Slider2_Callback(hObject, eventdata, handles)
4013slider2=get(handles.Slider2,'Value');
4014min_val=str2num(get(handles.num_MinVec,'String'));
4015max_val=str2num(get(handles.num_MaxVec,'String'));
4016col=min_val+(max_val-min_val)*slider2;
4017set(handles.num_ColCode2,'String',num2str(col))
4018if(get(handles.Slider1,'Value') > col)%move also the first slider at the same value if needed
4019    set(handles.Slider1,'Value',col)
4020    set(handles.num_ColCode1,'String',num2str(col))
4021end
4022set_vec_col_bar(handles)
4023update_plot(handles);
4024
4025%----------------------------------------------------------------
4026% --- Execute on return carriage on the edit box corresponding to slider 1
4027%----------------------------------------------------------------
4028function num_ColCode1_Callback(hObject, eventdata, handles)
4029set_vec_col_bar(handles)
4030update_plot(handles);
4031
4032%----------------------------------------------------------------
4033% --- Execute on return carriage on the edit box corresponding to slider 2
4034%----------------------------------------------------------------
4035function num_ColCode2_Callback(hObject, eventdata, handles)
4036set_vec_col_bar(handles)
4037update_plot(handles);
4038%------------------------------------------------------------------------
4039%-------------------------------------------------------
4040% --- Executes on button press in CheckFixVecColor.
4041%-------------------------------------------------------
4042function VecColBar_Callback(hObject, eventdata, handles)
4043set_vec_col_bar(handles)
4044
4045%------------------------------------------------------------------------
4046% --- Executes on button press in CheckFixVecColor.
4047function CheckFixVecColor_Callback(hObject, eventdata, handles)
4048%------------------------------------------------------------------------
4049if ~get(handles.CheckFixVecColor,'Value')
4050    update_plot(handles);
4051end
4052
4053%------------------------------------------------------------------------
4054% --- Executes on selection change in num_MaxVec.
4055function num_MinVec_Callback(hObject, eventdata, handles)
4056%------------------------------------------------------------------------
4057max_vec_Callback(hObject, eventdata, handles)
4058
4059%------------------------------------------------------------------------
4060% --- Executes on selection change in num_MaxVec.
4061function num_MaxVec_Callback(hObject, eventdata, handles)
4062%------------------------------------------------------------------------
4063set(handles.CheckFixVecColor,'Value',1)
4064CheckFixVecColor_Callback(hObject, eventdata, handles)
4065min_val=str2num(get(handles.num_MinVec,'String'));
4066max_val=str2num(get(handles.num_MaxVec,'String'));
4067slider1=get(handles.Slider1,'Value');
4068slider2=get(handles.Slider2,'Value');
4069colcode1=min_val+(max_val-min_val)*slider1;
4070colcode2=min_val+(max_val-min_val)*slider2;
4071set(handles.num_ColCode1,'String',num2str(colcode1))
4072set(handles.num_ColCode2,'String',num2str(colcode2))
4073update_plot(handles);
4074
4075%------------------------------------------------------------------------
4076% --- update the display of color code for vectors (on vecColBar)
4077function set_vec_col_bar(handles)
4078%------------------------------------------------------------------------
4079%get the image of the color display button 'VecColBar' in pixels
4080set(handles.VecColBar,'Unit','pixel');
4081pos_vert=get(handles.VecColBar,'Position');
4082set(handles.VecColBar,'Unit','Normalized');
4083width=ceil(pos_vert(3));
4084height=ceil(pos_vert(4));
4085
4086%get slider indications
4087list=get(handles.ColorCode,'String');
4088ichoice=get(handles.ColorCode,'Value');
4089colcode.ColorCode=list{ichoice};
4090colcode.MinVec=str2num(get(handles.num_MinVec,'String'));
4091colcode.MaxVec=str2num(get(handles.num_MaxVec,'String'));
4092test3color=strcmp(colcode.ColorCode,'rgb') || strcmp(colcode.ColorCode,'bgr');
4093if test3color
4094    colcode.ColCode1=str2num(get(handles.num_ColCode1,'String'));
4095    colcode.ColCode2=str2num(get(handles.num_ColCode2,'String'));
4096end
4097vec_C=colcode.MinVec+(colcode.MaxVec-colcode.MinVec)*(0.5:width-0.5)/width;%sample of vec_C values from min to max
4098[colorlist,col_vec]=set_col_vec(colcode,vec_C);
4099oneheight=ones(1,height);
4100A1=colorlist(col_vec,1)*oneheight;
4101A2=colorlist(col_vec,2)*oneheight;
4102A3=colorlist(col_vec,3)*oneheight;
4103A(:,:,1)=A1';
4104A(:,:,2)=A2';
4105A(:,:,3)=A3';
4106set(handles.VecColBar,'Cdata',A)
4107
4108%-------------------------------------------------------------------
4109function update_plot(handles)
4110%-------------------------------------------------------------------
4111UvData=get(handles.uvmat,'UserData');
4112AxeData=UvData.PlotAxes;% retrieve the current plotted data
4113PlotParam=read_GUI(handles.uvmat);
4114[tild,PlotParamOut]= plot_field(AxeData,handles.PlotAxes,PlotParam);
4115errormsg=fill_GUI(PlotParamOut,handles.uvmat);
4116%write_plot_param(handles,PlotParamOut); %update the auto plot parameters
4117
4118%------------------------------------------------------------------------
4119%------------------------------------------------------------------------
4120%   SELECTION AND EDITION OF PROJECTION OBJECTS
4121%------------------------------------------------------------------------
4122%------------------------------------------------------------------------
4123
4124% --- Executes on selection change in ListObject_1.
4125function ListObject_1_Callback(hObject, eventdata, handles)
4126list_str=get(handles.ListObject,'String');
4127UvData=get(handles.uvmat,'UserData');
4128ObjectData=UvData.ProjObject{get(handles.ListObject_1,'Value')};
4129
4130%% update the projection plot on uvmat
4131ProjData= proj_field(UvData.Field,ObjectData);%project the current input field on object ObjectData
4132plot_field(ProjData,handles.PlotAxes,read_GUI(handles.uvmat));% plot the projected field;
4133%replot all the objects within the new projected field
4134for IndexObj=1:numel(list_str)
4135        hobject=UvData.ProjObject{IndexObj}.DisplayHandle.uvmat;
4136        if isempty(hobject) || ~ishandle(hobject)
4137            hobject=handles.PlotAxes;
4138        end
4139        if isequal(IndexObj,get(handles.ListObject,'Value'))
4140            objectcolor='m'; %paint in magenta the currently selected object in ListObject
4141        else
4142            objectcolor='b';
4143        end
4144        UvData.ProjObject{IndexObj}.DisplayHandle.uvmat=plot_object(UvData.ProjObject{IndexObj},ObjectData,hobject,objectcolor);%draw the object in uvmat     
4145end
4146set(handles.uvmat,'UserData',UvData)
4147
4148%% display the object parameters if the GUI set_object is already opened
4149if ~get(handles.ViewObject,'Value')
4150    ZBounds=0; % default
4151    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4152        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4153        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4154    end
4155    ObjectData.Name=list_str{get(handles.ListObject_1,'Value')};
4156    set_object(ObjectData,[],ZBounds);
4157    set(handles.ViewObject,'Value',1)% show that the selected object in ListObject_1 is currently visualised
4158end
4159
4160%  desactivate the edit object mode
4161set(handles.edit_object,'Value',0)
4162% set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])
4163
4164%------------------------------------------------------------------------
4165% --- Executes on selection change in ListObject.
4166function ListObject_Callback(hObject, eventdata, handles)
4167%------------------------------------------------------------------------
4168list_str=get(handles.ListObject,'String');
4169IndexObj=get(handles.ListObject,'Value');%present object selection
4170
4171%% The object  is displayed in set_object if this GUI is already opened
4172UvData=get(handles.uvmat,'UserData');
4173ObjectData=UvData.ProjObject{IndexObj};
4174hset_object=findobj(allchild(0),'tag','set_object');
4175if ~isempty(hset_object)
4176    ZBounds=0; % default
4177    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4178        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4179        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4180    end
4181    ObjectData.Name=list_str{IndexObj};
4182    set_object(ObjectData,[],ZBounds);
4183    set(handles.ViewField,'Value',1)% show that the selected object in ListObject is currently visualised
4184end
4185
4186%%  desactivate the edit object mode
4187set(handles.edit_object,'Value',0)
4188% set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])
4189
4190%% update the  plot on view_field if view_field is already openened
4191hview_field=findobj(allchild(0),'tag','view_field');
4192if isempty(hview_field)
4193    hhview_field.PlotAxes=[];
4194else
4195    Data=get(hview_field,'UserData');
4196    hhview_field=guidata(hview_field);
4197    ProjData= proj_field(UvData.Field,ObjectData);%project the current interface field on ObjectData
4198    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.PlotAxes,read_GUI(hview_field));%read plotting parameters on the uvmat interface
4199   
4200    %write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
4201    haxes=findobj(hview_field,'tag','axes3');
4202    pos=get(hview_field,'Position'); 
4203    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
4204        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
4205        pos_table=get(h_TableDisplay,'Position');
4206        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
4207        drawnow% needed to change position before the next command
4208        set(hview_field,'UserData',Data);% restore the previously stored GUI position after GUI resizing
4209    else
4210        set(hview_field,'Position',Data.GUISize)% return to the previously stored GUI position and size
4211    end
4212end
4213
4214%% update the color of the graphic object representation: the selected object in magenta, others in blue
4215update_object_color(handles.PlotAxes,hhview_field.PlotAxes,UvData.ProjObject{IndexObj}.DisplayHandle.uvmat)
4216
4217%------------------------------------------------------------------------
4218%--- update the color representation of objects (indicating the selected ones)
4219function update_object_color(axes_uvmat,axes_view_field,DisplayHandle)
4220%------------------------------------------------------------------------
4221if isempty(axes_view_field)% case with no view_field plot
4222hother=[findobj(axes_uvmat,'Tag','proj_object');findobj(axes_uvmat,'Tag','DeformPoint')];%find all the proj object and deform point representations
4223else
4224hother=[findobj(axes_uvmat,'Tag','proj_object') ;findobj(axes_view_field,'Tag','proj_object');... %find all the proj object representations
4225findobj(axes_uvmat,'Tag','DeformPoint'); findobj(axes_view_field,'Tag','DeformPoint')];%find all the deform point representations
4226end
4227for iobj=1:length(hother)
4228    if isequal(get(hother(iobj),'Type'),'rectangle')||isequal(get(hother(iobj),'Type'),'patch')
4229        set(hother(iobj),'EdgeColor','b')
4230        if isequal(get(hother(iobj),'FaceColor'),'m')
4231            set(hother(iobj),'FaceColor','b')
4232        end
4233    elseif isequal(get(hother(iobj),'Type'),'image')
4234        Acolor=get(hother(iobj),'CData');
4235        Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2));
4236        set(hother(iobj),'CData',Acolor);
4237    else
4238        set(hother(iobj),'Color','b')
4239    end
4240    set(hother(iobj),'Selected','off')
4241end
4242if ishandle(DisplayHandle)
4243    linetype=get(DisplayHandle,'Type');
4244    if isequal(linetype,'line')
4245        set(DisplayHandle,'Color','m'); %set the selected object to magenta color
4246    elseif isequal(linetype,'rectangle')
4247        set(DisplayHandle,'EdgeColor','m'); %set the selected object to magenta color
4248    elseif isequal(linetype,'patch')
4249        set(DisplayHandle,'FaceColor','m'); %set the selected object to magenta color
4250    end
4251    SubObjectData=get(DisplayHandle,'UserData');
4252    if isfield(SubObjectData,'SubObject') & ishandle(SubObjectData.SubObject)
4253        for iobj=1:length(SubObjectData.SubObject)
4254            hsub=SubObjectData.SubObject(iobj);
4255            if isequal(get(hsub,'Type'),'rectangle')
4256                set(hsub,'EdgeColor','m'); %set the selected object to magenta color
4257            elseif isequal(get(hsub,'Type'),'image')
4258                Acolor=get(hsub,'CData');
4259                Acolor(:,:,1)=Acolor(:,:,3);
4260                set(hsub,'CData',Acolor);
4261            else
4262                set(hsub,'Color','m')
4263            end
4264        end
4265    end
4266    if isfield(SubObjectData,'DeformPoint') & ishandle(SubObjectData.DeformPoint)
4267        set(SubObjectData.DeformPoint,'Color','m')
4268    end
4269end
4270
4271%-------------------------------------------------------------------
4272% --- Executes on selection change in edit_object.
4273function edit_object_Callback(hObject, eventdata, handles)
4274%-------------------------------------------------------------------
4275hset_object=findobj(allchild(0),'Tag','set_object');
4276if get(handles.edit_object,'Value')
4277%     set(handles.edit_object,'BackgroundColor',[1,1,0]) 
4278    %suppress the other options
4279    set(handles.CheckZoom,'Value',0)
4280    CheckZoom_Callback(hObject, eventdata, handles)
4281    hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4282    if ishandle(hgeometry_calib)
4283        hhgeometry_calib=guidata(hgeometry_calib);
4284        set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4285        set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4286    end
4287    set(handles.ViewObject,'value',1)
4288    ViewObject_Callback(hObject, eventdata, handles)
4289else % desctivate object edit mode
4290%     set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4291    if ~isempty(hset_object)% open the
4292        hhset_object=guidata(hset_object);
4293        set(hhset_object.PLOT,'enable','off');
4294        set(get(hset_object,'children'),'enable','inactive')
4295    end
4296end
4297
4298
4299%------------------------------------------------------------------------
4300% --- Executes on button press in ViewObject.
4301function ViewObject_Callback(hObject, eventdata, handles)
4302%------------------------------------------------------------------------
4303check_view=get(handles.ViewObject,'Value');
4304
4305if check_view %activate set_object   
4306    IndexObj=get(handles.ListObject,'Value');
4307    list_object=get(handles.ListObject,'String');
4308    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4309    UvData.ProjObject{IndexObj}.Name=list_object{IndexObj};
4310    if numel(UvData.ProjObject)<IndexObj;% error in UvData
4311        msgbox_uvmat('ERROR','invalid object list')
4312        return
4313    end
4314    ZBounds=0; % default
4315    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4316        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4317        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4318    end
4319%     set(handles.ListObject_1,'Value',IndexObj);%restore ListObject selection after set_object deletion
4320    data=UvData.ProjObject{IndexObj};
4321    if ~isfield(data,'Type')% default plane
4322        data.Type='plane';
4323    end
4324%     if isfield(UvData,'Field')
4325%         Field=UvData.Field;
4326%         if isfield(UvData.Field,'Mesh')&&~isempty(UvData.Field.Mesh)
4327%             data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
4328%             if strcmp(data.Type,'line')||strcmp(data.Type,'polyline')
4329%                 data.RangeY=UvData.Field.Mesh;
4330%             else
4331%                 data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
4332%             end
4333%             data.DX=UvData.Field.Mesh;
4334%             data.DY=UvData.Field.Mesh;
4335%         end
4336%         if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
4337%             data.Coord=[0 0 0]; %default
4338%         end
4339%         if isfield(Field,'CoordUnit')
4340%             data.CoordUnit=Field.CoordUnit;
4341%         end
4342%     end
4343    hset_object=set_object(data,[],ZBounds);
4344    hhset_object=guidata(hset_object);
4345    if get(handles.edit_object,'Value')% edit mode
4346        set(hhset_object.PLOT,'Enable','on')
4347        set(get(hset_object,'children'),'enable','on')
4348    else
4349        set(hhset_object.PLOT,'Enable','off')
4350        set(get(hset_object,'children'),'enable','inactive')% deactivate the GUI except SAVE
4351        set(hhset_object.SAVE,'Enable','on')
4352    end
4353else
4354    hset_object=findobj(allchild(0),'tag','set_object');
4355    if ~isempty(hset_object)
4356        delete(hset_object)% delete existing version of set_object
4357    end
4358end
4359 
4360
4361%------------------------------------------------------------------------
4362% --- Executes on button press in ViewField.
4363function ViewField_Callback(hObject, eventdata, handles)
4364%------------------------------------------------------------------------
4365check_view=get(handles.ViewField,'Value');
4366
4367if check_view
4368    IndexObj=get(handles.ListObject,'Value');
4369    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4370    if numel(UvData.ProjObject)<IndexObj(end);% error in UvData
4371        msgbox_uvmat('ERROR','invalid object list')
4372        return
4373    end
4374    ZBounds=0; % default
4375    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4376        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4377        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4378    end
4379    set(handles.ListObject,'Value',IndexObj);%restore ListObject selection after set_object deletion
4380    if ~isfield(UvData.ProjObject{IndexObj(1)},'Type')% default plane
4381        UvData.ProjObject{IndexObj(1)}.Type='plane';
4382    end
4383    list_object=get(handles.ListObject,'String');
4384    UvData.ProjObject{IndexObj(end)}.Name=list_object{IndexObj(end)};
4385   
4386    %% show the projection of the selected object on view_field
4387    ProjData= proj_field(UvData.Field,UvData.ProjObject{IndexObj});%project the current field on ObjectData
4388    hview_field=findobj(allchild(0),'tag','view_field');
4389    if isempty(hview_field)
4390        hview_field=view_field;
4391    end
4392    hhview_field=guidata(hview_field);
4393    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.PlotAxes,read_GUI(hview_field));%read plotting parameters on the GUI view_field);
4394    errormsg=fill_GUI(PlotParam,hview_field);
4395    for list={'Scalar','Vectors'}
4396        if ~isfield(PlotParam,list{1})
4397            set(hhview_field.(list{1}),'Visible','off')
4398        end
4399    end
4400    %write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
4401    haxes=findobj(hview_field,'tag','axes3');
4402    pos=get(hview_field,'Position');
4403    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
4404        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
4405        pos_table=get(h_TableDisplay,'Position');
4406        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
4407    else
4408        Data=get(hview_field,'UserData');
4409        set(hview_field,'Position',Data.GUISize)% restore the size of view_field for plots
4410    end
4411else
4412    hview_field=findobj(allchild(0),'tag','view_field');
4413    if ~isempty(hview_field)
4414        delete(hview_field)% delete existing version of set_object
4415    end
4416end
4417
4418
4419%------------------------------------------------------------------------
4420% --- Executes on button press in delete_object.
4421%------------------------------------------------------------------------
4422function delete_object_Callback(hObject, eventdata, handles)
4423
4424IndexObj=get(handles.ListObject,'Value');%projection object selected for view_field
4425IndexObj_1=get(handles.ListObject_1,'Value');%projection object selected for uvmat plot
4426if IndexObj>1 && ~isequal(IndexObj,IndexObj_1) % do not delete the object used for the uvmat plot
4427    delete_object(IndexObj)
4428end
4429
4430%'delete_object': delete a projection object, defined by its index in the Uvmat list or by its graphic handle
4431%------------------------------------------------------------------------
4432% function delete_object(hObject)
4433%
4434% INPUT:
4435% hObject: object index (if integer) or handle of the graphic object. If
4436%          hObject is a subobject, the parent object is detected and deleted.
4437
4438function delete_object(IndexObj)
4439
4440huvmat=findobj('tag','uvmat');%handles of the uvmat interface
4441UvData=get(huvmat,'UserData');
4442hlist_object=findobj(huvmat,'Tag','ListObject');%handles of the object list in the uvmat interface
4443list_str=get(hlist_object,'String');%objet list
4444% if isequal(floor(hObject),hObject) %case of an index
4445    if  ~isempty(UvData) && isfield(UvData, 'ProjObject') && length(UvData.ProjObject)>=IndexObj
4446        if isfield(UvData.ProjObject{IndexObj},'DisplayHandle') && isfield(UvData.ProjObject{IndexObj}.DisplayHandle,'uvmat')
4447            hdisplay=UvData.ProjObject{IndexObj}.DisplayHandle.uvmat;
4448            for iview=1:length(hdisplay)
4449                if ishandle(hdisplay(iview)) && ~isequal(hdisplay(iview),0)
4450                    ObjectData=get(hdisplay(iview),'UserData');
4451                    if isfield(ObjectData,'SubObject') & ishandle(ObjectData.SubObject)
4452                        delete(ObjectData.SubObject);
4453                    end
4454                    if isfield(ObjectData,'DeformPoint') & ishandle(ObjectData.DeformPoint)
4455                        delete(ObjectData.DeformPoint);
4456                    end
4457                    delete(hdisplay(iview))
4458                end
4459                ishandle(hdisplay(iview))
4460            end
4461            for iobj=IndexObj+1:length(UvData.ProjObject)
4462                hdisplay=UvData.ProjObject{iobj}.DisplayHandle.uvmat;
4463                for iview=1:length(hdisplay)
4464                    if ishandle(hdisplay(iview)) && ~isequal(hdisplay(iview),0)
4465                        PlotData=get(hdisplay(iview),'UserData');
4466                        PlotData.IndexObj=iobj-1;
4467                        set(hdisplay(iview),'UserData',PlotData);
4468                    end
4469                end
4470            end
4471        end
4472        UvData.ProjObject(IndexObj)=[]; 
4473        if ~isempty(list_str)
4474            list_str(IndexObj)=[];
4475        end
4476    end
4477% elseif ishandle(hObject)%object handle
4478%     userdata=get(hObject,'UserData');
4479%     if ishandle(userdata)%the selected line depends on a parent line
4480%         hdisplay=userdata;% the parent object becomes the current one
4481%     else
4482%         hdisplay=hObject;% the selected object becomes the current one
4483%     end
4484%     PlotData=get(hdisplay,'UserData');
4485%     if isfield(PlotData,'SubObject') & ishandle(PlotData.SubObject)
4486%             delete(PlotData.SubObject);
4487%     end
4488%     if isfield(PlotData,'DeformPoint') & ishandle(PlotData.DeformPoint)
4489%            delete(PlotData.DeformPoint);
4490%     end
4491%     delete(hdisplay);
4492%     if isfield(PlotData,'IndexObj')
4493%         IndexObj=PlotData.IndexObj;
4494%         if  isequal(round(IndexObj),IndexObj) & IndexObj>=1 & length(list_str) > IndexObj
4495%             if isfield(UvData,'ProjObject')& length(UvData.ProjObject) > IndexObj
4496%                UvData.ProjObject(IndexObj)=[];
4497%             end
4498%             list_str(IndexObj)=[];
4499%         end
4500%     end
4501% end
4502set(huvmat,'UserData',UvData);
4503set(hlist_object,'String',list_str)
4504set(hlist_object,'Value',length(list_str))
4505hlist_object_1=findobj(huvmat,'Tag','ListObject_1');%handles of the first object list in the uvmat interface
4506old_index=get(hlist_object_1,'Value');
4507set(hlist_object_1,'String',list_str)
4508if IndexObj<=old_index
4509    set(hlist_object_1,'Value',old_index-1)
4510end
4511
4512%------------------------------------------------------------------------
4513%------------------------------------------------------------------------
4514%  II - TOOLS FROM THE UPPER MENU BAR
4515%------------------------------------------------------------------------
4516%------------------------------------------------------------------------
4517
4518%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4519% Export  Menu Callbacks
4520%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4521%------------------------------------------------------------------------
4522% --- Executes on button press in Menu/Export/field in workspace.
4523function MenuExportField_Callback(hObject, eventdata, handles)
4524%------------------------------------------------------------------------
4525global Data_uvmat
4526Data_uvmat=get(handles.uvmat,'UserData');
4527evalin('base','global Data_uvmat')%make CurData global in the workspace
4528display('current field :')
4529evalin('base','Data_uvmat') %display CurData in the workspace
4530commandwindow; %brings the Matlab command window to the front
4531
4532%------------------------------------------------------------------------
4533% --- Executes on button press in Menu/Export/extract figure.
4534function MenuExportFigure_Callback(hObject, eventdata, handles)
4535%------------------------------------------------------------------------
4536% huvmat=get(handles.MenuExport,'parent');
4537hfig=figure;
4538copyobj(handles.PlotAxes,hfig);
4539map=colormap(handles.PlotAxes);
4540colormap(map);%transmit the current colormap to the zoom fig
4541colorbar
4542
4543% --------------------------------------------------------------------
4544function MenuExportAxis_Callback(hObject, eventdata, handles)
4545ListFig=findobj(allchild(0),'Type','figure');
4546nb_option=0;
4547menu={};
4548for ilist=1:numel(ListFig)
4549    FigName=get(ListFig(ilist),'name');
4550    if isempty(FigName)
4551        FigName=['figure ' num2str(ListFig(ilist))];
4552    end
4553    if ~strcmp(FigName,'uvmat')
4554        ListAxes=findobj(ListFig(ilist),'Type','axes');
4555        ListTags=get(ListAxes,'Tag');
4556        if ~isempty(ListTags) && ~isempty(find(~strcmp('Colorbar',ListTags), 1))
4557            ListAxes=ListAxes(~strcmp('Colorbar',ListTags));
4558            if numel(ListAxes)==1
4559                nb_option=nb_option+1;
4560                menu{nb_option}=FigName ;
4561                AxesHandle(nb_option)=ListAxes;
4562            else
4563                nb_axis=0;
4564                for iaxes=1:numel(ListAxes)
4565                    nb_axis=nb_axis+1;
4566                    nb_option=nb_option+1;
4567                    menu{nb_option}=[FigName '_' num2str(nb_axis)];
4568                    AxesHandle(nb_option)=ListAxes(nb_axis);
4569                end
4570            end
4571        end
4572    end
4573end
4574if isempty(menu)
4575    answer=msgbox_uvmat('INPUT_Y-N','no existing plotting axes available, create new figure?');
4576    if strcmp(answer,'Yes')
4577        hfig=figure;
4578        copyobj(handles.PlotAxes,hfig);
4579    else
4580        return
4581    end
4582    map=colormap(handles.PlotAxes);
4583    colormap(map);%transmit the current colormap to the zoom fig
4584    colorbar
4585else
4586    answer=msgbox_uvmat('INPUT_MENU','select a figure/axis on which the current uvmat plot will be exported',menu);
4587    if isempty(answer)
4588        return
4589    else
4590        axes(AxesHandle(answer))
4591        hold on
4592        hchild=get(handles.PlotAxes,'children');
4593        copyobj(hchild,gca);
4594    end
4595end
4596
4597
4598%------------------------------------------------------------------------
4599% --------------------------------------------------------------------
4600function MenuExportMovie_Callback(hObject, eventdata, handles)
4601% --------------------------------------------------------------------
4602set(handles.MenuExportMovie,'BusyAction','queue')% activate the button
4603huvmat=get(handles.run0,'parent');
4604UvData=get(huvmat,'UserData');
4605%[xx,xx,FileBase]=read_file_boxes(handles);
4606[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
4607FileBase=fullfile(RootPath,RootFile);
4608 %read the current input file name
4609prompt = {'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)'};
4610dlg_title = 'select properties of the output avi movie';
4611num_lines= 1;
4612def     = {[FileBase '_out.avi'];'10';'1';'[0.03 0.05 0.95 0.92]';'10'};
4613answer = inputdlg(prompt,dlg_title,num_lines,def,'on');
4614aviname=answer{1};
4615fps=str2double(answer{2});
4616% check for existing file with output name aviname
4617if exist(aviname,'file')
4618    backup=aviname;
4619    testexist=2;
4620    while testexist==2
4621        backup=[backup '~'];
4622        testexist=exist(backup,'file');     
4623    end
4624    [success,message]=copyfile(aviname,backup);%make backup of the existing file
4625    if isequal(success,1)
4626        delete(aviname)%delete existing file
4627    else
4628        msgbox_uvmat('ERROR',message)
4629        return
4630    end
4631end
4632%create avi open
4633aviobj=avifile(aviname,'Compression','None','fps',fps);
4634
4635%display first view for tests
4636newfig=figure;
4637newaxes=copyobj(handles.PlotAxes,newfig);%new plotting axes in the new figure
4638set(newaxes,'Tag','movieaxes')
4639nbpix=[512 384]*str2double(answer{3});
4640set(gcf,'Position',[1 1 nbpix])% resolution XVGA
4641set(newaxes,'Position',eval(answer{4}));
4642map=colormap(handles.PlotAxes);
4643colormap(map);%transmit the current colormap to the zoom fig
4644msgbox_uvmat('INPUT_Y-N',{['adjust figure ' num2str(newfig) ' with its matlab edit menu '] ;...
4645        ['then press OK to get the avi movie as a copy of figure ' num2str(newfig) ' display']});
4646UvData.plotaxes=newaxes;% the axis in the new figure becomes the current main plotting axes
4647set(huvmat,'UserData',UvData);
4648increment=str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d
4649set(handles.STOP,'Visible','on')
4650set(handles.speed,'Visible','on')
4651set(handles.speed_txt,'Visible','on')
4652set(handles.Movie,'BusyAction','queue')
4653
4654%imin=str2double(get(handles.i1,'String'));
4655imax=str2double(answer{5});
4656% if isfield(UvData,'Time')
4657htitle=get(newaxes,'Title');
4658xlim=get(newaxes,'XLim');
4659ylim=get(newaxes,'YLim');
4660set(htitle,'Position',[xlim(2)+0.07*(xlim(2)-xlim(1)) ylim(2)-0.05*(ylim(2)-ylim(1)) 0])
4661time_str=get(handles.abs_time,'String');
4662set(htitle,'String',['t=' time_str])
4663set(handles.speed,'Value',1)
4664for i=1:imax
4665    if get(handles.speed,'Value')~=0 && isequal(get(handles.MenuExportMovie,'BusyAction'),'queue') % enable STOP command
4666            runpm(hObject,eventdata,handles,increment)% run plus
4667            drawnow
4668            time_str=get(handles.abs_time,'String');
4669            if ishandle(htitle)
4670             set(htitle,'String',['t=' time_str])
4671            end
4672            mov=getframe(newfig);
4673            aviobj=addframe(aviobj,mov);
4674    end
4675end
4676aviobj=close(aviobj);
4677UvData=rmfield(UvData,'plotaxes');
4678set(huvmat,'UserData',UvData);
4679msgbox_uvmat('CONFIRMATION',{['movie ' aviname ' created '];['with ' num2str(imax) ' frames']})
4680
4681
4682%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4683% Projection Objects Menu Callbacks
4684%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4685
4686% -----------------------------------------------------------------------
4687function Menupoints_Callback(hObject, eventdata, handles)
4688%------------------------------------------------------------------------
4689data.Type='points';
4690data.ProjMode='projection';%default
4691data.ProjModeMenu={};% do not restrict ProjMode menus
4692create_object(data,handles)
4693
4694% -----------------------------------------------------------------------
4695function Menuline_Callback(hObject, eventdata, handles)
4696%------------------------------------------------------------------------
4697data.Type='line';
4698data.ProjMode='projection';%default
4699data.ProjModeMenu={};% do not restrict ProjMode menus
4700create_object(data,handles)
4701
4702%------------------------------------------------------------------------
4703function Menupolyline_Callback(hObject, eventdata, handles)
4704%------------------------------------------------------------------------
4705data.Type='polyline';
4706data.ProjMode='projection';%default
4707data.ProjModeMenu={};% do not restrict ProjMode menus
4708create_object(data,handles)
4709
4710%------------------------------------------------------------------------
4711function Menupolygon_Callback(hObject, eventdata, handles)
4712%------------------------------------------------------------------------
4713data.Type='polygon';
4714data.ProjMode='inside';%default
4715data.ProjModeMenu={};% do not restrict ProjMode menus
4716create_object(data,handles)
4717
4718%------------------------------------------------------------------------
4719function Menurectangle_Callback(hObject, eventdata, handles)
4720%------------------------------------------------------------------------
4721data.Type='rectangle';
4722data.ProjMode='inside';%default
4723data.ProjModeMenu={};% do not restrict ProjMode menus
4724create_object(data,handles)
4725
4726%------------------------------------------------------------------------
4727function Menuellipse_Callback(hObject, eventdata, handles)
4728%------------------------------------------------------------------------
4729data.Type='ellipse';
4730data.ProjMode='inside';%default
4731data.ProjModeMenu={};% do not restrict ProjMode menus
4732create_object(data,handles)
4733
4734%------------------------------------------------------------------------
4735function MenuMaskObject_Callback(hObject, eventdata, handles)
4736%------------------------------------------------------------------------
4737data.Type='polygon';
4738data.TypeMenu={'polygon'};
4739data.ProjMode='mask_inside';%default
4740data.ProjModeMenu={'mask_inside';'mask_outside'};
4741create_object(data,handles)
4742
4743%------------------------------------------------------------------------
4744function Menuplane_Callback(hObject, eventdata, handles)
4745%------------------------------------------------------------------------
4746data.Type='plane';
4747data.ProjMode='projection';%default
4748data.ProjModeMenu={};% do not restrict ProjMode menus
4749create_object(data,handles)
4750
4751%------------------------------------------------------------------------
4752function Menuvolume_Callback(hObject, eventdata, handles)
4753%------------------------------------------------------------------------
4754data.Type='volume';
4755data.ProjMode='interp_lin';%default
4756data.ProjModeMenu={};
4757% set(handles.create,'Visible','on')
4758% set(handles.create,'Value',1)
4759% VOLUME_Callback(hObject,eventdata,handles)data.ProjModeMenu={};
4760create_object(data,handles)
4761
4762%------------------------------------------------------------------------
4763% --- generic function used for the creation of a projection object
4764function create_object(data,handles)
4765%------------------------------------------------------------------------
4766%% desactivate concurrent tools
4767hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');% search the GUI geometric calibration
4768if ishandle(hgeometry_calib)
4769    hhgeometry_calib=guidata(hgeometry_calib);
4770    set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4771end
4772set(handles.edit_object,'Value',0)  %desactivate the object edit mode
4773set(handles.CheckZoomFig,'Value',0) %desactivate zoom sub fig
4774set(handles.CheckZoom,'Value',0)    %desactivate the zoom action
4775if ishandle(handles.UVMAT_title)
4776    delete(handles.UVMAT_title)     %delete the initial display of uvmat if no field has been entered yet
4777end
4778
4779%% append a new line to the list of projection objects
4780ListObject=get(handles.ListObject,'String');
4781if isempty(ListObject)
4782    ListObject={''};
4783end
4784if ~strcmp(ListObject{end},'')
4785    ListObject=[ListObject;{''}]; %append a blank to the list (if nort already done) to indicate the creation of a new object
4786    set(handles.ListObject,'String',ListObject)
4787end
4788IndexObj=length(ListObject);
4789set(handles.ListObject,'Value',IndexObj)
4790UvData=get(handles.uvmat,'UserData');
4791UvData.ProjObject{IndexObj}=[]; %create a new empty object
4792UvData.ProjObject{IndexObj}.DisplayHandle.uvmat=handles.PlotAxes; % axes for plot_object
4793UvData.ProjObject{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation
4794set(handles.uvmat,'UserData',UvData)
4795
4796%% initiate the new projection object
4797data.Name=data.Type;% default name=type
4798data.Coord=[0 0]; %default
4799if isfield(UvData,'Field')
4800    Field=UvData.Field;
4801    if isfield(UvData.Field,'CoordMesh')&&~isempty(UvData.Field.CoordMesh)
4802        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
4803        if strcmp(data.Type,'line')||strcmp(data.Type,'polyline')||strcmp(data.Type,'points')
4804            data.RangeY=UvData.Field.CoordMesh;
4805        else
4806            data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
4807        end
4808        data.DX=UvData.Field.CoordMesh;
4809        data.DY=UvData.Field.CoordMesh;
4810        if strcmp(data.Type,'rectangle')||strcmp(data.Type,'ellipse')
4811            data.RangeX=UvData.Field.CoordMesh;
4812            data.RangeY=UvData.Field.CoordMesh;
4813        end
4814    end
4815    if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
4816         data.Coord=[0 0 0]; %default
4817    end
4818    if isfield(Field,'CoordUnit')
4819        data.CoordUnit=Field.CoordUnit;
4820    end
4821end
4822hset_object=set_object(data,handles);% call the GUI set_object
4823hchild=get(hset_object,'children');
4824set(hchild,'enable','on')
4825
4826
4827set(handles.delete_object,'Visible','on')
4828
4829%------------------------------------------------------------------------
4830function MenuBrowseObject_Callback(hObject, eventdata, handles)
4831%------------------------------------------------------------------------
4832%get the object file
4833[FileName, PathName, filterindex] = uigetfile( ...
4834       {'*.xml;*.mat', ' (*.xml,*.mat)';
4835       '*.xml',  '.xml files '; ...
4836        '*.mat',  '.mat matlab files '}, ...
4837        'Pick an xml Object file',get(handles.RootPath,'String'));
4838fileinput=[PathName FileName];%complete file name
4839sizf=size(fileinput);
4840if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
4841
4842%read the file
4843[data,heading]=xml2struct(fileinput);
4844if ~strcmp(heading,'ProjObject')
4845    msgbox_uvmat('WARNING','The xml file does not have the heading ProjObject for projection objects')
4846end
4847[tild,data.Name]=fileparts(FileName);% object name set as file name
4848ListObject=get(handles.ListObject,'String');
4849if ~strcmp(ListObject{end},'')
4850    ListObject=[ListObject;{''}]; %append a blank to the list (if not already done) to indicate the creation of a new object
4851    set(handles.ListObject,'String',ListObject)
4852end
4853IndexObj=length(ListObject);
4854
4855UvData=get(handles.uvmat,'UserData');
4856UvData.ProjObject{IndexObj}=[]; %create a new empty object
4857UvData.ProjObject{IndexObj}.DisplayHandle.uvmat=[]; %no plot handle before plot_field operation
4858UvData.ProjObject{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation
4859set(handles.uvmat,'UserData',UvData)
4860set(handles.ListObject,'Value',IndexObj)
4861hset_object=set_object(data);% call the set_object interface
4862set(get(hset_object,'children'),'enable','on')% enable edit action on elements on GUI set_object
4863set(handles.edit_object,'Value',0); %suppress the object edit mode
4864% set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4865set(handles.delete_object,'Visible','on')
4866
4867
4868%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4869% MenuEdit Callbacks
4870%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4871%------------------------------------------------------------------------
4872function MenuEditObject_Callback(hObject, eventdata, handles)
4873%------------------------------------------------------------------------
4874set(handles.edit_object,'Value',1)
4875edit_Callback(hObject, eventdata, handles)
4876
4877%------------------------------------------------------------------------
4878function MenuEditVectors_Callback(hObject, eventdata, handles)
4879%------------------------------------------------------------------------
4880set(handles.edit_vect,'Visible','on')
4881set(handles.edit_vect,'Value',1)
4882edit_vect_Callback(hObject, eventdata, handles)
4883
4884%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4885% MenuTools Callbacks
4886%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4887%------------------------------------------------------------------------
4888function MenuCalib_Callback(hObject, eventdata, handles)
4889%------------------------------------------------------------------------
4890
4891UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4892
4893%suppress competing options
4894set(handles.CheckZoom,'Value',0)
4895set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
4896set(handles.ListObject,'Value',1)     
4897% initiate display of GUI geometry_calib
4898data=[]; %default
4899if isfield(UvData,'CoordType')
4900    data.CoordType=UvData.CoordType;
4901end
4902[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
4903FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
4904set(handles.view_xml,'Backgroundcolor',[1 1 0])%indicate the reading of the current xml file by geometry_calib
4905pos_uvmat=get(handles.uvmat,'Position');
4906pos_cal(1)=pos_uvmat(1)+UvData.OpenParam.PosGeometryCalib(1)*pos_uvmat(3);
4907pos_cal(2)=pos_uvmat(2)+UvData.OpenParam.PosGeometryCalib(2)*pos_uvmat(4);
4908pos_cal(3:4)=UvData.OpenParam.PosGeometryCalib(3:4).* pos_uvmat(3:4);
4909geometry_calib(FileName,pos_cal);% call the geometry_calib interface   
4910set(handles.view_xml,'Backgroundcolor',[1 1 1])%indicate the end of reading of the current xml file by geometry_calib
4911set(handles.MenuCalib,'checked','on')% indicate that MenuCalib is activated, test used by mouse action
4912
4913
4914%-----------------------------------------------------------------------
4915function MenuLIFCalib_Callback(hObject, eventdata, handles)
4916%------------------------------------------------------------------------
4917%% read UvData properties stored on the uvmat interface
4918UvData=get(handles.uvmat,'UserData');
4919if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
4920    XmlData=UvData.XmlData{1};
4921else
4922    msgbox_uvmat('ERROR','geometric calibration needed: use Tools/geometric calibration in the menu bar');
4923    return
4924end
4925
4926%% read lines currently drawn
4927ListObj=UvData.ProjObject;
4928select=zeros(1,numel(ListObj));
4929for iobj=1:numel(ListObj);
4930    if isfield(ListObj{iobj},'Type') && strcmp(ListObj{iobj}.Type,'line')
4931        select(iobj)=1;
4932    end
4933end
4934val=find(select);
4935if numel(val)<2
4936    msgbox_uvmat('ERROR','light rays must be defined by at least two lines created by Projection object/line in the menu bar');
4937    return
4938else
4939    set(handles.ListObject,'Value',val);% show the selected lines on the list
4940    ObjectData=UvData.ProjObject(val);
4941    for iobj=1:length(ObjectData)
4942%         if isfield(ObjectData{iobj},'Coord')
4943            xA(iobj)=ObjectData{iobj}.Coord(1,1);
4944            yA(iobj)=ObjectData{iobj}.Coord(1,2);
4945            xB(iobj)=ObjectData{iobj}.Coord(2,1);
4946            yB(iobj)=ObjectData{iobj}.Coord(2,2);
4947%         end
4948    end
4949end
4950
4951%% find the origin as intersection of the two first lines (see http://www.ahristov.com/tutorial/geometry-games/intersection-lines.html )
4952x1=xA(1);x2=xB(1);
4953x3=xA(2);x4=xB(2);
4954y1=yA(1);y2=yB(1);
4955y3=yA(2);y4=yB(2);
4956D = (x1-x2)*(y3-y4) -(y1-y2)*(x3-x4);
4957if D==0
4958    msgbox_uvmat('ERROR','the two lines are parallel');
4959    return
4960end
4961x0=((x3-x4)*(x1*y2-y1*x2)-(x1-x2)*(x3*y4-y3*x4))/D;
4962y0=((y3-y4)*(x1*y2-y1*x2)-(y1-y2)*(x3*y4-y3*x4))/D;
4963XmlData.Illumination.Origin=[x0 y0];
4964XmlData.PolarCentre=[x0 y0];
4965
4966%% display the current image in polar coordinates with origin at the  illumination source
4967currentdir=pwd; 
4968uvmatpath=fileparts(which('uvmat'));
4969cd(fullfile(uvmatpath,'transform_field'));
4970phys_polar=str2func('phys_polar');
4971cd(currentdir)
4972DataOut=phys_polar(UvData.Field,XmlData);
4973view_field(DataOut);
4974
4975%% use the third line for reference luminosity
4976if numel(val)==3
4977    x_ref=linspace(ObjectData{3}.Coord(1,1),ObjectData{3}.Coord(2,1),10);
4978    y_ref=linspace(ObjectData{3}.Coord(1,2),ObjectData{3}.Coord(2,2),10);
4979    x_ref=x_ref-x0;
4980    y_ref=y_ref-y0;
4981    [theta_ref,r_ref] = cart2pol(x_ref,y_ref);%theta_ref  and r_ref are the polar coordinates of the points on the line
4982    theta_ref=theta_ref*180/pi;
4983    figure
4984    plot(theta_ref,r_ref)
4985    azimuth_ima=linspace(DataOut.AY(1),DataOut.AY(2),size(DataOut.A,1));%profile of x index on the transformed image
4986    dist_source = interp1(theta_ref,r_ref,azimuth_ima);
4987    dist_source_pixel=round(size(DataOut.A,2)*(dist_source-DataOut.AX(1))/(DataOut.AX(2)-DataOut.AX(1)));
4988    line_nan= isnan(dist_source_pixel);
4989    dist_source_pixel(line_nan)=1;
4990    width=20; %number of pixels used for reference
4991    DataOut.A=double(DataOut.A);
4992    Anorm=zeros(size(DataOut.A));
4993    Aval=mean(mean(DataOut.A));
4994    for iline=1:size(DataOut.A,1)
4995        lum(iline)=mean(DataOut.A(iline,dist_source_pixel(iline):dist_source_pixel(iline)+width));
4996        Anorm(iline,:)=uint16(Aval*DataOut.A(iline,:)/lum(iline));
4997    end
4998    lum(line_nan)=NaN;
4999    figure
5000    plot(1:size(DataOut.A,1),lum)
5001end
5002ImaName=regexprep([get(handles.RootFile,'String') get(handles.FileIndex,'String')],'//','');
5003NewImageName=fullfile(get(handles.RootPath,'String'),'polar',[ImaName get(handles.FileExt,'String')]);
5004imwrite(Anorm,NewImageName,'BitDepth',16)
5005
5006%% record the origin in the xml file
5007XmlFileName=find_imadoc(get(handles.RootPath,'String'),get(handles.SubDir,'String'),get(handles.RootFile,'String'),get(handles.FileExt,'String'));
5008answer=msgbox_uvmat('INPUT_Y-N','save the illumination origin in the current xml file?');
5009if strcmp(answer,'Yes')
5010    t=xmltree(XmlFileName); %read the file
5011    title=get(t,1,'name');
5012    if ~strcmp(title,'ImaDoc')
5013        msgbox_uvmat('ERROR','wrong xml file');
5014        return
5015    end
5016    % backup the output file if it already exist, and read it
5017    backupfile=XmlFileName;
5018    testexist=2;
5019    while testexist==2
5020        backupfile=[backupfile '~'];
5021        testexist=exist(backupfile,'file');
5022    end
5023    [success,message]=copyfile(XmlFileName,backupfile);%make backup
5024    if success~=1
5025        errormsg=['errror in xml file backup: ' message];
5026        return
5027    end
5028    uid_illumination=find(t,'ImaDoc/Illumination');
5029    if isempty(uid_illumination)  %if GeometryCalib does not already exists, create it
5030        [t,uid_illumination]=add(t,1,'element','Illumination');
5031    end
5032    uid_origin=find(t,'ImaDoc/Illumination/Origin');
5033    if ~isempty(uid_origin)  %if GeometryCalib does not already exists, create it
5034         t=delete(t,uid_origin);
5035    end
5036    % save the illumination origin
5037    t=struct2xml(XmlData.Illumination,t,uid_illumination);
5038    save(t,XmlFileName);
5039end
5040   
5041
5042
5043%------------------------------------------------------------------------
5044function MenuMask_Callback(hObject, eventdata, handles)
5045%------------------------------------------------------------------------
5046UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
5047ListObj=UvData.ProjObject;
5048select=zeros(1,numel(ListObj));
5049for iobj=1:numel(ListObj);
5050    if strcmp(ListObj{iobj}.ProjMode,'mask_inside')||strcmp(ListObj{iobj}.ProjMode,'mask_outside')
5051        select(iobj)=1;
5052    end
5053end
5054val=find(select);
5055if isempty(val)
5056    msgbox_uvmat('ERROR','polygons must be first created by Projection object/mask polygon in the menu bar');
5057    return
5058else
5059    set(handles.ListObject,'Value',val);
5060    flag=1;
5061    npx=size(UvData.Field.A,2);
5062    npy=size(UvData.Field.A,1);
5063    xi=0.5:npx-0.5;
5064    yi=0.5:npy-0.5;
5065    [Xi,Yi]=meshgrid(xi,yi);
5066        for iobj=1:length(UvData.ProjObject)
5067            ObjectData=UvData.ProjObject{iobj};
5068            if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
5069                flagobj=1;
5070                testphys=0; %coordinates in pixels by default
5071                if isfield(ObjectData,'CoordUnit') && ~isequal(ObjectData.CoordUnit,'pixel')
5072                    if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
5073                        Calib=UvData.XmlData{1}.GeometryCalib;
5074                        testphys=1;
5075                    end
5076                end
5077                if isfield(ObjectData,'Coord')&& isfield(ObjectData,'Type')
5078                    if isequal(ObjectData.Type,'polygon')
5079                        X=ObjectData.Coord(:,1);
5080                        Y=ObjectData.Coord(:,2);
5081                        if testphys
5082                            pos=[X Y zeros(size(X))];
5083                            if isfield(Calib,'SliceCoord') && length(Calib.SliceCoord)>=3
5084                                if isfield(Calib,'SliceAngle')&&~isequal(Calib.SliceAngle,[0 0 0])
5085                                    om=norm(Calib.SliceAngle);%norm of rotation angle in radians
5086                                    OmAxis=Calib.SliceAngle/om; %unit vector marking the rotation axis
5087                                    cos_om=cos(pi*om/180);
5088                                    sin_om=sin(pi*om/180);
5089                                    pos=cos_om*pos+sin_om*cross(OmAxis,pos)+(1-cos_om)*(OmAxis*pos')*OmAxis;
5090                                end
5091                                pos(:,1)=pos(:,1)+Calib.SliceCoord(1);
5092                                pos(:,2)=pos(:,2)+Calib.SliceCoord(2);
5093                                pos(:,3)=pos(:,3)+Calib.SliceCoord(3);
5094                            end                           
5095                            [X,Y]=px_XYZ(Calib,pos(:,1),pos(:,2),pos(:,3));
5096                        end
5097                        flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside
5098                    elseif isequal(ObjectData.Type,'ellipse')
5099                        if testphys
5100                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
5101                        end
5102                        RangeX=max(ObjectData.RangeX);
5103                        RangeY=max(ObjectData.RangeY);
5104                        X2Max=RangeX*RangeX;
5105                        Y2Max=RangeY*RangeY;
5106                        distX=(Xi-ObjectData.Coord(1,1));
5107                        distY=(Yi-ObjectData.Coord(1,2));
5108                        flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
5109                    elseif isequal(ObjectData.Type,'rectangle')
5110                        if testphys
5111                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
5112                        end
5113                        distX=abs(Xi-ObjectData.Coord(1,1));
5114                        distY=abs(Yi-ObjectData.Coord(1,2));
5115                        flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
5116                    end
5117                    if isequal(ObjectData.ProjMode,'mask_outside')
5118                        flagobj=~flagobj;
5119                    end
5120                    flag=flag & flagobj;
5121                end
5122            end
5123        end
5124%     end
5125    %mask name
5126    RootPath=get(handles.RootPath,'String');
5127    SubDir=get(handles.SubDir,'String');
5128    RootFile=get(handles.RootFile,'String');
5129    if ~isempty(RootFile)&&(isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
5130        RootFile(1)=[];
5131    end
5132    list=get(handles.masklevel,'String');
5133    masknumber=num2str(length(list));
5134    maskindex=get(handles.masklevel,'Value');
5135   % mask_name=fullfile_uvmat(RootPath,'',[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
5136    mask_name=fullfile_uvmat(RootPath,[SubDir '.mask'],'mask','.png','_1',maskindex);
5137    imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
5138    imflag=flipdim(imflag,1);
5139
5140    %display the mask
5141    hfigmask=figure;
5142    set(hfigmask,'Name','mask image')
5143    vec=linspace(0,1,256);%define a linear greyscale colormap
5144    map=[vec' vec' vec'];
5145    colormap(map)
5146    image(imflag);
5147    answer=msgbox_uvmat('INPUT_TXT','mask file name:', mask_name);
5148    if ~strcmp(answer,'Cancel')
5149        mask_dir=fileparts(answer);
5150        if ~exist(mask_dir,'dir')
5151            [xx,msg1]=mkdir(mask_dir);
5152            if ~strcmp(msg1,'')
5153                errormsg=['cannot create ' mask_dir ': ' msg1];%error message for directory creation
5154                return
5155            end
5156        end
5157        imwrite(imflag,answer,'BitDepth',8);
5158    end
5159    set(handles.ListObject,'Value',1)
5160end
5161
5162%------------------------------------------------------------------------
5163%-- open the GUI set_grid.fig to create grid
5164function MenuGrid_Callback(hObject, eventdata, handles)
5165%------------------------------------------------------------------------
5166%suppress the other options if grid is chosen
5167set(handles.edit_vect,'Value',0)
5168edit_vect_Callback(hObject, eventdata, handles)
5169% set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
5170set(handles.ListObject,'Value',1)     
5171
5172%prepare display of the set_grid GUI
5173[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
5174FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
5175UvData=get(handles.uvmat,'UserData');
5176% CoordList=get(handles.TransformName,'String');
5177% val=get(handles.TransformName,'Value');
5178set_grid(FileName,UvData.Field);% call the set_object interface
5179
5180
5181%------------------------------------------------------------------------
5182function MenuRuler_Callback(hObject, eventdata, handles)
5183%------------------------------------------------------------------------
5184set(handles.CheckZoom,'Value',0)
5185CheckZoom_Callback(handles.uvmat, [], handles)
5186set(handles.MenuRuler,'checked','on')
5187UvData=get(handles.uvmat,'UserData');
5188UvData.MouseAction='ruler';
5189set(handles.uvmat,'UserData',UvData);
5190
5191%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
5192% MenuRun Callbacks
5193%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
5194
5195%------------------------------------------------------------------------
5196% open the GUI 'series'
5197function MenuSeries_Callback(hObject, eventdata, handles)
5198%------------------------------------------------------------------------
5199[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
5200Param.FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];%first input file name
5201if isequal(get(handles.SubField,'Value'),1)
5202    [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
5203    FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
5204    if ~isequal(FileName_1,Param.FileName)
5205        Param.FileName_1=FileName_1;%second input file name if relevant
5206    end
5207end
5208Param.NomType=get(handles.NomType,'String');
5209Param.NomType_1=get(handles.NomType_1,'String');
5210Param.CheckFixPair=get(handles.CheckFixPair,'Value');
5211UvData=get(handles.uvmat,'UserData');
5212if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'Time')
5213    Param.Time=UvData.XmlData{1}.Time;
5214end
5215if isequal(get(handles.scan_i,'Value'),1)
5216    Param.incr_i=str2num(get(handles.num_IndexIncrement,'String'));
5217elseif isequal(get(handles.scan_j,'Value'),1)
5218    Param.incr_j=str2num(get(handles.num_IndexIncrement,'String'));
5219end
5220
5221%% transfer fields and coordinate names
5222Param.list_fields=get(handles.FieldName,'String');% list menu fields
5223FieldName=Param.list_fields{get(handles.FieldName,'Value')};
5224ind_image=find(strcmp('image',Param.list_fields));
5225if ~isempty(ind_image) && numel(Param.list_fields)>1
5226    Param.list_fields(ind_image)=[]; %suppress  'image' option
5227end
5228Param.index_fields=find(strcmp(FieldName,Param.list_fields));% selected string index
5229Param.list_fields_1=get(handles.FieldName_1,'String');% list menu fields
5230if ischar(Param.list_fields_1),Param.list_fields_1={Param.list_fields_1};end
5231FieldName_1=Param.list_fields_1{get(handles.FieldName_1,'Value')};
5232ind_image=find(strcmp('image',Param.list_fields_1));
5233if ~isempty(ind_image) && numel(Param.list_fields_1)>1
5234    Param.list_fields_1(ind_image)=[]; %suppress  'image' option
5235end
5236Param.index_fields_1=find(strcmp(FieldName_1,Param.list_fields_1));% selected string index
5237TransformList=get(handles.TransformName,'String');
5238Param.TransformName=TransformList{get(handles.TransformName,'Value')};
5239Param.Coord_x_str=get(handles.Coord_x,'String');
5240Param.Coord_x_val=get(handles.Coord_x,'Value');
5241Param.Coord_y_str=get(handles.Coord_y,'String');
5242Param.Coord_y_val=get(handles.Coord_y,'Value');
5243series(Param); %run the series interface
5244
5245%------------------------------------------------------------------------
5246% -- open the GUI civ.fig for PIV
5247function MenuPIV_Callback(hObject, eventdata, handles)
5248%------------------------------------------------------------------------
5249 [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
5250 FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
5251civ(FileName);% interface de civ(not in the uvmat file)
5252
5253% --------------------------------------------------------------------
5254function MenuHelp_Callback(hObject, eventdata, handles)
5255% --------------------------------------------------------------------
5256path_to_uvmat=which ('uvmat');% check the path of uvmat
5257pathelp=fileparts(path_to_uvmat);
5258helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
5259if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
5260else
5261    addpath (fullfile(pathelp,'uvmat_doc'))
5262    web(helpfile);
5263end
5264
5265% --- Executes on selection change in Coord_y.
5266function Coord_y_Callback(hObject, eventdata, handles)
5267
5268% --- Executes on selection change in Coord_x.
5269function Coord_x_Callback(hObject, eventdata, handles)
5270
5271
5272% --- Executes on button press in CheckColorBar.
5273function CheckColorBar_Callback(hObject, eventdata, handles)
5274
5275
5276
5277function TransformPath_Callback(hObject, eventdata, handles)
5278% hObject    handle to TransformPath (see GCBO)
5279% eventdata  reserved - to be defined in a future version of MATLAB
5280% handles    structure with handles and user data (see GUIDATA)
5281
5282% Hints: get(hObject,'String') returns contents of TransformPath as text
5283%        str2double(get(hObject,'String')) returns contents of TransformPath as a double
5284
5285
5286%TODO: use to modify fill_GUI
5287%'write_plot_param': update the plotting parameters on the uvmat or view_field interface after a plotting operation
5288function write_plot_param(handles,PlotParam)
5289%% coordinates
5290if isempty(PlotParam.Coordinates)
5291    set(handles.Coordinates,'Visible','off')
5292    set(handles.PlotAxes,'Visible','off')
5293    set(handles.text_display,'Visible','off')
5294    set(handles.TableDisplay,'Visible','on')
5295else
5296    set(handles.Coordinates,'Visible','on')
5297    set(handles.PlotAxes,'Visible','on')
5298    set(handles.text_display,'Visible','on')
5299    if isfield(handles,'TableDisplay')
5300    set(handles.TableDisplay,'Visible','off')
5301    end
5302    Coordinates=PlotParam.Coordinates;
5303    if isfield(Coordinates,'CheckFixAspectRatio')
5304        if Coordinates.CheckFixAspectRatio
5305            set(handles.CheckFixAspectRatio,'Value',1)
5306        else
5307            set(handles.CheckFixAspectRatio,'Value',0)
5308 
5309        end
5310    end
5311    if isfield(Coordinates,'AspectRatio')
5312        set(handles.num_AspectRatio,'String',num2str(Coordinates.AspectRatio))
5313    end
5314    if isfield(Coordinates,'MinX')
5315        set(handles.num_MinX,'String',num2str(Coordinates.MinX,4));
5316        set(handles.num_MaxX,'String',num2str(Coordinates.MaxX,4));
5317        set(handles.num_MinY,'String',num2str(Coordinates.MinY,4));
5318        set(handles.num_MaxY,'String',num2str(Coordinates.MaxY,4));
5319    else
5320        set(handles.num_MinX,'String','');
5321        set(handles.num_MaxX,'String','');
5322        set(handles.num_MinY,'String','');
5323        set(handles.num_MaxY,'String','');
5324    end
5325end
5326
5327%% scalar or image parameters
5328if isfield(PlotParam,'Scalar')
5329    set(handles.Scalar,'Visible','on')
5330    if isfield(PlotParam.Scalar,'MaxA')
5331        set(handles.num_MaxA,'String',num2str(PlotParam.Scalar.MaxA,3));
5332    end
5333    if isfield(PlotParam.Scalar,'MinA')
5334        set(handles.num_MinA,'String',num2str(PlotParam.Scalar.MinA,3));
5335    end   
5336    if isfield(PlotParam.Scalar,'IncrA')
5337        set(handles.num_IncrA,'String',num2str(PlotParam.Scalar.IncrA,3))
5338    end
5339    set(handles.CheckBW,'Value',PlotParam.Scalar.CheckBW)
5340    if isfield(PlotParam.Scalar,'Opacity')&&isfield(handles,'num_Opacity')
5341        set(handles.num_Opacity,'String',num2str(PlotParam.Scalar.Opacity))
5342    end
5343else
5344    set(handles.Scalar,'Visible','off')
5345end
5346
5347%% parameter for vector field
5348if isfield(PlotParam,'Vectors')
5349    set(handles.Vectors,'Visible','on')
5350    if isfield(PlotParam.Vectors,'VecScale')
5351        set(handles.num_VecScale,'String',num2str(PlotParam.Vectors.VecScale,3))
5352    end
5353    if isfield(PlotParam.Vectors,'MinC')&& isfield(PlotParam.Vectors,'MaxC')
5354        MinC=PlotParam.Vectors.MinC;
5355        MaxC=PlotParam.Vectors.MaxC;
5356        set(handles.num_MinVec,'String', num2str(MinC,3));
5357        set(handles.num_MaxVec,'String',num2str(MaxC,3));
5358        list=get(handles.ColorCode,'String');
5359        ichoice=get(handles.ColorCode,'Value');
5360        color_option=list{ichoice};
5361        test3color=strcmp(color_option,'rgb')||strcmp(color_option,'bgr');
5362        if test3color% need to update color thresholds
5363            set(handles.num_ColCode1,'Visible','on')
5364            set(handles.num_ColCode2,'Visible','on')
5365            set(handles.Slider1,'Visible','on')
5366            set(handles.Slider2,'Visible','on')
5367            %ColCode1=MinC+(MaxC-MinC)*PlotParam.Vectors.ColCode1;
5368            %ColCode2=MinC+(MaxC-MinC)*PlotParam.Vectors.ColCode2;
5369%             ColCode1=MinC+(MaxC-MinC)*PlotParam.Vectors.ColCode1;
5370            %ColCode2=MinC+(MaxC-MinC)*PlotParam.Vectors.ColCode2;
5371            set(handles.num_ColCode1,'String',num2str(PlotParam.Vectors.ColCode1,3))
5372            set(handles.num_ColCode2,'String',num2str(PlotParam.Vectors.ColCode2,3))
5373            set(handles.Slider1,'Value',(PlotParam.Vectors.ColCode1-MinC)/(MaxC-MinC))
5374            set(handles.Slider2,'Value',(PlotParam.Vectors.ColCode2-MinC)/(MaxC-MinC))
5375        else
5376            set(handles.num_ColCode1,'Visible','off')
5377            set(handles.num_ColCode2,'Visible','off')
5378            set(handles.Slider1,'Visible','off')
5379            set(handles.Slider2,'Visible','off')
5380        end
5381    end
5382else
5383    set(handles.Vectors,'Visible','off')
5384    if isfield(handles,'edit_vect')
5385        set(handles.edit_vect,'Visible','off')
5386        set(handles.record,'Visible','off')
5387    end
5388end
5389
5390
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