source: trunk/src/uvmat.m @ 713

Last change on this file since 713 was 713, checked in by sommeria, 11 years ago

improving figure extracting and keyboard callback

File size: 233.4 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 REFRESH_Callback) %%%%%%%%%%%%%%%%%%%%:
49%
50%
51% 1) Input filenames are determined by MenuBrowse (first field), MenuBrowseCampaign
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 CheckEditObject
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 CheckEditObject
114%            .CurrentLine: currently drawn menuline (A REVOIR)
115%            .CurrentObject: handle of the currently drawn CheckEditObject
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])
192UvData.OpenParam.PosColorbar=[0.80 0.02 0.018 0.445];
193% UvData.OpenParam.PosGeometryCalib=[0.95 -0.03 0.28 1 ];%position for geometry_calib
194AxeData.LimEditBox=1; %initialise AxeData
195set(handles.PlotAxes,'UserData',AxeData)
196% position of table Coord_y
197set(handles.Coord_y,'Unit','pixel')
198Pos=get(handles.Coord_y,'Position');
199set(handles.Coord_y,'Unit','normalized')
200set(handles.Coord_y,'ColumnWidth',{Pos(3)})
201set(handles.Coord_y,'ColumnFormat',{'char'})
202set(handles.Coord_y,'ColumnEditable',false)
203set(handles.Coord_y,'ColumnName',{''})
204
205%% set functions for the mouse and keyboard
206set(hObject,'WindowKeyPressFcn',{'keyboard_callback',handles})%set keyboard action function
207set(hObject,'WindowButtonMotionFcn',{'mouse_motion',handles})%set mouse action functio
208set(hObject,'WindowButtonDownFcn',{'mouse_down'})%set mouse click action function
209set(hObject,'WindowButtonUpFcn',{'mouse_up',handles})
210set(hObject,'DeleteFcn',{@closefcn})%
211set(hObject,'ResizeFcn',{@ResizeFcn,handles})%
212% set(handles.RootPath,'ButtonDownFcn',{'@mouse_down_control'})%set mouse click action function
213
214%% initialisation
215set(handles.FieldName,'Value',1)
216set(handles.FieldName,'string',{''})
217UvData.ProjObject={[]};
218
219%% TRANSFORM menu: builtin fcts
220transform_menu={'';'sub_field';'phys';'phys_polar'};
221UvData.OpenParam.NbBuiltin=numel(transform_menu); %number of functions
222transform_path=fullfile(path_uvmat,'transform_field');
223path_list=cell(UvData.OpenParam.NbBuiltin,1);
224path_list{1}='';
225for ilist=2:UvData.OpenParam.NbBuiltin
226path_list{ilist}=transform_path; % set transform_path to the path_list
227end
228
229%% load the list of previously browsed files in menus Open, Open_1 and TransformName
230dir_perso=prefdir; % path to the directory .matlab containing the personal data of the current user
231profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmat_perso.mat' in .matlab
232if exist(profil_perso,'file')% if the file exists
233    h=load (profil_perso); % open the personal file
234    if isfield(h,'MenuFile')% load the saved menu of previously opened files
235        for ifile=1:min(length(h.MenuFile),5)
236            set(handles.(['MenuFile_' num2str(ifile)]),'Label',h.MenuFile{ifile});
237        end
238    end
239    if isfield(h,'MenuCampaign')% load the saved menu of previously opened campaigns
240        for ifile=1:min(length(h.MenuCampaign),5)
241            set(handles.(['MenuCampaign_' num2str(ifile)]),'Label',h.MenuCampaign{ifile});
242        end
243    end
244    if isfield(h,'RootPath')
245        set(handles.RootPath,'UserData',h.RootPath); %store the previous campaign in the UserData of RootPath
246    end
247    if isfield(h,'transform_fct') && iscell(h.transform_fct) % load the menu of transform fct set by user
248        for ilist=1:length(h.transform_fct);
249            if exist(h.transform_fct{ilist},'file')
250                [path,file]=fileparts(h.transform_fct{ilist});
251                transform_menu=[transform_menu; {file}];
252                path_list=[path_list; {path}];
253            end
254        end
255    end
256end
257transform_menu=[transform_menu;{'more...'}];%append the option more.. to the menu
258set(handles.TransformName,'String',transform_menu)% display the menu of transform fcts
259set(handles.TransformName,'UserData',path_list)% store the corresponding list of path in UserData of uicontrol transform_fct
260set(handles.TransformPath,'String','')
261set(handles.TransformPath,'UserData',[])
262
263%% case of an input argument for uvmat
264testinputfield=0;
265inputfile=[];
266Field=[];
267if exist('input','var')
268    if ishandle(handles.UVMAT_title)
269        delete(handles.UVMAT_title)
270    end   
271    if isstruct(input)
272        if isfield(input,'InputFile')
273            inputfile=input.InputFile;
274        end
275        if isfield(input,'TimeIndex')
276            set(handles.i1,num2str(input.TimeIndex))
277        end
278        if isfield(input,'FieldsString')
279            UvData.FieldsString=input.FieldsString;
280        end
281    elseif ischar(input)% file name introduced as input
282           inputfile=input;
283    elseif isnumeric(input)%simple matrix introduced as input
284        sizinput=size(input);
285        if sizinput(1)<=1 || sizinput(2)<=1
286            msgbox_uvmat('ERROR','bad input for uvmat: file name, structure or numerical matrix accepted')
287            return
288        end
289        UvData.Field.ListVarName={'A','coord_y','coord_x'};
290        UvData.Field.VarDimName={{'coord_y','coord_x'},'cord_y','coord_x'};
291        UvData.Field.A=input;
292        UvData.Field.coord_x=[0.5 size(input,2)-0.5];
293        UvData.Field.coord_y=[size(input,1)-0.5 0.5];
294        testinputfield=1;
295    end
296else
297    %% check the path and date of modification of all functions in uvmat
298    path_to_uvmat=which ('uvmat');% check the path detected for source file uvmat
299    [infomsg,date_str,svn_info]=check_files;%check the path of the functions called by uvmat.m   
300    date_str=['last modification: ' date_str];
301    if ishandle(handles.UVMAT_title)
302        set(handles.UVMAT_title,'String',...
303            [{'Copyright  LEGI UMR 5519 /CNRS-UJF-Grenoble INP, 2010'};...
304            {'GNU General Public License'};...
305            {path_to_uvmat};...
306            {date_str};...
307            infomsg]);
308    end
309end
310set(handles.uvmat,'UserData',UvData)
311if ~isempty(inputfile)
312    %%%%% display the input field %%%%%%%
313    display_file_name(handles,inputfile)
314    %%%%%%%
315end
316
317set_vec_col_bar(handles) %update the display of color code for vectors
318
319%------------------------------------------------------------------------
320% --- Outputs from this function are returned to the command menuline.
321function varargout = uvmat_OutputFcn(hObject, eventdata, handles)
322%------------------------------------------------------------------------   
323varargout{1} = handles.output;% the only output argument is the handle to the GUI figure
324
325%------------------------------------------------------------------------
326% --- executed when closing uvmat: delete or desactivate the associated figures if exist
327function closefcn(gcbo,eventdata)
328%------------------------------------------------------------------------
329% delete GUI 'view_field' if detected
330hh=findobj(allchild(0),'tag','view_field');
331if ~isempty(hh)
332    delete(hh)
333end
334% delete GUI 'geometry_calib' if detected
335hh=findobj(allchild(0),'tag','geometry_calib');
336if ~isempty(hh)
337    delete(hh)
338end
339% desable set_object editing action if detected
340hh=findobj(allchild(0),'tag','set_object');
341if ~isempty(hh)
342    hhh=findobj(hh,'tag','PLOT');
343    set(hhh,'enable','off')
344end
345%delete the bowser if detected
346hh=findobj(allchild(0),'tag','browser');
347if ~isempty(hh)
348    delete(hh)
349end
350
351%------------------------------------------------------------------------
352%--- activated when resizing the GUI view_field
353 function ResizeFcn(gcbo,eventdata,handles)
354%------------------------------------------------------------------------     
355set(handles.uvmat,'Units','pixels')
356size_fig=get(handles.uvmat,'Position');
357ColumnWidth=max(150,0.18*size_fig(3));
358ColumnWidth=min(ColumnWidth,250); % width of the right side display column, between 150 and 250, depending on the fig width
359
360%% position of panel InputFile
361set(handles.InputFile,'Units','pixels')
362pos_InputFile=get(handles.InputFile,'Position');% [lower x lower y width height] for text_display
363pos_InputFile(1)=0;
364pos_InputFile(2)=size_fig(4)-pos_InputFile(4);             % set frame InputFile to the top of the fig
365pos_InputFile(3)=size_fig(3);
366set(handles.InputFile,'Position',pos_InputFile);% [lower x lower y width height] for text_display
367
368%% reset position of text_display and TableDisplay
369% if strcmp(get(handles.TableDisplay,'Visible'),'off')
370    set(handles.text_display,'Units','pixels')
371    pos_1=get(handles.text_display,'Position');% [lower x lower y width height] for text_display
372        pos_1(3)=1.2*ColumnWidth;
373    pos_1(1)=size_fig(3)-pos_1(3);             % set text display to the right of the fig
374    pos_1(2)=size_fig(4)-pos_InputFile(4)-pos_1(4);             % set text display to the top of the fig
375    set(handles.text_display,'Position',pos_1)
376    % reset position of TableDisplay
377% else
378%     set(handles.TableDisplay,'Units','pixels')
379%     pos_1=get(handles.TableDisplay,'Position');
380%     pos_1(3)=1.2*ColumnWidth;
381%     pos_1(1)=size_fig(3)-pos_1(3);
382%     pos_1(2)=size_fig(4)-pos_InputFile(4)-pos_1(4);
383    set(handles.TableDisplay,'Position',pos_1)
384    % reset position of CheckTable
385    set(handles.CheckTable,'Unit','pixels')
386pos_CheckTable=get(handles.CheckTable,'Position');% [lower x lower y width height] for CheckHold
387pos_CheckTable(1)=pos_1(1)-pos_CheckTable(3);       % set 'CheckHold' to the right of the fig
388pos_CheckTable(2)=pos_InputFile(2)-pos_CheckTable(4);          % set 'CheckHold' to the lower edge of text display
389set(handles.CheckTable,'Position',pos_CheckTable)
390% end
391
392%% reset position of CheckHold
393% pos_CheckHold=get(handles.CheckHold,'Position');% [lower x lower y width height] for CheckHold
394% pos_CheckHold(1)=size_fig(3)-pos_CheckHold(3);       % set 'CheckHold' to the right of the fig
395% pos_CheckHold(2)=pos_1(2)-pos_CheckHold(4);          % set 'CheckHold' to the lower edge of text display
396% set(handles.CheckHold,'Position',pos_CheckHold)
397
398%% reset position of Coordinates
399set(handles.Coordinates,'Units','pixels')
400pos_2=get(handles.Coordinates,'Position');% [lower x lower y width height] for frame 'Coordinates'
401pos_2(3)=ColumnWidth;
402pos_2(1)=size_fig(3)-pos_2(3);       % set 'Coordinates' to the right of the fig
403pos_2(2)=pos_1(2)-pos_2(4);          % set 'Coordinates' to the lower edge of text display, allowing a margin for CheckHold
404set(handles.Coordinates,'Position',pos_2)
405
406%% reset position of  Scalar
407set(handles.Scalar,'Units','pixels')
408pos_3=get(handles.Scalar,'Position'); % [lower x lower y width height] for frame 'Scalar'
409pos_3(3)=ColumnWidth;
410pos_3(1)=size_fig(3)-pos_3(3);         % set 'Scalar' to the right of the fig
411if strcmp(get(handles.Scalar,'Visible'),'on')
412    pos_3(2)=pos_2(2)-pos_3(4); % set 'Scalar' to the lower edge of frame 'Coordinates' if visible
413else
414    pos_3(2)=pos_2(2);% set 'Scalar' to the lower edge of frame 'text display' if  unvisible
415end
416set(handles.Scalar,'Position',pos_3)
417
418%% reset position of  Vectors
419set(handles.Vectors,'Units','pixels')
420pos_4=get(handles.Vectors,'Position');
421pos_4(3)=ColumnWidth;
422pos_4(1)=size_fig(3)-pos_4(3);
423if strcmp(get(handles.Vectors,'visible'),'on')
424    pos_4(2)=pos_3(2)-pos_4(4);
425else
426    pos_4(2)=pos_3(2);
427end
428set(handles.Vectors,'Position',pos_4)
429
430%% reset position and scale of axis
431pos(1)=0.2*size_fig(3)+35;
432pos(2)=35;
433pos(3)=0.77*size_fig(3)-1.2*ColumnWidth;
434pos(4)=size_fig(4)-60;
435set(handles.PlotAxes,'Units','pixels')
436set(handles.PlotAxes,'Position',pos)
437set(handles.PlotAxes,'Units','normalized')
438
439
440%------------------------------------------------------------------------
441%------------------------------------------------------------------------
442%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
443% automatically sets the global properties when the rootfile name is introduced
444% then activate the view-field action if selected
445% it is activated either by clicking on the RootPath window or by the
446% browser
447%------------------------------------------------------------------------
448%------------------------------------------------------------------------
449% --- Executes on the menu Open/Browse...
450% search the files, recognize their type according to their name and fill the rootfile input windows
451function MenuBrowse_Callback(hObject, eventdata, handles)
452[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
453oldfile=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
454if isempty(oldfile) %loads the previously stored file name and set it as default in the file_input box
455    oldfile=get(handles.RootPath,'UserData');
456end
457fileinput=uigetfile_uvmat('pick an input file',oldfile);
458hh=dir(fileinput);
459if numel(hh)>1
460    msgbox_uvmat('ERROR','invalid input, probably a broken link');
461else
462
463    %% display the selected field and related information
464    if ~isempty(fileinput)
465        set(handles.SubField,'Value',0)
466        desable_subfield(handles)
467        display_file_name(handles,fileinput)
468    end
469end
470
471% -----------------------------------------------------------------------
472% --- Open again the file whose name has been recorded in MenuFile_1
473function MenuFile_Callback(hObject, eventdata, handles)
474%------------------------------------------------------------------------
475fileinput=get(hObject,'Label');
476    set(handles.SubField,'Value',0)
477    desable_subfield(handles)
478display_file_name( handles,fileinput)
479
480
481% -----------------------------------------------------------------------
482% --- Executes on the menu Open/Browse campaign...
483% --- search the file inside a campaign, using the GUI browse_data
484% -----------------------------------------------------------------------
485function MenuBrowseCampaign_Callback(hObject, eventdata, handles)
486set(handles.MenuOpenCampaign,'ForegroundColor',[1 1 0])
487drawnow
488RootPath=get(handles.RootPath,'String');
489if isempty(RootPath)
490    RootPath=get(handles.RootPath,'UserData');%use Rootpath recored from the personal file at uvmat opening
491end
492CampaignPath=fileparts(fileparts(RootPath));
493DirFull=uigetfile_uvmat('define this path as the Campaign folder:',CampaignPath,'uigetdir');
494%DirFull = uigetdir(CampaignPath,'Select a Campaign dir, then press OK');
495if isempty(DirFull)
496    return
497end
498OutPut=browse_data(DirFull);% open the GUI browse_data to get select a campaign dir, experiment and device
499if ~isfield(OutPut,'Campaign')
500    return
501end
502DirName=fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.DataSeries{1});
503ListStruct=dir(DirName); %list files and the dir DataSeries
504% select the first appropriate file in the dir
505FileName='';
506for ilist=1:numel(ListStruct)
507    if ~isequal(ListStruct(ilist).isdir,1)%look for files, not dir
508        FileName=ListStruct(ilist).name;
509        FileType=get_file_type(fullfile(DirName,FileName));
510        switch FileType
511            case {'image','multimage','civx','civdata','netcdf'}
512                break
513        end
514    end
515end
516if isempty(FileName)
517    msgbox_uvmat('ERROR',['no appropriate input file in the DataSeries folder ' fullfile(DirName)])
518    return
519end
520
521%% update the list of campaigns in the menubar
522MenuCampaign=[{get(handles.MenuCampaign_1,'Label')};{get(handles.MenuCampaign_2,'Label')};...
523    {get(handles.MenuCampaign_3,'Label')};{get(handles.MenuCampaign_4,'Label')};{get(handles.MenuCampaign_5,'Label')}];
524check_dir=isempty(find(strcmp(DirFull,MenuCampaign)));
525if check_dir %insert the new campaign in the list if it is not found
526    MenuCampaign(end)=[]; %suppress the last item
527    MenuCampaign=[{DirFull};MenuCampaign];%insert the new campaign
528    for ilist=1:numel(MenuCampaign)
529        set(handles.(['MenuCampaign_' num2str(ilist)]),'Label',MenuCampaign{ilist})
530    end
531    % save the list for future opening:
532    dir_perso=prefdir;
533    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
534    if exist(profil_perso,'file')
535        save (profil_perso,'MenuCampaign','RootPath','-append'); %store the file names for future opening of uvmat
536    else
537        save (profil_perso,'MenuCampaign','RootPath','-V6'); %store the file names for future opening of uvmat
538    end
539end
540
541%% display the selected field and related information
542display_file_name( handles,fullfile(DirName,FileName))
543
544set(handles.MenuOpenCampaign,'ForegroundColor',[0 0 0])
545
546% -----------------------------------------------------------------------
547% --- Open again as second field the file whose name has been recorded in MenuFile_1
548% -----------------------------------------------------------------------
549function MenuCampaign_Callback(hObject, eventdata, handles)
550
551set(handles.MenuOpenCampaign,'ForegroundColor',[1 1 0])
552OutPut=browse_data(get(hObject,'Label'));% open the GUI browse_data to get select a campaign dir, experiment and device
553if ~isfield(OutPut,'Campaign')
554    return
555end
556DirName=fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.DataSeries{1});
557hdir=dir(DirName); %list files and dirs
558FileName='';
559for ilist=1:numel(hdir)
560    if ~isequal(hdir(ilist).isdir,1)%look for files, not dir
561        FileName=hdir(ilist).name;
562        FileType=get_file_type(fullfile(DirName,FileName));
563        switch FileType
564            case {'image','multimage','civx','civdata','netcdf'}
565            break
566        end
567    end
568end
569if isempty(FileName)
570    msgbox_uvmat('ERROR','no valid input file in the selected directory')
571else
572display_file_name(handles,fullfile(DirName,FileName))
573end
574set(handles.MenuOpenCampaign,'ForegroundColor',[0 0 0])
575
576%------------------------------------------------------------------------
577% --- Called by action in FileIndex edit box
578function FileIndex_Callback(hObject, eventdata, handles)
579%------------------------------------------------------------------------
580[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
581set(handles.i1,'String',num2str(i1));
582set(handles.i2,'String',num2str(i2));
583set(handles.j1,'String',num2str(j1));
584set(handles.j2,'String',num2str(j2));
585
586
587%------------------------------------------------------------------------
588% --- Called by action in NomType edit box
589function NomType_Callback(hObject, eventdata, handles)
590%------------------------------------------------------------------------
591i1=str2num(get(handles.i1,'String'));
592i2=str2num(get(handles.i2,'String'));
593j1=str2num(get(handles.j1,'String'));
594j2=str2num(get(handles.j2,'String'));
595FileIndex=fullfile_uvmat('','','','',get(handles.NomType,'String'),i1,i2,j1,j2);
596set(handles.FileIndex,'String',FileIndex)
597% inputfilerefresh the current settings and inputfilerefresh the field view
598RootPath_Callback(hObject,eventdata,handles)
599
600%------------------------------------------------------------------------
601% --- Called by action in NomType edit box
602function NomType_1_Callback(hObject, eventdata, handles)
603%------------------------------------------------------------------------
604i1=str2num(get(handles.i1,'String'));
605i2=str2num(get(handles.i2,'String'));
606j1=str2num(get(handles.j1,'String'));
607j2=str2num(get(handles.j2,'String'));
608FileIndex=fullfile_uvmat('','','','',get(handles.NomType_1,'String'),i1,i2,j1,j2);
609set(handles.FileIndex_1,'String',FileIndex)
610% inputfilerefresh the current settings and inputfilerefresh the field view
611RootPath_1_Callback(hObject,eventdata,handles)
612
613%------------------------------------------------------------------------
614% --- Executes on button press in InputFileREFRESH.
615function InputFileREFRESH_Callback(hObject, eventdata, handles)
616%------------------------------------------------------------------------   
617set(handles.InputFileREFRESH,'BackgroundColor',[1 1 0])% set button color to yellow to indicate that refresh is under action
618% read the current input file name:
619[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
620% if ~exist(fullfile(RootPath,SubDir),'dir')
621%     msgbox_uvmat('ERROR',['directory ' fullfile(RootPath,SubDir) ' does not exist'])
622%     return
623% end
624% detect the file type, get the movie object if relevant, and look for the corresponding file series:
625[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,FileInfo,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
626% initiate the input file series and inputfilerefresh the current field view:
627errormsg=update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,1);
628% inputfilerefresh the second series if selected
629if get(handles.SubField,'Value')
630    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
631    if ~exist(fullfile(RootPath,SubDir),'dir')
632        msgbox_uvmat('ERROR',['directory ' fullfile(RootPath,SubDir) ' does not exist'])
633        return
634    end
635    % detect the file type, get the movie object if relevant, and look for the corresponding file series:
636    [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
637    % initiate the input file series and inputfilerefresh the current field view:
638    errormsg=update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,2);
639end
640
641if isempty(errormsg)
642set(handles.InputFileREFRESH,'BackgroundColor',[1 0 0])% set button color to red to indicate that refresh has been updated
643else
644    set(handles.InputFileREFRESH,'BackgroundColor',[1 0 1])% keep button color magenta, input not succesfull
645end
646
647%------------------------------------------------------------------------
648% --- Fills the edit boxes RootPath, RootFile,NomType...from an input file name 'fileinput'
649function display_file_name(handles,fileinput,index)
650%------------------------------------------------------------------------
651%% look for the input file existence
652if ~exist(fileinput,'file')
653    msgbox_uvmat('ERROR',['input file ' fileinput  ' does not exist'])
654    return
655end
656
657%% define the relevant handles for the first field series (index=1) or the second file series (index=2)
658if ~exist('index','var')
659    index=1;
660end
661if index==1
662    handles_RootPath=handles.RootPath;
663    handles_SubDir=handles.SubDir;
664    handles_RootFile=handles.RootFile;
665    handles_FileIndex=handles.FileIndex;
666    handles_NomType=handles.NomType;
667    handles_FileExt=handles.FileExt;
668elseif index==2
669    handles_RootPath=handles.RootPath_1;
670    handles_SubDir=handles.SubDir_1;
671    handles_RootFile=handles.RootFile_1;
672    handles_FileIndex=handles.FileIndex_1;
673    handles_NomType=handles.NomType_1;
674    handles_FileExt=handles.FileExt_1;
675    set(handles.RootPath_1,'Visible','on')
676    set(handles.RootFile_1,'Visible','on')
677    set(handles.SubDir_1,'Visible','on');
678    set(handles.FileIndex_1,'Visible','on');
679    set(handles.FileExt_1,'Visible','on');
680    set(handles.NomType_1,'Visible','on');
681    set(handles.TimeName_1,'Visible','on')
682    set(handles.TimeValue_1,'Visible','on')
683end
684set(handles.InputFileREFRESH,'BackgroundColor',[1 1 0])% paint REFRESH button to yellow to visualise root file input
685set(handles.uvmat,'Pointer','watch') % set the mouse pointer to 'watch'
686drawnow
687
688%% detect root name, nomenclature and indices in the input file name:
689[FilePath,FileName,FileExt]=fileparts(fileinput);
690% detect the file type, get the movie object if relevant, and look for the corresponding file series:
691% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
692[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]);
693
694if strcmp(FileType,'txt')
695    try
696        edit(fileinput)
697    catch ME
698        msgbox_uvmat('ERROR','invalid intput file')
699    end
700    return
701elseif strcmp(FileType,'xml')
702    editxml(fileinput)
703     return
704elseif strcmp(FileType,'figure')
705    open(fileinput)
706     return
707end
708
709%% open the file or fill the GUI uvmat according to the detected file type
710switch FileType
711    case ''
712        msgbox_uvmat('ERROR','invalid input file type')
713    case 'txt'
714        edit(fileinput)
715    case 'figure'                           %display matlab figure
716        hfig=open(fileinput);
717        set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
718        set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
719        set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
720    case 'xml'                % edit xml files
721        t=xmltree(fileinput);
722        % the xml file marks a project or project link, open datatree_browser
723        if strcmp(get(t,1,'name'),'Project')&& exist(regexprep(fileinput,'.xml$',''),'dir')
724            datatree_browser(fileinput)
725        else % other xml file, open the xml editor
726            editxml(fileinput);
727        end
728    case 'xls'% Excel file opended by editxml
729        editxml(fileinput);
730    otherwise
731        set(handles_RootPath,'String',RootPath);
732        rootname=fullfile(RootPath,SubDir,RootFile);
733        set(handles_SubDir,'String',['/' SubDir]);
734        set(handles_RootFile,'String',['/' RootFile]); %display the separator
735        indices=fileinput(length(rootname)+1:end);
736        indices(end-length(FileExt)+1:end)=[]; %remove extension
737        set(handles_FileIndex,'String',indices);
738        set(handles_NomType,'String',NomType);
739        set(handles_FileExt,'String',FileExt);
740        if index==1
741            % fill file index counters if the first file series is opened
742            set(handles.i1,'String',num2str(i1));
743            set(handles.i2,'String',num2str(i2));
744            set(handles.j1,'String',num2stra(j1,NomType));
745            set(handles.j2,'String',num2stra(j2,NomType));
746        else %read the current field index to synchronise with the first series
747            i1_s=str2num(get(handles.i1,'String'));
748            i2_0=str2num(get(handles.i2,'String'));
749            if ~isempty(i2_0)
750                i2_s=i2_0;
751            else
752               i2_s=i2;
753            end
754            j1_0=stra2num(get(handles.j1,'String'));
755            if ~isempty(j1_0)
756                j1_s=j1_0;
757            else
758                j1_s=j1;
759            end
760            j2_0=stra2num(get(handles.j2,'String'));
761            if ~isempty(j2_0)
762                j2_s=j2_0;
763            else
764                j2_s=j2;
765            end
766        end
767       
768        % synchronise indices of the second  input file if it exists
769        if get(handles.SubField,'Value')==1% if the subfield button is activated, update the field numbers
770            Input=read_GUI(handles.InputFile);
771            if ~isfield(Input,'RootPath_1')||strcmp(Input.RootPath_1,'"')
772                Input.RootPath_1=Input.RootPath;
773            end
774            if ~isfield(Input,'SubDir_1')||strcmp(Input.SubDir_1,'"')
775                Input.SubDir_1=Input.SubDir;
776            end
777            if ~isfield(Input,'RootFile_1')||strcmp(Input.RootFile_1,'"')
778                Input.RootFile_1=Input.RootFile;
779            end
780            if ~isfield(Input,'FileExt_1')||strcmp(Input.FileExt_1,'"')
781                Input.FileExt_1=Input.FileExt;
782            end
783            if ~isfield(Input,'NomType_1')||strcmp(Input.NomType_1,'"')
784                Input.NomType_1=Input.NomType;
785            end
786            %updtate the indices of the second field series to correspond to the newly opened one
787            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);
788            if exist(FileName_1,'file')
789                FileIndex_1=fullfile_uvmat('','','','',Input.NomType_1,i1_s,i2_s,j1_s,j2_s);
790            else
791                FileIndex_1=fullfile_uvmat('','','','',Input.NomType_1,i1,i2,j1,j2);
792                msgbox_uvmat('WARNING','unable to synchronise the indices of the two series')
793            end
794            set(handles.FileIndex_1,'String',FileIndex_1)
795        end
796       
797        %enable other menus
798        set(handles.MenuOpenCampaign,'Enable','on')
799        set(handles.MenuExport,'Enable','on')
800        set(handles.MenuExportFigure,'Enable','on')
801        set(handles.MenuExportMovie,'Enable','on')
802        set(handles.MenuTools,'Enable','on')
803
804        % initiate input file series and inputfilerefresh the current field view:     
805        update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,index);
806
807end
808
809%% update list of recent files in the menubar and save it for future opening
810MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
811    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
812str_find=strcmp(fileinput,MenuFile);
813if isempty(find(str_find,1))
814    MenuFile=[{fileinput};MenuFile];%insert the current file if not already in the list
815end
816for ifile=1:min(length(MenuFile),5)
817    set(handles.(['MenuFile_' num2str(ifile)]),'Label',MenuFile{ifile});
818    %set(handles.(['MenuFile_' num2str(ifile) '_1']),'Label',MenuFile{ifile});
819end
820dir_perso=prefdir;
821profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
822if exist(profil_perso,'file')
823    save (profil_perso,'MenuFile','RootPath','-append'); %store the file names for future opening of uvmat
824else
825    save (profil_perso,'MenuFile','RootPath','-V6'); %store the file names for future opening of uvmat
826end
827
828set(handles.InputFileREFRESH,'BackgroundColor',[1 0 0])% paint back button to red to indicate update is finished
829set(handles.uvmat,'Pointer','arrow')% set back the mouse pointer to arrow
830
831
832%------------------------------------------------------------------------
833% --- Update information about a new field series (indices to scan, timing,
834%     calibration from an xml file, then inputfilerefresh current plots
835function errormsg=update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,VideoObject,index)
836%------------------------------------------------------------------------
837errormsg=''; %default error msg
838%% define the relevant handles depending on the index (1=first file series, 2= second file series)
839if ~exist('index','var')
840    index=1;
841end
842if index==1
843    handles_Fields=handles.FieldName;
844elseif index==2
845    handles_Fields=handles.FieldName_1;
846end
847
848set(handles.FieldName,'UserData',[])% reinialize data from uvmat opening
849UvData=get(handles.uvmat,'UserData');%huvmat=handles of the uvmat interface
850UvData.NewSeries=1; %flag for REFRESH: begin a new series
851UvData.FileName_1='';% name of the current second field (used to detect a  constant field during file scanning)
852UvData.FileType{index}=FileType;
853UvData.i1_series{index}=i1_series;
854UvData.i2_series{index}=i2_series;
855UvData.j1_series{index}=j1_series;
856UvData.j2_series{index}=j2_series;
857set(handles.FixVelType,'Value',0); %desactivate fixed veltype
858if index==1
859    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
860else
861    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
862end
863FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
864FileBase=fullfile(RootPath,RootFile);
865if ~exist(FileName,'file')
866    errormsg=['input file ' FileName ' not found'];
867   msgbox_uvmat('ERROR',errormsg);   
868    return
869end
870
871%% read timing and total frame number from the current file (movie files) !! may be overrid by xml file
872TimeUnit='';%default
873TimeName='';%default
874XmlData.Time=[];%default
875imainfo=[];
876ColorType='falsecolor'; %default
877UvData.MovieObject{index}=VideoObject;
878if ~isempty(VideoObject)% case of video data
879    imainfo=get(VideoObject);
880    TimeUnit='s';
881    if isempty(j1_series); %frame index along i
882        XmlData.Time=zeros(imainfo.NumberOfFrames+1,2);
883        XmlData.Time(:,2)=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)';
884    else
885        XmlData.Time=[0;ones(size(i1_series,3)-1,1)]*(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate);
886    end
887    %set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FrameRate) 'ms']);%display the elementary time interval in millisec
888    TimeName='video';
889    ColorType='truecolor';
890elseif ~isempty(FileExt(2:end))&&(~isempty(imformats(FileExt(2:end))) || isequal(FileExt,'.vol'))%&& isequal(NomType,'*')% multi-frame image
891    if ~isequal(SubDir,'')
892        imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]);
893    else
894        imainfo=imfinfo([FileBase FileIndices FileExt]);
895    end
896    ColorType=imainfo.ColorType;%='truecolor' for color images
897end
898if isfield(imainfo,'Width') && isfield(imainfo,'Height')
899    if length(imainfo)>1
900        set(handles.num_Npx,'String',num2str(imainfo(1).Width));%fills nbre of pixels x box
901        set(handles.num_Npy,'String',num2str(imainfo(1).Height));%fills nbre of pixels x box
902    else
903        set(handles.num_Npx,'String',num2str(imainfo.Width));%fills nbre of pixels x box
904        set(handles.num_Npy,'String',num2str(imainfo.Height));%fills nbre of pixels x box
905    end
906else
907    set(handles.num_Npx,'String','');%fills nbre of pixels x box
908    set(handles.num_Npy,'String','');%fills nbre of pixels x box
909end
910set(handles.CheckBW,'Value',strcmp(ColorType,'grayscale'))% select handles.CheckBW if grayscale image
911
912%% read parameters (time, geometric calibration..) from a documentation file (.xml advised)
913XmlData.GeometryCalib=[];%default
914XmlFileName=find_imadoc(RootPath,SubDir,RootFile,FileExt);
915[tild,tild,DocExt]=fileparts(XmlFileName);
916warntext='';%default warning message
917NbSlice=1;%default
918ImaDoc_str='';
919set(handles.InputFileREFRESH,'BackgroundColor',[1 1 0])
920if ~isempty(XmlFileName)
921    set(handles.view_xml,'Visible','on')
922    set(handles.view_xml,'BackgroundColor',[1 1 0])% paint  to yellow color to indicate reading of the xml file
923    set(handles.view_xml,'String','view .xml')
924    drawnow
925    [XmlDataRead,warntext]=imadoc2struct(XmlFileName);
926    if ~isempty(warntext)
927        msgbox_uvmat('WARNING',warntext)
928    end
929    if ~isempty(XmlDataRead)
930        ImaDoc_str=['view ' DocExt];  % DocExt= '.xml' or .civ (obsolete case)
931        %XmlData=XmlDataRead;
932        if isfield(XmlDataRead,'TimeUnit')&& ~isempty(XmlDataRead.TimeUnit)
933            TimeUnit=XmlDataRead.TimeUnit;
934        end
935        if isfield(XmlDataRead,'Time')&& ~isempty(XmlDataRead.Time)
936            XmlData.Time=XmlDataRead.Time;
937        end
938        set(handles.view_xml,'BackgroundColor',[1 1 1])% paint back to white
939        drawnow
940        if isfield(XmlDataRead, 'GeometryCalib') && ~isempty(XmlDataRead.GeometryCalib)
941            XmlData.GeometryCalib=XmlDataRead.GeometryCalib;
942            if isfield(XmlData.GeometryCalib,'VolumeScan') && isequal(XmlData.GeometryCalib.VolumeScan,'y')
943                set (handles.slices,'String','volume')
944            end
945            % check whether the GUI geometry_calib is opened
946            hgeometry_calib=findobj('tag','geometry_calib');
947            if ~isempty(hgeometry_calib) % check whether the display of the GUI geometry_calib is consistent with the current calib param
948                GUserData=get(hgeometry_calib,'UserData');
949                if ~(isfield(GUserData,'XmlInputFile') && strcmp(GUserData.XmlInputFile,XmlFileName))
950                    answer=msgbox_uvmat('INPUT_Y-N','refresh the display of the GUI geometry_calib with the new input data?');
951                    if strcmp(answer,'Yes')
952                        geometry_calib(XmlFileName);%diplay the new calibration points and parameters in geometry_calib
953                    end
954                end
955            end
956        end
957    end
958end
959if isempty(ImaDoc_str)
960    set(handles.view_xml,'Visible','off') % no .xml (or .civ) file detected
961else
962    set(handles.view_xml,'String',ImaDoc_str)% indicate that a xml file has been detected
963end
964
965%% Define timing
966% time not set by the input file: images or civ data: indicate that time is read from the xml file
967if isfield(XmlData,'Time')&& ~isempty(XmlData.Time) && ...
968        (strcmp(FileType,'image')|| strcmp(FileType,'multimage')||strcmp(FileType,'civdata')||strcmp(FileType,'civx'))
969    TimeName='xml';
970elseif strcmp(FileType,'civdata')
971    TimeName='civdata';
972elseif strcmp(FileType,'civx')
973    TimeName='civx';
974end
975if index==1
976    set(handles.TimeName,'String',TimeName)
977else
978    set(handles.TimeName_1,'String',TimeName)
979    set(handles.TimeName_1,'Visible','on')
980end
981
982%% store last index in handles.MaxIndex_i and .MaxIndex_j
983nbfield=max(max(max(i2_series)));
984if isempty(nbfield)
985    nbfield=max(max(max(i1_series)));
986end
987nbfield_j=max(max(max(j2_series)));
988if isempty(nbfield_j)
989    nbfield_j=max(max(max(j1_series)));
990end
991if isfield(XmlData,'Time')&& ~isempty(XmlData.Time)
992    %transform .Time to a column vector if it is a line vector the nomenclature uses a single index
993    if isequal(size(XmlData.Time,1),1)
994        XmlData.Time=(XmlData.Time)';
995    end
996end
997last_i_cell=get(handles.MaxIndex_i,'String');
998if isempty(nbfield)
999    last_i_cell{index}='';
1000else
1001    last_i_cell{index}=num2str(nbfield);
1002end
1003set(handles.MaxIndex_i,'String',last_i_cell)
1004last_j_cell=get(handles.MaxIndex_j,'String');
1005if isempty(nbfield_j)
1006     last_j_cell{index}='';
1007else
1008     last_j_cell{index}=num2str(nbfield_j);
1009end
1010set(handles.MaxIndex_j,'String',last_j_cell);
1011
1012%% store geometric calibration in UvData
1013if isfield(XmlData,'GeometryCalib')
1014    GeometryCalib=XmlData.GeometryCalib;
1015    if isempty(GeometryCalib)
1016        set(handles.pxcmx,'String','')
1017        set(handles.pxcmy,'String','')
1018        set(handles.pxcmx,'Visible','off')
1019        set(handles.pxcmy,'Visible','off')
1020        set(handles.TransformName,'Value',1); %  no transform by default
1021    else
1022        set(handles.pxcmx,'Visible','on')
1023        set(handles.pxcmy,'Visible','on')
1024        if (isfield(GeometryCalib,'R')&& ~isequal(GeometryCalib.R(2,1),0) && ~isequal(GeometryCalib.R(1,2),0)) ||...
1025            (isfield(GeometryCalib,'kappa1')&& ~isequal(GeometryCalib.kappa1,0))
1026            set(handles.pxcmx,'String','var')
1027            set(handles.pxcmy,'String','var')
1028        elseif isfield(GeometryCalib,'fx_fy')
1029            pixcmx=GeometryCalib.fx_fy(1);%*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx);
1030            pixcmy=GeometryCalib.fx_fy(2);%*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy);
1031            set(handles.pxcmx,'String',num2str(pixcmx))
1032            set(handles.pxcmy,'String',num2str(pixcmy))
1033        end
1034        if ~get(handles.CheckFixLimits,'Value')
1035            set(handles.TransformName,'Value',3); % phys transform by default if fixedLimits is off
1036        end
1037        if isfield(GeometryCalib,'SliceCoord')           
1038           siz=size(GeometryCalib.SliceCoord);
1039           if siz(1)>1
1040               NbSlice=siz(1);
1041               set(handles.slices,'Visible','on')
1042               set(handles.slices,'Value',1)
1043           end
1044           if isfield(GeometryCalib,'VolumeScan') && isequal(GeometryCalib.VolumeScan,'y')
1045               set(handles.num_NbSlice,'Visible','off')
1046           else
1047               set(handles.num_NbSlice,'Visible','on')
1048               set(handles.num_NbSlice,'String',num2str(NbSlice))
1049           end
1050           slices_Callback([],[], handles)
1051        end           
1052    end
1053end
1054
1055%% update the data attached to the uvmat interface
1056if ~isempty(TimeUnit)
1057    if index==2 && isfield(UvData,'TimeUnit') && ~strcmp(UvData.TimeUnit,TimeUnit)
1058        msgbox_uvmat('WARNING',['time unit for second file series ' TimeUnit ' inconsistent with first series'])
1059    else
1060        UvData.TimeUnit=TimeUnit;
1061    end
1062end
1063UvData.XmlData{index}=XmlData;
1064UvData.NewSeries=1;
1065
1066%display warning message
1067if ~isequal(warntext,'')
1068    msgbox_uvmat('WARNING',warntext);
1069end
1070
1071%% set default options in menu 'FieldName'
1072switch FileType
1073    case {'civx','civdata'}
1074        [FieldList,ColorList]=set_field_list('U','V','C');
1075        set(handles_Fields,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data
1076        set(handles_Fields,'Value',2) % set menu to 'velocity
1077        if index==1
1078            set(handles.FieldName_1,'Value',1);
1079            set(handles.FieldName_1,'String',[{''};{'image'};FieldList;{'get_field...'}]);%standard menu for civx data reproduced for the second field
1080        end
1081        set(handles.ColorScalar,'Value',1)
1082        set(handles.ColorScalar,'String',ColorList)
1083        set(handles.Vectors,'Visible','on')
1084        set(handles.Coord_x,'Value',1);
1085        set(handles.Coord_x,'String','X');
1086%         set(handles.Coord_y,'Value',1);
1087        set(handles.Coord_y,'Data',{'Y'});
1088    case 'netcdf'
1089        set(handles_Fields,'Value',1)
1090        set(handles_Fields,'String',{'get_field...'})
1091        if index==1
1092            FieldName_Callback([],[], handles)
1093        else
1094            FieldName_1_Callback([],[], handles)
1095        end
1096    otherwise
1097        set(handles_Fields,'Value',1) % set menu to 'image'
1098        set(handles_Fields,'String',{'image'})
1099        set(handles.Coord_x,'Value',1);
1100        set(handles.Coord_x,'String','AX');
1101    set(handles.Coord_y,'Data',{'AY'});
1102end
1103set(handles.uvmat,'UserData',UvData)
1104
1105%% set index navigation options and inputfilerefresh plots
1106scan_option='i';%default
1107state_j='off'; %default
1108if index==2
1109    if get(handles.scan_j,'Value')
1110        scan_option='j'; %keep the scan option for the second file series
1111    end
1112    if strcmp(get(handles.j1,'Visible'),'on')
1113        state_j='on';
1114    end
1115end
1116[ref_j,ref_i]=find(squeeze(i1_series(1,:,:)));
1117if ~isempty(j1_series)
1118        state_j='on';
1119        if index==1
1120            if isequal(ref_i,ref_i(1)*ones(size(ref_j)))% if ref_i is always equal to its first value
1121                scan_option='j'; %scan j indext               
1122            end
1123        end
1124end
1125if isequal(scan_option,'i')
1126    diff_ref_i=diff(ref_i,1);
1127    if isempty(diff_ref_i)
1128        diff_ref_i=1;
1129    end
1130    if isequal (diff_ref_i,diff_ref_i(1)*ones(size(diff_ref_i)))
1131        set(handles.num_IndexIncrement,'String',num2str(diff_ref_i(1)))
1132    end
1133     set(handles.scan_i,'Value',1)
1134     scan_i_Callback([],[], handles);
1135else
1136    diff_ref_j=diff(ref_j);
1137    if isempty(diff_ref_j)
1138        diff_ref_j=1;
1139    end
1140    if isequal (diff_ref_j,diff_ref_j(1)*ones(size(diff_ref_j)))
1141        set(handles.num_IndexIncrement,'String',num2str(diff_ref_j(1)))
1142    end
1143     set(handles.scan_j,'Value',1)
1144     scan_j_Callback([],[], handles);
1145end
1146set(handles.scan_j,'Visible',state_j)
1147set(handles.j1,'Visible',state_j)
1148set(handles.j2,'Visible',state_j)
1149set(handles.MaxIndex_j,'Visible',state_j);
1150%set(handles.frame_j,'Visible',state_j);
1151set(handles.j_text,'Visible',state_j);
1152if ~isempty(i2_series)||~isempty(j2_series)
1153    set(handles.CheckFixPair,'Visible','on')
1154elseif index==1
1155    set(handles.CheckFixPair,'Visible','off')
1156end
1157
1158%% apply the effect of the transform fct and view the field 
1159transform=get(handles.TransformPath,'UserData');
1160if index==2 && (~isa(transform,'function_handle')||nargin(transform)<3)
1161    set(handles.TransformName,'value',2); % set transform to sub_field if the current fct doe not accept two input fields
1162end
1163TransformName_Callback([],[],handles)
1164mask_test=get(handles.CheckMask,'value');
1165if mask_test
1166    MaskData=get(handles.CheckMask,'UserData');
1167    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1168          delete(MaskData.maskhandle)    %delete old mask
1169    end
1170    CheckMask_Callback([],[],handles)
1171end
1172
1173%------------------------------------------------------------------------
1174% --- switch file index scanning options scan_i and scan_j in an exclusive way
1175%------------------------------------------------------------------------
1176function scan_i_Callback(hObject, eventdata, handles)
1177
1178if get(handles.scan_i,'Value')==1
1179    set(handles.scan_j,'Value',0)
1180else
1181    set(handles.scan_j,'Value',1)
1182end
1183scan_j_Callback(hObject, eventdata, handles)
1184
1185%------------------------------------------------------------------------
1186% --- switch file index scanning options scan_i and scan_j in an exclusive way
1187%------------------------------------------------------------------------
1188function scan_j_Callback(hObject, eventdata, handles)
1189
1190if get(handles.scan_j,'Value')==1
1191    set(handles.scan_i,'Value',0)
1192else
1193    set(handles.scan_i,'Value',1)
1194    set(handles.CheckFixPair,'Visible','off')
1195end
1196
1197%------------------------------------------------------------------------
1198function i1_Callback(hObject, eventdata, handles)
1199%------------------------------------------------------------------------
1200update_ij(handles,1)
1201
1202%------------------------------------------------------------------------
1203function i2_Callback(hObject, eventdata, handles)
1204%------------------------------------------------------------------------
1205update_ij(handles,2)
1206
1207%------------------------------------------------------------------------
1208function j1_Callback(hObject, eventdata, handles)
1209%------------------------------------------------------------------------
1210update_ij(handles,3)
1211
1212%------------------------------------------------------------------------
1213function j2_Callback(hObject, eventdata, handles)
1214%------------------------------------------------------------------------
1215update_ij(handles,4)
1216
1217%------------------------------------------------------------------------
1218%--- update the index display after action on edit boxes i1, i2, j1 or j2
1219%------------------------------------------------------------------------
1220function update_ij(handles,index_rank)
1221   
1222NomType=get(handles.NomType,'String');
1223indices=get(handles.FileIndex,'String');
1224[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(indices);% the indices for the second series taken from FileIndex
1225switch index_rank
1226    case 1
1227        indices=fullfile_uvmat('','','','',NomType,stra2num(get(handles.i1,'String')),i2,j1,j2);
1228        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
1229    case 2
1230        indices=fullfile_uvmat('','','','',NomType,i1,stra2num(get(handles.i2,'String')),j1,j2);
1231        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
1232    case 3
1233        indices=fullfile_uvmat('','','','',NomType,i1,i2,stra2num(get(handles.j1,'String')),j2);
1234        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
1235    case 4
1236        indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,stra2num(get(handles.j2,'String')));
1237        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
1238end
1239set(handles.FileIndex,'String',indices)
1240set(handles.FileIndex,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation
1241% update the second index if relevant
1242if strcmp(get(handles.FileIndex_1,'Visible'),'on')
1243    NomType_1=get(handles.NomType_1,'String');
1244    indices_1=get(handles.FileIndex_1,'String');
1245    [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
1246    switch index_rank
1247        case 1
1248            indices_1=fullfile_uvmat('','','','',NomType_1,stra2num(get(handles.i1,'String')),i2_1,j1_1,j2_1);
1249        case 2
1250            indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,stra2num(get(handles.i2,'String')),j1_1,j2_1);
1251        case 3
1252            indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,i2_1,stra2num(get(handles.j1,'String')),j2_1);
1253        case 4
1254            indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,i2_1,j1_1,stra2num(get(handles.j2,'String')));
1255    end
1256    set(handles.FileIndex_1,'String',indices_1)
1257    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
1258end
1259   
1260%------------------------------------------------------------------------
1261
1262%------------------------------------------------------------------------
1263function slices_Callback(hObject, eventdata, handles)
1264%------------------------------------------------------------------------
1265if strcmp(get(handles.slices,'String'),'slices')
1266    if get(handles.slices,'Value')==1
1267        set(handles.num_NbSlice,'Visible','on')
1268        set(handles.z_text,'Visible','on')
1269        set(handles.z_index,'Visible','on')
1270        num_NbSlice_Callback(hObject, eventdata, handles)
1271    else
1272        set(handles.num_NbSlice,'Visible','off')
1273        set(handles.z_text,'Visible','off')
1274        set(handles.z_index,'Visible','off')
1275        set(handles.masklevel,'Value',1)
1276        set(handles.masklevel,'String',{'1'})
1277    end
1278end
1279
1280%------------------------------------------------------------------------
1281function num_NbSlice_Callback(hObject, eventdata, handles)
1282%------------------------------------------------------------------------
1283mode=get(handles.slices,'String');
1284nb_slice_str=get(handles.num_NbSlice,'String');
1285if strcmp(mode,'volume')
1286    z=stra2num(get(handles.j1,'String'));
1287else
1288    num=str2double(get(handles.i1,'String'));
1289    nbslice=str2double(get(handles.num_NbSlice,'String'));
1290    z=mod(num-1,nbslice)+1;
1291end
1292set(handles.z_index,'String',num2str(z))
1293for ilist=1:nbslice
1294    list_index{ilist,1}=num2str(ilist);
1295end   
1296set(handles.masklevel,'String',list_index)
1297set(handles.masklevel,'Value',z)
1298
1299%------------------------------------------------------------------------
1300% --- Executes on button press in view_xml.
1301%------------------------------------------------------------------------
1302function view_xml_Callback(hObject, eventdata, handles)
1303
1304% if TimeName defined, open the xml file corresponding to the first file
1305% series, else open the xml file corresponding to the second series
1306if isempty(get(handles.TimeName,'String'))% open the xml file corresponding to the secodn file series
1307    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
1308else
1309   [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1310end
1311option=get(handles.view_xml,'String');
1312if isequal(option,'view .xml')     
1313    FileXml=fullfile(RootPath,[SubDir '.xml']);
1314    if ~exist(FileXml,'file')% case of civ files , removes the extension for subdir
1315        FileXml=fullfile(RootPath,[regexprep(SubDir,'\..+$','') '.xml']);
1316    end
1317    heditxml=editxml(FileXml);
1318end
1319
1320%------------------------------------------------------------------------
1321% --- Executes on button press in CheckMask.
1322function CheckMask_Callback(hObject, eventdata, handles)
1323%------------------------------------------------------------------------
1324%case of view mask selection
1325if isequal(get(handles.CheckMask,'Value'),1)
1326    [RootPath,SubDir]=read_file_boxes(handles);
1327    MaskSubDir=regexprep(SubDir,'\..*','');%take the root part of SubDir, before the first dot '.'
1328    MaskPath=fullfile(RootPath,[MaskSubDir '.mask']);
1329    mdetect=0;
1330    if exist(MaskPath,'dir')
1331        ListStruct=dir(MaskPath);%look for a mask file
1332        ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray
1333        check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files
1334        ListFiles=ListCells(1,:);%list of file and dri names
1335        ListFiles=ListFiles(~check_dir);%list of file names (excluding dir)
1336        if ~isempty(ListFiles)
1337            for ifile=1:numel(ListFiles)
1338                [tild,tild,MaskExt]=fileparts(ListFiles{1});
1339                [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileType]=find_file_series(MaskPath,ListFiles{ifile},0);
1340                if strcmp(MaskFileType,'image') && isempty(i2_series) && isempty(j2_series)
1341                    mdetect=1;
1342                end
1343                if ~strcmp(MaskFile{ifile},MaskFile{1})
1344                    mdetect=0;% cancel detection test in case of multiple masks, use the brower for selection
1345                    break
1346                end
1347            end
1348        end
1349        RootPath=MaskPath;
1350    end
1351    if mdetect==0
1352        MaskFullName=uigetfile_uvmat('pick a mask image file:',RootPath,'image');
1353        if isempty(MaskFullName)
1354            set(handles.CheckMask,'Value',0)
1355        end
1356        [MaskPath,MaskName,MaskExt]=fileparts(MaskFullName);
1357        [tild,tild,MaskFile,i1_series,i2_series,j1_series,j2_series,MaskNomType]=find_file_series(MaskPath,[MaskName MaskExt],0);
1358        if ~(isempty(i2_series) && isempty(j2_series))
1359            MaskNomType='*';
1360        end
1361    end
1362    Mask.Path=MaskPath;
1363    if isempty(MaskFile)
1364        Mask.File='';
1365    else
1366        Mask.File=MaskFile{1};
1367    end
1368    Mask.Ext=MaskExt;
1369    Mask.NomType=MaskNomType;
1370    set(handles.CheckMask,'UserData',Mask);
1371    errormsg=update_mask(handles);
1372else % desactivate mask display
1373    MaskData=get(handles.CheckMask,'UserData');
1374    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1375        delete(MaskData.maskhandle)
1376    end
1377    set(handles.CheckMask,'UserData',[])
1378    UvData=get(handles.uvmat,'UserData');
1379    if isfield(UvData,'MaskName')
1380        UvData=rmfield(UvData,'MaskName');
1381        set(handles.uvmat,'UserData',UvData)
1382    end
1383    set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1384end
1385
1386%------------------------------------------------------------------------
1387function errormsg=update_mask(handles)
1388%------------------------------------------------------------------------
1389errormsg=[];%default
1390Mask=get(handles.CheckMask,'UserData');
1391MaskIndex=1;
1392if strcmp(get(handles.z_index,'Visible'),'on')
1393    MaskIndex=str2num(get(handles.z_index,'String'));
1394end
1395if isfield(Mask,'maskhandle')&& ishandle(Mask.maskhandle)
1396    uistack(Mask.maskhandle,'top');
1397end
1398MaskName=fullfile_uvmat(Mask.Path,'',Mask.File,Mask.Ext,Mask.NomType,MaskIndex);
1399UvData=get(handles.uvmat,'UserData');
1400
1401%% update mask image if the mask is new
1402if ~ (isfield(UvData,'MaskName') && isequal(UvData.MaskName,MaskName))
1403    UvData.MaskName=MaskName; %update the recorded name on UvData
1404    set(handles.uvmat,'UserData',UvData);
1405    if ~exist(MaskName,'file')
1406        if isfield(Mask,'maskhandle')&& ishandle(Mask.maskhandle)
1407            delete(Mask.maskhandle)   
1408        end
1409    else
1410        %read mask image
1411        [MaskField,tild,errormsg] = read_field(MaskName,'image');
1412        if ~isempty(errormsg)
1413            return
1414        end
1415        npxy=size(MaskField.A);
1416        if length(npxy)>2
1417            errormsg=[MaskName ' is not a grey scale image'];
1418            return
1419        elseif ~isa(MaskField.A,'uint8')
1420            errormsg=[MaskName ' is not a 8 bit grey level image'];
1421            return
1422        end
1423        MaskField.ZIndex=MaskIndex;
1424        %px to phys or other transform on field
1425         menu_transform=get(handles.TransformName,'String');
1426        choice_value=get(handles.TransformName,'Value');
1427        transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1428        transform=get(handles.TransformPath,'UserData');
1429        if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
1430            if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
1431                Calib=UvData.XmlData{1}.GeometryCalib;
1432                MaskField=transform(MaskField,UvData.XmlData{1});
1433            end
1434        end
1435        flagmask=MaskField.A < 200;
1436       
1437        %make brown color image
1438        imflag(:,:,1)=0.9*flagmask;
1439        imflag(:,:,2)=0.7*flagmask;
1440        imflag(:,:,3)=zeros(size(flagmask));
1441       
1442        %update mask image
1443        hmask=[]; %default
1444        if isfield(Mask,'maskhandle')&& ishandle(Mask.maskhandle)
1445            hmask=Mask.maskhandle;
1446        end
1447        if ~isempty(hmask)
1448            set(hmask,'CData',imflag)   
1449            set(hmask,'AlphaData',flagmask*0.6)
1450            set(hmask,'XData',MaskField.AX);
1451            set(hmask,'YData',MaskField.AY);
1452%             uistack(hmask,'top')
1453        else
1454            axes(handles.PlotAxes)
1455            hold on   
1456            Mask.maskhandle=image(MaskField.AX,MaskField.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*ones(size(flagmask)));
1457            set(handles.CheckMask,'UserData',Mask)
1458        end
1459    end
1460end
1461
1462%------------------------------------------------------------------------
1463%------------------------------------------------------------------------
1464% III - MAIN InputFileREFRESH FUNCTIONS : 'FRAME PLOT'
1465%------------------------------------------------------------------------
1466
1467%------------------------------------------------------------------------
1468% --- Executes on button press in runplus: make one step forward and call
1469% --- InputFileREFRESH. The step forward is along the fieldname series 1 or 2 depending on
1470% --- the scan_i and scan_j check box (exclusive each other)
1471function runplus_Callback(hObject, eventdata, handles)
1472%------------------------------------------------------------------------
1473
1474set(handles.runplus,'BackgroundColor',[1 1 0])%paint the command button in yellow
1475drawnow
1476increment=str2double(get(handles.num_IndexIncrement,'String')); %get the field increment d
1477if isnan(increment)% case of free increment: move to next available field index
1478    increment='+';
1479end
1480errormsg=runpm(hObject,eventdata,handles,increment);
1481if ~isempty(errormsg)
1482    msgbox_uvmat('ERROR',errormsg);
1483end
1484set(handles.runplus,'BackgroundColor',[1 0 0])%paint the command button back to red
1485
1486%------------------------------------------------------------------------
1487% --- Executes on button press in runmin: make one step backward and call
1488% --- InputFileREFRESH. The step backward is along the fieldname series 1 or 2 depending on
1489% --- the scan_i and scan_j check box (exclusive each other)
1490function runmin_Callback(hObject, eventdata, handles)
1491%------------------------------------------------------------------------
1492
1493set(handles.runmin,'BackgroundColor',[1 1 0])%paint the command button in yellow
1494drawnow
1495increment=-str2double(get(handles.num_IndexIncrement,'String')); %get the field increment d
1496if isnan(increment)% case of free increment: move to previous available field index
1497    increment='-';
1498end
1499errormsg=runpm(hObject,eventdata,handles,increment);
1500if ~isempty(errormsg)
1501    msgbox_uvmat('ERROR',errormsg);
1502end
1503set(handles.runmin,'BackgroundColor',[1 0 0])%paint the command button back to red
1504
1505%------------------------------------------------------------------------
1506% -- Executes on button press in Movie: make a series of +> steps
1507function Movie_Callback(hObject, eventdata, handles)
1508%------------------------------------------------------------------------
1509
1510set(handles.Movie,'BackgroundColor',[1 1 0])%paint the command button in yellow
1511drawnow
1512increment=str2double(get(handles.num_IndexIncrement,'String')); %get the field increment d
1513if isnan(increment)% case of free increment: move to next available field index
1514    increment='+';
1515end
1516set(handles.STOP,'Visible','on')
1517set(handles.speed,'Visible','on')
1518set(handles.speed_txt,'Visible','on')
1519set(handles.Movie,'BusyAction','queue')
1520UvData=get(handles.uvmat,'UserData');
1521
1522while get(handles.Movie,'Value')==1 && get(handles.speed,'Value')~=0 && isequal(get(handles.Movie,'BusyAction'),'queue') % enable STOP command
1523        errormsg=runpm(hObject,eventdata,handles,increment);
1524        if ~isempty(errormsg)
1525            set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1526            return
1527        end
1528        pause(1.02-get(handles.speed,'Value'))% wait for next image
1529end
1530if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1531    UvData.aviobj=close(UvData.aviobj);
1532   set(handles.uvmat,'UserData',UvData);
1533end
1534set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1535
1536%------------------------------------------------------------------------
1537% -- Executes on button press in Movie: make a series of <- steps
1538function MovieBackward_Callback(hObject, eventdata, handles)
1539%------------------------------------------------------------------------
1540set(handles.MovieBackward,'BackgroundColor',[1 1 0])%paint the command button in yellow
1541drawnow
1542increment=-str2double(get(handles.num_IndexIncrement,'String')); %get the field increment d
1543if isnan(increment)% case of free increment: move to next available field index
1544    increment='-';
1545end
1546set(handles.STOP,'Visible','on')
1547set(handles.speed,'Visible','on')
1548set(handles.speed_txt,'Visible','on')
1549set(handles.MovieBackward,'BusyAction','queue')
1550UvData=get(handles.uvmat,'UserData');
1551
1552while get(handles.MovieBackward,'Value')==1 && get(handles.speed,'Value')~=0 && isequal(get(handles.MovieBackward,'BusyAction'),'queue') % enable STOP command
1553        errormsg=runpm(hObject,eventdata,handles,increment);
1554        if ~isempty(errormsg)
1555            set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1556            return
1557        end
1558        pause(1.02-get(handles.speed,'Value'))% wait for next image
1559end
1560if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1561    UvData.aviobj=close(UvData.aviobj);
1562   set(handles.uvmat,'UserData',UvData);
1563end
1564set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1565
1566%------------------------------------------------------------------------
1567function STOP_Callback(hObject, eventdata, handles)
1568%------------------------------------------------------------------------
1569set(handles.movie_pair,'BusyAction','Cancel')
1570set(handles.movie_pair,'value',0)
1571set(handles.Movie,'BusyAction','Cancel')
1572set(handles.MovieBackward,'BusyAction','Cancel')
1573set(handles.MenuExportMovie,'BusyAction','Cancel')
1574%set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1575set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1576set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1577
1578%------------------------------------------------------------------------
1579% --- function activated by runplus and run minus
1580function errormsg=runpm(hObject,eventdata,handles,increment)
1581%------------------------------------------------------------------------
1582errormsg='';%default
1583%% check for movie pair status
1584movie_status=get(handles.movie_pair,'Value');
1585if isequal(movie_status,1)
1586    STOP_Callback(hObject, eventdata, handles)%interrupt movie pair if active
1587end
1588
1589%% read the current input file name(s) and field indices
1590InputFile=read_GUI(handles.InputFile);
1591InputFile.RootFile=regexprep(InputFile.RootFile,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1592InputFile.SubDir=regexprep(InputFile.SubDir,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1593FileExt=InputFile.FileExt;
1594NomType=InputFile.NomType;
1595% i1=str2num(get(handles.i1,'String'));%read the field indices (for movie, it is not given by the file name)
1596% i2=[];%default
1597% if strcmp(get(handles.i2,'Visible'),'on')
1598%     i2=str2num(get(handles.i2,'String'));
1599% end
1600% j1=[];
1601% if strcmp(get(handles.j1,'Visible'),'on')
1602%     j1=stra2num(get(handles.j1,'String'));
1603% end
1604% j2=j1;
1605% if strcmp(get(handles.j2,'Visible'),'on')
1606%     j2=stra2num(get(handles.j2,'String'));
1607% end
1608[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(InputFile.FileIndex);% check back the indices used
1609if isempty(i1)
1610    i1=str2num(get(handles.i1,'String'));%read the field indices (for movie, it is not given by the file name)
1611elseif isempty(j1) && strcmp(get(handles.j1,'Visible'),'on')
1612    j1=str2num(get(handles.j1,'String'));%case of indexed movie
1613end
1614sub_value= get(handles.SubField,'Value');
1615if sub_value % a second input file has been entered
1616    [InputFile.RootPath_1,InputFile.SubDir_1,InputFile.RootFile_1,InputFile.FileIndex_1,InputFile.FileExt_1,InputFile.NomType_1]=read_file_boxes_1(handles);
1617    [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
1618    if isempty(i1_1)
1619        i1_1=str2num(get(handles.i1,'String'));%read the field indices (for movie, it is not given by the file name)
1620    elseif isempty(j1_1) && strcmp(get(handles.j1,'Visible'),'on')
1621        j1_1=str2num(get(handles.j1,'String'));%case of indexed movie
1622    end
1623else
1624    filename_1=[];
1625end
1626
1627%% increment (or decrement) the field indices and update the input filename(s)
1628if ~isnumeric(increment)% undefined increment value
1629    set(handles.CheckFixPair,'Value',0)
1630end
1631CheckFixPair=get(handles.CheckFixPair,'Value')||(isempty(i2)&&isempty(j2));
1632
1633% the pair i1-i2 or j1-j2 is imposed (check box CheckFixPair selected)
1634if CheckFixPair && isnumeric(increment)
1635    if get(handles.scan_i,'Value')==1% case of scanning along index i
1636        i1=i1+increment;
1637        i2=i2+increment;
1638        if sub_value
1639            i1_1=i1_1+increment;
1640            i2_1=i2_1+increment;
1641        end
1642    else % case of scanning along index j (burst numbers)
1643        j1=j1+increment;
1644        j2=j2+increment;
1645        if sub_value
1646            j1_1=j1_1+increment;
1647            j2_1=j2_1+increment;
1648        end
1649    end
1650   
1651    % the pair i1-i2 or j1-j2 is free (check box CheckFixPair not selected): the list of existing indices recorded in UvData is used
1652else
1653    UvData=get(handles.uvmat,'UserData');
1654    ref_i=i1;
1655    if ~isempty(i2)
1656        ref_i=floor((i1+i2)/2);% current reference index i
1657    end
1658    ref_j=1;
1659    if ~isempty(j1)
1660        ref_j=j1;
1661        if ~isempty(j2)
1662            ref_j=floor((j1+j2)/2);% current reference index j
1663        end
1664    end
1665    if isnumeric(increment)
1666        if get(handles.scan_i,'Value')==1% case of scanning along index i
1667            ref_i=ref_i+increment;% increment the current reference index i
1668        else % case of scanning along index j (burst numbers)
1669            ref_j=ref_j+increment;% increment the current reference index j if scan_j option is used
1670        end
1671    else % free increment
1672        runaction=get(gcbo,'tag');
1673        if strcmp(increment,'+')% if runplus or movie is activated
1674            step=1;
1675        else
1676            step=-1;
1677        end
1678        if get(handles.scan_i,'Value')==1% case of scanning along index i
1679            ref_i=ref_i+step;
1680            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
1681                ref_i=ref_i+step;
1682            end
1683        else % case of scanning along index j (burst numbers)
1684            ref_j=ref_j+step;
1685            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
1686                ref_j=ref_j+step;
1687            end
1688        end
1689    end
1690    if ref_i<0
1691        errormsg='minimum i index reached';
1692    elseif ref_j<0
1693        errormsg='minimum j index reached';
1694    elseif ref_i+1>size(UvData.i1_series{1},3)
1695        errormsg='maximum i index reached (reload the input file to update the index bound)';
1696    elseif ref_j+1>size(UvData.i1_series{1},2)
1697        errormsg='maximum j index reached (reload the input file to update the index bound)';
1698    end
1699    if ~isempty(errormsg),return,end
1700    siz=size(UvData.i1_series{1});
1701    ref_indices=ref_i*siz(1)*siz(2)+ref_j*siz(1)+1:ref_i*siz(1)*siz(2)+(ref_j+1)*siz(1);
1702    i1_subseries=UvData.i1_series{1}(ref_indices);
1703    ref_indices=ref_indices(i1_subseries>0);
1704    if isempty(ref_indices)% case of pairs (free index i)
1705        ref_indices=ref_i*siz(1)*siz(2)+1:(ref_i+1)*siz(1)*siz(2);
1706        i1_subseries=UvData.i1_series{1}(ref_indices);
1707        ref_indices=ref_indices(i1_subseries>0);
1708    end
1709    if isempty(ref_indices),errormsg='no next frame: set num_IndexIncrement =''*'' to reach the next existing file';return
1710    end
1711    i1=UvData.i1_series{1}(ref_indices(end));
1712    if ~isempty(UvData.i2_series{1})
1713        i2=UvData.i2_series{1}(ref_indices(end));
1714    end
1715    if ~isempty(UvData.j1_series{1})
1716        j1=UvData.j1_series{1}(ref_indices(end));
1717    end
1718    if ~isempty(UvData.j2_series{1})
1719        j2=UvData.j2_series{1}(ref_indices(end));
1720    end
1721   
1722    % case of a second file series
1723    if sub_value
1724        ref_i_1=i1_1;
1725        if ~isempty(i2_1)
1726            ref_i_1=floor((i1_1+i2_1)/2);% current reference index i
1727        end
1728        ref_j_1=1;
1729        if ~isempty(j1_1)
1730            ref_j_1=j1_1;
1731            if ~isempty(j2_1)
1732                ref_j_1=floor((j1_1+j2_1)/2);% current reference index j
1733            end
1734        end
1735        if isnumeric(increment)
1736            if get(handles.scan_i,'Value')==1% case of scanning along index i
1737                ref_i_1=ref_i_1+increment;% increment the current reference index i
1738            else % case of scanning along index j (burst numbers)
1739                ref_j_1=ref_j_1+increment;% increment the current reference index j if scan_j option is used
1740            end
1741        else % free increment, synchronise the ref indices with the first series
1742            ref_i_1=ref_i;
1743            ref_j_1=ref_j;
1744        end
1745        if numel(UvData.i1_series)==1
1746            UvData.i1_series{2}=UvData.i1_series{1};
1747            UvData.j1_series{2}=UvData.j1_series{1};
1748            UvData.i2_series{2}=UvData.i2_series{1};
1749            UvData.j2_series{2}=UvData.j2_series{1};
1750        end
1751        if ref_i_1<0
1752            errormsg='minimum i index reached';
1753        elseif ref_j_1<0
1754            errormsg='minimum j index reached';
1755        elseif ref_i_1+1>size(UvData.i1_series{2},3)
1756            errormsg='maximum i index reached for the second series (reload the input file to update the index bound)';
1757        elseif ref_j_1+1>size(UvData.i1_series{2},2)
1758            errormsg='maximum j index reached for the second series(reload the input file to update the index bound)';
1759        end
1760        if ~isempty(errormsg),return,end
1761        siz=size(UvData.i1_series{2});
1762        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);
1763        i1_subseries=UvData.i1_series{2}(ref_indices);
1764        ref_indices=ref_indices(i1_subseries>0);
1765        if isempty(ref_indices)% case of pairs (free index i)
1766            ref_indices=ref_i_1*siz(1)*siz(2)+1:(ref_i_1+1)*siz(1)*siz(2);
1767            i1_subseries=UvData.i1_series{2}(ref_indices);
1768            ref_indices=ref_indices(i1_subseries>0);
1769        end
1770        i1_1=UvData.i1_series{2}(ref_indices(end));
1771        if ~isempty(UvData.i2_series{2})
1772            i2_1=UvData.i2_series{2}(ref_indices(end));
1773        end
1774        if ~isempty(UvData.j1_series{2})
1775            j1_1=UvData.j1_series{2}(ref_indices(end));
1776        end
1777        if ~isempty(UvData.j2_series{2})
1778            j2_1=UvData.j2_series{1}(ref_indices(end));
1779        end
1780    else% the second series (if needed) is the same file as the first
1781        i1_1=i1;
1782        i2_1=i2;
1783        j1_1=j1;
1784        j2_1=j2;
1785    end
1786end
1787filename=fullfile_uvmat(InputFile.RootPath,InputFile.SubDir,InputFile.RootFile,FileExt,NomType,i1,i2,j1,j2);
1788
1789%% inputfilerefresh plots
1790if sub_value
1791    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);
1792    errormsg=refresh_field(handles,filename,filename_1,i1,i2,j1,j2,i1_1,i2_1,j1_1,j2_1);
1793else
1794    errormsg=refresh_field(handles,filename,filename_1,i1,i2,j1,j2);
1795end
1796set(handles.InputFileREFRESH,'BackgroundColor',[1 0 0])
1797
1798%% update the index counters if the index move is successfull
1799if isempty(errormsg)
1800    set(handles.i1,'String',num2stra(i1,NomType,1));
1801    if isequal(i2,i1)
1802        set(handles.i2,'String','');
1803    else
1804        set(handles.i2,'String',num2stra(i2,NomType,1));
1805    end
1806    set(handles.j1,'String',num2stra(j1,NomType,2));
1807    if isequal(j2,j1)
1808        set(handles.j2,'String','');
1809    else
1810        set(handles.j2,'String',num2stra(j2,NomType,2));
1811    end
1812    indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1813    set(handles.FileIndex,'String',indices);
1814    if ~isempty(filename_1)
1815        indices_1=fullfile_uvmat('','','','',InputFile.NomType_1,i1_1,i2_1,j1_1,j2_1);
1816        set(handles.FileIndex_1,'String',indices_1);
1817    end
1818    if isequal(movie_status,1)
1819        set(handles.movie_pair,'Value',1)
1820        movie_pair_Callback(hObject, eventdata, handles); %reactivate moviepair if it was activated
1821    else
1822        if isempty(i2), set(handles.i2,'String',''); end % suppress the second index display if not used
1823        if isempty(j2), set(handles.j2,'String',''); end
1824    end
1825    set(handles.i1,'BackgroundColor',[1 1 1])
1826    set(handles.i2,'BackgroundColor',[1 1 1])
1827    set(handles.j1,'BackgroundColor',[1 1 1])
1828    set(handles.j2,'BackgroundColor',[1 1 1])
1829    set(handles.FileIndex,'BackgroundColor',[1 1 1])
1830    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
1831end
1832
1833%------------------------------------------------------------------------
1834% --- Executes on button press in movie_pair: create an alternating movie with two view
1835function movie_pair_Callback(hObject, eventdata, handles)
1836%------------------------------------------------------------------------
1837
1838%% stop movie action if the movie_pair button is off
1839if ~get(handles.movie_pair,'value')
1840    set(handles.movie_pair,'BusyAction','Cancel')%stop movie pair if button is 'off'
1841    set(handles.i2,'String','')
1842    set(handles.j2,'String','')
1843    set(handles.Dt_txt,'String','')
1844    return
1845else
1846    set(handles.movie_pair,'BusyAction','queue')
1847    set(handles.InputFileREFRESH,'BackgroundColor',[1 0 0])
1848end
1849
1850%% initialisation
1851set(handles.movie_pair,'BackgroundColor',[1 1 0])%paint the command button in yellow
1852drawnow
1853list_fields=get(handles.FieldName,'String');% list menu fields
1854index_fields=get(handles.FieldName,'Value');% selected string index
1855FieldName=list_fields{index_fields}; % selected field
1856UvData=get(handles.uvmat,'UserData');
1857if isequal(FieldName,'image')
1858    index=1;
1859    [RootPath,SubDir,RootFile,FileIndices,Ext]=read_file_boxes(handles);
1860    NomType=get(handles.NomType,'String');
1861else
1862    list_fields=get(handles.FieldName_1,'String');% list menu fields
1863    index_fields=get(handles.FieldName_1,'Value');% selected string index
1864    FieldName=list_fields{index_fields}; % selected field
1865    if isequal(FieldName,'image')
1866        index=2;
1867        [RootPath,SubDir,RootFile,FileIndex_1,Ext,NomType]=read_file_boxes_1(handles);% get info from the second input line
1868    else
1869        msgbox_uvmat('ERROR','an image or movie must be first introduced as input')
1870        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1871        set(handles.movie_pair,'Value',0)
1872        return
1873    end
1874end
1875num_i1=str2num(get(handles.i1,'String'));
1876num_j1=stra2num(get(handles.j1,'String'));
1877num_i2=str2num(get(handles.i2,'String'));
1878num_j2=stra2num(get(handles.j2,'String'));
1879imaname_1='';
1880if isempty(num_j2)
1881    if isempty(num_i2)
1882        if strcmp(get(handles.j2,'Visible'),'on') %if the j box is visible
1883            imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,Ext,NomType,num_i1,[],num_j1+1);
1884        end
1885        if exist(imaname_1,'file')
1886            num_j2=num_j1+1;% look by default for the next j index as the second file
1887            set(handles.j2,'String',num2stra(num_j2,NomType));
1888        else
1889            imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,Ext,NomType,num_i1+1,[],num_j1);
1890            if exist(imaname_1,'file')
1891                num_i2=num_i1+1;
1892                set(handles.i2,'String',num2str(num_i2));
1893            else
1894                msgbox_uvmat('ERROR', 'a second image index i2 or j2 is needed to show the pair as a movie')
1895                set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1896                set(handles.movie_pair,'Value',0)
1897                return
1898            end
1899        end
1900    else
1901        num_j2=num_j1;%repeat the index i1 by default
1902    end
1903end
1904if isempty(num_i2)
1905    num_i2=num_i1;%repeat the index i1 by default
1906end
1907if isempty(num_j1)
1908    num_j1=1;
1909end
1910if isempty(num_j2)
1911    num_j2=num_j1;%repeat the index i1 by default
1912end
1913imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,Ext,NomType,num_i2,[],num_j2);
1914if strcmp(NomType,'*')
1915    num_frame=num_i2;
1916else
1917    num_frame=num_j2;
1918end
1919if ~exist(imaname_1,'file')
1920      msgbox_uvmat('ERROR',['second input open (-)  ' imaname_1 ' not found']);
1921      set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1922       set(handles.movie_pair,'Value',0)
1923      return
1924end
1925
1926%% display time interval for the image pair
1927if isfield(UvData,'XmlData')&&isfield(UvData.XmlData{1},'Time')...
1928        && size(UvData.XmlData{1}.Time,1)>=num_i2+1 && size(UvData.XmlData{1}.Time,2)>=num_j2+1
1929    dt=(UvData.XmlData{1}.Time(num_i2+1,num_j2+1)-UvData.XmlData{1}.Time(num_i1+1,num_j1+1));
1930    if  isfield(UvData,'TimeUnit')
1931        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  m' UvData.TimeUnit] )
1932    else
1933        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  10^(-3)'] )
1934    end
1935else
1936    set(handles.Dt_txt,'String','')
1937end
1938
1939%% get the first image
1940%Field.AName='image';
1941if index==1
1942    Field_a=UvData.Field;% movie on the second field
1943else
1944    Field_a=UvData.Field_1;% movie on the first field
1945end
1946
1947%% read the second image
1948MovieObject=[];
1949if numel(UvData.MovieObject)>=index
1950    MovieObject=UvData.MovieObject{index};
1951end
1952[Field_b,ParamOut,errormsg] = read_field(imaname_1,UvData.FileType{index},MovieObject,num_frame);
1953
1954%px to phys or other transform on field
1955transform=get(handles.TransformPath,'UserData');
1956if  ~isempty(transform)
1957    if isfield(UvData,'XmlData') && numel(UvData.XmlData)>=index %use geometry calib recorded from the ImaDoc xml file as first priority
1958        if index==2
1959        Field_a=transform(Field_a,UvData.XmlData{index});%the first field has been stored without transform
1960        end
1961        if nargin(transform)>=2
1962        Field_b=transform(Field_b,UvData.XmlData{index});
1963        else
1964          Field_b=transform(Field_b);
1965        end
1966    end
1967end
1968
1969% make movie until movie speed is set to 0 or STOP is activated
1970hima=findobj(handles.PlotAxes,'Tag','ima');% %handles.PlotAxes =main plotting window (A GENERALISER)
1971set(handles.STOP,'Visible','on')
1972set(handles.speed,'Visible','on')
1973set(handles.speed_txt,'Visible','on')
1974set(handles.i2,'BackgroundColor',[1 1 1])% mark the edit box in white to indicate its use as input
1975set(handles.j2,'BackgroundColor',[1 1 1])% mark the edit box in white to indicate its use as input
1976set(handles.FileIndex,'BackgroundColor',[1 1 1])% mark the edit box in white to indicate its use as input
1977while get(handles.speed,'Value')~=0 && isequal(get(handles.movie_pair,'BusyAction'),'queue') % enable STOP command
1978    % read and plot the series of images in non erase mode
1979    set(hima,'CData',Field_b.A);
1980    pause(1.02-get(handles.speed,'Value'));% wait for next image
1981    set(hima,'CData',Field_a.A);
1982    pause(1.02-get(handles.speed,'Value'));% wait for next image
1983end
1984set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1985set(handles.movie_pair,'Value',0)
1986set(handles.Dt_txt,'String','')
1987
1988%------------------------------------------------------------------------
1989% --- Executes on button press in InputFileREFRESH.
1990function REFRESH_Callback(hObject, eventdata, handles)
1991%------------------------------------------------------------------------
1992set(handles.REFRESH,'BackgroundColor',[1 1 0])%paint the command button in yellow
1993drawnow
1994[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
1995[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(FileIndex);% check back the indices used
1996if isempty(i2), set(handles.i2,'String',''); end % suppress the second index display if not used
1997if isempty(j2), set(handles.j2,'String',''); end
1998filename=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
1999filename_1='';%default
2000FileIndex_1='';
2001if get(handles.SubField,'Value')
2002    [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
2003    filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
2004end
2005num_i1=stra2num(get(handles.i1,'String'));
2006num_i2=stra2num(get(handles.i2,'String'));
2007num_j1=stra2num(get(handles.j1,'String'));
2008num_j2=stra2num(get(handles.j2,'String'));
2009[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
2010if isempty(j1_1)% case of movies, the index is not given by file index
2011    j1_1=num_j1;
2012end
2013
2014errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1);
2015
2016if ~isempty(errormsg)
2017      msgbox_uvmat('ERROR',errormsg);
2018else
2019    set(handles.i1,'BackgroundColor',[1 1 1])
2020    set(handles.i2,'BackgroundColor',[1 1 1])
2021    set(handles.j1,'BackgroundColor',[1 1 1])
2022    set(handles.j2,'BackgroundColor',[1 1 1])
2023    set(handles.FileIndex,'BackgroundColor',[1 1 1])
2024    set(handles.FileIndex_1,'BackgroundColor',[1 1 1]) 
2025    set(handles.REFRESH,'BackgroundColor',[1 0 0])
2026end   
2027
2028%------------------------------------------------------------------------
2029% --- read the input files and inputfilerefresh all the plots, including projection.
2030% OUTPUT:
2031%  errormsg: error message char string  =[] by default
2032% INPUT:
2033% FileName: first input file (=[] in the absence of input file)
2034% FileName_1: second input file (=[] in the asbsence of second input file)
2035% num_i1,num_i2,num_j1,num_j2; frame indices
2036% i1_1,i2_1,j1_1,j2_1: frame indices for the second input file  (needed if FileName_1 is not empty)
2037%------------------------------------------------------------------------
2038function errormsg=refresh_field(handles,FileName,FileName_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1)
2039%------------------------------------------------------------------------
2040
2041%% initialisation
2042if ~exist('Field','var')
2043    Field={};
2044end
2045UvData=get(handles.uvmat,'UserData');
2046if ishandle(handles.UVMAT_title) %remove title panel on uvmat
2047    delete(handles.UVMAT_title)
2048end
2049
2050%% determine the main input file information for action
2051if ~exist(FileName,'file')
2052    errormsg=['input file ' FileName ' does not exist'];
2053    return
2054end
2055NomType=get(handles.NomType,'String');
2056NomType_1='';
2057if strcmp(get(handles.NomType_1,'Visible'),'on')
2058    NomType_1=get(handles.NomType_1,'String');
2059end
2060%update the z position index
2061mode_slice=get(handles.slices,'String');
2062if strcmp(mode_slice,'volume')
2063    z_index=num_j1;
2064    set(handles.z_index,'String',num2str(z_index))
2065else
2066    nbslice=str2num(get(handles.num_NbSlice,'String'));
2067    z_index=mod(num_i1-1,nbslice)+1;
2068    set(handles.z_index,'String',num2str(z_index))
2069end
2070% inputfilerefresh menu for save_mask if relevant
2071masknumber=get(handles.masklevel,'String');
2072if length(masknumber)>=z_index
2073    set(handles.masklevel,'Value',z_index)
2074end
2075
2076%% test for need of tps
2077check_proj_tps=0;
2078if  (strcmp(UvData.FileType{1},'civdata')||strcmp(UvData.FileType{1},'civx'))
2079    for iobj=1:numel(UvData.ProjObject)
2080        if isfield(UvData.ProjObject{iobj},'ProjMode')&& strcmp(UvData.ProjObject{iobj}.ProjMode,'interp_tps')
2081            check_proj_tps=1;
2082            break
2083        end
2084    end
2085end
2086
2087%% read the first input field
2088ParamIn.ColorVar='';%default variable name for vector color
2089frame_index=1;%default
2090FieldName='';%default
2091VelType='';%default
2092switch UvData.FileType{1}
2093    case {'civx','civdata','netcdf'};
2094        list_fields=get(handles.FieldName,'String');% list menu fields
2095        FieldName= list_fields{get(handles.FieldName,'Value')}; % selected field
2096        if ~strcmp(FieldName,'get_field...')
2097            if get(handles.FixVelType,'Value')
2098                VelTypeList=get(handles.VelType,'String');
2099                VelType=VelTypeList{get(handles.VelType,'Value')};
2100            end
2101        end
2102        % case of input vector field, get the scalar used for vector color
2103        if ~isempty(regexp(FieldName,'^vec('))
2104            list_code=get(handles.ColorCode,'String');% list menu fields
2105            index_code=get(handles.ColorCode,'Value');% selected string index
2106            if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2107                list_code=get(handles.ColorScalar,'String');% list menu fields
2108                index_code=get(handles.ColorScalar,'Value');% selected string index
2109                ParamIn.ColorVar= list_code{index_code}; % selected field
2110            end
2111        end
2112    case {'video','mmreader'}
2113        ParamIn=UvData.MovieObject{1};     
2114        if strcmp(NomType,'*')
2115            frame_index=num_i1;%frame index from a single movies or multimage
2116        else
2117            frame_index=num_j1;% frame index from a set of indexed movies
2118        end
2119    case 'multimage'
2120        if ~strcmp(NomType,'*')
2121            frame_index=num_j1;%frame index for movies or multimage
2122        else
2123            frame_index=num_i1;
2124        end
2125    case 'vol' %TODO: update
2126        if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2127            ParamIn.Npy=UvData.XmlData.Npy;
2128            ParamIn.Npx=UvData.XmlData.Npx;
2129        else           
2130            errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2131            return
2132        end
2133end
2134if isstruct (ParamIn)
2135    ParamIn.FieldName=FieldName;
2136    ParamIn.VelType=VelType;
2137    ParamIn.Coord_x=get(handles.Coord_x,'String');
2138    ParamIn.Coord_y=get(handles.Coord_y,'Data');
2139end
2140check_tps = 0;         
2141if strcmp(UvData.FileType{1},'civdata')&&~strcmp(ParamIn.FieldName,'velocity')&&~strcmp(ParamIn.FieldName,'get_field...')
2142       check_tps=1;%tps needed to get the requested field
2143end
2144[Field{1},ParamOut,errormsg] = read_field(FileName,UvData.FileType{1},ParamIn,frame_index);
2145if ~isempty(errormsg)
2146    errormsg=['uvmat / refresh_field / read_field( ' FileName ') / ' errormsg];
2147    return
2148end 
2149if isfield(ParamOut,'Npx')&& isfield(ParamOut,'Npy')
2150    set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2151    set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2152end
2153Field{1}.ZIndex=z_index; %used for multiplane 3D calibration
2154
2155%% choose and read a second field FileName_1 if defined
2156VelType_1=[];%default
2157FieldName_1=[];
2158ParamIn_1=[];
2159ParamOut_1=[];
2160frame_index_1=1;
2161if ~isempty(FileName_1)
2162    if ~exist(FileName_1,'file')
2163        errormsg=['second file ' FileName_1 ' does not exist'];
2164        return
2165    end
2166    switch UvData.FileType{2}
2167        case {'civx','civdata','netcdf'};
2168            list_fields=get(handles.FieldName_1,'String');% list menu fields
2169            if ischar(list_fields),list_fields={list_fields};end
2170            FieldName_1= list_fields{get(handles.FieldName_1,'Value')}; % selected field
2171            if ~strcmp(FieldName,'get_field...')
2172                if get(handles.FixVelType,'Value')
2173                    VelTypeList=get(handles.VelType_1,'String');
2174                    VelType_1=VelTypeList{get(handles.VelType_1,'Value')};% read the velocity type.
2175                end
2176            end
2177            if strcmp(FieldName_1,'velocity')&& strcmp(get(handles.ColorCode,'Visible'),'on')
2178                list_code=get(handles.ColorCode,'String');% list menu fields
2179                index_code=get(handles.ColorCode,'Value');% selected string index
2180                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2181                    list_code=get(handles.ColorScalar,'String');% list menu fields
2182                    index_code=get(handles.ColorScalar,'Value');% selected string index
2183                    ParamIn_1.ColorVar= list_code{index_code}; % selected field for vector color display                 
2184                end
2185            end
2186        case {'video','mmreader'}
2187            ParamIn_1=UvData.MovieObject{2};
2188                        if ~strcmp(NomType_1,'*')
2189                frame_index_1=j1_1;%frame index for movies or multimage
2190            else
2191                frame_index_1=i1_1;
2192            end 
2193         case 'multimage'
2194            if strcmp(NomType_1,'*')%frame index for movies or multimage
2195                frame_index_1=i1_1;
2196            else
2197                frame_index_1=j1_1;
2198            end   
2199        case 'vol' %TODO: update
2200            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2201                ParamIn_1.Npy=UvData.XmlData.Npy;
2202                ParamIn_1.Npx=UvData.XmlData.Npx;
2203            else
2204                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2205                return
2206            end
2207    end
2208    if isequal(get(handles.NomType_1,'Visible'),'on')
2209    NomType_1=get(handles.NomType_1,'String');
2210    else
2211        NomType_1=get(handles.NomType,'String');
2212    end
2213    test_keepdata_1=0;% test for keeping the previous stored data if the input files are unchanged
2214    if ~isequal(NomType_1,'*')&& isfield(UvData,'FileName_1')
2215           test_keepdata_1= strcmp(FileName_1,UvData.FileName_1) ;
2216    end
2217    if test_keepdata_1
2218        Field{2}=UvData.Field_1;% keep the stored field
2219        ParamOut_1=UvData.ParamOut_1;
2220    else
2221        if isempty(ParamIn_1) || isstruct(ParamIn_1)
2222        ParamIn_1.FieldName=FieldName_1;
2223        ParamIn_1.VelType=VelType_1;
2224        ParamIn_1.Coord_x=get(handles.Coord_x,'String');
2225        ParamIn_1.Coord_y=get(handles.Coord_y,'Data');
2226        end 
2227        [Field{2},ParamOut_1,errormsg] = read_field(FileName_1,UvData.FileType{2},ParamIn_1,frame_index_1);
2228        if ~isempty(errormsg)
2229            errormsg=['error in reading ' FieldName_1 ' in ' FileName_1 ': ' errormsg];
2230            return
2231        end
2232        if isstruct(ParamOut_1)&&~strcmp(ParamOut_1.FieldName,'get_field...')&& (strcmp(UvData.FileType{2},'civdata')||strcmp(UvData.FileType{2},'civx'))...
2233                &&~strcmp(ParamOut_1.FieldName,'velocity') && ~strcmp(ParamOut_1.FieldName,'get_field...')
2234            if ~check_proj_tps
2235            end
2236        end
2237    end
2238    Field{2}.ZIndex=z_index;%used for multi-plane 3D calibration
2239end
2240
2241%% update uvmat interface
2242if isfield(ParamOut,'Npx')
2243    set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2244    set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2245elseif isfield(ParamOut_1,'Npx')
2246    set(handles.num_Npx,'String',num2str(ParamOut_1.Npx));% display image size on the interface
2247    set(handles.num_Npy,'String',num2str(ParamOut_1.Npy));
2248end
2249
2250%% update the display menu for the first velocity type (first menuline)
2251test_veltype=0;
2252if (strcmp(UvData.FileType{1},'civx')||strcmp(UvData.FileType{1},'civdata'))&& ~strcmp(FieldName,'get_field...')
2253    test_veltype=1;
2254    set(handles.VelType,'Visible','on')
2255    set(handles.VelType_1,'Visible','on')
2256    set(handles.FixVelType,'Visible','on')
2257    menu=set_veltype_display(ParamOut.CivStage,UvData.FileType{1});
2258    index_menu=strcmp(ParamOut.VelType,menu);%look for VelType in  the menu
2259    index_val=find(index_menu,1);
2260    if isempty(index_val)
2261        index_val=1;
2262    end
2263    set(handles.VelType,'Value',index_val)
2264    if ~get(handles.SubField,'value')
2265        set(handles.VelType,'String',menu)
2266        set(handles.VelType_1,'Value',1)
2267        set(handles.VelType_1,'String',[{''};menu])
2268    end
2269else
2270    set(handles.VelType,'Visible','off')
2271end
2272
2273%% update the display menu for the second velocity type (second menuline)
2274test_veltype_1=0;
2275if isempty(FileName_1)
2276    %     set(handles.FieldName_1,'Value',1); %update the field menu
2277    %     if isstruct(ParamOut)
2278    %     set(handles.FieldName_1,'String',[{''};ParamOut.FieldList]); %update the field menu
2279    %     end
2280elseif ~test_keepdata_1
2281    if (strcmp(UvData.FileType{2},'civx')||strcmp(UvData.FileType{2},'civdata'))&& ~strcmp(FieldName_1,'get_field...')
2282%     if (~strcmp(UvData.FileType{2},'netcdf')&&~strcmp(UvData.FileType{2},'civdata')&&~strcmp(UvData.FileType{2},'civx'))|| isequal(FieldName_1,'get_field...')
2283        test_veltype_1=1;
2284        set(handles.VelType_1,'Visible','on')
2285        menu=set_veltype_display(ParamOut_1.CivStage,UvData.FileType{2});
2286        index_menu=strcmp(ParamOut_1.VelType,menu);
2287        set(handles.VelType_1,'Value',1+find(index_menu,1))
2288        set(handles.VelType_1,'String',[{''};menu])
2289    else
2290         set(handles.VelType_1,'Visible','off')
2291    end
2292    % update the second field menu: the same quantity
2293    if isstruct(ParamOut_1)
2294        % display the FieldName menu from the input file and pick the selected one:
2295        FieldList=get(handles.FieldName_1,'String');
2296        field_index=strcmp(ParamOut_1.FieldName,FieldList);
2297        if ~isempty(field_index)
2298            set(handles.FieldName_1,'Value',find(field_index,1))
2299        end
2300    end
2301end
2302if test_veltype||test_veltype_1
2303    set(handles.FixVelType,'Visible','on')
2304else
2305    set(handles.FixVelType,'Visible','off')
2306end
2307   
2308%% introduce w as background image by default for a new series (only for nbdim=2)
2309if ~isfield(UvData,'NewSeries')
2310    UvData.NewSeries=1;
2311end
2312%put W as background image by default if NbDim=2:
2313if  UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W) && ~isequal(Field{1}.NbDim,3);
2314        set(handles.SubField,'Value',1);
2315        set(handles.RootPath_1,'String','"')
2316        set(handles.RootFile_1,'String','"')
2317        set(handles.SubDir_1,'String','"');
2318         indices=fullfile_uvmat('','','','',NomType,num_i1,num_i2,num_j1,num_j2);
2319        set(handles.FileIndex_1,'String',indices)
2320        set(handles.FileExt_1,'String','"');
2321        set(handles.FieldName_1,'Visible','on');
2322        set(handles.FieldName_1,'Visible','on');
2323        set(handles.RootPath_1,'Visible','on')
2324        set(handles.RootFile_1,'Visible','on')
2325        set(handles.SubDir_1,'Visible','on');
2326        set(handles.FileIndex_1,'Visible','on');
2327        set(handles.FileExt_1,'Visible','on');
2328        set(handles.FieldName_1,'Visible','on');
2329        Field{1}.AName='w';
2330end           
2331
2332%% display time value of the current file
2333abstime=[];%default inputs
2334dt=[];
2335TimeUnit='';
2336if isfield(UvData,'TimeUnit')
2337TimeUnit=UvData.TimeUnit;%retrieve info from update_rootinfo
2338end
2339% time from xml file or video movie
2340TimeName=get(handles.TimeName,'String');% indicate that time is from xml
2341if strcmp(TimeName,'xml')||strcmp(TimeName,'video')
2342    if isempty(num_i2)||isnan(num_i2)
2343        num_i2=num_i1;
2344    end
2345    if isempty(num_j1)||isnan(num_j1)
2346        num_j1=1;
2347    end
2348    if isempty(num_j2)||isnan(num_j2)
2349        num_j2=num_j1;
2350    end
2351    siz=size(UvData.XmlData{1}.Time);
2352    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)
2353        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
2354        dt=(UvData.XmlData{1}.Time(num_i2+1,num_j2+1)-UvData.XmlData{1}.Time(num_i1+1,num_j1+1));
2355        Field{1}.Dt=dt;
2356        if isfield(UvData.XmlData{1},'TimeUnit')
2357            TimeUnit=UvData.XmlData{1}.TimeUnit;
2358        end
2359    end
2360end
2361
2362% get time in the input file, not defined in a xml file or movie
2363if isempty(abstime)
2364    if strcmp(TimeName,'civdata')||strcmp(TimeName,'civx')
2365        abstime=Field{1}.Time;
2366    elseif ~isempty(regexp(TimeName,'^att:'))||~isempty(regexp(TimeName,'^var:'))
2367        abstime=Field{1}.(TimeName(5:end));%the time is an attribute or variale selected by get_file
2368    elseif ~isempty(regexp(TimeName,'^dim:'))
2369        abstime=str2num(get(handles.i1,'String'));
2370    end
2371    if isfield(Field{1},'Dt')
2372        dt=Field{1}.Dt;%dt read from the netcdf input file
2373        if isfield(Field{1},'TimeUnit')
2374            TimeUnit=Field{1}.TimeUnit;
2375        end
2376    elseif numel(Field)==2 && isfield(Field{2},'Dt')%dt obtained from the second field if not defined in the first
2377        dt=Field{2}.Dt;%dt read from the netcdf input file
2378        if isfield(Field{2},'TimeUnit')
2379            TimeUnit=Field{2}.TimeUnit;
2380        end
2381    end
2382end
2383set(handles.TimeValue,'String',num2str(abstime))
2384
2385%% display time value of the second current file if relevant
2386abstime_1=[];
2387if ~isempty(FileName_1)
2388    TimeName_1=get(handles.TimeName_1,'String');% indicate whether time is from xml or video
2389    % time from xml file or video movie as a second file series
2390    if strcmp(TimeName_1,'xml')||strcmp(TimeName_1,'video')
2391        if numel(UvData.XmlData)==2
2392            if isempty(i2_1)
2393                i2_1=num_i1;
2394            end
2395            if isempty(j1_1)
2396                j1_1=1;
2397            end
2398            if isempty(j2_1)
2399                j2_1=j1_1;
2400            end
2401            siz=size(UvData.XmlData{2}.Time);
2402            if ~isempty(i1_1) && siz(1)>=max(i1_1+1,i2_1+1) && siz(2)>=max(j1_1+1,j2_1+1)
2403                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
2404                Field{2}.Dt=(UvData.XmlData{2}.Time(i2_1+1,j2_1+1)-UvData.XmlData{2}.Time(i1_1+1,j1_1+1));
2405            end
2406        end
2407    end
2408   
2409    % get time in the input file of the second series, not defined in a xml file or movie
2410    if isempty(abstime_1) && numel(Field)==2
2411         if strcmp(TimeName_1,'civdata')||strcmp(TimeName_1,'civx')
2412        abstime_1=Field{2}.Time;
2413         elseif  ~isempty(regexp(TimeName_1,'^att:')) ||~isempty(regexp(TimeName_1,'^dim:'))||~isempty(regexp(TimeName_1,'^var:'))
2414        abstime_1=Field{2}.(TimeName_1(5:end));%the time is an attribute or variale selected by get_file
2415         end
2416    end
2417    set(handles.TimeValue_1,'String',num2str(abstime_1,5))
2418end
2419
2420if isempty(dt)||isequal(dt,0)
2421    set(handles.Dt_txt,'String','')
2422else
2423    if  isempty(TimeUnit)
2424        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  10^(-3)'] )
2425    else
2426        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  m' TimeUnit] )
2427    end
2428end
2429
2430%% Time title with unit
2431if isempty(abstime)&&isempty(abstime_1)
2432    Time_title='';
2433else
2434    Time_title='Time';
2435    if ~isempty(TimeUnit)
2436        Time_title=['Time (' TimeUnit ')'];
2437    end
2438end
2439set(handles.Time_title,'String',Time_title)
2440
2441%% store the current open names, fieldname and vel types in uvmat interface
2442UvData.FileName_1=FileName_1;
2443UvData.ParamOut_1=ParamOut_1;
2444if numel(Field)==2
2445    UvData.Field_1=Field{2}; %store the second field for possible use at next RUN
2446end
2447
2448%% apply coordinate transform or other user fct
2449transform=get(handles.TransformPath,'UserData');
2450if isempty(transform)
2451    UvData.Field=Field{1};
2452else
2453    XmlData=[];%default
2454    XmlData_1=[];%default
2455    if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority
2456        XmlData=UvData.XmlData{1};
2457        if numel(UvData.XmlData)==2
2458            XmlData_1=UvData.XmlData{2};
2459        end
2460    end
2461    switch nargin(transform)
2462        case 4
2463            if length(Field)==2
2464                UvData.Field=transform(Field{1},XmlData,Field{2},XmlData_1);
2465            else
2466                UvData.Field=transform(Field{1},XmlData);
2467            end
2468        case 3
2469            if length(Field)==2
2470                UvData.Field=transform(Field{1},XmlData,Field{2});
2471            else
2472                UvData.Field=transform(Field{1},XmlData);
2473            end
2474        case 2
2475            UvData.Field=transform(Field{1},XmlData);
2476        case 1
2477            UvData.Field=transform(Field{1});
2478    end
2479end
2480
2481%% calculate tps coefficients if needed
2482UvData.Field=tps_coeff_field(UvData.Field,check_proj_tps);
2483
2484%% get bounds and dimensions of the input field
2485UvData.Field=find_field_bounds(UvData.Field);
2486
2487if UvData.Field.NbDim>1
2488    % default projection plane
2489    if isempty(UvData.ProjObject{1})
2490        UvData.ProjObject{1}.Type='plane';%main plotting plane
2491        UvData.ProjObject{1}.ProjMode='projection';%main plotting plane
2492       % UvData.ProjObject{1}.Coord=[0 0 0];
2493        UvData.ProjObject{1}.DisplayHandle.uvmat=[]; %plane not visible in uvmat
2494        UvData.ProjObject{1}.DisplayHandle.view_field=[]; %plane not visible in uvmat
2495    end
2496    %% 3D case (menuvolume)
2497    if UvData.Field.NbDim==3% && UvData.NewSeries
2498        test_set_object=1;
2499        hset_object=findobj(allchild(0),'tag','set_object');% look for the set_object GUI
2500        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
2501        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
2502        if ~isempty(hset_object) %if set_object is detected
2503            delete(hset_object);% delete the GUI set_object if it does not fit
2504        end
2505        if test_set_object% reinitiate the GUI set_object
2506            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
2507            UvData.ProjObject{1}.NbDim=NbDim;%test for 3D objects
2508            UvData.ProjObject{1}.RangeZ=UvData.Field.CoordMesh;%main plotting plane
2509            UvData.ProjObject{1}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen
2510            UvData.ProjObject{1}.Angle=[0 0 0];
2511            UvData.ProjObject{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR
2512            UvData.ProjObject{1}.Name='1-PLANE';
2513            UvData.ProjObject{1}.enable_plot=1;
2514            set_object(UvData.ProjObject{1},handles,ZBounds);
2515            set(handles.ListObject,'Value',1);
2516            set(handles.ListObject,'String',{'1-PLANE'});
2517            set(handles.CheckEditObject,'Value',1)% put the plane in edit mode to enable the z cursor
2518            CheckEditObject_Callback([],[], handles)
2519        end
2520        %multilevel case (single menuplane in a 3D space)
2521    elseif isfield(UvData,'Z')
2522        if isfield(UvData,'CoordType')&& isequal(UvData.CoordType,'phys') && isfield(UvData,'XmlData')
2523            XmlData=UvData.XmlData{1};
2524            if isfield(XmlData,'PlanePos')
2525                UvData.ProjObject{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:);
2526            end
2527            if isfield(XmlData,'PlaneAngle')
2528                siz=size(XmlData.PlaneAngle);
2529                indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning)
2530                UvData.ProjObject{1}.PlaneAngle=XmlData.PlaneAngle(indangle,:);
2531            end
2532        elseif isfield(UvData,'ZIndex')
2533            UvData.ProjObject{1}.ZObject=UvData.ZIndex;
2534        end
2535    end
2536end
2537
2538testnewseries=UvData.NewSeries;
2539UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback)
2540set(handles.uvmat,'UserData',UvData)
2541
2542%% reset the min and max of scalar if only the mask is displayed(TODO: check the need)
2543% if isfield(UvData,'Mask')&& ~isfield(UvData,'A')
2544%     set(handles.num_MinA,'String','0')
2545%     set(handles.num_MaxA,'String','255')
2546% end
2547
2548%% usual 1D (x,y) plots
2549if UvData.Field.NbDim<=1
2550    set(handles.Objects,'Visible','off')
2551%     set(handles.ListObject_1_title,'Visible','off')
2552%     set(handles.ListObject_1,'Visible','off')
2553    [PlotType,PlotParamOut]=plot_field(UvData.Field,handles.PlotAxes,read_GUI(handles.uvmat));
2554    errormsg=fill_GUI(PlotParamOut,handles.uvmat);
2555    for list={'Scalar','Vectors'}
2556        if ~isfield(PlotParamOut,list{1})
2557            set(handles.(list{1}),'Visible','off')
2558        end
2559    end
2560   
2561%% 2D or 3D fieldname are generally projected
2562else
2563    set(handles.Objects,'Visible','on')
2564%     set(handles.ListObject_1_title,'Visible','on')
2565%     set(handles.ListObject_1,'Visible','on')
2566   
2567    %% Plot the projections on the selected  projection objects
2568    % main projection object (uvmat display)
2569    list_object=get(handles.ListObject_1,'String');
2570    if isequal(list_object,{''})||isequal(list_object,' ')%refresh list of objects if the menu is empty
2571        set(handles.ListObject,'Value',1)
2572        set(handles.ListObject,'String',{'plane'})
2573        UvData.ProjObject{1}.Type='plane';%main plotting plane
2574        UvData.ProjObject{1}.ProjMode='projection';%main plotting plane
2575        UvData.ProjObject{1}.DisplayHandle.uvmat=[]; %plane not visible in uvmat
2576        UvData.ProjObject{1}.DisplayHandle.view_field=[]; %plane not visible in uvmat
2577        set(handles.ListObject_1,'Value',1)
2578        set(handles.ListObject_1,'String',{'plane'})
2579    end
2580    IndexObj=get(handles.ListObject_1,'Value');%selected projection object for main view
2581    if IndexObj> numel(UvData.ProjObject)
2582        IndexObj=1;%select the first object if the selected one does not exist
2583        set(handles.ListObject_1,'Value',1)
2584    end
2585    if get(handles.CheckViewField,'Value')
2586        IndexObj_2=get(handles.ListObject,'Value');%selected projection object for view_field
2587        if ~isequal(IndexObj_2,IndexObj(1))
2588            IndexObj(2)=IndexObj_2;
2589        end
2590    end
2591    plot_handles{1}=handles;
2592    if isfield(UvData,'plotaxes')%case of movies
2593        haxes(1)=UvData.plotaxes;
2594    else
2595        haxes(1)=handles.PlotAxes;
2596    end
2597    PlotParam{1}=read_GUI(handles.uvmat);
2598    %default settings if vectors not visible
2599    if ~isfield(PlotParam{1},'Vectors')
2600        PlotParam{1}.Vectors.MaxVec=1;
2601        PlotParam{1}.Vectors.MinVec=0;
2602        PlotParam{1}.Vectors.CheckFixVecColor=1;
2603        PlotParam{1}.Vectors.ColCode1=0.33;
2604        PlotParam{1}.Vectors.ColCode2=0.66;
2605        PlotParam{1}.Vectors.ColorScalar={''};
2606        PlotParam{1}.Vectors.ColorCode= {'rgb'};
2607    end
2608    PosColorbar{1}=UvData.OpenParam.PosColorbar;%prescribe the colorbar position on the uvmat interface
2609   
2610    %% second projection object (view_field display)
2611    if length( IndexObj)>=2
2612        view_field_handle=findobj(allchild(0),'tag','view_field');%handles of the view_field GUI
2613        if ~isempty(view_field_handle)
2614            plot_handles{2}=guidata(view_field_handle);
2615            haxes(2)=plot_handles{2}.PlotAxes;
2616            PlotParam{2}=read_GUI(view_field_handle);
2617           % PlotParam{2}=read_GUI(handles.uvmat);%read plotting parameters on the uvmat interface
2618            PosColorbar{2}='*'; %TODO: deal with colorbar position on view_field
2619        end
2620    end
2621   
2622    %% loop on the projection objects: one or two
2623   
2624    for imap=1:numel(IndexObj)
2625        iobj=IndexObj(imap);
2626        if numel(UvData.ProjObject)<iobj
2627            break
2628        end
2629        [ObjectData,errormsg]=proj_field(UvData.Field,UvData.ProjObject{iobj});% project field on the object
2630        if ~isempty(errormsg)
2631            return
2632        end
2633        if testnewseries
2634            PlotParam{imap}.Scalar.CheckBW=[]; %B/W option depends on the input field (image or scalar)
2635            if isfield(ObjectData,'CoordUnit')
2636                PlotParam{imap}.Coordinates.CheckFixAspectRatio=1;% set x and y scaling equal if CoordUnit is defined (common unit for x and y)
2637                PlotParam{imap}.Coordinates.AspectRatio=1; %set aspect ratio to 1
2638            end
2639        end
2640        %use of mask (TODO: check)
2641        if isfield(ObjectData,'NbDim') && isequal(ObjectData.NbDim,2) && isfield(ObjectData,'Mask') && isfield(ObjectData,'A')
2642            flag_mask=double(ObjectData.Mask>200);%=0 for masked regions
2643            AX=ObjectData.AX;%x coordiantes for the scalar field
2644            AY=ObjectData.AY;%y coordinates for the scalar field
2645            MaskX=ObjectData.MaskX;%x coordiantes for the mask
2646            MaskY=ObjectData.MaskY;%y coordiantes for the mask
2647            if ~isequal(MaskX,AX)||~isequal(MaskY,AY)
2648                nxy=size(flag_mask);
2649                sizpx=(ObjectData.MaskX(end)-ObjectData.MaskX(1))/(nxy(2)-1);%size of a mask pixel
2650                sizpy=(ObjectData.MaskY(1)-ObjectData.MaskY(end))/(nxy(1)-1);
2651                x_mask=ObjectData.MaskX(1):sizpx:ObjectData.MaskX(end); % pixel x coordinates for image display
2652                y_mask=ObjectData.MaskY(1):-sizpy:ObjectData.MaskY(end);% pixel x coordinates for image display
2653                %project on the positions of the scalar
2654                npxy=size(ObjectData.A);
2655                dxy(1)=(ObjectData.AY(end)-ObjectData.AY(1))/(npxy(1)-1);%grid mesh in y
2656                dxy(2)=(ObjectData.AX(end)-ObjectData.AX(1))/(npxy(2)-1);%grid mesh in x
2657                xi=ObjectData.AX(1):dxy(2):ObjectData.AX(end);
2658                yi=ObjectData.AY(1):dxy(1):ObjectData.AY(end);
2659                [XI,YI]=meshgrid(xi,yi);% creates the matrix of regular coordinates
2660                flag_mask = interp2(x_mask,y_mask,flag_mask,XI,YI);
2661            end
2662            AClass=class(ObjectData.A);
2663            ObjectData.A=flag_mask.*double(ObjectData.A);
2664            ObjectData.A=feval(AClass,ObjectData.A);
2665        end
2666        if ~isempty(ObjectData)
2667            %PlotType='none'; %default
2668            if imap==2 && isempty(view_field_handle)
2669                view_field(ObjectData)
2670            else
2671              %  ObjectData.VarAttribute{5}.Role='scalar';TODO    CORRECT
2672                [PlotType,PlotParamOut]=plot_field(ObjectData,haxes(imap),PlotParam{imap},PosColorbar{imap});
2673                if imap==1
2674                    errormsg=fill_GUI(PlotParamOut,handles.uvmat);
2675                else
2676                    errormsg=fill_GUI(PlotParamOut,view_field_handle);
2677                end
2678                for list={'Scalar','Vectors'}
2679                    if ~isfield(PlotParamOut,list{1})
2680                        set(plot_handles{imap}.(list{1}),'Visible','off')
2681                    end
2682                end
2683                if isfield(Field,'CoordMesh')&&~isempty(Field.CoordMesh)
2684                    ObjectData.CoordMesh=Field.CoordMesh; % gives an estimated mesh size (useful for mouse action on the plot)
2685                end
2686            end
2687        end
2688    end
2689   
2690    %% update the mask
2691    if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
2692        update_mask(handles);
2693    end
2694   
2695    %% prepare the menus of histograms and plot them (histogram of the whole volume in 3D case)
2696    menu_histo=(UvData.Field.ListVarName)';%list of field variables to be displayed for the menu of histogram display
2697    ind_skip=[];
2698    % nb_histo=1;
2699    Ustring='';
2700    Vstring='';
2701    % suppress coordinates from the histogram menu
2702    for ivar=1:numel(menu_histo)%l loop on field variables:
2703        if isfield(UvData.Field,'VarAttribute') && numel(UvData.Field.VarAttribute)>=ivar && isfield(UvData.Field.VarAttribute{ivar},'Role')
2704            Role=UvData.Field.VarAttribute{ivar}.Role;
2705            switch Role
2706                case {'coord_x','coord_y','coord_z','dimvar'}
2707                    ind_skip=[ind_skip ivar];
2708                case {'vector_x'}
2709                    Ustring=UvData.Field.ListVarName{ivar};
2710                    ind_skip=[ind_skip ivar];
2711                case {'vector_y'}
2712                    Vstring=UvData.Field.ListVarName{ivar};
2713                    ind_skip=[ind_skip ivar];
2714            end
2715        end
2716        DimCell=UvData.Field.VarDimName{ivar};
2717        DimName='';
2718        if ischar(DimCell)
2719            DimName=DimCell;
2720        elseif iscell(DimCell)&& numel(DimCell)==1
2721            DimName=DimCell{1};
2722        end
2723        if strcmp(DimName,menu_histo{ivar})
2724            ind_skip=[ind_skip ivar];
2725        end
2726    end
2727    menu_histo(ind_skip)=[];% remove skipped items
2728    if ~isempty(Ustring)
2729        menu_histo=[{[Ustring ',' Vstring]};menu_histo];% add U, V at the beginning if they exist
2730    end
2731   
2732    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2733    % display menus and plot histograms
2734    test_v=0;
2735    if ~isempty(menu_histo)
2736        set(handles.histo1_menu,'Value',1)
2737        set(handles.histo1_menu,'String',menu_histo)
2738        histo1_menu_Callback(handles.histo1_menu, [], handles)% plot first histogram
2739    end
2740end
2741ResizeFcn(handles.uvmat,[],handles)
2742
2743%------------------------------------------------------------------------
2744function histo1_menu_Callback(hObject, eventdata, handles)
2745%--------------------------------------------
2746histo_menu=get(handles.histo1_menu,'String');
2747histo_value=get(handles.histo1_menu,'Value');
2748FieldName=histo_menu{histo_value};
2749
2750UvData=get(handles.uvmat,'UserData');
2751Field=UvData.Field;
2752r=regexp(FieldName,'(?<var1>.*)(?<sep>,)(?<var2>.*)','names');
2753FieldName_2='';
2754if ~isempty(r)
2755    FieldName=r.var1;
2756    FieldName_2=r.var2;
2757end
2758if ~isfield(UvData.Field,FieldName)
2759    msgbox_uvmat('ERROR',['no field  ' FieldName ' for histogram'])
2760    return
2761end
2762FieldHisto=Field.(FieldName);
2763if isfield(Field,'FF') && ~isempty(Field.FF) && isequal(size(Field.FF),size(FieldHisto))
2764    indsel=find(Field.FF==0);%find values marked as false
2765    if ~isempty(indsel)
2766        FieldHisto=FieldHisto(indsel);
2767        if ~isempty(FieldName_2)
2768            FieldHisto(:,:,2)=Field.(FieldName_2)(indsel);
2769        end
2770    end
2771elseif ~isempty(FieldName_2)
2772    FieldHisto(:,:,2)=Field.(FieldName_2);
2773end
2774if isempty(Field)
2775    msgbox_uvmat('ERROR',['empty field ' FieldName])
2776else
2777    nxy=size(FieldHisto);
2778    Amin=double(min(min(min(FieldHisto))));%min of field value
2779    Amax=double(max(max(max(FieldHisto))));%max of field value
2780    if isequal(Amin,Amax)
2781        cla(handles.HistoAxes)
2782    else
2783        Histo.ListVarName={FieldName,'histo'};
2784        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
2785            Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
2786        else
2787            if numel(nxy)==2
2788                Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
2789            else
2790                Histo.VarDimName={FieldName,{FieldName,'component'}}; %dimensions for the histogram
2791            end
2792        end
2793        %unit
2794        units=[]; %default
2795        for ivar=1:numel(Field.ListVarName)
2796            if strcmp(Field.ListVarName{ivar},FieldName)
2797                if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'units')
2798                    units=Field.VarAttribute{ivar}.units;
2799                    break
2800                end
2801            end
2802        end
2803        if ~isempty(units)
2804            Histo.VarAttribute{1}.units=units;
2805        end
2806        eval(['Histo.' FieldName '=linspace(Amin,Amax,50);'])%absissa values for histo
2807        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
2808            C=reshape(double(FieldHisto),1,[]);% reshape in a vector
2809            Histo.histo(:,1)=hist(C, Histo.(FieldName));  %calculate histogram
2810        else
2811            for col=1:size(FieldHisto,3)
2812                B=FieldHisto(:,:,col);
2813                C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector
2814                Histo.histo(:,col)=hist(C, Histo.(FieldName));  %calculate histogram
2815            end
2816        end
2817        plot_field(Histo,handles.HistoAxes);
2818        hlegend=legend;
2819        if isempty(FieldName_2)
2820        set(hlegend,'String',FieldName)
2821        else
2822            set(hlegend,'String',{FieldName;FieldName_2})
2823        end
2824    end
2825end
2826
2827%------------------------------------------------------------------------
2828% --- translate coordinate to matrix index
2829%------------------------------------------------------------------------
2830function [indx,indy]=pos2ind(x0,rangx0,nxy)
2831indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel 
2832indy=1+round((nxy(1)-1)*(y12-rangy0(1))/(rangy0(2)-rangy0(1)));% index y of pixel
2833
2834%------------------------------------------------------------------------
2835% --- Executes on button press in 'CheckZoom'.
2836%------------------------------------------------------------------------
2837function CheckZoom_Callback(hObject, eventdata, handles)
2838
2839    if get(handles.CheckZoom,'Value')
2840        set(handles.CheckFixLimits,'Value',1)% propose by default fixed limits for the plotting axes
2841        set(handles.CheckZoomFig,'Value',0)%desactivate zoom fig
2842    end
2843
2844
2845%------------------------------------------------------------------------
2846% --- Executes on button press in CheckZoomFig.
2847%------------------------------------------------------------------------
2848function CheckZoomFig_Callback(hObject, eventdata, handles)
2849
2850if get(handles.CheckZoomFig,'Value')
2851    set(handles.CheckZoom,'value',0)
2852end
2853
2854%------------------------------------------------------------------------
2855% --- Executes on button press in 'CheckFixLimits'.
2856%------------------------------------------------------------------------
2857function CheckFixLimits_Callback(hObject, eventdata, handles)
2858
2859if ~get(handles.CheckFixLimits,'Value')
2860    update_plot(handles)
2861    set(handles.CheckZoom,'Value',0)
2862end
2863
2864%------------------------------------------------------------------------
2865% --- Executes on button press in CheckFixAspectRatio.
2866function CheckFixAspectRatio_Callback(hObject, eventdata, handles)
2867%------------------------------------------------------------------------
2868
2869% if get(handles.CheckFixAspectRatio,'Value')
2870    update_plot(handles);
2871% else
2872%     update_plot(handles);
2873% end
2874
2875%------------------------------------------------------------------------
2876function num_AspectRatio_Callback(hObject, eventdata, handles)
2877%------------------------------------------------------------------------
2878set(handles.CheckFixAspectRatio,'Value',1)% select the fixed aspect ratio button
2879update_plot(handles);
2880
2881%------------------------------------------------------------------------
2882%----Executes on button press in 'record': records the current flags of manual correction.
2883%------------------------------------------------------------------------
2884function record_Callback(hObject, eventdata, handles)
2885
2886[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
2887FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
2888[erread,message]=fileattrib(FileName);
2889if ~isempty(message) && ~isequal(message.UserWrite,1)
2890     msgbox_uvmat('ERROR',['no writting access to ' FileName])
2891     return
2892end
2893MenuVelType=get(handles.VelType,'String');
2894test_civ2=strcmp(MenuVelType{get(handles.VelType,'Value')},'civ2');
2895test_civ1=strcmp(MenuVelType{get(handles.VelType,'Value')},'civ1');
2896if ~test_civ2 && ~test_civ1
2897    msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
2898end
2899if test_civ2
2900    nbname='nb_vec_2';
2901   flagname='Civ2_FF';
2902   CivStage=5;
2903end
2904if test_civ1
2905    nbname='nb_vec_1';
2906   flagname='Civ1_FF';
2907    CivStage=2;
2908end
2909%write fix flags in the netcdf file
2910UvData=get(handles.uvmat,'UserData');
2911hhh=which('netcdf.open');% look for built-in matlab netcdf library
2912if ~isequal(hhh,'')% case of  builtin Matlab netcdf library
2913    nc=netcdf.open(FileName,'NC_WRITE');
2914    netcdf.reDef(nc);
2915    netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),'CivStage',CivStage);
2916    dimid = netcdf.inqDimID(nc,nbname);
2917    try
2918        varid = netcdf.inqVarID(nc,flagname);% look for already existing fixflag variable
2919    catch
2920        varid=netcdf.defVar(nc,flagname,'double',dimid);%create fixflag variable if it does not exist
2921    end
2922    netcdf.endDef(nc);
2923    netcdf.putVar(nc,varid,UvData.PlotAxes.FF);
2924    netcdf.close(nc); 
2925else %old netcdf library
2926    netcdf_toolbox(FileName,AxeData,attrname,nbname,flagname)
2927end
2928
2929%-------------------------------------------------------------------
2930%----Correct the netcdf file, using toolbox (old versions of Matlab).
2931%-------------------------------------------------------------------
2932function netcdf_toolbox(FileName,AxeData,attrname,nbname,flagname)
2933nc=netcdf(FileName,'write'); %open netcdf file
2934result=redef(nc);
2935eval(['nc.' attrname '=1;']);
2936theDim=nc(nbname) ;% get the number of velocity vectors
2937nb_vectors=size(theDim);
2938var_FixFlag=ncvar(flagname,nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag
2939var_FixFlag(1:nb_vectors)=AxeData.FF;%
2940fin=close(nc);
2941
2942%-----------------------------------------------------------------------
2943% --- Executes on button press in SubField
2944%-----------------------------------------------------------------------
2945function SubField_Callback(hObject, eventdata, handles)
2946
2947if get(handles.SubField,'Value')==0% if the subfield button is desactivated 
2948    desable_subfield(handles)
2949    transform_fct_list=get(handles.TransformName,'String');
2950    transform_fct=transform_fct_list(get(handles.TransformName,'Value'));
2951    if strcmp(transform_fct,'sub_field')
2952        set(handles.TransformName,'Value',1)%suppress the sub_field transform
2953        TransformName_Callback(hObject, eventdata, handles);
2954    else
2955        REFRESH_Callback(hObject, eventdata, handles)
2956    end 
2957else
2958    fileinput_1=uigetfile_uvmat('select a second input file:',get(handles.RootPath,'String'));
2959    if isempty(fileinput_1)
2960        set(handles.SubField,'Value',0)
2961    else       
2962        % refresh the current displayed field
2963        display_file_name(handles,fileinput_1,2)
2964       
2965        %update list of recent files in the menubar
2966        MenuFile_1=fileinput_1;
2967        MenuFile_2=get(handles.MenuFile_1,'Label');
2968        MenuFile_3=get(handles.MenuFile_2,'Label');
2969        MenuFile_4=get(handles.MenuFile_3,'Label');
2970        MenuFile_5=get(handles.MenuFile_4,'Label');
2971        set(handles.MenuFile_1,'Label',MenuFile_1)
2972        set(handles.MenuFile_2,'Label',MenuFile_2)
2973        set(handles.MenuFile_3,'Label',MenuFile_3)
2974        set(handles.MenuFile_4,'Label',MenuFile_4)
2975        set(handles.MenuFile_5,'Label',MenuFile_5)
2976    end
2977end
2978
2979%-----------------------------------------------------------------------
2980% --- desactivate display used for a second file series
2981%-----------------------------------------------------------------------
2982function desable_subfield(handles)
2983   
2984set(handles.RootPath_1,'String','')
2985set(handles.RootFile_1,'String','')
2986set(handles.SubDir_1,'String','');
2987set(handles.FileIndex_1,'String','');
2988set(handles.FileExt_1,'String','');
2989set(handles.RootPath_1,'Visible','off')
2990set(handles.RootFile_1,'Visible','off')
2991set(handles.SubDir_1,'Visible','off');
2992set(handles.NomType_1,'Visible','off');
2993set(handles.FileIndex_1,'Visible','off');
2994set(handles.FileExt_1,'Visible','off');
2995set(handles.TimeName_1,'String','');
2996set(handles.TimeName_1,'Visible','off');
2997set(handles.TimeValue_1,'String','');
2998set(handles.TimeValue_1,'Visible','off');
2999set(handles.FieldName_1,'Value',1);%set to blank state
3000set(handles.VelType_1,'Value',1);%set to blank state
3001set(handles.num_Opacity,'String','')% desactivate opacity setting
3002FieldList=get(handles.FieldName,'String');
3003if numel(FieldList)>1   % if a choice of fields exists
3004    set(handles.FieldName_1,'Value',1)% set second field choice to blank
3005    set(handles.FieldName_1,'String',[{''};FieldList])% reproduce the menu FieldName plus a blank option
3006else
3007    set(handles.FieldName_1,'String',{''})% set second field choice to blank
3008end
3009if ~strcmp(get(handles.VelType,'Visible'),'on')
3010    set(handles.VelType_1,'Visible','off')
3011end
3012UvData=get(handles.uvmat,'UserData');
3013if isfield(UvData,'XmlData_1')
3014    UvData=rmfield(UvData,'XmlData_1');
3015end
3016set(handles.uvmat,'UserData',UvData);
3017
3018%------------------------------------------------------------------------
3019% --- read the data displayed for the input rootfile windows (new): TODO use read_GUI
3020%------------------------------------------------------------------------
3021function [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles)
3022
3023InputFile=read_GUI(handles.InputFile);
3024RootPath=InputFile.RootPath;
3025SubDir=regexprep(InputFile.SubDir,'/|\','');
3026RootFile=regexprep(InputFile.RootFile,'/|\','');
3027FileIndices=InputFile.FileIndex;
3028FileExt=InputFile.FileExt;
3029
3030
3031%------------------------------------------------------------------------
3032% ---- read the data displayed for the second input rootfile windows
3033%------------------------------------------------------------------------
3034function [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1,NomType_1]=read_file_boxes_1(handles)
3035
3036RootPath_1=get(handles.RootPath_1,'String'); % read the data from the file1_input window
3037if isequal(get(handles.RootPath_1,'Visible'),'off') || isequal(RootPath_1,'"')
3038    RootPath_1=get(handles.RootPath,'String');
3039end;
3040SubDir_1=get(handles.SubDir_1,'String');
3041if isequal(get(handles.SubDir_1,'Visible'),'off')|| isequal(SubDir_1,'"')
3042    SubDir_1=get(handles.SubDir,'String');
3043end
3044SubDir_1=regexprep(SubDir_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3045RootFile_1=get(handles.RootFile_1,'String');
3046if isequal(get(handles.RootFile_1,'Visible'),'off') || isequal(RootFile_1,'"')
3047    RootFile_1=get(handles.RootFile,'String');
3048end
3049RootFile_1=regexprep(RootFile_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3050FileIndex_1=get(handles.FileIndex_1,'String');
3051if isequal(get(handles.FileIndex_1,'Visible'),'off')|| isequal(FileIndex_1,'"')
3052    FileIndex_1=get(handles.FileIndex,'String');
3053end
3054FileExt_1=get(handles.FileExt_1,'String');
3055if isequal(get(handles.FileExt_1,'Visible'),'off') || isequal(FileExt_1,'"')
3056    FileExt_1=get(handles.FileExt,'String');%read FileExt by default
3057end
3058NomType_1=get(handles.NomType_1,'String');
3059if isequal(get(handles.NomType_1,'Visible'),'off') || isequal(NomType_1,'"')
3060    NomType_1=get(handles.NomType,'String');%read FileExt by default
3061end
3062%------------------------------------------------------------------------
3063% --- Executes on menu selection FieldName
3064function FieldName_Callback(hObject, eventdata, handles)
3065%------------------------------------------------------------------------
3066
3067%% read data from uvmat
3068UvData=get(handles.uvmat,'UserData');
3069list_fields=get(handles.FieldName,'String');% list menu fields
3070index_fields=get(handles.FieldName,'Value');% selected string index
3071field= list_fields{index_fields(1)}; % selected string
3072[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3073FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3074[tild,tild,tild,i1,i2,j1,j2,tild,NomType]=fileparts_uvmat(['xxx' get(handles.FileIndex,'String') FileExt]);
3075
3076switch field
3077   
3078    case 'get_field...'
3079        %% fill the coordinates and variables from selections in get_field
3080        ParamIn=[];
3081        % in case of civ data, we use the civ choice as default input for the GUI get_field
3082        if strcmp(get(handles.VelType,'Visible'),'on')
3083            ParamIn.SwitchVarIndexTime='attribute';
3084            ListVelType=get(handles.VelType,'String');
3085            VelType=ListVelType{get(handles.VelType,'Value')};
3086            switch VelType
3087                case 'civ1'
3088                    ParamIn.TimeAttrName='Civ1_Time';
3089                    ParamIn.vector_x='Civ1_U';
3090                    ParamIn.vector_y='Civ1_V';
3091                    ParamIn.vec_color='Civ1_C';
3092                case 'filter1'
3093                    ParamIn.TimeAttrName='Civ1_Time';
3094                    ParamIn.vector_x='Civ1_U_smooth';
3095                    ParamIn.vector_y='Civ1_V_smooth';
3096                case 'civ2'
3097                    ParamIn.TimeAttrName='Civ2_Time';
3098                    ParamIn.vector_x='Civ2_U';
3099                    ParamIn.vector_y='Civ2_V';
3100                case 'filter2'
3101                    ParamIn.TimeAttrName='Civ2_Time';
3102                    ParamIn.vector_x='Civ2_U_smooth';
3103                    ParamIn.vector_y='Civ2_V_smooth';
3104                    ParamIn.vec_color='Civ2_C';
3105            end
3106        end
3107       
3108        % VelType menu desactivated
3109        set(handles.FixVelType,'visible','off')
3110        set(handles.VelType,'Visible','off')
3111       
3112        %read selection from get_field
3113        [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3114        FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3115        GetFieldData=get_field(FileName,ParamIn);% inport field names from the GUI get_field
3116        FieldList={};
3117        VecColorList={};
3118        switch GetFieldData.FieldOption
3119            case 'vectors'
3120                UName=GetFieldData.PanelVectors.vector_x;
3121                VName=GetFieldData.PanelVectors.vector_y;
3122                YName={GetFieldData.Coordinates.Coord_y};
3123                CName=GetFieldData.PanelVectors.vec_color;
3124                FieldList={['vec(' UName ',' VName ')'];...
3125                    ['norm(' UName ',' VName ')'];...
3126                    UName;VName};
3127                VecColorList={['norm(' UName ',' VName ')'];...
3128                    UName;VName};
3129                if ~isempty(CName)
3130                    VecColorList=[{CName};VecColorList];
3131                end
3132            case 'scalar'
3133                AName=GetFieldData.PanelScalar.scalar;
3134                YName={GetFieldData.Coordinates.Coord_y};
3135                FieldList={AName};
3136            case '1D plot'
3137                YName=GetFieldData.PanelOrdinate.ordinate;
3138            case 'civdata...'%reinitiate input, return to automatic civ data reading
3139                display_file_name(handles,FileName,1)
3140        end
3141        if ~strcmp(GetFieldData.FieldOption,'civdata...')
3142            XName=GetFieldData.Coordinates.Coord_x;
3143            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
3144            switch TimeNameStr
3145                case 'file index'
3146                    set(handles.TimeName,'String','');
3147                case 'attribute'
3148                    set(handles.TimeName,'String',['att:' GetFieldData.Time.TimeName]);
3149                case 'variable'
3150                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
3151                    set(handles.NomType,'String','*')
3152                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
3153                    set(handles.FileIndex,'String','')
3154                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
3155                case 'matrix_index'
3156                    set(handles.TimeName,'String',['dim:' GetFieldData.Time.TimeName]);
3157                    set(handles.NomType,'String','*')
3158                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
3159                    set(handles.FileIndex,'String','')
3160                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
3161            end
3162            set(handles.Coord_x,'String',XName)
3163            if ischar(YName)
3164                YName={YName};
3165            end
3166            set(handles.Coord_y,'Data',YName)
3167            set(handles.FieldName,'Value',1)
3168            set(handles.FieldName,'String',[FieldList; {'get_field...'}]);
3169            set(handles.ColorScalar,'Value',1)
3170            set(handles.ColorScalar,'String',VecColorList);
3171            UvData.FileType{1}='netcdf';
3172            set(handles.uvmat,'UserData',UvData)
3173            REFRESH_Callback(hObject, eventdata, handles)
3174        end
3175       
3176    case 'image'
3177        %% look for image corresponding to civ data
3178        if  isfield(UvData.Field,'Civ2_ImageA')%get the corresponding input image in the netcdf file
3179            imagename=UvData.Field.Civ2_ImageA;
3180        elseif isfield(UvData.Field,'Civ1_ImageA')%
3181            imagename=UvData.Field.Civ1_ImageA;
3182        else
3183            SubDirBase=regexprep(SubDir,'\..*','');%take the root part of SubDir, before the first dot '.'
3184            imagename=fullfile_uvmat(RootPath,SubDirBase,RootFile,'.png',NomType,i1,[],j1,[]);
3185        end
3186        if ~exist(imagename,'file')
3187            imagename=uigetfile_uvmat('Pick an image file',imagename,'image');
3188            if isempty(imagename)
3189                return
3190            end
3191        end
3192        % display the selected field and related information
3193        display_file_name(handles,imagename)%display the image
3194    otherwise
3195        REFRESH_Callback(hObject, eventdata, handles)
3196end
3197
3198%----------------------------------------------------------------
3199% --- Executes on menu selection FieldName
3200function FieldName_1_Callback(hObject, eventdata, handles)
3201%-------------------------------------------------
3202
3203%%%%%% TODO: modify like FieldName_Callback
3204%% read input data
3205check_new=~get(handles.SubField,'Value'); %check_new=1 if a second field was not previously entered
3206UvData=get(handles.uvmat,'UserData');
3207if check_new && isfield(UvData,'XmlData')
3208    UvData.XmlData{2}=UvData.XmlData{1};
3209end
3210if isfield(UvData,'Field_1')
3211    UvData=rmfield(UvData,'Field_1');% remove the stored second field (a new one needs to be read)
3212end
3213UvData.FileName_1='';% desactivate the use of a constant second file
3214list_fields=get(handles.FieldName,'String');% list menu fields
3215field= list_fields{get(handles.FieldName,'Value')}; % selected string
3216list_fields=get(handles.FieldName_1,'String');% list menu fields
3217field_1= list_fields{get(handles.FieldName_1,'Value')}; % selected string for the second field
3218if isempty(field_1)%||(numel(UvData.FileType)>=2 && strcmp(UvData.FileType{2},'image'))
3219    set(handles.SubField,'Value',0)
3220    SubField_Callback(hObject, eventdata, handles)
3221    return
3222else
3223    set(handles.SubField,'Value',1)%state that a second field is now entered
3224end
3225
3226%% read the rootfile input display
3227[RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
3228FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
3229[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
3230switch field_1
3231    case 'get_field...'
3232         %% fill the coordinates and variables from selections in get_field
3233        ParamIn=[];
3234        % in case of civ data, we use the civ choice as default input for the GUI get_field
3235        if strcmp(get(handles.VelType_1,'Visible'),'on')
3236            ParamIn.SwitchVarIndexTime='attribute';
3237            ListVelType=get(handles.VelType_1,'String');
3238            VelType=ListVelType{get(handles.VelType_1,'Value')};
3239            switch VelType
3240                case 'civ1'
3241                    ParamIn.TimeAttrName='Civ1_Time';
3242                    ParamIn.vector_x='Civ1_U';
3243                    ParamIn.vector_y='Civ1_V';
3244                    ParamIn.vec_color='Civ1_C';
3245                case 'filter1'
3246                    ParamIn.TimeAttrName='Civ1_Time';
3247                    ParamIn.vector_x='Civ1_U_smooth';
3248                    ParamIn.vector_y='Civ1_V_smooth';
3249                case 'civ2'
3250                    ParamIn.TimeAttrName='Civ2_Time';
3251                    ParamIn.vector_x='Civ2_U';
3252                    ParamIn.vector_y='Civ2_V';
3253                case 'filter2'
3254                    ParamIn.TimeAttrName='Civ2_Time';
3255                    ParamIn.vector_x='Civ2_U_smooth';
3256                    ParamIn.vector_y='Civ2_V_smooth';
3257                    ParamIn.vec_color='Civ2_C';
3258            end
3259        end
3260       
3261        % VelType menu desactivated
3262        set(handles.FixVelType,'visible','off')
3263        set(handles.VelType,'Visible','off')
3264       
3265        %read selection from get_field
3266        [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
3267        FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3268        GetFieldData=get_field(FileName,ParamIn);% inport field names from the GUI get_field
3269        FieldList={};
3270        VecColorList={};
3271        switch GetFieldData.FieldOption
3272            case 'vectors'
3273                UName=GetFieldData.PanelVectors.vector_x;
3274                VName=GetFieldData.PanelVectors.vector_y;
3275                YName={GetFieldData.Coordinates.Coord_y};
3276                CName=GetFieldData.PanelVectors.vec_color;
3277                FieldList={['vec(' UName ',' VName ')'];...
3278                    ['norm(' UName ',' VName ')'];...
3279                    UName;VName};
3280                VecColorList={['norm(' UName ',' VName ')'];...
3281                    UName;VName};
3282                if ~isempty(CName)
3283                    VecColorList=[{CName};VecColorList];
3284                end
3285            case 'scalar'
3286                AName=GetFieldData.PanelScalar.scalar;
3287                YName={GetFieldData.Coordinates.Coord_y};
3288                FieldList={AName};
3289            case '1D plot'
3290                YName=GetFieldData.PanelOrdinate.ordinate;
3291            case 'civdata...'%reinitiate input, return to automatic civ data reading
3292                display_file_name(handles,FileName,1)
3293        end
3294        if ~strcmp(GetFieldData.FieldOption,'civdata...')
3295            XName=GetFieldData.Coordinates.Coord_x;
3296            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
3297            switch TimeNameStr
3298                case 'file index'
3299                    set(handles.TimeName_1,'String','');
3300                case 'attribute'
3301                    set(handles.TimeName_1,'String',['att:' GetFieldData.Time.TimeName]);
3302                case 'variable'
3303                    set(handles.TimeName_1,'String',['var:' GetFieldData.Time.TimeName])
3304                    set(handles.NomType_1,'String','*')
3305                    set(handles.RootFile_1,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
3306                    set(handles.FileIndex_1,'String','')
3307                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
3308                case 'matrix_index'
3309                    set(handles.TimeName_1,'String',['dim:' GetFieldData.Time.TimeName]);
3310                    set(handles.NomType_1,'String','*')
3311                    set(handles.RootFile_1,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
3312                    set(handles.FileIndex_1,'String','')
3313                    ParamIn.TimeDimName_1=GetFieldData.Time.TimeName;
3314            end
3315            set(handles.Coord_x,'String',XName)
3316            if ischar(YName)
3317                YName={YName};
3318            end
3319            set(handles.Coord_y,'Data',YName)
3320            set(handles.FieldName_1,'Value',1)
3321            set(handles.FieldName_1,'String',[FieldList; {'get_field...'}]);
3322            set(handles.ColorScalar,'Value',1)
3323            set(handles.ColorScalar,'String',VecColorList);
3324            UvData.FileType{2}='netcdf';
3325            set(handles.uvmat,'UserData',UvData)
3326            REFRESH_Callback(hObject, eventdata, handles)
3327        end
3328         
3329%         set_veltype_display(0) % no veltype display
3330%         hget_field=findobj(allchild(0),'name','get_field_1');
3331%         if ~isempty(hget_field)
3332%             delete(hget_field)
3333%         end
3334%         hget_field=get_field(FileName_1);
3335%         set(hget_field,'name','get_field_1')
3336%         hhget_field=guidata(hget_field);
3337%         set(hhget_field.list_fig,'Value',1)
3338%         set(hhget_field.list_fig,'String',{'uvmat'})
3339%         if check_new
3340%             UvData.FileType{2}=UvData.FileType{1};
3341%             set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3342%               set(handles.uvmat,'UserData',UvData)
3343%         end
3344    case 'image'
3345        %% look for image corresponding to civ data
3346        imagename='';
3347        if  isfield(UvData.Field,'Civ2_ImageA')%get the corresponding input image in the netcdf file
3348            imagename=UvData.Field.Civ2_ImageA;
3349        elseif isfield(UvData.Field,'Civ1_ImageA')%
3350            imagename=UvData.Field.Civ1_ImageA;
3351        else
3352            SubDirBase=regexprep(SubDir,'\..*','');%take the root part of SubDir, before the first dot '.'
3353            imagename=fullfile_uvmat(RootPath,SubDirBase,RootFile,'.png',NomType,i1,[],j1,[]);
3354        end
3355        if ~exist(imagename,'file')
3356            imagename=uigetfile_uvmat('Pick an image file',imagename,'image');
3357           
3358        end
3359        if isempty(imagename)
3360            set(handles.SubField,'Value',0)
3361            return
3362        else
3363            display_file_name(handles,imagename,2)%display the image as second field
3364        end
3365    otherwise
3366        check_refresh=1;
3367        if check_new% if a second field was not previously entered, we just read another field in the first input file
3368            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3369            set(handles.FileExt_1,'String',get(handles.FileExt,'String'))
3370           
3371            UvData.FileType{2}=UvData.FileType{1};
3372            UvData.XmlData{2}= UvData.XmlData{1};
3373            transform=get(handles.TransformPath,'UserData');
3374             if (~isa(transform,'function_handle')||nargin(transform)<3)
3375                set(handles.uvmat,'UserData',UvData)
3376                set(handles.TransformName,'value',2); % set transform fct to 'sub_field' if the current fct does not accept two input fields
3377                TransformName_Callback(hObject, eventdata, handles)% activate transform_fct_Callback and refresh current plot
3378                 check_refresh=0;
3379             end             
3380        end
3381        if ~isequal(field,'image')
3382            set(handles.TitleNpxy,'Visible','off')% visible npx,pxcm... buttons
3383            set(handles.num_Npx,'Visible','off')
3384            set(handles.num_Npy,'Visible','off')
3385        end
3386        set(handles.uvmat,'UserData',UvData)
3387 
3388        if check_refresh && ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3389            REFRESH_Callback(hObject, eventdata, handles)
3390        end
3391end
3392
3393%------------------------------------------------------------------------
3394% --- set the visibility of relevant velocity type menus:
3395function menu=set_veltype_display(Civ,FileType)
3396%------------------------------------------------------------------------
3397if ~exist('FileType','var')
3398    FileType='civx';
3399end
3400switch FileType
3401    case 'civx'
3402        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3403        if isequal(Civ,0)
3404            imax=0;
3405        elseif isequal(Civ,1) || isequal(Civ,2)
3406            imax=1;
3407        elseif isequal(Civ,3)
3408            imax=3;
3409        elseif isequal(Civ,4) || isequal(Civ,5)
3410            imax=4;
3411        elseif isequal(Civ,6) %patch2
3412            imax=6;
3413        end
3414    case 'civdata'
3415        menu={'civ1';'filter1';'civ2';'filter2'};
3416        if isequal(Civ,0)
3417            imax=0;
3418        elseif isequal(Civ,1) || isequal(Civ,2)
3419            imax=1;
3420        elseif isequal(Civ,3)
3421            imax=2;
3422        elseif isequal(Civ,4) || isequal(Civ,5)
3423            imax=3;
3424        elseif isequal(Civ,6) %patch2
3425            imax=4;
3426        end
3427end
3428menu=menu(1:imax);
3429
3430%------------------------------------------------------------------------
3431% --- Executes on button press in FixVelType.
3432function FixVelType_Callback(hObject, eventdata, handles)
3433%------------------------------------------------------------------------
3434% inputfilerefresh the current plot if the fixed  veltype is unselected
3435if ~get(handles.FixVelType,'Value')
3436    REFRESH_Callback(hObject, eventdata, handles)
3437end
3438
3439%------------------------------------------------------------------------
3440% --- Executes on button press in VelType.
3441function VelType_Callback(hObject, eventdata, handles)
3442%------------------------------------------------------------------------
3443set(handles.FixVelType,'Value',1)
3444REFRESH_Callback(hObject, eventdata, handles)
3445
3446%------------------------------------------------------------------------
3447% --- Executes on choice selection in VelType_1.
3448function VelType_1_Callback(hObject, eventdata, handles)
3449%------------------------------------------------------------------------
3450set(handles.FixVelType,'Value',1)% the velocity type is now imposed by the GUI (not automatic)
3451UvData=get(handles.uvmat,'UserData');
3452set(handles.InputFileREFRESH,'BackgroundColor',[1 1 0])%paint REFRESH button in yellow to indicate its activation
3453drawnow   
3454InputFile=read_GUI(handles.InputFile);% read the input file parameters
3455[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
3456[RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
3457FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];% name of the first input file
3458
3459check_refresh=0;
3460if isempty(InputFile.VelType_1)
3461        FileName_1='';% we plot the first input field without the second field
3462        set(handles.SubField,'Value',0)
3463        SubField_Callback(hObject, eventdata, handles)% activate SubField_Callback and refresh current plot, removing the second field
3464elseif get(handles.SubField,'Value')% if subfield is already 'on'
3465     FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];% name of the second input file
3466     check_refresh=1;%will refresh the current plot
3467else% we introduce the same file (with a different field) for the second series
3468     FileName_1=FileName;% we compare two fields in the same file
3469     UvData.FileType{2}=UvData.FileType{1};
3470     UvData.XmlData{2}= UvData.XmlData{1};
3471     set(handles.SubField,'Value',1)
3472     transform=get(handles.TransformPath,'UserData');
3473     if (~isa(transform,'function_handle')||nargin(transform)<3)
3474        set(handles.uvmat,'UserData',UvData)
3475        set(handles.TransformName,'value',2); % set transform fct to 'sub_field' if the current fct does not accept two input fields
3476        TransformName_Callback(hObject, eventdata, handles)% activate transform_fct_Callback and refresh current plot
3477     else
3478         check_refresh=1;
3479     end 
3480end
3481
3482% inputfilerefresh the current plot if it has not been done previously
3483if check_refresh
3484    UvData.FileName_1='';% desactivate the use of a constant second file
3485    set(handles.uvmat,'UserData',UvData)
3486    num_i1=stra2num(get(handles.i1,'String'));
3487    num_i2=stra2num(get(handles.i2,'String'));
3488    num_j1=stra2num(get(handles.j1,'String'));
3489    num_j2=stra2num(get(handles.j2,'String'));
3490    [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(['xx' FileIndex_1]);
3491    errormsg=refresh_field(handles,FileName,FileName_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1);
3492    if ~isempty(errormsg)
3493        msgbox_uvmat('ERROR',errormsg);
3494    else
3495        set(handles.i1,'BackgroundColor',[1 1 1])
3496        set(handles.i2,'BackgroundColor',[1 1 1])
3497        set(handles.j1,'BackgroundColor',[1 1 1])
3498        set(handles.j2,'BackgroundColor',[1 1 1])
3499        set(handles.FileIndex,'BackgroundColor',[1 1 1])
3500        set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
3501    end
3502    set(handles.InputFileREFRESH,'BackgroundColor',[1 0 0])
3503end
3504
3505
3506%------------------------------------------------------------------------
3507% --- reset civ buttons
3508function reset_vel_type(handles_civ0,handle1)
3509%------------------------------------------------------------------------
3510for ibutton=1:length(handles_civ0)
3511    set(handles_civ0(ibutton),'BackgroundColor',[0.831 0.816 0.784])
3512    set(handles_civ0(ibutton),'Value',0)
3513end
3514if exist('handle1','var')%handles of selected button
3515        set(handle1,'BackgroundColor',[1 1 0]) 
3516end
3517
3518%-----------------------------------------------------------------------
3519% --- Executes on button press in MENUVOLUME.
3520function VOLUME_Callback(hObject, eventdata, handles)
3521%-----------------------------------------------------------------------
3522%errordlg('command VOL not implemented yet')
3523if ishandle(handles.UVMAT_title)
3524    delete(handles.UVMAT_title)
3525end
3526UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3527if isequal(get(handles.VOLUME,'Value'),1)
3528    set(handles.CheckZoom,'Value',0)
3529%     set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3530    set(handles.edit_vect,'Value',0)
3531    edit_vect_Callback(hObject, eventdata, handles)
3532    set(handles.CheckEditObject,'Value',0)
3533%     set(handles.CheckEditObject,'BackgroundColor',[0.7 0.7 0.7])
3534%     set(handles.cal,'Value',0)
3535%     set(handles.cal,'BackgroundColor',[0 1 0])
3536    set(handles.edit_vect,'Value',0)
3537    edit_vect_Callback(hObject, eventdata, handles)
3538    %initiate set_object GUI
3539    data.Name='VOLUME';
3540    if isfield(UvData,'CoordType')
3541        data.CoordType=UvData.CoordType;
3542    end
3543    if isfield(UvData.Field,'CoordMesh')&~isempty(UvData.Field.CoordMesh)
3544        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
3545        data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
3546        data.DX=UvData.Field.CoordMesh;
3547        data.DY=UvData.Field.CoordMesh;
3548    elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3549        np=size(UvData.Field.A);
3550        meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
3551        meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
3552        data.RangeY=max(meshx,meshy);
3553        data.RangeX=max(meshx,meshy);
3554        data.DX=max(meshx,meshy);
3555    end
3556    data.ParentButton=handles.VOLUME;
3557    PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
3558    [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes,
3559                                                      % associate the set_object interface handle to the plotting axes
3560    %set(hset_object,'Position',get(handles.uvmat,'Position')+UvData.OpenParam.PosSetObject)
3561    UvData.MouseAction='create_object';
3562else
3563    set(handles.VOLUME,'BackgroundColor',[0 1 0])
3564end
3565set(handles.uvmat,'UserData',UvData)
3566
3567%-------------------------------------------------------
3568function edit_vect_Callback(hObject, eventdata, handles)
3569%-------------------------------------------------------
3570%
3571if isequal(get(handles.edit_vect,'Value'),1)
3572    VelTypeMenu=get(handles.VelType,'String');
3573    VelType=VelTypeMenu{get(handles.VelType,'Value')};
3574    if ~strcmp(VelType,'civ2') && ~strcmp(VelType,'civ1')
3575        msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
3576    end
3577    set(handles.record,'Visible','on')
3578    set(handles.edit_vect,'BackgroundColor',[1 1 0])
3579    set(handles.CheckEditObject,'Value',0)
3580    set(handles.CheckZoom,'Value',0)
3581%     set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3582%     set(handles.CheckEditObject,'BackgroundColor',[0.7 0.7 0.7])
3583    set(gcf,'Pointer','arrow')
3584else
3585    set(handles.record,'Visible','off')
3586    set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7])
3587end
3588
3589%----------------------------------------------
3590function save_mask_Callback(hObject, eventdata, handles)
3591%-----------------------------------------------------------------------
3592UvData=get(handles.uvmat,'UserData');
3593
3594flag=1;
3595npx=size(UvData.Field.A,2);
3596npy=size(UvData.Field.A,1);
3597xi=0.5:npx-0.5;
3598yi=0.5:npy-0.5;
3599[Xi,Yi]=meshgrid(xi,yi);
3600if isfield(UvData,'ProjObject')
3601    for iobj=1:length(UvData.ProjObject)
3602        ObjectData=UvData.ProjObject{iobj};
3603        if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
3604            flagobj=1;
3605            testphys=0; %coordinates in pixels by default
3606            if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys')
3607                if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
3608                    Calib=UvData.XmlData{1}.GeometryCalib;
3609                    testphys=1;
3610                end
3611            end
3612            if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style')
3613                if isequal(ObjectData.Type,'polygon')
3614                    X=ObjectData.Coord(:,1);
3615                    Y=ObjectData.Coord(:,2);
3616                    if testphys
3617                        [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
3618                    end
3619                    flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside                 
3620                elseif isequal(ObjectData.Type,'ellipse')
3621                    if testphys
3622                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3623                    end
3624                    RangeX=max(ObjectData.RangeX);
3625                    RangeY=max(ObjectData.RangeY);
3626                    X2Max=RangeX*RangeX;
3627                    Y2Max=RangeY*RangeY;
3628                    distX=(Xi-ObjectData.Coord(1,1));
3629                    distY=(Yi-ObjectData.Coord(1,2));
3630                    flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
3631                elseif isequal(ObjectData.Type,'rectangle')
3632                    if testphys
3633                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3634                    end
3635                    distX=abs(Xi-ObjectData.Coord(1,1));
3636                    distY=abs(Yi-ObjectData.Coord(1,2));
3637                    flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
3638                end
3639                if isequal(ObjectData.ProjMode,'mask_outside')
3640                    flagobj=~flagobj;
3641                end
3642                flag=flag & flagobj;
3643            end
3644        end
3645    end
3646end
3647% flag=~flag;
3648%mask name
3649RootPath=get(handles.RootPath,'String');
3650RootFile=get(handles.RootFile,'String');
3651RootFile=regexprep(RootFile,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3652filebase=fullfile(RootPath,RootFile);
3653list=get(handles.masklevel,'String');
3654masknumber=num2str(length(list));
3655maskindex=get(handles.masklevel,'Value');
3656mask_name=fullfile_uvmat(RootPath,SubDir,[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
3657%mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
3658imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
3659imflag=flipdim(imflag,1);
3660% imflag=uint8(255*flag);% =0 for flag=0 (vectors=0 when 20<imflag<200)
3661msgbox_uvmat('CONFIRMATION',[mask_name ' saved'])
3662imwrite(imflag,mask_name,'BitDepth',8);
3663
3664%display the mask
3665figure;
3666vec=linspace(0,1,256);%define a linear greyscale colormap
3667map=[vec' vec' vec'];
3668colormap(map)
3669
3670image(imflag);
3671
3672%------------------------------------------------------------------------
3673%------------------------------------------------------------------------
3674%  - FUNCTIONS FOR SETTING PLOTTING PARAMETERS
3675
3676%------------------------------------------------------------------------
3677%------------------------------------------------------------------------
3678% --- Executes on selection change in TransformName.
3679
3680function TransformName_Callback(hObject, eventdata, handles)
3681%------------------------------------------------------------------------
3682UvData=get(handles.uvmat,'UserData');
3683menu=get(handles.TransformName,'String');%refresh
3684ichoice=get(handles.TransformName,'Value');%item number in the menu
3685transform_name=menu{ichoice};% choice of the transform fct
3686list_path=get(handles.TransformName,'UserData');
3687
3688%% handles uicontrol visibility
3689if isempty(transform_name)
3690    set(handles.TransformPath,'Visible','off')
3691else
3692    set(handles.TransformPath,'Visible','on')
3693end
3694
3695
3696%% add a new item to the menu if the option 'more...' has been selected
3697prev_path=fullfile(get(handles.TransformPath,'String'));
3698if ~exist(prev_path,'dir')
3699    prev_path=fullfile(fileparts(which('uvmat')),'transform_field');
3700end
3701if strcmp(transform_name,'more...');
3702    transform_fct_chosen=uigetfile_uvmat('Pick the transform function',prev_path,'.m');
3703    if ~isempty(transform_fct_chosen)
3704        [PathName,transform_name]=fileparts(transform_fct_chosen);
3705        ichoice=find(strcmp(transform_name,menu),1);%look for the selected fct in the existing menu
3706        if isempty(ichoice)% if the item is not found, add it to the menu (before 'more...' and select it)
3707            menu=[menu(1:end-1);{transform_name};{'more...'}];
3708            ichoice=numel(menu)-1;
3709        end
3710        list_path{ichoice}=PathName;%update the list fo fct paths
3711        set(handles.TransformName,'String',menu)
3712        set(handles.TransformName,'Value',ichoice)
3713       
3714        % save the new menu in the personal file 'uvmat_perso.mat'
3715        dir_perso=prefdir;%personal Matalb directory
3716        profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3717        if exist(profil_perso,'file')
3718            nb_builtin=UvData.OpenParam.NbBuiltin;% number of 'builtin' (basic) transform fcts in uvmat
3719            if nb_builtin<numel(list_path)
3720                for ilist=nb_builtin+1:numel(list_path)
3721                    transform_fct{ilist-nb_builtin}=[fullfile(list_path{ilist},menu{ilist}) '.m'];
3722                end
3723                save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
3724            end
3725        end
3726    end
3727end
3728
3729%% create the function handle of the selected fct
3730if isempty(list_path{ichoice})% case of no selected fct
3731    transform_handle=[];
3732else
3733    if ~exist(list_path{ichoice},'dir')
3734        msgbox_uvmat('ERROR','invalid fct path: select the transform fct again with the option more...')
3735        return
3736    end
3737    current_dir=pwd;%current working dir
3738    cd(list_path{ichoice})
3739    transform_handle=str2func(transform_name);
3740    cd(current_dir)
3741end
3742set(handles.TransformPath,'String',list_path{ichoice})
3743set(handles.TransformPath,'UserData',transform_handle)
3744set(handles.TransformName,'UserData',list_path)
3745
3746%% update the ToolTip string of the menu TransformName with the first line of the selected fct file
3747if isempty(list_path{ichoice})% case of no selected fct
3748    set(handles.TransformName,'ToolTipString','transform_fct:choose a transform function')
3749else
3750    try
3751        [fid,errormsg] =fopen([fullfile(list_path{ichoice},transform_name) '.m']);
3752        InputText=textscan(fid,'%s',1,'delimiter','\n');
3753        fclose(fid)
3754        set(handles.TransformName,'ToolTipString',['transform_fct: ' InputText{1}{1}])% put the first line of the selected function as tooltip help
3755    end
3756end
3757
3758%% adapt the GUI to the input/output conditions of the selected transform fct
3759DataOut=[];
3760CoordUnit='';
3761CoordUnitPrev='';
3762if isfield(UvData,'Field')&&isfield(UvData.Field,'CoordUnit')
3763    CoordUnitPrev=UvData.Field.CoordUnit;
3764end
3765if ~isempty(list_path{ichoice})
3766    if nargin(transform_handle)>1 && isfield(UvData,'XmlData')&&~isempty(UvData.XmlData)
3767        XmlData=UvData.XmlData{1};
3768        DataOut=feval(transform_handle,'*',XmlData);
3769        if isfield(DataOut,'CoordUnit')% set the requested coord unit (info used to possibly delete the current projection objects)
3770            CoordUnit=DataOut.CoordUnit;
3771        end
3772        if isfield(DataOut,'InputFieldType')% to be used to impose a type of input file (eg. for image transform)
3773            UvData.InputFieldType=DataOut.InputFieldType;
3774        end
3775        if isfield(DataOut,'XmlData')%  used to add transform parameters at selection of the transform fct
3776            ListFields=fieldnames(DataOut.XmlData);
3777            for ilist=1:numel(ListFields)
3778            UvData.XmlData{1}.(ListFields{ilist})=DataOut.XmlData.(ListFields{ilist});
3779            end
3780        end
3781    else
3782        DataOut=feval(transform_handle,'*');
3783    end
3784end
3785
3786
3787%% delete drawn objects if the output CooordUnit is different from the previous one
3788if ~strcmp(CoordUnit,CoordUnitPrev)
3789    set(handles.CheckFixLimits,'Value',0)
3790% set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
3791    hother=findobj('Tag','proj_object');%find all the proj objects
3792    for iobj=1:length(hother)
3793        delete_object(hother(iobj))
3794    end
3795    hother=findobj('Tag','DeformPoint');%find all the proj objects
3796    for iobj=1:length(hother)
3797        delete_object(hother(iobj))
3798    end
3799    hh=findobj('Tag','calib_points');
3800    if ~isempty(hh)
3801        delete(hh)
3802    end
3803    hhh=findobj('Tag','calib_marker');
3804    if ~isempty(hhh)
3805        delete(hhh)
3806    end
3807    set(handles.ListObject,'Value',1)
3808    set(handles.ListObject,'String',{''})
3809    set(handles.ListObject_1,'Value',1)
3810    set(handles.ListObject_1,'String',{''})
3811    set(handles.CheckViewObject,'value',0)
3812    CheckViewObject_Callback(hObject, eventdata, handles)
3813    set(handles.CheckViewField,'value',0)
3814    CheckViewField_Callback(hObject, eventdata, handles)
3815    set(handles.CheckEditObject,'Value',0)
3816    CheckEditObject_Callback(hObject, eventdata, handles)
3817    UvData.ProjObject={[]};
3818end
3819set(handles.uvmat,'UserData',UvData)
3820
3821%% inputfilerefresh the current plot
3822if isempty(list_path{ichoice}) || nargin(transform_handle)<3
3823    set(handles.SubField,'Value',0)
3824    SubField_Callback(hObject, eventdata, handles)
3825else
3826    REFRESH_Callback(hObject, eventdata, handles)
3827end
3828
3829%------------------------------------------------
3830%CALLBACKS FOR PLOTTING PARAMETERS
3831%-------------------------------------------------
3832%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3833% Plot coordinates
3834%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3835%------------------------------------------------------------------------
3836function num_MinX_Callback(hObject, eventdata, handles)
3837%------------------------------------------------------------------------
3838set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3839% set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3840update_plot(handles);
3841
3842%------------------------------------------------------------------------
3843function num_MaxX_Callback(hObject, eventdata, handles)
3844%------------------------------------------------------------------------
3845set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3846% set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3847update_plot(handles);
3848
3849%------------------------------------------------------------------------
3850function num_MinY_Callback(hObject, eventdata, handles)
3851%------------------------------------------
3852set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3853% set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3854update_plot(handles);
3855
3856%------------------------------------------------------------------------
3857function num_MaxY_Callback(hObject, eventdata, handles)
3858%------------------------------------------------------------------------
3859set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3860% set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3861update_plot(handles);
3862
3863%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3864% Scalar or image representation
3865%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3866%------------------------------------------------------------------------
3867function num_MinA_Callback(hObject, eventdata, handles)
3868%------------------------------------------
3869set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3870% set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3871MinA=str2double(get(handles.num_MinA,'String'));
3872MaxA=str2double(get(handles.num_MaxA,'String'));
3873if MinA>MaxA% switch minA and maxA in case of error
3874    MinA_old=MinA;
3875    MinA=MaxA;
3876    MaxA=MinA_old;
3877    set(handles.num_MinA,'String',num2str(MinA,5));
3878    set(handles.num_MaxA,'String',num2str(MaxA,5));
3879end
3880update_plot(handles);
3881
3882%------------------------------------------------------------------------
3883function num_MaxA_Callback(hObject, eventdata, handles)
3884%------------------------------------------------------------------------
3885set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3886% set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3887MinA=str2double(get(handles.num_MinA,'String'));
3888MaxA=str2double(get(handles.num_MaxA,'String'));
3889if MinA>MaxA% switch minA and maxA in case of error
3890        MinA_old=MinA;
3891    MinA=MaxA;
3892    MaxA=MinA_old;
3893    set(handles.num_MinA,'String',num2str(MinA,5));
3894    set(handles.num_MaxA,'String',num2str(MaxA,5));
3895end
3896update_plot(handles);
3897
3898%------------------------------------------------------------------------
3899function CheckFixScalar_Callback(hObject, eventdata, handles)
3900%------------------------------------------------------------------------
3901test=get(handles.CheckFixScalar,'Value');
3902if test
3903%     set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3904else
3905%     set(handles.CheckFixScalar,'BackgroundColor',[0.7 0.7 0.7])
3906    update_plot(handles);
3907end
3908
3909%-------------------------------------------------------------------
3910function CheckBW_Callback(hObject, eventdata, handles)
3911%-------------------------------------------------------------------
3912update_plot(handles);
3913
3914%-------------------------------------------------------------------
3915function num_Opacity_Callback(hObject, eventdata, handles)
3916update_plot(handles);
3917%-------------------------------------------------------------------
3918
3919%-------------------------------------------------------------------
3920function ListContour_Callback(hObject, eventdata, handles)
3921%-------------------------------------------------------------------
3922val=get(handles.ListContour,'Value');
3923if val==2% option 'contours'
3924    set(handles.interval_txt,'Visible','on')
3925    set(handles.num_IncrA,'Visible','on')
3926    set(handles.num_IncrA,'String','')% refresh contour interval
3927%     set(handles.opacity_txt,'Visible','off')
3928%     set(handles.num_Opacity,'Visible','off')
3929else % option 'image'
3930    set(handles.interval_txt,'Visible','off')
3931    set(handles.num_IncrA,'Visible','off')
3932%     set(handles.opacity_txt,'Visible','on')
3933%     set(handles.num_Opacity,'Visible','on')
3934end
3935update_plot(handles);
3936
3937%-------------------------------------------------------------------
3938function num_IncrA_Callback(hObject, eventdata, handles)
3939%-------------------------------------------------------------------
3940update_plot(handles);
3941
3942
3943%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3944% Vector representation
3945%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3946%-------------------------------------------------------------------
3947function CheckHideWarning_Callback(hObject, eventdata, handles)
3948%-------------------------------------------------------------------
3949update_plot(handles);
3950
3951%-------------------------------------------------------------------
3952function CheckHideFalse_Callback(hObject, eventdata, handles)
3953%-------------------------------------------------------------------
3954update_plot(handles);
3955
3956%-------------------------------------------------------------------
3957function num_VecScale_Callback(hObject, eventdata, handles)
3958%-------------------------------------------------------------------
3959set(handles.CheckFixVectors,'Value',1);
3960set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3961update_plot(handles);
3962
3963%-------------------------------------------------------------------
3964function CheckFixVectors_Callback(hObject, eventdata, handles)
3965%-------------------------------------------------------------------
3966if ~get(handles.CheckFixVectors,'Value')
3967    update_plot(handles);
3968end
3969
3970%------------------------------------------------------------------------
3971% --- Executes on selection change in CheckDecimate4 (nb_vec/4).
3972%------------------------------------------------------------------------
3973function CheckDecimate4_Callback(hObject, eventdata, handles)
3974
3975if isequal(get(handles.CheckDecimate4,'Value'),1)
3976    set(handles.CheckDecimate16,'Value',0)
3977end
3978update_plot(handles);
3979
3980%------------------------------------------------------------------------
3981% --- Executes on selection change in CheckDecimate16 (nb_vec/16).
3982%------------------------------------------------------------------------
3983function CheckDecimate16_Callback(hObject, eventdata, handles)
3984
3985if isequal(get(handles.CheckDecimate16,'Value'),1)
3986    set(handles.CheckDecimate4,'Value',0)
3987end
3988update_plot(handles);
3989
3990%------------------------------------------------------------------------
3991% --- Executes on selection change in ColorCode menu
3992function ColorCode_Callback(hObject, eventdata, handles)
3993%------------------------------------------------------------------------
3994% edit the choice for color code
3995update_color_code_boxes(handles);
3996update_plot(handles);
3997
3998%------------------------------------------------------------------------
3999function update_color_code_boxes(handles)
4000%------------------------------------------------------------------------
4001list_code=get(handles.ColorCode,'String');% list menu fields
4002colcode= list_code{get(handles.ColorCode,'Value')}; % selected field
4003enable_slider='off';%default
4004enable_bounds='off';%default
4005enable_scalar='off';%default
4006switch colcode
4007    case {'rgb','bgr'}
4008        enable_slider='on';
4009        enable_bounds='on';
4010        enable_scalar='on';
4011    case '64 colors'
4012        enable_bounds='on';
4013        enable_scalar='on';
4014end
4015set(handles.Slider1,'Visible',enable_slider)
4016set(handles.Slider2,'Visible', enable_slider)
4017set(handles.num_ColCode1,'Visible',enable_slider)
4018set(handles.num_ColCode2,'Visible',enable_slider)
4019set(handles.TitleColCode1,'Visible',enable_slider)
4020set(handles.TitleColCode2,'Visible',enable_slider)
4021set(handles.CheckFixVecColor,'Visible',enable_bounds)
4022set(handles.num_MinVec,'Visible',enable_bounds)
4023set(handles.num_MaxVec,'Visible',enable_bounds)
4024set(handles.ColorScalar,'Visible',enable_scalar)
4025set_vec_col_bar(handles)
4026
4027%------------------------------------------------------------------
4028% --- Executes on selection change in ColorScalar: choice of the color code.
4029function ColorScalar_Callback(hObject, eventdata, handles)
4030%------------------------------------------------------------------
4031% edit the choice for color code
4032list_scalar=get(handles.ColorScalar,'String');% list menu fields
4033col_scalar= list_scalar{get(handles.ColorScalar,'Value')}; % selected field
4034if isequal(col_scalar,'ima_cor')
4035    set(handles.CheckFixVecColor,'Value',1)%fixed scale by default
4036    ColorCode='rgb';
4037    set(handles.num_MinVec,'String','0')
4038    set(handles.num_MaxVec,'String','1')
4039    set(handles.num_ColCode1,'String','0.333')
4040    set(handles.num_ColCode2,'String','0.666')
4041else
4042    set(handles.CheckFixVecColor,'Value',0)%auto scale between min,max by default
4043    ColorCode='64 colors';
4044end
4045ColorCodeList=get(handles.ColorCode,'String');
4046ichoice=find(strcmp(ColorCode,ColorCodeList),1);
4047set(handles.ColorCode,'Value',ichoice)% set color code in the menu
4048
4049update_color_code_boxes(handles);
4050%replot the current graph
4051REFRESH_Callback(hObject, eventdata, handles)
4052
4053%----------------------------------------------------------------
4054% -- Executes on slider movement to set the color code
4055%
4056function Slider1_Callback(hObject, eventdata, handles)
4057%------------------------------------------------------------------
4058slider1=get(handles.Slider1,'Value');
4059min_val=str2num(get(handles.num_MinVec,'String'));
4060max_val=str2num(get(handles.num_MaxVec,'String'));
4061col=min_val+(max_val-min_val)*slider1;
4062set(handles.num_ColCode1,'String',num2str(col))
4063if(get(handles.Slider2,'Value') < col)%move also the second slider at the same value if needed
4064    set(handles.Slider2,'Value',col)
4065    set(handles.num_ColCode2,'String',num2str(col))
4066end
4067set_vec_col_bar(handles)
4068update_plot(handles);
4069
4070%----------------------------------------------------------------
4071% Executes on slider movement to set the color code
4072%----------------------------------------------------------------
4073function Slider2_Callback(hObject, eventdata, handles)
4074slider2=get(handles.Slider2,'Value');
4075min_val=str2num(get(handles.num_MinVec,'String'));
4076max_val=str2num(get(handles.num_MaxVec,'String'));
4077col=min_val+(max_val-min_val)*slider2;
4078set(handles.num_ColCode2,'String',num2str(col))
4079if(get(handles.Slider1,'Value') > col)%move also the first slider at the same value if needed
4080    set(handles.Slider1,'Value',col)
4081    set(handles.num_ColCode1,'String',num2str(col))
4082end
4083set_vec_col_bar(handles)
4084update_plot(handles);
4085
4086%----------------------------------------------------------------
4087% --- Execute on return carriage on the edit box corresponding to slider 1
4088%----------------------------------------------------------------
4089function num_ColCode1_Callback(hObject, eventdata, handles)
4090set_vec_col_bar(handles)
4091update_plot(handles);
4092
4093%----------------------------------------------------------------
4094% --- Execute on return carriage on the edit box corresponding to slider 2
4095%----------------------------------------------------------------
4096function num_ColCode2_Callback(hObject, eventdata, handles)
4097set_vec_col_bar(handles)
4098update_plot(handles);
4099%------------------------------------------------------------------------
4100%-------------------------------------------------------
4101% --- Executes on button press in CheckFixVecColor.
4102%-------------------------------------------------------
4103function VecColBar_Callback(hObject, eventdata, handles)
4104set_vec_col_bar(handles)
4105
4106%------------------------------------------------------------------------
4107% --- Executes on button press in CheckFixVecColor.
4108function CheckFixVecColor_Callback(hObject, eventdata, handles)
4109%------------------------------------------------------------------------
4110if ~get(handles.CheckFixVecColor,'Value')
4111    update_plot(handles);
4112end
4113
4114%------------------------------------------------------------------------
4115% --- Executes on selection change in num_MaxVec.
4116function num_MinVec_Callback(hObject, eventdata, handles)
4117%------------------------------------------------------------------------
4118num_MaxVec_Callback(hObject, eventdata, handles)
4119
4120%------------------------------------------------------------------------
4121% --- Executes on selection change in num_MaxVec.
4122function num_MaxVec_Callback(hObject, eventdata, handles)
4123%------------------------------------------------------------------------
4124set(handles.CheckFixVecColor,'Value',1)
4125CheckFixVecColor_Callback(hObject, eventdata, handles)
4126min_val=str2num(get(handles.num_MinVec,'String'));
4127max_val=str2num(get(handles.num_MaxVec,'String'));
4128slider1=get(handles.Slider1,'Value');
4129slider2=get(handles.Slider2,'Value');
4130colcode1=min_val+(max_val-min_val)*slider1;
4131colcode2=min_val+(max_val-min_val)*slider2;
4132set(handles.num_ColCode1,'String',num2str(colcode1))
4133set(handles.num_ColCode2,'String',num2str(colcode2))
4134update_plot(handles);
4135
4136%------------------------------------------------------------------------
4137% --- update the display of color code for vectors (on vecColBar)
4138function set_vec_col_bar(handles)
4139%------------------------------------------------------------------------
4140%get the image of the color display button 'VecColBar' in pixels
4141set(handles.VecColBar,'Unit','pixel');
4142pos_vert=get(handles.VecColBar,'Position');
4143set(handles.VecColBar,'Unit','Normalized');
4144width=ceil(pos_vert(3));
4145height=ceil(pos_vert(4));
4146
4147%get slider indications
4148list=get(handles.ColorCode,'String');
4149ichoice=get(handles.ColorCode,'Value');
4150colcode.ColorCode=list{ichoice};
4151colcode.MinVec=str2num(get(handles.num_MinVec,'String'));
4152colcode.MaxVec=str2num(get(handles.num_MaxVec,'String'));
4153test3color=strcmp(colcode.ColorCode,'rgb') || strcmp(colcode.ColorCode,'bgr');
4154if test3color
4155    colcode.ColCode1=str2num(get(handles.num_ColCode1,'String'));
4156    colcode.ColCode2=str2num(get(handles.num_ColCode2,'String'));
4157end
4158vec_C=colcode.MinVec+(colcode.MaxVec-colcode.MinVec)*(0.5:width-0.5)/width;%sample of vec_C values from min to max
4159[colorlist,col_vec]=set_col_vec(colcode,vec_C);
4160oneheight=ones(1,height);
4161A1=colorlist(col_vec,1)*oneheight;
4162A2=colorlist(col_vec,2)*oneheight;
4163A3=colorlist(col_vec,3)*oneheight;
4164A(:,:,1)=A1';
4165A(:,:,2)=A2';
4166A(:,:,3)=A3';
4167set(handles.VecColBar,'Cdata',A)
4168
4169%-------------------------------------------------------------------
4170function update_plot(handles)
4171%-------------------------------------------------------------------
4172set(handles.REFRESH,'BackgroundColor',[1 1 0]);% display plot activity by yellow color
4173drawnow
4174UvData=get(handles.uvmat,'UserData');
4175AxeData=UvData.PlotAxes;% retrieve the current plotted data
4176PlotParam=read_GUI(handles.uvmat);
4177[tild,PlotParamOut]= plot_field(AxeData,handles.PlotAxes,PlotParam);
4178errormsg=fill_GUI(PlotParamOut,handles.uvmat);
4179if ~isempty(errormsg)
4180    msgbox_uvmat('ERROR',errormsg)
4181    return
4182end
4183set(handles.REFRESH,'BackgroundColor',[1 0 0]);
4184
4185%------------------------------------------------------------------------
4186%------------------------------------------------------------------------
4187%   SELECTION AND EDITION OF PROJECTION OBJECTS
4188%------------------------------------------------------------------------
4189%------------------------------------------------------------------------
4190
4191% --- Executes on selection change in ListObject_1.
4192function ListObject_1_Callback(hObject, eventdata, handles)
4193list_str=get(handles.ListObject,'String');
4194UvData=get(handles.uvmat,'UserData');
4195ObjectData=UvData.ProjObject{get(handles.ListObject_1,'Value')};
4196
4197%% update the projection plot on uvmat
4198ProjData= proj_field(UvData.Field,ObjectData);%project the current input field on object ObjectData
4199plot_field(ProjData,handles.PlotAxes,read_GUI(handles.uvmat));% plot the projected field;
4200%replot all the objects within the new projected field
4201for IndexObj=1:numel(list_str)
4202        hobject=UvData.ProjObject{IndexObj}.DisplayHandle.uvmat;
4203        if isempty(hobject) || ~ishandle(hobject)
4204            hobject=handles.PlotAxes;
4205        end
4206        if isequal(IndexObj,get(handles.ListObject,'Value'))
4207            objectcolor='m'; %paint in magenta the currently selected object in ListObject
4208        else
4209            objectcolor='b';
4210        end
4211        UvData.ProjObject{IndexObj}.DisplayHandle.uvmat=plot_object(UvData.ProjObject{IndexObj},ObjectData,hobject,objectcolor);%draw the object in uvmat     
4212end
4213set(handles.uvmat,'UserData',UvData)
4214
4215%% display the object parameters if the GUI set_object is already opened
4216if ~get(handles.CheckViewObject,'Value')
4217    ZBounds=0; % default
4218    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4219        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4220        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4221    end
4222    ObjectData.Name=list_str{get(handles.ListObject_1,'Value')};
4223    set_object(ObjectData,[],ZBounds);
4224    set(handles.CheckViewObject,'Value',1)% show that the selected object in ListObject_1 is currently visualised
4225end
4226
4227%  desactivate the edit object mode
4228set(handles.CheckEditObject,'Value',0)
4229% set(handles.CheckEditObject,'BackgroundColor',[0.7,0.7,0.7])
4230
4231%------------------------------------------------------------------------
4232% --- Executes on selection change in ListObject.
4233function ListObject_Callback(hObject, eventdata, handles)
4234%------------------------------------------------------------------------
4235list_str=get(handles.ListObject,'String');
4236IndexObj=get(handles.ListObject,'Value');%present object selection
4237UvData=get(handles.uvmat,'UserData');
4238ObjectData=UvData.ProjObject{IndexObj};
4239    ZBounds=0; % default
4240    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4241        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4242        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4243    end
4244
4245%% show object features if view_object isselected
4246if get(handles.CheckViewObject,'value')
4247    set_object(ObjectData,[],ZBounds);
4248end
4249
4250%% The object  is displayed in set_object if this GUI is already opened
4251%
4252% hset_object=findobj(allchild(0),'tag','set_object');
4253% if ~isempty(hset_object)
4254%
4255%     ObjectData.Name=list_str{IndexObj};
4256%     set_object(ObjectData,[],ZBounds);
4257%     set(handles.CheckViewField,'Value',1)% show that the selected object in ListObject is currently visualised
4258% end
4259
4260%%  desactivate the edit object mode for security
4261set(handles.CheckEditObject,'Value',0)
4262
4263% set(handles.CheckEditObject,'BackgroundColor',[0.7,0.7,0.7])
4264
4265%% update the  plot on view_field if view_field is already openened
4266hview_field=findobj(allchild(0),'tag','view_field');
4267if isempty(hview_field)
4268    hhview_field.PlotAxes=[];
4269else
4270    Data=get(hview_field,'UserData');
4271    hhview_field=guidata(hview_field);
4272    ProjData= proj_field(UvData.Field,ObjectData);%project the current interface field on ObjectData
4273    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.PlotAxes,read_GUI(hview_field));%read plotting parameters on the uvmat interface
4274   
4275    %write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
4276    haxes=findobj(hview_field,'tag','axes3');
4277    pos=get(hview_field,'Position'); 
4278    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
4279        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
4280        pos_table=get(h_TableDisplay,'Position');
4281        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
4282        drawnow% needed to change position before the next command
4283        set(hview_field,'UserData',Data);% restore the previously stored GUI position after GUI resizing
4284    else
4285%         set(hview_field,'Position',Data.GUISize)% return to the previously stored GUI position and size
4286    end
4287end
4288
4289%% update the color of the graphic object representation: the selected object in magenta, others in blue
4290update_object_color(handles.PlotAxes,hhview_field.PlotAxes,UvData.ProjObject{IndexObj}.DisplayHandle.uvmat)
4291
4292%------------------------------------------------------------------------
4293%--- update the color representation of objects (indicating the selected ones)
4294function update_object_color(axes_uvmat,axes_view_field,DisplayHandle)
4295%------------------------------------------------------------------------
4296if isempty(axes_view_field)% case with no view_field plot
4297hother=[findobj(axes_uvmat,'Tag','proj_object');findobj(axes_uvmat,'Tag','DeformPoint')];%find all the proj object and deform point representations
4298else
4299hother=[findobj(axes_uvmat,'Tag','proj_object') ;findobj(axes_view_field,'Tag','proj_object');... %find all the proj object representations
4300findobj(axes_uvmat,'Tag','DeformPoint'); findobj(axes_view_field,'Tag','DeformPoint')];%find all the deform point representations
4301end
4302for iobj=1:length(hother)
4303    if isequal(get(hother(iobj),'Type'),'rectangle')||isequal(get(hother(iobj),'Type'),'patch')
4304        set(hother(iobj),'EdgeColor','b')
4305        if isequal(get(hother(iobj),'FaceColor'),'m')
4306            set(hother(iobj),'FaceColor','b')
4307        end
4308    elseif isequal(get(hother(iobj),'Type'),'image')
4309        Acolor=get(hother(iobj),'CData');
4310        Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2));
4311        set(hother(iobj),'CData',Acolor);
4312    else
4313        set(hother(iobj),'Color','b')
4314    end
4315    set(hother(iobj),'Selected','off')
4316end
4317if ishandle(DisplayHandle)
4318    linetype=get(DisplayHandle,'Type');
4319    if isequal(linetype,'line')
4320        set(DisplayHandle,'Color','m'); %set the selected object to magenta color
4321    elseif isequal(linetype,'rectangle')
4322        set(DisplayHandle,'EdgeColor','m'); %set the selected object to magenta color
4323    elseif isequal(linetype,'patch')
4324        set(DisplayHandle,'FaceColor','m'); %set the selected object to magenta color
4325    end
4326    SubObjectData=get(DisplayHandle,'UserData');
4327    if isfield(SubObjectData,'SubObject') & ishandle(SubObjectData.SubObject)
4328        for iobj=1:length(SubObjectData.SubObject)
4329            hsub=SubObjectData.SubObject(iobj);
4330            if isequal(get(hsub,'Type'),'rectangle')
4331                set(hsub,'EdgeColor','m'); %set the selected object to magenta color
4332            elseif isequal(get(hsub,'Type'),'image')
4333                Acolor=get(hsub,'CData');
4334                Acolor(:,:,1)=Acolor(:,:,3);
4335                set(hsub,'CData',Acolor);
4336            else
4337                set(hsub,'Color','m')
4338            end
4339        end
4340    end
4341    if isfield(SubObjectData,'DeformPoint') & ishandle(SubObjectData.DeformPoint)
4342        set(SubObjectData.DeformPoint,'Color','m')
4343    end
4344end
4345
4346%-------------------------------------------------------------------
4347% --- Executes on selection change in CheckEditObject.
4348function CheckEditObject_Callback(hObject, eventdata, handles)
4349%-------------------------------------------------------------------
4350hset_object=findobj(allchild(0),'Tag','set_object');
4351if get(handles.CheckEditObject,'Value')
4352    %suppress the other options
4353    set(handles.MenuObject,'checked','off')
4354    set(handles.CheckZoom,'Value',0)
4355    CheckZoom_Callback(hObject, eventdata, handles)
4356    hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4357    if ishandle(hgeometry_calib)
4358        hhgeometry_calib=guidata(hgeometry_calib);
4359        set(hhgeometry_calib.CheckEnableMouse,'Value',0)% desactivate mouse action in geometry_calib
4360        set(hhgeometry_calib.CheckEnableMouse,'BackgroundColor',[0.7 0.7 0.7])
4361    end
4362    set(handles.CheckViewObject,'value',1)
4363    CheckViewObject_Callback(hObject, eventdata, handles)
4364else % desactivate object edit mode
4365    if ~isempty(hset_object)% open the
4366        set(get(hset_object,'children'),'Enable','off')
4367        hSAVE=findobj(hset_object,'Tag','SAVE');
4368        set(hSAVE,'Enable','on')
4369    end
4370end
4371
4372
4373%------------------------------------------------------------------------
4374% --- Executes on button press in CheckViewObject.
4375function CheckViewObject_Callback(hObject, eventdata, handles)
4376%------------------------------------------------------------------------
4377check_view=get(handles.CheckViewObject,'Value');
4378
4379if check_view %activate set_object   
4380    IndexObj=get(handles.ListObject,'Value');
4381    list_object=get(handles.ListObject,'String');
4382    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4383    UvData.ProjObject{IndexObj}.Name=list_object{IndexObj};
4384    if numel(UvData.ProjObject)<IndexObj;% error in UvData
4385        msgbox_uvmat('ERROR','invalid object list')
4386        return
4387    end
4388    ZBounds=0; % default
4389    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4390        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4391        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4392    end
4393    data=UvData.ProjObject{IndexObj};
4394    if ~isfield(data,'Type')% default plane
4395        data.Type='plane';
4396    end
4397    hset_object=set_object(data,[],ZBounds);
4398    hhset_object=guidata(hset_object);
4399    if get(handles.CheckEditObject,'Value')% edit mode
4400        set(get(hset_object,'children'),'Enable','on')
4401    else
4402        set(get(hset_object,'children'),'Enable','off')% deactivate the GUI except SAVE
4403        set(hhset_object.SAVE,'Enable','on')
4404    end
4405else
4406    hset_object=findobj(allchild(0),'tag','set_object');
4407    if ~isempty(hset_object)
4408        delete(hset_object)% delete existing version of set_object
4409    end
4410end
4411 
4412
4413%------------------------------------------------------------------------
4414% --- Executes on button press in CheckViewField.
4415function CheckViewField_Callback(hObject, eventdata, handles)
4416%------------------------------------------------------------------------
4417check_view=get(handles.CheckViewField,'Value');
4418
4419if check_view
4420    IndexObj=get(handles.ListObject,'Value');
4421    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4422    if numel(UvData.ProjObject)<IndexObj(end);% error in UvData
4423        msgbox_uvmat('ERROR','invalid object list')
4424        return
4425    end
4426    ZBounds=0; % default
4427    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4428        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4429        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4430    end
4431    set(handles.ListObject,'Value',IndexObj);%restore ListObject selection after set_object deletion
4432    if ~isfield(UvData.ProjObject{IndexObj(1)},'Type')% default plane
4433        UvData.ProjObject{IndexObj(1)}.Type='plane';
4434    end
4435    list_object=get(handles.ListObject,'String');
4436    UvData.ProjObject{IndexObj(end)}.Name=list_object{IndexObj(end)};
4437   
4438    %% show the projection of the selected object on view_field
4439    ProjData= proj_field(UvData.Field,UvData.ProjObject{IndexObj});%project the current field on ObjectData
4440    hview_field=findobj(allchild(0),'tag','view_field');
4441    if isempty(hview_field)
4442        hview_field=view_field;
4443    end
4444    hhview_field=guidata(hview_field);
4445    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.PlotAxes,read_GUI(hview_field));%read plotting parameters on the GUI view_field);
4446    errormsg=fill_GUI(PlotParam,hview_field);
4447    for list={'Scalar','Vectors'}
4448        if ~isfield(PlotParam,list{1})
4449            set(hhview_field.(list{1}),'Visible','off')
4450        end
4451    end
4452    %write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
4453    haxes=findobj(hview_field,'tag','axes3');
4454    pos=get(hview_field,'Position');
4455    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
4456        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
4457        pos_table=get(h_TableDisplay,'Position');
4458        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
4459    else
4460        Data=get(hview_field,'UserData');
4461%         set(hview_field,'Position',Data.GUISize)% restore the size of view_field for plots
4462    end
4463else
4464    hview_field=findobj(allchild(0),'tag','view_field');
4465    if ~isempty(hview_field)
4466        delete(hview_field)% delete existing version of set_object
4467    end
4468end
4469
4470
4471%------------------------------------------------------------------------
4472% --- Executes on button press in DeleteObject.
4473%------------------------------------------------------------------------
4474function DeleteObject_Callback(hObject, eventdata, handles)
4475
4476IndexObj=get(handles.ListObject,'Value');%projection object selected for view_field
4477IndexObj_1=get(handles.ListObject_1,'Value');%projection object selected for uvmat plot
4478if IndexObj>1 && ~isequal(IndexObj,IndexObj_1) % do not delete the object used for the uvmat plot
4479    delete_object(IndexObj)
4480end
4481
4482%'DeleteObject': delete a projection object, defined by its index in the Uvmat list or by its graphic handle
4483%------------------------------------------------------------------------
4484% function DeleteObject(hObject)
4485%
4486% INPUT:
4487% hObject: object index (if integer) or handle of the graphic object. If
4488%          hObject is a subobject, the parent object is detected and deleted.
4489
4490function delete_object(IndexObj)
4491
4492huvmat=findobj('tag','uvmat');%handles of the uvmat interface
4493UvData=get(huvmat,'UserData');
4494hlist_object=findobj(huvmat,'Tag','ListObject');%handles of the object list in the uvmat interface
4495list_str=get(hlist_object,'String');%objet list
4496if  ~isempty(UvData) && isfield(UvData, 'ProjObject') && length(UvData.ProjObject)>=IndexObj
4497    if isfield(UvData.ProjObject{IndexObj},'DisplayHandle') && isfield(UvData.ProjObject{IndexObj}.DisplayHandle,'uvmat')
4498        hdisplay=UvData.ProjObject{IndexObj}.DisplayHandle.uvmat;%handle of the object graphic representation in uvmat
4499        for iview=1:length(hdisplay)
4500            if ishandle(hdisplay(iview)) && ~isequal(hdisplay(iview),0)
4501                ObjectData=get(hdisplay(iview),'UserData');
4502                if isfield(ObjectData,'SubObject') && ~isempty(ObjectData.SubObject)
4503                    delete(ObjectData.SubObject(ishandle(ObjectData.SubObject)));% delete the graphic 'sub-objects (e.g. projection bounds)
4504                end
4505                if isfield(ObjectData,'DeformPoint')&& ~isempty(ObjectData.DeformPoint)
4506                    delete(ObjectData.DeformPoint(ishandle(ObjectData.DeformPoint)));% delete the graphic deformation points
4507                    delete(hdisplay(iview))% delete the main graphic representation of the object
4508                end
4509            end
4510            ishandle(hdisplay(iview))
4511        end
4512        for iobj=IndexObj+1:length(UvData.ProjObject)
4513            hdisplay=UvData.ProjObject{iobj}.DisplayHandle.uvmat;
4514            for iview=1:length(hdisplay)
4515                if ishandle(hdisplay(iview)) && ~isequal(hdisplay(iview),0)
4516                    PlotData=get(hdisplay(iview),'UserData');
4517                    PlotData.IndexObj=iobj-1;
4518                    set(hdisplay(iview),'UserData',PlotData);
4519                end
4520            end
4521        end
4522    end
4523    UvData.ProjObject(IndexObj)=[];
4524    if ~isempty(list_str)
4525        list_str(IndexObj)=[];
4526    end
4527end
4528set(huvmat,'UserData',UvData);
4529set(hlist_object,'String',list_str)
4530set(hlist_object,'Value',length(list_str))
4531hlist_object_1=findobj(huvmat,'Tag','ListObject_1');%handles of the first object list in the uvmat interface
4532old_index=get(hlist_object_1,'Value');
4533set(hlist_object_1,'String',list_str)
4534if IndexObj<=old_index
4535    set(hlist_object_1,'Value',old_index-1)
4536end
4537
4538%------------------------------------------------------------------------
4539%------------------------------------------------------------------------
4540%  II - TOOLS FROM THE UPPER MENU BAR
4541%------------------------------------------------------------------------
4542%------------------------------------------------------------------------
4543
4544%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4545% Export  Menu Callbacks
4546%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4547%------------------------------------------------------------------------
4548% --- Executes on button press in Menu/Export/field in workspace.
4549function MenuExportField_Callback(hObject, eventdata, handles)
4550%------------------------------------------------------------------------
4551global Data_uvmat
4552Data_uvmat=get(handles.uvmat,'UserData');
4553evalin('base','global Data_uvmat')%make CurData global in the workspace
4554display('current field :')
4555evalin('base','Data_uvmat') %display CurData in the workspace
4556commandwindow; %brings the Matlab command window to the front
4557
4558%------------------------------------------------------------------------
4559% --- Executes on button press in Menu/Export/extract figure.
4560function MenuExportFigure_Callback(hObject, eventdata, handles)
4561%------------------------------------------------------------------------
4562hfig=figure;
4563copyobj(handles.PlotAxes,hfig);
4564h=findobj(handles.PlotAxes,'tag','ima'); %look for image in the plot
4565if ~isempty(h)
4566map=colormap(handles.PlotAxes);
4567colormap(map);%transmit the current colormap to the zoom fig
4568colorbar
4569end
4570
4571% --------------------------------------------------------------------
4572function MenuExportAxis_Callback(hObject, eventdata, handles)
4573ListFig=findobj(allchild(0),'Type','figure');
4574nb_option=0;
4575menu={};
4576for ilist=1:numel(ListFig)
4577    FigName=get(ListFig(ilist),'name');
4578    if isempty(FigName)
4579        FigName=['figure ' num2str(ListFig(ilist))];
4580    end
4581    if ~strcmp(FigName,'uvmat')
4582        ListAxes=findobj(ListFig(ilist),'Type','axes');
4583        ListTags=get(ListAxes,'Tag');
4584        if ~isempty(ListTags) && ~isempty(find(~strcmp('Colorbar',ListTags), 1))
4585            ListAxes=ListAxes(~strcmp('Colorbar',ListTags));
4586            if numel(ListAxes)==1
4587                nb_option=nb_option+1;
4588                menu{nb_option}=FigName ;
4589                AxesHandle(nb_option)=ListAxes;
4590            else
4591                nb_axis=0;
4592                for iaxes=1:numel(ListAxes)
4593                    nb_axis=nb_axis+1;
4594                    nb_option=nb_option+1;
4595                    menu{nb_option}=[FigName '_' num2str(nb_axis)];
4596                    AxesHandle(nb_option)=ListAxes(nb_axis);
4597                end
4598            end
4599        end
4600    end
4601end
4602if isempty(menu)
4603    answer=msgbox_uvmat('INPUT_Y-N','no existing plotting axes available, create new figure?');
4604    if strcmp(answer,'Yes')
4605        hfig=figure;
4606        copyobj(handles.PlotAxes,hfig);
4607    else
4608        return
4609    end
4610    map=colormap(handles.PlotAxes);
4611    colormap(map);%transmit the current colormap to the zoom fig
4612    colorbar
4613else
4614    answer=msgbox_uvmat('INPUT_MENU','select a figure/axis on which the current uvmat plot will be exported',menu);
4615    if isempty(answer)
4616        return
4617    else
4618        axes(AxesHandle(answer))
4619        hold on
4620        hchild=get(handles.PlotAxes,'children');
4621        copyobj(hchild,gca);
4622    end
4623end
4624
4625
4626%------------------------------------------------------------------------
4627% --------------------------------------------------------------------
4628function MenuExportMovie_Callback(hObject, eventdata, handles)
4629% --------------------------------------------------------------------
4630set(handles.MenuExportMovie,'BusyAction','queue')% activate the button
4631huvmat=get(handles.InputFileREFRESH,'parent');
4632UvData=get(huvmat,'UserData');
4633%[xx,xx,FileBase]=read_file_boxes(handles);
4634[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
4635FileBase=fullfile(RootPath,RootFile);
4636 %read the current input file name
4637prompt = {'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)'};
4638dlg_title = 'select properties of the output avi movie';
4639num_lines= 1;
4640def     = {[FileBase '_out.avi'];'10';'1';'[0.03 0.05 0.95 0.92]';'10'};
4641answer = inputdlg(prompt,dlg_title,num_lines,def,'on');
4642aviname=answer{1};
4643fps=str2double(answer{2});
4644% check for existing file with output name aviname
4645if exist(aviname,'file')
4646    backup=aviname;
4647    testexist=2;
4648    while testexist==2
4649        backup=[backup '~'];
4650        testexist=exist(backup,'file');     
4651    end
4652    [success,message]=copyfile(aviname,backup);%make backup of the existing file
4653    if isequal(success,1)
4654        delete(aviname)%delete existing file
4655    else
4656        msgbox_uvmat('ERROR',message)
4657        return
4658    end
4659end
4660%create avi open
4661aviobj=avifile(aviname,'Compression','None','fps',fps);
4662
4663%display first view for tests
4664newfig=figure;
4665newaxes=copyobj(handles.PlotAxes,newfig);%new plotting axes in the new figure
4666set(newaxes,'Tag','movieaxes')
4667nbpix=[512 384]*str2double(answer{3});
4668set(gcf,'Position',[1 1 nbpix])% resolution XVGA
4669set(newaxes,'Position',eval(answer{4}));
4670map=colormap(handles.PlotAxes);
4671colormap(map);%transmit the current colormap to the zoom fig
4672msgbox_uvmat('INPUT_Y-N',{['adjust figure ' num2str(newfig) ' with its matlab edit menu '] ;...
4673        ['then press OK to get the avi movie as a copy of figure ' num2str(newfig) ' display']});
4674UvData.plotaxes=newaxes;% the axis in the new figure becomes the current main plotting axes
4675set(huvmat,'UserData',UvData);
4676increment=str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d
4677set(handles.STOP,'Visible','on')
4678set(handles.speed,'Visible','on')
4679set(handles.speed_txt,'Visible','on')
4680set(handles.Movie,'BusyAction','queue')
4681
4682%imin=str2double(get(handles.i1,'String'));
4683imax=str2double(answer{5});
4684% if isfield(UvData,'Time')
4685htitle=get(newaxes,'Title');
4686xlim=get(newaxes,'XLim');
4687ylim=get(newaxes,'YLim');
4688set(htitle,'Position',[xlim(2)+0.07*(xlim(2)-xlim(1)) ylim(2)-0.05*(ylim(2)-ylim(1)) 0])
4689time_str=get(handles.TimeValue,'String');
4690set(htitle,'String',['t=' time_str])
4691set(handles.speed,'Value',1)
4692for i=1:imax
4693    if get(handles.speed,'Value')~=0 && isequal(get(handles.MenuExportMovie,'BusyAction'),'queue') % enable STOP command
4694            runpm(hObject,eventdata,handles,increment)% run plus
4695            drawnow
4696            time_str=get(handles.TimeValue,'String');
4697            if ishandle(htitle)
4698             set(htitle,'String',['t=' time_str])
4699            end
4700            mov=getframe(newfig);
4701            aviobj=addframe(aviobj,mov);
4702    end
4703end
4704aviobj=close(aviobj);
4705UvData=rmfield(UvData,'plotaxes');
4706set(huvmat,'UserData',UvData);
4707msgbox_uvmat('CONFIRMATION',{['movie ' aviname ' created '];['with ' num2str(imax) ' frames']})
4708
4709
4710%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4711% Projection Objects Menu Callbacks
4712%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4713
4714% -----------------------------------------------------------------------
4715function Menupoints_Callback(hObject, eventdata, handles)
4716%------------------------------------------------------------------------
4717data.Type='points';
4718data.ProjMode='projection';%default
4719data.ProjModeMenu={};% do not restrict ProjMode menus
4720create_object(data,handles)
4721
4722% -----------------------------------------------------------------------
4723% --- Callback of the Menu command line
4724%------------------------------------------------------------------------
4725function Menuline_Callback(hObject, eventdata, handles)
4726%------------------------------------------------------------------------
4727data.Type='line';
4728data.ProjMode='projection';%default
4729data.ProjModeMenu={};% do not restrict ProjMode menus
4730create_object(data,handles)
4731
4732% -----------------------------------------------------------------------
4733% --- Callback of the Menu command line_x
4734%------------------------------------------------------------------------
4735function Menuline_x_Callback(hObject, eventdata, handles)
4736
4737data.Type='line_x';
4738data.ProjMode='projection';%default
4739data.ProjModeMenu={};% do not restrict ProjMode menus
4740create_object(data,handles)
4741
4742% -----------------------------------------------------------------------
4743% --- Callback of the Menu command line_y
4744% -----------------------------------------------------------------------
4745function Menuline_y_Callback(hObject, eventdata, handles)
4746
4747data.Type='line_y';
4748data.ProjMode='projection';%default
4749data.ProjModeMenu={};% do not restrict ProjMode menus
4750create_object(data,handles)
4751
4752%------------------------------------------------------------------------
4753function Menupolyline_Callback(hObject, eventdata, handles)
4754%------------------------------------------------------------------------
4755data.Type='polyline';
4756data.ProjMode='projection';%default
4757data.ProjModeMenu={};% do not restrict ProjMode menus
4758create_object(data,handles)
4759
4760%------------------------------------------------------------------------
4761function Menupolygon_Callback(hObject, eventdata, handles)
4762%------------------------------------------------------------------------
4763data.Type='polygon';
4764data.ProjMode='inside';%default
4765data.ProjModeMenu={};% do not restrict ProjMode menus
4766create_object(data,handles)
4767
4768%------------------------------------------------------------------------
4769function Menurectangle_Callback(hObject, eventdata, handles)
4770%------------------------------------------------------------------------
4771data.Type='rectangle';
4772data.ProjMode='inside';%default
4773data.ProjModeMenu={};% do not restrict ProjMode menus
4774create_object(data,handles)
4775
4776%------------------------------------------------------------------------
4777function Menuellipse_Callback(hObject, eventdata, handles)
4778%------------------------------------------------------------------------
4779data.Type='ellipse';
4780data.ProjMode='inside';%default
4781data.ProjModeMenu={};% do not restrict ProjMode menus
4782create_object(data,handles)
4783
4784%------------------------------------------------------------------------
4785function MenuMaskObject_Callback(hObject, eventdata, handles)
4786%------------------------------------------------------------------------
4787data.Type='polygon';
4788data.TypeMenu={'polygon'};
4789data.ProjMode='mask_inside';%default
4790data.ProjModeMenu={'mask_inside';'mask_outside'};
4791create_object(data,handles)
4792
4793%------------------------------------------------------------------------
4794function Menuplane_Callback(hObject, eventdata, handles)
4795%------------------------------------------------------------------------
4796data.Type='plane';
4797data.ProjMode='projection';%default
4798data.ProjModeMenu={};% do not restrict ProjMode menus
4799create_object(data,handles)
4800
4801%------------------------------------------------------------------------
4802function Menuvolume_Callback(hObject, eventdata, handles)
4803%------------------------------------------------------------------------
4804data.Type='volume';
4805data.ProjMode='interp_lin';%default
4806data.ProjModeMenu={};
4807% set(handles.create,'Visible','on')
4808% set(handles.create,'Value',1)
4809% VOLUME_Callback(hObject,eventdata,handles)data.ProjModeMenu={};
4810create_object(data,handles)
4811
4812%------------------------------------------------------------------------
4813% --- generic function used for the creation of a projection object
4814function create_object(data,handles)
4815%------------------------------------------------------------------------
4816%% desactivate concurrent tools
4817hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');% search the GUI geometric calibration
4818if ishandle(hgeometry_calib)
4819    hhgeometry_calib=guidata(hgeometry_calib);
4820    set(hhgeometry_calib.CheckEnableMouse,'Value',0)% desactivate mouse action in geometry_calib
4821    set(hhgeometry_calib.CheckEnableMouse,'BackgroundColor',[0.7 0.7 0.7])
4822end
4823set(handles.CheckEditObject,'Value',0)  %desactivate the object edit mode
4824CheckEditObject_Callback([],[],handles)
4825set(handles.CheckViewObject,'Value',0) % desactivate view_object (new object created)
4826set(handles.CheckZoomFig,'Value',0) %desactivate zoom sub fig
4827set(handles.CheckZoom,'Value',0)    %desactivate the zoom action
4828set(handles.MenuObject,'checked','on')% indicate object creation for mouse pointer display
4829if ishandle(handles.UVMAT_title)
4830    delete(handles.UVMAT_title)     %delete the initial display of uvmat if no field has been entered yet
4831end
4832
4833%% initiate the new projection object
4834UvData=get(handles.uvmat,'UserData');
4835data.Name=data.Type;% default name=type
4836data.Coord=[0 0]; %default
4837check_plot=0;
4838if isfield(UvData,'Field')
4839    Field=UvData.Field;
4840    if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
4841         data.Coord=[0 0 0]; %default
4842    end
4843    if isfield(Field,'CoordUnit')
4844        data.CoordUnit=Field.CoordUnit;
4845    end
4846    if isfield(UvData.Field,'CoordMesh')&&~isempty(UvData.Field.CoordMesh)
4847        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
4848        switch data.Type
4849            case {'line','polyline','points'}
4850                data.RangeY=UvData.Field.CoordMesh;
4851            case 'line_x'
4852                check_plot=1; %plot the line directly when set_object is opened
4853                data.Type='line';
4854                data.RangeX=UvData.Field.XMin ;
4855                data.RangeY=UvData.Field.CoordMesh;
4856                data.Coord=[UvData.Field.XMin (UvData.Field.YMin +UvData.Field.YMax)/2;...
4857                           UvData.Field.XMax (UvData.Field.YMin +UvData.Field.YMax)/2];% put line at the middle of the y axis
4858            case 'line_y'
4859                check_plot=1; %plot the line directly when set_object is opened
4860                data.Type='line';
4861                data.RangeX=UvData.Field.YMin ;
4862                data.RangeY=UvData.Field.CoordMesh;
4863                data.Coord=[(UvData.Field.XMin+UvData.Field.XMax)/2 UvData.Field.YMin;...
4864                            (UvData.Field.XMin +UvData.Field.XMax)/2 UvData.Field.YMax];% put line at the middle of the y axis
4865            case {'rectangle','ellipse'}
4866                data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
4867                data.RangeX=UvData.Field.CoordMesh;
4868                data.RangeY=UvData.Field.CoordMesh;
4869            otherwise
4870                data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
4871        end
4872        data.DX=UvData.Field.CoordMesh;
4873        data.DY=UvData.Field.CoordMesh;
4874    end
4875end
4876
4877hset_object=set_object(data,handles);% call the GUI set_object
4878hchild=get(hset_object,'children');
4879set(hchild,'enable','on')
4880set(handles.DeleteObject,'Visible','on')% make the object delete button visible
4881if check_plot
4882    hhset_object=guidata(hset_object);
4883    set_object('REFRESH_Callback',1,[],hhset_object);% call the GUI set_object
4884end
4885set(handles.CheckViewField,'Visible','on')
4886set(handles.DeleteObject,'Visible','on')
4887set(handles.ListObject_1,'Visible','on')
4888set(handles.ListObject_1_title,'Visible','on')
4889
4890%------------------------------------------------------------------------
4891function MenuBrowseObject_Callback(hObject, eventdata, handles)
4892%------------------------------------------------------------------------
4893%get the object file
4894fileinput=uigetfile_uvmat('pick an xml object file:',get(handles.RootPath,'String'),'.xml');
4895if ~isempty(fileinput)
4896    %read the file
4897    [data,heading]=xml2struct(fileinput);
4898    if ~strcmp(heading,'ProjObject')
4899        msgbox_uvmat('WARNING','The xml file does not have the heading ProjObject for projection objects')
4900    end
4901    ListObject=get(handles.ListObject,'String');
4902    ListObject=[ListObject;{data.Name}];
4903    IndexObj=length(ListObject);
4904    UvData=get(handles.uvmat,'UserData');
4905    UvData.ProjObject{IndexObj}=[]; %create a new empty object
4906    UvData.ProjObject{IndexObj}.DisplayHandle.uvmat=[]; %no plot handle before plot_field operation
4907    UvData.ProjObject{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation
4908    set(handles.uvmat,'UserData',UvData)
4909    set(handles.CheckViewObject,'Value',1)
4910    set(handles.CheckViewField,'Value',1)
4911    hset_object=set_object(data);% call the set_object interface
4912    hhset_object=guidata(hset_object);
4913    set_object('REFRESH_Callback',hObject,eventdata,hhset_object);% plot projection
4914    set(handles.CheckEditObject,'Value',0); %suppress the object edit mode
4915    CheckEditObject_Callback([],[],handles)
4916    set(handles.DeleteObject,'Visible','on')
4917end
4918
4919%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4920% MenuTools Callbacks
4921%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4922%------------------------------------------------------------------------
4923function MenuCalib_Callback(hObject, eventdata, handles)
4924%------------------------------------------------------------------------
4925
4926UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4927
4928%suppress competing options
4929set(handles.CheckZoom,'Value',0)
4930set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
4931set(handles.ListObject,'Value',1)     
4932% initiate display of GUI geometry_calib
4933data=[]; %default
4934if isfield(UvData,'CoordType')
4935    data.CoordType=UvData.CoordType;
4936end
4937[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
4938FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
4939set(handles.view_xml,'BackgroundColor',[1 1 0])%indicate the reading of the current xml file by geometry_calib
4940geometry_calib(FileName);% call the geometry_calib interface   
4941set(handles.view_xml,'BackgroundColor',[1 1 1])%indicate the end of reading of the current xml file by geometry_calib
4942set(handles.MenuCalib,'checked','on')% indicate that MenuCalib is activated, test used by mouse action
4943
4944
4945%-----------------------------------------------------------------------
4946function MenuLIFCalib_Callback(hObject, eventdata, handles)
4947%------------------------------------------------------------------------
4948%% read UvData properties stored on the uvmat interface
4949UvData=get(handles.uvmat,'UserData');
4950if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
4951    XmlData=UvData.XmlData{1};
4952else
4953    msgbox_uvmat('ERROR','geometric calibration needed: use Tools/geometric calibration in the menu bar');
4954    return
4955end
4956
4957%% read lines currently drawn
4958ListObj=UvData.ProjObject;
4959select=zeros(1,numel(ListObj));
4960for iobj=1:numel(ListObj);
4961    if isfield(ListObj{iobj},'Type') && strcmp(ListObj{iobj}.Type,'line')
4962        select(iobj)=1;
4963    end
4964end
4965val=find(select);
4966if numel(val)<2
4967    msgbox_uvmat('ERROR','light rays must be defined by at least two lines created by Projection object/line in the menu bar');
4968    return
4969else
4970    set(handles.ListObject,'Value',val);% show the selected lines on the list
4971    ObjectData=UvData.ProjObject(val);
4972    for iobj=1:length(ObjectData)
4973            xA(iobj)=ObjectData{iobj}.Coord(1,1);
4974            yA(iobj)=ObjectData{iobj}.Coord(1,2);
4975            xB(iobj)=ObjectData{iobj}.Coord(2,1);
4976            yB(iobj)=ObjectData{iobj}.Coord(2,2);
4977    end
4978end
4979
4980%% find the origin as intersection of the two first lines (see http://www.ahristov.com/tutorial/geometry-games/intersection-lines.html )
4981x1=xA(1);x2=xB(1);
4982x3=xA(2);x4=xB(2);
4983y1=yA(1);y2=yB(1);
4984y3=yA(2);y4=yB(2);
4985D = (x1-x2)*(y3-y4) -(y1-y2)*(x3-x4);
4986if D==0
4987    msgbox_uvmat('ERROR','the two lines are parallel');
4988    return
4989end
4990x0=((x3-x4)*(x1*y2-y1*x2)-(x1-x2)*(x3*y4-y3*x4))/D;
4991y0=((y3-y4)*(x1*y2-y1*x2)-(y1-y2)*(x3*y4-y3*x4))/D;
4992XmlData.Illumination.Origin=[x0 y0];
4993XmlData.PolarCentre=[x0 y0];
4994
4995%% display the current image in polar coordinates with origin at the  illumination source
4996currentdir=pwd; 
4997uvmatpath=fileparts(which('uvmat'));
4998cd(fullfile(uvmatpath,'transform_field'));
4999phys_polar=str2func('phys_polar');
5000cd(currentdir)
5001DataOut=phys_polar(UvData.Field,XmlData);
5002view_field(DataOut);
5003
5004%% use the third line for reference luminosity
5005if numel(val)==3
5006    x_ref=linspace(ObjectData{3}.Coord(1,1),ObjectData{3}.Coord(2,1),10);
5007    y_ref=linspace(ObjectData{3}.Coord(1,2),ObjectData{3}.Coord(2,2),10);
5008    x_ref=x_ref-x0;
5009    y_ref=y_ref-y0;
5010    [theta_ref,r_ref] = cart2pol(x_ref,y_ref);%theta_ref  and r_ref are the polar coordinates of the points on the line
5011    theta_ref=theta_ref*180/pi;
5012    figure
5013    plot(theta_ref,r_ref)
5014    azimuth_ima=linspace(DataOut.AY(1),DataOut.AY(2),size(DataOut.A,1));%profile of x index on the transformed image
5015    dist_source = interp1(theta_ref,r_ref,azimuth_ima);
5016    dist_source_pixel=round(size(DataOut.A,2)*(dist_source-DataOut.AX(1))/(DataOut.AX(2)-DataOut.AX(1)));
5017    line_nan= isnan(dist_source_pixel);
5018    dist_source_pixel(line_nan)=1;
5019    width=20; %number of pixels used for reference
5020    DataOut.A=double(DataOut.A);
5021    Anorm=zeros(size(DataOut.A));
5022    Aval=mean(mean(DataOut.A));
5023    for iline=1:size(DataOut.A,1)
5024        lum(iline)=mean(DataOut.A(iline,dist_source_pixel(iline):dist_source_pixel(iline)+width));
5025        Anorm(iline,:)=uint16(Aval*DataOut.A(iline,:)/lum(iline));
5026    end
5027    lum(line_nan)=NaN;
5028    figure
5029    plot(1:size(DataOut.A,1),lum)
5030end
5031ImaName=regexprep([get(handles.RootFile,'String') get(handles.FileIndex,'String')],'//','');
5032NewImageName=fullfile(get(handles.RootPath,'String'),'polar',[ImaName get(handles.FileExt,'String')]);
5033imwrite(Anorm,NewImageName,'BitDepth',16)
5034
5035%% record the origin in the xml file
5036XmlFileName=find_imadoc(get(handles.RootPath,'String'),get(handles.SubDir,'String'),get(handles.RootFile,'String'),get(handles.FileExt,'String'));
5037answer=msgbox_uvmat('INPUT_Y-N','save the illumination origin in the current xml file?');
5038if strcmp(answer,'Yes')
5039    t=xmltree(XmlFileName); %read the file
5040    title=get(t,1,'name');
5041    if ~strcmp(title,'ImaDoc')
5042        msgbox_uvmat('ERROR','wrong xml file');
5043        return
5044    end
5045    % backup the output file if it already exist, and read it
5046    backupfile=XmlFileName;
5047    testexist=2;
5048    while testexist==2
5049        backupfile=[backupfile '~'];
5050        testexist=exist(backupfile,'file');
5051    end
5052    [success,message]=copyfile(XmlFileName,backupfile);%make backup
5053    if success~=1
5054        errormsg=['errror in xml file backup: ' message];
5055        return
5056    end
5057    uid_illumination=find(t,'ImaDoc/Illumination');
5058    if isempty(uid_illumination)  %if GeometryCalib does not already exists, create it
5059        [t,uid_illumination]=add(t,1,'element','Illumination');
5060    end
5061    uid_origin=find(t,'ImaDoc/Illumination/Origin');
5062    if ~isempty(uid_origin)  %if GeometryCalib does not already exists, create it
5063         t=delete(t,uid_origin);
5064    end
5065    % save the illumination origin
5066    t=struct2xml(XmlData.Illumination,t,uid_illumination);
5067    save(t,XmlFileName);
5068end
5069   
5070
5071
5072%------------------------------------------------------------------------
5073function MenuMask_Callback(hObject, eventdata, handles)
5074%------------------------------------------------------------------------
5075UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
5076ListObj=UvData.ProjObject;
5077select=zeros(1,numel(ListObj));
5078for iobj=1:numel(ListObj);
5079    if strcmp(ListObj{iobj}.ProjMode,'mask_inside')||strcmp(ListObj{iobj}.ProjMode,'mask_outside')
5080        select(iobj)=1;
5081    end
5082end
5083val=find(select);
5084if isempty(val)
5085    msgbox_uvmat('ERROR','polygons must be first created by Projection object/mask polygon in the menu bar');
5086    return
5087else
5088    set(handles.ListObject,'Value',val);
5089    flag=1;
5090    if ~isfield(UvData.Field,'A')
5091            msgbox_uvmat('ERROR','an image needs to be opened to set the mask size');
5092    return
5093    end
5094    npx=size(UvData.Field.A,2);
5095    npy=size(UvData.Field.A,1);
5096    xi=0.5:npx-0.5;
5097    yi=0.5:npy-0.5;
5098    [Xi,Yi]=meshgrid(xi,yi);
5099        for iobj=1:length(UvData.ProjObject)
5100            ObjectData=UvData.ProjObject{iobj};
5101            if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
5102                flagobj=1;
5103                testphys=0; %coordinates in pixels by default
5104                if isfield(ObjectData,'CoordUnit') && ~isequal(ObjectData.CoordUnit,'pixel')
5105                    if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
5106                        Calib=UvData.XmlData{1}.GeometryCalib;
5107                        testphys=1;
5108                    end
5109                end
5110                if isfield(ObjectData,'Coord')&& isfield(ObjectData,'Type')
5111                    if isequal(ObjectData.Type,'polygon')
5112                        X=ObjectData.Coord(:,1);
5113                        Y=ObjectData.Coord(:,2);
5114                        if testphys
5115                            pos=[X Y zeros(size(X))];
5116                            if isfield(Calib,'SliceCoord') && length(Calib.SliceCoord)>=3
5117                                if isfield(Calib,'SliceAngle')&&~isequal(Calib.SliceAngle,[0 0 0])
5118                                    om=norm(Calib.SliceAngle);%norm of rotation angle in radians
5119                                    OmAxis=Calib.SliceAngle/om; %unit vector marking the rotation axis
5120                                    cos_om=cos(pi*om/180);
5121                                    sin_om=sin(pi*om/180);
5122                                    pos=cos_om*pos+sin_om*cross(OmAxis,pos)+(1-cos_om)*(OmAxis*pos')*OmAxis;
5123                                end
5124                                pos(:,1)=pos(:,1)+Calib.SliceCoord(1);
5125                                pos(:,2)=pos(:,2)+Calib.SliceCoord(2);
5126                                pos(:,3)=pos(:,3)+Calib.SliceCoord(3);
5127                            end                           
5128                            [X,Y]=px_XYZ(Calib,pos(:,1),pos(:,2),pos(:,3));
5129                        end
5130                        flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside
5131                    elseif isequal(ObjectData.Type,'ellipse')
5132                        if testphys
5133                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
5134                        end
5135                        RangeX=max(ObjectData.RangeX);
5136                        RangeY=max(ObjectData.RangeY);
5137                        X2Max=RangeX*RangeX;
5138                        Y2Max=RangeY*RangeY;
5139                        distX=(Xi-ObjectData.Coord(1,1));
5140                        distY=(Yi-ObjectData.Coord(1,2));
5141                        flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
5142                    elseif isequal(ObjectData.Type,'rectangle')
5143                        if testphys
5144                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
5145                        end
5146                        distX=abs(Xi-ObjectData.Coord(1,1));
5147                        distY=abs(Yi-ObjectData.Coord(1,2));
5148                        flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
5149                    end
5150                    if isequal(ObjectData.ProjMode,'mask_outside')
5151                        flagobj=~flagobj;
5152                    end
5153                    flag=flag & flagobj;
5154                end
5155            end
5156        end
5157    %mask name
5158    RootPath=get(handles.RootPath,'String');
5159    SubDir=get(handles.SubDir,'String');
5160    RootFile=get(handles.RootFile,'String');
5161    if ~isempty(RootFile)&&(isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
5162        RootFile(1)=[];
5163    end
5164    list=get(handles.masklevel,'String');
5165    masknumber=num2str(length(list));
5166    maskindex=get(handles.masklevel,'Value');
5167    mask_name=fullfile_uvmat(RootPath,[SubDir '.mask'],'mask','.png','_1',maskindex);
5168    imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
5169    imflag=flipdim(imflag,1);
5170
5171    %display the mask
5172    hfigmask=figure;
5173    set(hfigmask,'Name','mask image')
5174    vec=linspace(0,1,256);%define a linear greyscale colormap
5175    map=[vec' vec' vec'];
5176    colormap(map)
5177    image(imflag);
5178    answer=msgbox_uvmat('INPUT_TXT','mask file name:', mask_name);
5179    if ~strcmp(answer,'Cancel')
5180        mask_dir=fileparts(answer);
5181        if ~exist(mask_dir,'dir')
5182            [xx,msg1]=mkdir(mask_dir);
5183            if ~strcmp(msg1,'')
5184                errormsg=['cannot create ' mask_dir ': ' msg1];%error message for directory creation
5185                return
5186            end
5187        end
5188        imwrite(imflag,answer,'BitDepth',8);
5189    end
5190    set(handles.ListObject,'Value',1)
5191end
5192
5193%------------------------------------------------------------------------
5194%-- open the GUI set_grid.fig to create grid
5195function MenuGrid_Callback(hObject, eventdata, handles)
5196%------------------------------------------------------------------------
5197%suppress the other options if grid is chosen
5198set(handles.edit_vect,'Value',0)
5199edit_vect_Callback(hObject, eventdata, handles)
5200set(handles.ListObject,'Value',1)     
5201
5202%prepare display of the set_grid GUI
5203[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
5204FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
5205UvData=get(handles.uvmat,'UserData');
5206% CoordList=get(handles.TransformName,'String');
5207% val=get(handles.TransformName,'Value');
5208set_grid(FileName,UvData.Field);% call the set_object interface
5209
5210
5211%------------------------------------------------------------------------
5212function MenuRuler_Callback(hObject, eventdata, handles)
5213%------------------------------------------------------------------------
5214set(handles.CheckZoom,'Value',0)
5215CheckZoom_Callback(handles.uvmat, [], handles)
5216set(handles.MenuRuler,'checked','on')
5217UvData=get(handles.uvmat,'UserData');
5218UvData.MouseAction='ruler';
5219set(handles.uvmat,'UserData',UvData);
5220
5221%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
5222% MenuRun Callbacks
5223%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
5224
5225%------------------------------------------------------------------------
5226% open the GUI 'series'
5227function MenuSeries_Callback(hObject, eventdata, handles)
5228%------------------------------------------------------------------------
5229Param=read_param(handles);
5230series(Param); %run the series interface
5231
5232% --------------------------------------------------------------------
5233function MenuPIV_Callback(hObject, eventdata, handles)
5234    Param=read_param(handles);
5235%     Param.ActionName='civ_series';
5236hseries=series(Param);
5237hhseries=guidata(hseries);
5238ActionMenu=get(hhseries.ActionName,'String');
5239index_action=find(strcmp('civ_series',ActionMenu));
5240set(hhseries.ActionName,'Value',index_action);
5241series('ActionName_Callback',hObject,eventdata,hhseries); %file input with xml reading  in uvmat, show the image in phys coordinates
5242
5243
5244%------------------------------------------------------------------------
5245% -- open the GUI civ.fig for PIV
5246function MenuCIVx_Callback(hObject, eventdata, handles)
5247%------------------------------------------------------------------------
5248 [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
5249 FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
5250civ(FileName);% interface de civ(not in the uvmat file)
5251
5252function Param=read_param(handles)
5253   
5254[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
5255Param.FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];%first input file name
5256if isequal(get(handles.SubField,'Value'),1)
5257    [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
5258    FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
5259    if ~isequal(FileName_1,Param.FileName)
5260        Param.FileName_1=FileName_1;%second input file name if relevant
5261    end
5262end
5263Param.NomType=get(handles.NomType,'String');
5264Param.NomType_1=get(handles.NomType_1,'String');
5265Param.CheckFixPair=get(handles.CheckFixPair,'Value');
5266UvData=get(handles.uvmat,'UserData');
5267if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'Time')
5268    Param.Time=UvData.XmlData{1}.Time;
5269end
5270if isequal(get(handles.scan_i,'Value'),1)
5271    Param.incr_i=str2num(get(handles.num_IndexIncrement,'String'));
5272elseif isequal(get(handles.scan_j,'Value'),1)
5273    Param.incr_j=str2num(get(handles.num_IndexIncrement,'String'));
5274end
5275
5276%% transfer fields and coordinate names
5277Param.list_fields=get(handles.FieldName,'String');% list menu fields
5278FieldName=Param.list_fields{get(handles.FieldName,'Value')};
5279ind_image=find(strcmp('image',Param.list_fields));
5280if ~isempty(ind_image) && numel(Param.list_fields)>1
5281    Param.list_fields(ind_image)=[]; %suppress  'image' option
5282end
5283Param.index_fields=find(strcmp(FieldName,Param.list_fields));% selected string index
5284Param.list_fields_1=get(handles.FieldName_1,'String');% list menu fields
5285if ischar(Param.list_fields_1),Param.list_fields_1={Param.list_fields_1};end
5286FieldName_1=Param.list_fields_1{get(handles.FieldName_1,'Value')};
5287ind_image=find(strcmp('image',Param.list_fields_1));
5288if ~isempty(ind_image) && numel(Param.list_fields_1)>1
5289    Param.list_fields_1(ind_image)=[]; %suppress  'image' option
5290end
5291Param.index_fields_1=find(strcmp(FieldName_1,Param.list_fields_1));% selected string index
5292TransformList=get(handles.TransformName,'String');
5293Param.TransformName=TransformList{get(handles.TransformName,'Value')};
5294Param.Coord_x_str=get(handles.Coord_x,'String');
5295Param.Coord_x_val=get(handles.Coord_x,'Value');
5296Param.Coord_y_str=get(handles.Coord_y,'Data');
5297
5298% --------------------------------------------------------------------
5299function MenuHelp_Callback(hObject, eventdata, handles)
5300% --------------------------------------------------------------------
5301web('http://servforge.legi.grenoble-inp.fr/projects/soft-uvmat/wiki/UvmatHelp')
5302
5303% path_to_uvmat=which ('uvmat');% check the path of uvmat
5304% pathelp=fileparts(path_to_uvmat);
5305% helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
5306% if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
5307% else
5308%     addpath (fullfile(pathelp,'uvmat_doc'))
5309%     web(helpfile);
5310% end
5311
5312% --- Executes on selection change in Coord_y.
5313function Coord_y_Callback(hObject, eventdata, handles)
5314
5315% --- Executes on selection change in Coord_x.
5316function Coord_x_Callback(hObject, eventdata, handles)
5317
5318
5319% --- Executes on button press in CheckColorBar.
5320function CheckColorBar_Callback(hObject, eventdata, handles)
5321
5322
5323
5324function TransformPath_Callback(hObject, eventdata, handles)
5325% hObject    handle to TransformPath (see GCBO)
5326% eventdata  reserved - to be defined in a future version of MATLAB
5327% handles    structure with handles and user data (see GUIDATA)
5328
5329% Hints: get(hObject,'String') returns contents of TransformPath as text
5330%        str2double(get(hObject,'String')) returns contents of TransformPath as a double
5331
5332
5333%TODO: use to modify fill_GUI
5334%'write_plot_param': update the plotting parameters on the uvmat or view_field interface after a plotting operation
5335function write_plot_param(handles,PlotParam)
5336%% coordinates
5337if isempty(PlotParam.Coordinates)
5338    set(handles.Coordinates,'Visible','off')
5339    set(handles.PlotAxes,'Visible','off')
5340    set(handles.text_display,'Visible','off')
5341    set(handles.TableDisplay,'Visible','on')
5342else
5343    set(handles.Coordinates,'Visible','on')
5344    set(handles.PlotAxes,'Visible','on')
5345    set(handles.text_display,'Visible','on')
5346    if isfield(handles,'TableDisplay')
5347    set(handles.TableDisplay,'Visible','off')
5348    end
5349    Coordinates=PlotParam.Coordinates;
5350    if isfield(Coordinates,'CheckFixAspectRatio')
5351        if Coordinates.CheckFixAspectRatio
5352            set(handles.CheckFixAspectRatio,'Value',1)
5353        else
5354            set(handles.CheckFixAspectRatio,'Value',0)
5355 
5356        end
5357    end
5358    if isfield(Coordinates,'AspectRatio')
5359        set(handles.num_AspectRatio,'String',num2str(Coordinates.AspectRatio))
5360    end
5361    if isfield(Coordinates,'MinX')
5362        set(handles.num_MinX,'String',num2str(Coordinates.MinX,4));
5363        set(handles.num_MaxX,'String',num2str(Coordinates.MaxX,4));
5364        set(handles.num_MinY,'String',num2str(Coordinates.MinY,4));
5365        set(handles.num_MaxY,'String',num2str(Coordinates.MaxY,4));
5366    else
5367        set(handles.num_MinX,'String','');
5368        set(handles.num_MaxX,'String','');
5369        set(handles.num_MinY,'String','');
5370        set(handles.num_MaxY,'String','');
5371    end
5372end
5373
5374%% scalar or image parameters
5375if isfield(PlotParam,'Scalar')
5376    set(handles.Scalar,'Visible','on')
5377    if isfield(PlotParam.Scalar,'MaxA')
5378        set(handles.num_MaxA,'String',num2str(PlotParam.Scalar.MaxA,3));
5379    end
5380    if isfield(PlotParam.Scalar,'MinA')
5381        set(handles.num_MinA,'String',num2str(PlotParam.Scalar.MinA,3));
5382    end   
5383    if isfield(PlotParam.Scalar,'IncrA')
5384        set(handles.num_IncrA,'String',num2str(PlotParam.Scalar.IncrA,3))
5385    end
5386    set(handles.CheckBW,'Value',PlotParam.Scalar.CheckBW)
5387    if isfield(PlotParam.Scalar,'Opacity')&&isfield(handles,'num_Opacity')
5388        set(handles.num_Opacity,'String',num2str(PlotParam.Scalar.Opacity))
5389    end
5390else
5391    set(handles.Scalar,'Visible','off')
5392end
5393
5394%% parameter for vector field
5395if isfield(PlotParam,'Vectors')
5396    set(handles.Vectors,'Visible','on')
5397    if isfield(PlotParam.Vectors,'VecScale')
5398        set(handles.num_VecScale,'String',num2str(PlotParam.Vectors.VecScale,3))
5399    end
5400    if isfield(PlotParam.Vectors,'MinC')&& isfield(PlotParam.Vectors,'MaxC')
5401        MinC=PlotParam.Vectors.MinC;
5402        MaxC=PlotParam.Vectors.MaxC;
5403        set(handles.num_MinVec,'String', num2str(MinC,3));
5404        set(handles.num_MaxVec,'String',num2str(MaxC,3));
5405        list=get(handles.ColorCode,'String');
5406        ichoice=get(handles.ColorCode,'Value');
5407        color_option=list{ichoice};
5408        test3color=strcmp(color_option,'rgb')||strcmp(color_option,'bgr');
5409        if test3color% need to update color thresholds
5410            set(handles.num_ColCode1,'Visible','on')
5411            set(handles.num_ColCode2,'Visible','on')
5412            set(handles.Slider1,'Visible','on')
5413            set(handles.Slider2,'Visible','on')
5414            set(handles.num_ColCode1,'String',num2str(PlotParam.Vectors.ColCode1,3))
5415            set(handles.num_ColCode2,'String',num2str(PlotParam.Vectors.ColCode2,3))
5416            set(handles.Slider1,'Value',(PlotParam.Vectors.ColCode1-MinC)/(MaxC-MinC))
5417            set(handles.Slider2,'Value',(PlotParam.Vectors.ColCode2-MinC)/(MaxC-MinC))
5418        else
5419            set(handles.num_ColCode1,'Visible','off')
5420            set(handles.num_ColCode2,'Visible','off')
5421            set(handles.Slider1,'Visible','off')
5422            set(handles.Slider2,'Visible','off')
5423        end
5424    end
5425else
5426    set(handles.Vectors,'Visible','off')
5427    if isfield(handles,'edit_vect')
5428        set(handles.edit_vect,'Visible','off')
5429        set(handles.record,'Visible','off')
5430    end
5431end
5432
5433
5434% --- Executes on button press in CheckTable.
5435function CheckTable_Callback(hObject, eventdata, handles)
5436if get(handles.CheckTable,'Value')
5437    set(handles.TableDisplay,'Visible','on')
5438else
5439    set(handles.TableDisplay,'Visible','off')
5440end
Note: See TracBrowser for help on using the repository browser.