source: trunk/src/uvmat.m @ 243

Last change on this file since 243 was 243, checked in by sommeria, 10 years ago

bug repair in uvmat

File size: 212.8 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 fields (with fields
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:
31%    'Strings' of all edit boxes and menus: get(handles.Tag,'String')
32%    'Values' of all menus and toggle buttons: get(handles.Tag,'Value')
33%     Matlab structure called UvData stored as 'UserData' of the figure uvmat.fig,(can be obtained by right mouse click on the interface).
34%          It contains the following fields:
35%     - Fixed specifiacation of plotting figures and axes (defined bu uvmat_OpeningFcn)
36%          .PosColorbar: [0.8210 0.4710 0.0190 0.4450]; specified position of the colorbar on figures
37%     - Information read in the documentation open of a series (activated by RootPath_Callback) :
38%          .XmlData, with fields:
39%               .Time: matrix of times of the images with index i and j
40%               .GeometryCalib: [1x1 struct]
41%     - Information defined from the interface:
42%           .NewSeries: =1 when the first view of a new field series is displayed, else 0
43%           .filename:(char string)
44%           .VelType:(char string) type of velocity field selected
45%           .VelType_1:(char string)  REMPLACER LE CELL ACTUEL
46%           .FieldName: (char string) main field selected('image', 'velocity'...)
47%           .FieldName_1:(char string) second field selected('image', 'velocity'...)
48%           .CName: (char string)name of the scalar used for vector colors
49%          .MovieObject: movie object representing an input movie
50%          .MovieObject_1: idem for a second input series (_1)
51%          .filename_1 : last second input file name (to deal with a constant second input without reading again the file)
52%          .VelType_1: last velocity type (VelType, civ2...) for the second input series
53%          .FieldName_1: last field name(velocity, vorticity...) for the second input series
54%          .ZMin, .ZMax: range of the z coordinate
55%..... to complement
56%     - Information on  projection objects
57%           .Object: {[1x1 struct]}
58%           .CurrentObjectIndex: index of the projection object .Object currently selected for editing
59%     -Information on the current field (Field{i})
60%            .Txt : text information to display (e.g. error message)
61%            .NbDim: number of dimensions (=0 by default)
62%            .NbCoord: number of vector components
63%            .CoordType: expresses the type of coordinate ('px' for image, 'sig' for instruments, or 'phys')
64%            .dt: time interval for the corresponding image pair
65%            .Mesh: estimated typical distance between vectors
66%            .ZMax:
67%            .ZMin:
68%            .X, .Y, .Z: set of vector coordinates
69%            .U,.V,.W: corresponding set of vector components
70%            .F: corresponding set of warning flags
71%            .FF: corresponding set of false flags, =0 for good vectors
72%            .C: corresponding values of the scalar used for vector color
73%             (.X, .Y, .Z,.U,.V,.W,.F,.FF,.C are matlab vectors of the same length,
74%                     equal to the number of vectors stored in the input open)
75%            .CName: name of the scalar .C
76%            .CType: type of the scalar .C, setting how the scalar is obtained (see 'Scalars' below)
77%            .A image or scalar
78%            .AX: vector of dimension 2 representing the first and last values
79%              of the X coordinates for the image or scalar known on a regular grid,
80%              or vector of dimension .A for a scaler defined on irregular grid.
81%            .AY: same as .AX along the Y direction
82%            .AName: name of the scalar, ='image' for an image
83
84% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%   DATA FLOW  (for run0_Callback) %%%%%%%%%%%%%%%%%%%%:
85%
86% fields are opened and visualised by the sub-function refresh_field.m
87% (called by uvmat_opening, RUN0, runp and runm)
88% The function first reads the name of the input file from the edit boxes  of the GUI
89% A second input file can be introduced for filed comparison
90% It then reads the input file(s) with the appropriate function, read for
91% images, read_civxdata.m for CIVx PIV data, nc2struct for other netcdf
92% files.
93%               Main input open   second input open(_1)        second image (pair animation)
94%            |                 |                             
95%            |                 |                                               
96%                     Field{1}         Field{2}               
97%                                                                         |
98% coord transform (phys.m) or other user defined  fct acting on Field{i}  |
99%                                                                   Field{i}
100%                                                                    |
101% calc_field.m: calculate scalar or other derived fields (vort, div..).
102%
103% sub_field.m: combine the input Field{i} in a single set of fields (vector + scalar):
104%              Field{i=1->3}.X --> UvData.X                          |
105%                                                                    |
106%                                                                 UvData
107%                                                                    |
108% plot histograms of the whole  field
109% proj_field.m: project the set of fields on the current projection objects defined by UvData.Object
110%                                                                    |                                                                          |
111%                                                                ObjectData
112%                                                                    |
113% plot_field.m: plot the projected fields and store them as          |
114% UvData.axes3                                        |
115%                                                                    |
116%                                                                AxeData
117%
118%%%%%%%%%%%%%%    SCALARS: %%%%%%%%%%%%??%%%
119% scalars are displayed either as an image or countour plot, either as a color of
120% velocity vectors. The scalar values in the first case is represented by
121% UvData.Field.A, and by UvData.Field.C in the second case. The corresponding set of X
122% and Y coordinates are represented by UvData.Field.AX and UvData.Field.AY, and .X and
123% .Y for C (the same as velocity vectors). If A is a nxxny matrix (scalar
124% on a regtular grid), then .AX andf.AY contains only two elements, represneting the
125% coordinates of the four image corners. The scalar name is represented by
126% the strings .AName and/or .CName.
127% If the scalar exists in an input open (image or scalar stored under its
128% name in a netcdf open), it is directly read at the level of Field{1}or Field{2}.
129% Else only its name AName is recorded in Field{i}, and its field is then calculated
130%by the fuction calc_scal after the coordinate transform or after projection on an edit_object
131     
132% Properties attached to plotting figures (standard Matlab properties):
133%    'CurrentAxes'= gca or get(gcf,'CurrentAxes');
134%    'CurrentPoint'=get(gcf,'CurrentPoint'): figure coordinates of the point over which the mouse is positioned
135%    'CurrentCharacter'=get(gcf,'CurrentCharacter'): last character typed  over the figure where the mouse is positioned
136%    'WindowButtonMotionFcn': function permanently called by mouse motion over the figure
137%    'KeyPressFcn': function called by pressing a key on the key board
138%    'WindowButtonDownFcn':  function called by pressing the mouse over the  figure
139%    'WindowButtonUpFcn': function called by releasing  the mouse pressure over the  figure
140
141% Properties attached to plotting axes:
142%    'CurrentPoint'=get(gca,'CurrentPoint'); (standard Matlab) same as for the figure, but position in plot coordinates.
143%     AxeData:=get(gca,'UserData');
144%     AxeData.Drawing  = create: create a new object
145%                       = deform: modify an existing object by moving its defining create
146%                      = off: no current drawing action
147%                     = translate: translate an existing object
148%                    = calibration: move a calibration point
149%                    = zoom: isolate a subregion for zoom in=1 if an object is being currently drawn, 0 else (set to 0 by releasing mouse button)
150%            .CurrentOrigin: Origin of a curently drawn edit_object
151%            .CurrentLine: currently drawn menuline (A REVOIR)
152%            .CurrentObject: handle of the currently drawn edit_object
153%            .CurrentRectZoom: current rectangle used for zoom
154
155% Properties attached to projection objects (create, menuline, menuplane...):
156%    'Tag'='proj_object': for all projection objects
157%    ObjectData.Style=...: style of projection object:
158%              .ProjMode
159%              .Coord: defines the position of the object
160%              .XMin,YMin....
161%              .XMax,YMax....
162%              .DX,DY,DZ
163%              .Phi, .Theta, .Psi : Euler angles
164%              .X,.Y,.U,.V.... : field data projected on the object
165%              .IndexObj: index in the list of UvData.Object
166           %during plotting
167%               .plotaxes: handles of the current axes used to plot the  result of field projection on the object
168%               .plothandle: vector of handle(s) of the object graphic represnetation in all the opened plotting axes
169% To each projection object #iobj, corresponds an axis
170% Object{iobj}.plotaxes and nbobj representation graphs  Object{iobj}.plothandles(:) (where nbobj is the
171% nbre of current objects opened in uvmat. Note that Object{iobj}.plothandles(iobj)=[] : an object is not represented in its own projection field;
172
173%------------------------------------------------------------------------
174%------------------------------------------------------------------------
175%  I - MAIN FUNCTION UVMAT (DO NOT MODIFY)
176%------------------------------------------------------------------------
177%------------------------------------------------------------------------
178function varargout = uvmat(varargin)
179
180% Begin initialization code - DO NOT EDIT
181gui_Singleton = 1;
182gui_State = struct('gui_Name',          mfilename, ...
183                   'gui_Singleton',     gui_Singleton, ...
184                   'gui_OpeningFcn',    @uvmat_OpeningFcn, ...
185                   'gui_OutputFcn',     @uvmat_OutputFcn, ...
186                   'gui_LayoutFcn',     [], ...
187                   'gui_Callback',      []);
188if nargin && ischar(varargin{1})&& ~isempty(regexp(varargin{1},'_Callback','once'))
189    gui_State.gui_Callback = str2func(varargin{1});
190end
191
192if nargout
193    varargout{1:nargout} = gui_mainfcn(gui_State, varargin{:});
194else
195    gui_mainfcn(gui_State, varargin{:});
196end
197% End initialization code - DO NOT EDIT
198
199%------------------------------------------------------------------------
200% --- Executes just before the GUI uvmat is made visible.
201function uvmat_OpeningFcn(hObject, eventdata, handles, input )
202%------------------------------------------------------------------------
203
204%% Choose default command menuline output for uvmat (standard GUI)
205handles.output = hObject;
206
207%% Update handles structure (standard GUI)
208guidata(hObject, handles);
209
210%% set the position of colorbar and ancillary GUIs:
211set(hObject,'Units','Normalized')
212movegui(hObject,'center')
213UvData.OpenParam.PosColorbar=[0.805 0.022 0.019 0.445];
214UvData.OpenParam.SetObjectOrigin=[-0.05 -0.03]; %position for set_object
215UvData.OpenParam.SetObjectSize=[0.3 0.7];
216UvData.OpenParam.CalOrigin=[0.95 -0.03];%position for geometry_calib (TO IMPROVE)
217UvData.OpenParam.CalSize=[0.28 1];
218UvData.axes3=[];%initiate the record of plotted field
219UvData.axes2=[];
220UvData.axes1=[];
221AxeData.LimEditBox=1; %initialise AxeData
222set(handles.axes3,'UserData',AxeData)
223
224%% set functions for the mouse and keyboard
225set(handles.histo_u,'NextPlot','replacechildren');
226set(handles.histo_v,'NextPlot','replacechildren');
227set(hObject,'KeyPressFcn',{'keyboard_callback',handles})%set keyboard action function
228set(hObject,'WindowButtonMotionFcn',{'mouse_motion',handles})%set mouse action functio
229set(hObject,'WindowButtonDownFcn',{'mouse_down'})%set mouse click action function
230set(hObject,'WindowButtonUpFcn',{'mouse_up',handles})
231set(hObject,'DeleteFcn',{@closefcn})%
232
233%% refresh projection plane
234UvData.Object{1}.ProjMode='projection';%main plotting plane
235set(handles.Fields,'Value',1)
236set(handles.Fields,'string',{''})
237
238%% TRANSFORM menu: builtin fcts
239menu_str={'';'phys';'px';'phys_polar'};
240UvData.OpenParam.NbBuiltin=numel(menu_str); %number of functions
241path_uvmat=fileparts(which('uvmat'));
242addpath(fullfile(path_uvmat,'transform_field'))
243fct_handle{1,1}=[];
244testexist=zeros(size(menu_str'));%default
245testexist(1)=1;
246for ilist=2:length(menu_str)
247    if exist(menu_str{ilist},'file')
248        fct_handle{ilist,1}=str2func(menu_str{ilist});
249        testexist(ilist)=1;
250    else
251        testexist(ilist)=0;
252    end
253end
254rmpath(fullfile(path_uvmat,'transform_field'))
255
256%% load the list of previously browsed files in menus Open and Open_1
257 dir_perso=prefdir; % path to the directory .matlab for personal data
258 profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmauvmat_perso.mat' in .matlab
259 if exist(profil_perso,'file')
260      h=load (profil_perso);
261      if isfield(h,'MenuFile_1')
262          set(handles.MenuFile_1,'Label',h.MenuFile_1);
263          set(handles.MenuFile_1_1,'Label',h.MenuFile_1);
264      end
265      if isfield(h,'MenuFile_2')
266          set(handles.MenuFile_2,'Label',h.MenuFile_2);
267          set(handles.MenuFile_2_1,'Label',h.MenuFile_2);
268      end
269      if isfield(h,'MenuFile_3')
270          set(handles.MenuFile_3,'Label',h.MenuFile_3);
271          set(handles.MenuFile_3_1,'Label',h.MenuFile_3);
272      end
273      if isfield(h,'MenuFile_4')
274          set(handles.MenuFile_4,'Label',h.MenuFile_4);
275          set(handles.MenuFile_4_1,'Label',h.MenuFile_4);
276      end
277      if isfield(h,'MenuFile_5')
278          set(handles.MenuFile_5,'Label',h.MenuFile_5);
279          set(handles.MenuFile_5_1,'Label',h.MenuFile_5);
280      end
281      if isfield(h,'transform_fct') && iscell(h.transform_fct)
282         for ilist=1:length(h.transform_fct);
283             if exist(h.transform_fct{ilist},'file')
284                [path,file]=fileparts(h.transform_fct{ilist});
285                addpath(path)
286                h_func=str2func(file);
287                rmpath(path)
288                testexist=[testexist 1];
289             else
290                file='';
291                h_func=[];
292                testexist=[testexist 0];
293             end
294             fct_handle=[fct_handle; {h_func}]; %concatene the list of paths
295             menu_str=[menu_str; {file}];
296         end
297      end
298 end
299menu_str=menu_str(testexist==1);%=menu_str(testexist~=0)
300fct_handle=fct_handle(testexist==1);
301menu_str=[menu_str;{'more...'}];
302set(handles.transform_fct,'String',menu_str)
303set(handles.transform_fct,'UserData',fct_handle)% store the list of path in UserData of ACTION
304
305
306%% check the path and date of modification of all functions in uvmat
307path_to_uvmat=which ('uvmat');% check the path detected for source file uvmat
308[errormsg,date_str]=check_functions;%check the path of the functions called by uvmat.m
309date_str=['last modification: ' date_str];
310
311%% case of an input argument for uvmat
312testinputfield=0;
313inputfile=[];
314Field=[];
315if exist('input','var')
316    if ~isempty(errormsg)
317        msgbox_uvmat('WARNING',errormsg)
318    end
319    if ishandle(handles.UVMAT_title)
320        delete(handles.UVMAT_title)
321    end   
322    if isstruct(input)
323        if isfield(input,'InputFile')
324            inputfile=input.InputFile;
325        end
326        if isfield(input,'TimeIndex')
327            set(handles.i1,num2str(input.TimeIndex))
328        end
329        if isfield(input,'FieldsString')
330%             set(handles.Fields,'Value',1)
331            UvData.FieldsString=input.FieldsString;
332        end
333    elseif ischar(input)% file name introduced as input
334           inputfile=input;
335    elseif isnumeric(input)%simple matrix introduced as input
336        sizinput=size(input);
337        if sizinput(1)<=1 || sizinput(2)<=1
338            msgbox_uvmat('ERROR','bad input for uvmat: file name, structure or numerical matrix accepted')
339            return
340        end
341        UvData.Field.ListVarName={'A','coord_y','coord_x'};
342        UvData.Field.VarDimName={{'coord_y','coord_x'},'cord_y','coord_x'};
343        UvData.Field.A=input;
344        UvData.Field.coord_x=[0.5 size(input,2)-0.5];
345        UvData.Field.coord_y=[size(input,1)-0.5 0.5];
346        testinputfield=1;
347    end
348else
349   if ishandle(handles.UVMAT_title)
350       fid=fopen('revision.info');
351       if fid~=-1
352         a=textscan(fid,'%s%s%s',1,'HeaderLines',4,'Delimiter',' ');
353         set(handles.UVMAT_title,'String',[{'Copyright Joel Sommeria, 2008, Coriolis/ LEGI / CNRS-UJF-INPG'};{'GNU General Public License'}; {path_to_uvmat}; ...
354           {['at revision ' a{3}{1}]};{date_str};errormsg]);
355         fclose(fid);
356       else
357          set(handles.UVMAT_title,'String',[{'Copyright Joel Sommeria, 2008, Coriolis/ LEGI / CNRS-UJF-INPG'};{'GNU General Public License'};{path_to_uvmat};...
358               {date_str};errormsg]);
359       end
360   end
361end
362set(handles.uvmat,'UserData',UvData)
363if ~isempty(inputfile)
364    %%%%% display the input field %%%%%%%
365    display_file_name(hObject, eventdata, handles,inputfile)
366    %%%%%%%
367    testinputfield=1;
368end
369
370%% plot input field if exists
371if testinputfield
372    %delete drawn objects
373    hother=findobj(handles.axes3,'Tag','proj_object');%find all the proj objects
374    for iobj=1:length(hother)
375        delete_object(hother(iobj))
376    end 
377    if isempty(inputfile)
378        errormsg=refresh_field(handles,[],[],[],[],[],[],{Field});
379        set(handles.MenuTools,'Enable','on')
380        set(handles.OBJECT_txt,'Visible','on')
381        set(handles.edit_object,'Visible','on')
382        set(handles.list_object_1,'Visible','on')
383        set(handles.frame_object,'Visible','on')
384        if ~isempty(errormsg)
385            msgbox_uvmat('ERROR',errormsg)
386        end
387    end
388end
389
390set_vec_col_bar(handles) %update the display of color code for vectors
391
392%------------------------------------------------------------------------
393% --- Outputs from this function are returned to the command menuline.
394function varargout = uvmat_OutputFcn(hObject, eventdata, handles)
395varargout{1} = handles.output;% the only output argument is the handle to the GUI figure
396
397%------------------------------------------------------------------------
398%------------------------------------------------------------------------
399%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
400% automatically sets the global properties when the rootfile name is introduced
401% then activate the view-field action if selected
402% it is activated either by clicking on the RootPath window or by the
403% browser
404%------------------------------------------------------------------------
405%------------------------------------------------------------------------
406% --- Executes on the menu Open/Browse...
407% search the files, recognize their type according to their name and fill the rootfile input windows
408function MenuBrowse_Callback(hObject, eventdata, handles)
409oldfile=read_file_boxes(handles);
410
411if isempty(oldfile)||isequal(oldfile,'') %loads the previously stored file name and set it as default in the file_input box
412         dir_perso=prefdir;
413         profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
414         if exist(profil_perso,'file')
415              h=load (profil_perso);
416             if isfield(h,'MenuFile_1')
417                  oldfile=h.MenuFile_1;
418             end
419         end
420end
421[FileName, PathName] = uigetfile( ...
422       {'*.xml;*.xls;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol;*.nc;*.cmx;*.fig;*.log;*.dat;*.bat;', ' (*.xml,*.xls,*.civ,*.jpg ,*.png, .tif, *.avi,*.vol,*.nc,*.cmx,*.fig,*.log,*.dat,*.bat)';
423       '*.xml',  '.xml files '; ...
424        '*.xls',  '.xls files '; ...
425        '*.civ',  '.civ files '; ...
426        '*.jpg',' jpeg image files'; ...
427        '*.png','.png image files'; ...
428        '*.tif','.tif image files'; ...
429        '*.avi;*.AVI','.avi movie files'; ...
430        '*.vol','.volume images (png)'; ...
431        '*.nc','.netcdf files'; ...
432        '*.cdf','.netcdf files'; ...
433        '*.cmx','.cmx text files ';...
434        '*.fig','.fig files (matlab fig)';...
435        '*.log','.log text files ';...
436        '*.dat','.dat text files ';...
437        '*.bat','.bat system command text files';...
438        '*.*',  'All Files (*.*)'}, ...
439        'Pick a file',oldfile);
440fileinput=[PathName FileName];%complete file name
441sizf=size(fileinput);
442if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
443
444% display the selected field and related information
445display_file_name(hObject, eventdata, handles,fileinput)
446
447%update list of recent files in the menubar
448MenuFile_1=fileinput;
449MenuFile_2=get(handles.MenuFile_1,'Label');
450MenuFile_3=get(handles.MenuFile_2,'Label');
451MenuFile_4=get(handles.MenuFile_3,'Label');
452MenuFile_5=get(handles.MenuFile_4,'Label');
453set(handles.MenuFile_1,'Label',MenuFile_1)
454set(handles.MenuFile_2,'Label',MenuFile_2)
455set(handles.MenuFile_3,'Label',MenuFile_3)
456set(handles.MenuFile_4,'Label',MenuFile_4)
457set(handles.MenuFile_5,'Label',MenuFile_5)
458set(handles.MenuFile_1_1,'Label',MenuFile_1)
459set(handles.MenuFile_2_1,'Label',MenuFile_2)
460set(handles.MenuFile_3_1,'Label',MenuFile_3)
461set(handles.MenuFile_4_1,'Label',MenuFile_4)
462set(handles.MenuFile_5_1,'Label',MenuFile_5)
463dir_perso=prefdir;
464profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
465if exist(profil_perso,'file')
466    save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
467else
468    txt=ver('MATLAB');
469    Release=txt.Release;
470    relnumb=str2double(Release(3:4));
471    if relnumb >= 14
472        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
473    else
474        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
475    end
476end
477
478% -----------------------------------------------------------------------
479% --- Open again the file whose name has been recorded in MenuFile_1
480function MenuFile_1_Callback(hObject, eventdata, handles)
481%------------------------------------------------------------------------
482fileinput=get(handles.MenuFile_1,'Label');
483display_file_name(hObject, eventdata, handles,fileinput)
484
485% -----------------------------------------------------------------------
486% --- Open again the file whose name has been recorded in MenuFile_2
487function MenuFile_2_Callback(hObject, eventdata, handles)
488%------------------------------------------------------------------------
489fileinput=get(handles.MenuFile_2,'Label');
490display_file_name(hObject, eventdata, handles,fileinput)
491
492% -----------------------------------------------------------------------
493% --- Open again the file whose name has been recorded in MenuFile_3
494function MenuFile_3_Callback(hObject, eventdata, handles)
495%------------------------------------------------------------------------
496fileinput=get(handles.MenuFile_3,'Label');
497display_file_name(hObject, eventdata, handles,fileinput)
498
499% -----------------------------------------------------------------------
500% --- Open again the file whose name has been recorded in MenuFile_4
501function MenuFile_4_Callback(hObject, eventdata, handles)
502%------------------------------------------------------------------------
503fileinput=get(handles.MenuFile_4,'Label');
504display_file_name(hObject, eventdata, handles,fileinput)
505
506% -----------------------------------------------------------------------
507% --- Open again the file whose name has been recorded in MenuFile_5
508function MenuFile_5_Callback(hObject, eventdata, handles)
509%------------------------------------------------------------------------
510fileinput=get(handles.MenuFile_5,'Label');
511display_file_name(hObject, eventdata, handles,fileinput)
512
513%------------------------------------------------------------------------
514% --- Fills the edit boxes RootPath, RootFile,NomType...from an input file name 'fileinput'
515function display_file_name(hObject, eventdata, handles,fileinput)
516%------------------------------------------------------------------------
517if ~exist(fileinput,'file')
518    msgbox_uvmat('ERROR',['input file ' fileinput  ' does not exist'])
519    return
520end
521[RootPath,RootFile,i1,i2,str_a,str_b,ext,NomType,SubDir]=name2display(fileinput);%extract information from the file name
522ext_test=''; %default
523if ~isempty(ext) % if a file extension is detected
524    form=imformats(ext(2:end));%test valid Matlab image formats
525    if ~isempty(form)
526        ext_test='.image';
527        imainfo=imfinfo(fileinput); 
528        if length(imainfo) >1 %case of image with multiple frames
529            i1='1'; % set the frame counter to 1 by default
530            i2='';
531            str_a='';
532            str_b='';
533            NomType='*'; %indicate a set of indexed frames within a single file
534            [RootPath,RootFile]=fileparts(fileinput); %include the indices in the root file
535        end
536    elseif isequal(lower(ext),'.avi')%case of avi movie file
537        ext_test='.image';
538        i1='1'; % set the frame counter to 1 by default
539        i2='';
540        str_a='';
541        str_b='';
542        NomType='*'; %indicate a set of indexed frames within a single file
543        [RootPath,RootFile]=fileparts(fileinput); %include the indices in the root file
544    else
545        ext_test=lower(ext);
546    end
547end
548switch ext_test
549    case {'.civ','.log','.cmx','.cmx2','.txt','.bat'}  %display text file
550        edit(fileinput) 
551    case '.fig'                           %display matlab figure
552        hfig=open(fileinput);
553        set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
554        set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
555        set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
556    case {'.xml','.xls'}                % edit xml or Excel files
557       editxml(fileinput);
558    case {'.avi','.image','.vol','.nc','.cdf'}   
559        set(handles.RootPath,'String',RootPath);
560        if  isequal(SubDir,'')
561            rootname=fullfile(RootPath,RootFile);
562        else
563            rootname=fullfile(RootPath,SubDir,RootFile);
564            SubDir=['/' SubDir]; %display the separator
565        end
566        set(handles.SubDir,'String',SubDir);
567        set(handles.RootFile,'String',['/' RootFile]); %display the separator
568        indices=fileinput(length(rootname)+1:end);
569        indices(end-length(ext)+1:end)=[]; %remove extension
570        set(handles.FileIndex,'String',indices);       
571        set(handles.FileIndex,'UserData',NomType);
572        set(handles.FileExt,'String',ext);
573        % fill file index counters
574        set(handles.i1,'String',i1);   
575        set(handles.i2,'String',i2);
576        set(handles.j1,'String',str_a);
577        set(handles.j2,'String',str_b);
578       
579        % synchronise indices of the second  input file if it exists
580        if get(handles.SubField,'Value')==1% if the subfield button is activated, update the field numbers
581            [ff,rr,FileBase_1,ii,FileExt_1,SubDir_1]=read_file_boxes_1(handles);
582            NomType_1=get(handles.FileIndex_1,'UserData');     
583            FileName_1=name_generator(FileBase_1,str2double(i1),str2double(i2),FileExt_1,NomType_1,1,stra2num(str_a),stra2num(str_b),SubDir_1);
584            if exist(FileName_1,'file')
585                FileIndex_1=name_generator('',str2double(i1),str2double(i2),'',NomType_1,1,stra2num(str_a),stra2num(str_b),'');
586                set(handles.FileIndex_1,'String',FileIndex_1)
587            else
588                set(handles.SubField,'Value',0)
589                SubField_Callback(hObject, eventdata, handles)
590            end
591        end 
592
593        %enable other menus
594        set(handles.MenuOpen_1,'Enable','on')
595        set(handles.MenuFile_1_1,'Enable','on')
596        set(handles.MenuFile_2_1,'Enable','on')
597        set(handles.MenuFile_3_1,'Enable','on')
598        set(handles.MenuFile_4_1,'Enable','on')
599        set(handles.MenuFile_5_1,'Enable','on')
600        set(handles.MenuExport,'Enable','on')
601        set(handles.MenuExportFigure,'Enable','on')
602        set(handles.MenuExportMovie,'Enable','on')
603        set(handles.MenuTools,'Enable','on')
604        set(handles.OBJECT_txt,'Visible','on')
605        set(handles.edit_object,'Visible','on')
606        set(handles.list_object_1,'Visible','on')
607        set(handles.frame_object,'Visible','on')
608         %%%%%% initiate input file:
609        update_rootinfo(hObject,eventdata,handles); 
610    otherwise
611       msgbox_uvmat('ERROR',['invalid input file extension' ext])
612end
613
614%------------------------------------------------------------------------
615% --- Called by action in RootPath edit box
616function RootPath_Callback(hObject,eventdata,handles)
617%------------------------------------------------------------------------
618update_rootinfo(hObject,eventdata,handles);
619
620%------------------------------------------------------------------------
621% --- Called by action in RootFile edit box
622function SubDir_Callback(hObject, eventdata, handles)
623%------------------------------------------------------------------------
624%refresh the menu of input fields
625Fields_Callback(hObject, eventdata, handles);
626% refresh the current field
627run0_Callback(hObject, eventdata, handles);
628
629%------------------------------------------------------------------------
630% --- Called by action in RootFile edit box
631function RootFile_Callback(hObject, eventdata, handles)
632%------------------------------------------------------------------------
633update_rootinfo(hObject,eventdata,handles)
634
635%------------------------------------------------------------------------
636% --- Called by action in FileIndex edit box
637function FileIndex_Callback(hObject, eventdata, handles)
638%------------------------------------------------------------------------
639FileIndices=get(handles.FileIndex,'String');
640if isempty(str2num(FileIndices))
641    [pp,ff,str1,str2,str_a,str_b]=name2display(FileIndices);
642else
643    str1=FileIndices;
644    str2='';
645    str_a='';
646    str_b='';
647end
648set(handles.i1,'String',str1);
649set(handles.i2,'String',str2);
650set(handles.j1,'String',str_a);
651set(handles.j2,'String',str_b);
652run0_Callback(hObject, eventdata, handles)
653
654%------------------------------------------------------------------------
655% --- Update information about a new field series (indices to scan, timing,
656%     calibration from an xml file, then refresh current plots
657function update_rootinfo(hObject,eventdata,handles)
658%------------------------------------------------------------------------
659set(handles.RootPath,'BackgroundColor',[1 1 0])
660drawnow
661set(handles.Fields,'UserData',[])% reinialize data from uvmat opening
662UvData=get(handles.uvmat,'UserData');%huvmat=handles of the uvmat interface
663UvData.NewSeries=1; %flag for run0: begin a new series
664UvData.TestInputFile=1;
665set(handles.fix_pair,'Value',1) % activate by default the comp_input '-'input window
666set(handles.FixVelType,'Value',0); %desactivate fixed veltype
667[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles);
668if ~exist(FileName,'file')
669   msgbox_uvmat('ERROR',['input file ' FileName ' not found']);
670    return
671end
672nbfield=[];%default
673nburst=[];%default
674
675% read timing and total frame number from the current file (movie files) !! may be overrid by xml file
676XmlData.Time=[];%default
677XmlData.GeometryCalib=[];%default
678TimeUnit=[];%default
679testima=0; %test for image input
680imainfo=[];
681ColorType='falsecolor'; %default
682hhh='';
683if isequal(lower(FileExt),'.avi') %.avi file
684    testima=1;
685    imainfo=aviinfo([FileBase FileIndices FileExt]);
686    nbfield=imainfo.NumFrames;
687    nburst=1;
688    set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FramesPerSecond) 'ms']);%display the elementary time interval in millisec
689    XmlData.Time=(0:1/imainfo.FramesPerSecond:(imainfo.NumFrames-1)/imainfo.FramesPerSecond)';
690    TimeUnit='s';
691    hhh=which('mmreader');
692    ColorType=imainfo.ImageType;%='truecolor' for color images
693elseif ~isempty(FileExt(2:end))&&(~isempty(imformats(FileExt(2:end))) || isequal(FileExt,'.vol'))%&& isequal(NomType,'*')% multi-frame image
694    testima=1;
695    if ~isequal(SubDir,'')
696       RootFile=get(handles.RootFile,'String');
697        imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]);
698    else
699        imainfo=imfinfo([FileBase FileIndices FileExt]);
700    end
701    ColorType=imainfo.ColorType;%='truecolor' for color images
702    if length(imainfo) >1 %case of image with multiple frames
703        nbfield=length(imainfo);
704        nburst=1;
705    end
706end
707if ~strcmp(hhh,'')&& mmreader.isPlatformSupported()% if the function is found (recent version of matlab)
708    UvData.MovieObject=mmreader([FileBase FileIndices FileExt]);
709elseif isfield(UvData,'MovieObject')
710    UvData=rmfield(UvData,'MovieObject');
711end
712if isfield(imainfo,'Width') && isfield(imainfo,'Height')
713    set(handles.npx,'String',num2str(imainfo.Width));%fills nbre of pixels x box
714    set(handles.npy,'String',num2str(imainfo.Height));%fills nbre of pixels x box
715else
716    set(handles.npx,'String','');%fills nbre of pixels x box
717    set(handles.npy,'String','');%fills nbre of pixels x box
718end
719set(handles.BW,'Value',strcmp(ColorType,'grayscale'))% select handles.BW if grayscale image
720
721% read parameters (time, geometric calibration..) from a documentation file (.xml advised)
722filexml=[FileBase '.xml'];
723fileciv=[FileBase '.civ'];
724warntext='';%default warning message
725NbSlice=1;%default
726
727if exist(filexml,'file')
728    set(handles.view_xml,'Visible','on')
729    set(handles.view_xml,'BackgroundColor',[1 1 0])
730    set(handles.RootPath,'BackgroundColor',[1 1 1])
731    set(handles.view_xml,'String','view .xml')
732    drawnow
733    [XmlData,warntext]=imadoc2struct(filexml);
734    if ~isempty(warntext)
735        msgbox_uvmat('WARNING',warntext)
736    end
737    if isfield(XmlData,'TimeUnit')
738        if isfield(XmlData,'TimeUnit')&& ~isempty(XmlData.TimeUnit)
739            TimeUnit=XmlData.TimeUnit;
740        end
741    end
742    set(handles.view_xml,'BackgroundColor',[1 1 1])
743    drawnow
744    if isfield(XmlData, 'GeometryCalib') && ~isempty(XmlData.GeometryCalib)
745        XmlData.GeometryCalib
746        if isfield(XmlData.GeometryCalib,'VolumeScan') && isequal(XmlData.GeometryCalib.VolumeScan,'y')
747            set (handles.nb_slice,'String','volume')
748        end
749        hgeometry_calib=findobj('tag','geometry_calib');
750        if ~isempty(hgeometry_calib)
751            GUserData=get(hgeometry_calib,'UserData');
752            if ~(isfield(GUserData,'XmlInputFile') && strcmp(GUserData.XmlInputFile,filexml))
753                answer=msgbox_uvmat('INPUT_Y-N','replace the display of geometry_calib with the new input data?');
754                if strcmp(answer,'Yes')
755                    geometry_calib(filexml);%diplay the new calibration points and parameters in geometry_calib
756                end
757            end
758        end
759    end 
760elseif exist(fileciv,'file')% if .civ file found
761    [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']);
762    GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
763    GeometryCalib.Tx=0;
764    GeometryCalib.Ty=0;
765    GeometryCalib.Tz=1;
766    GeometryCalib.dpx=1;
767    GeometryCalib.dpy=1;
768    GeometryCalib.sx=1;
769    GeometryCalib.Cx=0;
770    GeometryCalib.Cy=0;
771    GeometryCalib.f=1;
772    GeometryCalib.kappa1=0;
773    GeometryCalib.CoordUnit='cm';
774    XmlData.GeometryCalib=GeometryCalib;
775    if error==2, warntext=['no file ' FileBase '.civ'];
776    elseif error==1, warntext='inconsistent number of fields in the .civ file';
777    end 
778    set(handles.npx,'String',num2str(npx));%fills nbre of pixels x box
779    set(handles.npy,'String',num2str(npy));%fills nbre of pixels y box
780    set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box
781    set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box
782    set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box
783    set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box
784    set(handles.view_xml,'Visible','on')   
785    set(handles.view_xml,'String','view .civ')
786else
787    set(handles.view_xml,'Visible','off')
788end
789
790% store last index in handles.lat_i and .last_j
791if ~isempty(XmlData.Time)
792    nbfield=size(XmlData.Time,1);
793    nburst=size(XmlData.Time,2);
794    %transform .Time to a column vector if it is a line vector the nomenclature uses a single index
795    if isequal(nbfield,1) && ~isequal(nburst,1)% .Time is a line vector
796        NomType=get(handles.FileIndex,'UserData');
797        if numel(NomType)>=2 &&(strcmp(NomType,'_i')||strcmp(NomType(1:2),'%0')||strcmp(NomType(1:2),'_%'))
798            XmlData.Time=(XmlData.Time)';
799            nbfield=nburst;
800            nburst=1;
801        end
802    end
803end
804last_i_cell=get(handles.last_i,'String');
805if isempty(nbfield)
806    last_i_cell{1}='';
807else
808    last_i_cell{1}=num2str(nbfield);
809end
810set(handles.last_i,'String',last_i_cell)
811last_j_cell=get(handles.last_j,'String');
812if isempty(nburst)
813     last_j_cell{1}='';
814else
815     last_j_cell{1}=num2str(nburst);
816end
817set(handles.last_j,'String',last_j_cell);
818
819% store geometric calibration in UvData
820if isfield(XmlData,'GeometryCalib')
821    GeometryCalib=XmlData.GeometryCalib;
822    if isempty(GeometryCalib)
823        set(handles.pxcm,'String','')
824        set(handles.pycm,'String','')
825        set(handles.transform_fct,'Value',1); %  no transform by default
826    else
827        if (isfield(GeometryCalib,'R')&& ~isequal(GeometryCalib.R(2,1),0) && ~isequal(GeometryCalib.R(1,2),0)) ||...
828            (isfield(GeometryCalib,'kappa1')&& ~isequal(GeometryCalib.kappa1,0))
829            set(handles.pxcm,'String','var')
830            set(handles.pycm,'String','var')
831        elseif isfield(GeometryCalib,'fx_fy')
832            pixcmx=GeometryCalib.fx_fy(1);%*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx);
833            pixcmy=GeometryCalib.fx_fy(2);%*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy);
834            set(handles.pxcm,'String',num2str(pixcmx))
835            set(handles.pycm,'String',num2str(pixcmy))
836        end
837        if ~get(handles.FixLimits,'Value')
838            set(handles.transform_fct,'Value',2); % phys transform by default if fixedLimits is off
839        end
840        if isfield(GeometryCalib,'SliceCoord')
841           
842           siz=size(GeometryCalib.SliceCoord);
843           if siz(1)>1
844               NbSlice=siz(1);
845               set(handles.slices,'Visible','on')
846               set(handles.slices,'Value',1)
847           end
848           if isfield(GeometryCalib,'VolumeScan') && isequal(GeometryCalib.VolumeScan,'y')
849               set(handles.nb_slice,'String','volume')
850           else
851               set(handles.nb_slice,'String',num2str(NbSlice))
852           end
853           slices_Callback(hObject, eventdata, handles)
854        end           
855    end
856end
857
858%update the data attached to the uvmat interface
859if ~isempty(TimeUnit)
860    set(handles.time_txt,'String',['time (' TimeUnit ')'])
861end
862UvData.TimeUnit=TimeUnit;
863UvData.XmlData=XmlData;
864UvData.NewSeries=1;
865
866
867%display warning message
868if ~isequal(warntext,'')
869    msgbox_uvmat('WARNING',warntext);
870end
871
872% set default options in menu 'Fields'
873
874if ~testima
875    testcivx=0;
876    if isfield(UvData,'FieldsString') && isequal(UvData.FieldsString,{'get_field...'})% field menu defined as input (from get_field)
877        set(handles.Fields,'Value',1)
878        set(handles.Fields,'String',{'get_field...'})
879        UvData=rmfield(UvData,'FieldsString');
880    else
881        Data=nc2struct(FileName,'ListGlobalAttribute','Conventions','absolut_time_T0','civ');
882        if strcmp(Data.Conventions,'uvmat/civdata') ||( ~isempty(Data.absolut_time_T0)&& ~isequal(Data.civ,0))%if the new input is Civx
883            FieldList=calc_field;
884            set(handles.Fields,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data
885            set(handles.Fields,'Value',2) % set menu to 'velocity'
886            col_vec=FieldList;
887            col_vec(1)=[];%remove 'velocity' option for vector color (must be a scalar)
888            testcivx=1;
889        end
890        if ~testcivx
891            set(handles.Fields,'Value',1) % set menu to 'get_field...
892            set(handles.Fields,'String',{'get_field...'})
893            col_vec={'get_field...'};
894        end
895        set(handles.col_vec,'String',col_vec)
896    end
897end
898set(handles.uvmat,'UserData',UvData)
899
900%% set index navigation options and refresh plots
901set(handles.RootPath,'BackgroundColor',[1 1 1])
902drawnow
903set_scan_options(hObject, eventdata, handles)
904
905%------------------------------------------------------------------------
906%--- Set index navigation options for new series input and refresh plot
907%------------------------------------------------------------------------
908function set_scan_options(hObject, eventdata, handles)
909
910%  set the corresponding index navigation options
911NomType=get(handles.FileIndex,'UserData');       
912NomType_1=get(handles.FileIndex_1,'UserData');
913last_i_str=get(handles.last_i,'String');
914nbfield=str2num(last_i_str{1});
915if numel(last_i_str)==2
916    nbfield=min(nbfield,str2num(last_i_str{2}));
917end 
918state_j='off'; %default
919scan_option='i';%default
920NomTypeRaw=regexprep(NomType(2:end), '-', '');
921if numel(regexp(NomTypeRaw,'\D'))>=1
922        state_j='on';
923        if isequal(nbfield,1)
924            scan_option='j'; %scan j index by default if nbfield=1               
925        end
926end
927if ~isempty(NomType_1)
928    NomTypeRaw=regexprep(NomType_1(2:end), '-', '');
929    if numel(regexp(NomTypeRaw,'\D'))>=1
930            state_j='on';
931            if isequal(nbfield,1)
932                scan_option='j';                 
933            end           
934    end
935end
936if isequal(scan_option,'i')
937     set(handles.scan_i,'Value',1)
938     scan_i_Callback(hObject, eventdata, handles);
939else
940     set(handles.scan_j,'Value',1)
941     scan_j_Callback(hObject, eventdata, handles);
942end
943set(handles.scan_j,'Visible',state_j)
944set(handles.j1,'Visible',state_j)
945set(handles.j2,'Visible',state_j)
946set(handles.last_j,'Visible',state_j);
947set(handles.frame_j,'Visible',state_j);
948set(handles.j_text,'Visible',state_j);
949if strcmp(state_j,'on')
950    set(handles.fix_pair,'Visible','on')
951else
952    set(handles.fix_pair,'Visible','off')
953end
954
955%% view the field 
956run0_Callback(hObject, eventdata, handles); %view field
957mask_test=get(handles.mask_test,'value');
958if mask_test
959    MaskData=get(handles.mask_test,'UserData');
960    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
961          delete(MaskData.maskhandle)    %delete old mask
962    end
963    mask_test_Callback(hObject, eventdata, handles)
964end
965
966%------------------------------------------------------------------------
967% --- Executes on the menu Open/Browse_1 for the second input field,
968%     search the files, recognize their type according to their name and fill the rootfile input windows
969function MenuBrowse_1_Callback(hObject, eventdata, handles)
970%------------------------------------------------------------------------
971% huvmat=get(handles.run0,'parent');
972UvData=get(handles.uvmat,'UserData');
973
974RootPath=get(handles.RootPath,'String');
975[FileName, PathName, filterindex] = uigetfile( ...
976       {'*.xml;*.xls;*.civ;*.jpg;*.png;*.avi;*.AVI;*.nc;*.cmx;*.fig;*.log;*.dat', ' (*.xml,*.xls,*.civ, *.jpg,*.png, *.avi,*.nc,*.cmx ,*.fig,*.log,*.dat)';
977       '*.xml',  '.xml files '; ...
978        '*.xls',  '.xls files '; ...
979        '*.civ',  '.civ files '; ...
980        '*.jpg','.jpg image files'; ...
981        '*.png','.png image files'; ...
982        '*.avi;*.AVI','.avi movie files'; ...
983        '*.nc','.netcdf files'; ...
984        '*.cdf','.netcdf files'; ...
985        '*.cmx','.cmx text files';...
986        '*.cmx2','.cmx2 text files';...
987        '*.fig','.fig files (matlab fig)';...
988        '*.log','.log text files ';...
989        '*.dat','.dat text files ';...
990        '*.*',  'All Files (*.*)'}, ...
991        'Pick a second file for comparison',RootPath);
992fileinput_1=[PathName FileName];%complete file name
993sizf=size(fileinput_1);
994if (~ischar(fileinput_1)||~isequal(sizf(1),1)),return;end
995
996% refresh the current displayed field
997display_file_name_1(hObject,eventdata,handles,fileinput_1)
998
999%update list of recent files in the menubar
1000MenuFile_1=fileinput_1;
1001MenuFile_2=get(handles.MenuFile_1,'Label');
1002MenuFile_3=get(handles.MenuFile_2,'Label');
1003MenuFile_4=get(handles.MenuFile_3,'Label');
1004MenuFile_5=get(handles.MenuFile_4,'Label');
1005set(handles.MenuFile_1,'Label',MenuFile_1)
1006set(handles.MenuFile_2,'Label',MenuFile_2)
1007set(handles.MenuFile_3,'Label',MenuFile_3)
1008set(handles.MenuFile_4,'Label',MenuFile_4)
1009set(handles.MenuFile_5,'Label',MenuFile_5)
1010set(handles.MenuFile_1_1,'Label',MenuFile_1)
1011set(handles.MenuFile_2_1,'Label',MenuFile_2)
1012set(handles.MenuFile_3_1,'Label',MenuFile_3)
1013set(handles.MenuFile_4_1,'Label',MenuFile_4)
1014set(handles.MenuFile_5_1,'Label',MenuFile_5)
1015dir_perso=prefdir;
1016profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1017if exist(profil_perso,'file')
1018    save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
1019else
1020    txt=ver('MATLAB');
1021    Release=txt.Release;
1022    relnumb=str2double(Release(3:4));
1023    if relnumb >= 14
1024        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
1025    else
1026        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
1027    end
1028end
1029
1030% -----------------------------------------------------------------------
1031% --- Open again as second field the file whose name has been recorded in MenuFile_1
1032function MenuFile_1_1_Callback(hObject, eventdata, handles)
1033% -----------------------------------------------------------------------
1034fileinput_1=get(handles.MenuFile_1_1,'Label');
1035display_file_name_1(hObject,eventdata,handles,fileinput_1)
1036
1037% -----------------------------------------------------------------------
1038% --- Open again as second field the file whose name has been recorded in MenuFile_2
1039function MenuFile_2_1_Callback(hObject, eventdata, handles)
1040% -----------------------------------------------------------------------
1041fileinput_1=get(handles.MenuFile_2_1,'Label');
1042display_file_name_1(hObject,eventdata,handles,fileinput_1)
1043
1044% -----------------------------------------------------------------------
1045% --- Open again as second field the file whose name has been recorded in MenuFile_3
1046function MenuFile_3_1_Callback(hObject, eventdata, handles)
1047% -----------------------------------------------------------------------
1048fileinput_1=get(handles.MenuFile_3_1,'Label');
1049display_file_name_1(hObject,eventdata,handles,fileinput_1)
1050
1051% -----------------------------------------------------------------------
1052% --- Open again as second field the file whose name has been recorded in MenuFile_4
1053function MenuFile_4_1_Callback(hObject, eventdata, handles)
1054% -----------------------------------------------------------------------
1055fileinput_1=get(handles.MenuFile_4_1,'Label');
1056display_file_name_1(hObject,eventdata,handles,fileinput_1)
1057
1058% -----------------------------------------------------------------------
1059% --- Open again as second field the file whose name has been recorded in MenuFile_5
1060function MenuFile_5_1_Callback(hObject, eventdata, handles)
1061% -----------------------------------------------------------------------
1062fileinput_1=get(handles.MenuFile_5_1,'Label');
1063display_file_name_1(hObject,eventdata,handles,fileinput_1)
1064
1065%------------------------------------------------------------------------
1066% fills the edit boxes RootPath_1, RootFile_1,NomType_1...from an input file name 'fileinput_1'
1067%------------------------------------------------------------------------
1068function display_file_name_1(hObject,eventdata,handles,fileinput_1)
1069
1070%[path,name,ext]=fileparts(fileinput_1);
1071[RootPath_1,RootFile_1,field_count,str2,str_a,str_b,FileExt_1,NomType_1,SubDir_1]=name2display(fileinput_1);
1072nbfield_1=1; %default
1073ext_test=FileExt_1;%default
1074form=imformats(FileExt_1(2:end));
1075if ~isempty(form) % if the extension corresponds to an image format recognized by Matlab
1076    imainfo=imfinfo(fileinput_1); 
1077    nbfield_1=length(imainfo);
1078    ext_test='.image';
1079elseif isequal(lower(FileExt_1),'.avi')
1080    info=aviinfo(fileinput_1);
1081    nbfield_1=info.NumFrames;
1082    ext_test='.image';
1083end
1084
1085%open directly fig or text files
1086switch ext_test
1087    case {'.civ','.log','.cmx','.cmx2','.txt'}  %display text file
1088        edit(fileinput) 
1089        return
1090    case '.fig'                           %display matlab figure
1091        hfig=open(fileinput);
1092        set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
1093        set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
1094        set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
1095        return
1096    case {'.xml','.xls'}                % edit xml or Excel files
1097       heditxml=editxml(fileinput);
1098       return
1099    case {'.image','.nc','.cdf'}
1100%         set(handles.FileIndex,'UserData',NomType_1);
1101    otherwise
1102        msgbox_uvmat(['invalid input file extension ' FileExt_1 ' for uvmat'],'ERROR')
1103        return
1104end
1105
1106% test for image series in a single file and synchronise file indices of the two series
1107if nbfield_1 >1 %case of image with multiple frames
1108    if nbfield_1 < num_i1
1109        msgbox_uvmat('ERROR','current frame index beyond the input movie length')
1110        return
1111    else
1112        NomType_1='*'; %indicate a set of indexed frames within a single file
1113        filename_new=fileinput_1;
1114    end
1115else  % cases of data files   
1116    RootPath=get(handles.RootPath,'String');
1117    RootFile=get(handles.RootFile,'String');
1118    FileBase=fullfile(RootPath,RootFile);
1119    FileBase_1=fullfile(RootPath_1,RootFile_1);
1120    if isequal(FileBase,FileBase_1)
1121        filename_new=fileinput_1;
1122    else       
1123        num_i1=stra2num(get(handles.i1,'String'));%get the current file indices from counters
1124        num_j1=stra2num(get(handles.j1,'String'));
1125        num_i2=stra2num(get(handles.i2,'String'));
1126        num_j2=stra2num(get(handles.j2,'String'));
1127        [filename_new,idetect]=...
1128           name_generator(FileBase_1,num_i1,num_j1,FileExt_1,NomType_1,1,num_i2,num_j2,SubDir_1);%create name with indices synchronised with the first file
1129        indices=''; %default
1130        if ~idetect
1131            msgbox_uvmat('ERROR','second input file with indices corresponding to the first one does not exist')
1132            return
1133        end
1134    end
1135end
1136set(handles.FileIndex_1,'UserData',NomType_1);
1137
1138% make visible and fill the second raw of edit boxes
1139set(handles.RootPath_1,'Visible','on')
1140set(handles.RootFile_1,'Visible','on')
1141set(handles.SubDir_1,'Visible','on');
1142set(handles.FileIndex_1,'Visible','on');
1143set(handles.FileExt_1,'Visible','on');
1144[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles);
1145if isequal(FileBase,FileBase_1)
1146    set(handles.RootPath_1,'String','"')
1147    set(handles.RootFile_1,'String','"');
1148else
1149    set(handles.RootPath_1,'String',RootPath_1)
1150    set(handles.RootFile_1,'String',['/' RootFile_1]);
1151end
1152if  isequal(SubDir_1,'')
1153     set(handles.SubDir_1,'String','');
1154     FileBaseSub_1=FileBase_1;
1155else 
1156    set(handles.SubDir_1,'String',['/' SubDir_1]);
1157    FileBaseSub_1=fullfile(FileBase_1,SubDir_1);
1158end
1159indices=filename_new(length(FileBaseSub_1)+1:end);
1160indices(end-length(FileExt_1)+1:end)=[]; %remove extension
1161set(handles.FileIndex_1,'String',indices)
1162set(handles.FileIndex_1,'UserData',NomType_1)
1163set(handles.FileExt_1,'String',FileExt_1);
1164
1165% % default choice of fields
1166%set(handles.SubField,'Visible','on')
1167set(handles.SubField,'Value',1)
1168RootPath_1_Callback(hObject,eventdata,handles); 
1169
1170%-----------------------------------------------------------------------
1171% --- Called by action in RootPath_1 edit box
1172function RootPath_1_Callback(hObject,eventdata,handles)
1173% -----------------------------------------------------------------------
1174update_rootinfo_1(hObject,eventdata,handles)
1175
1176%-----------------------------------------------------------------------
1177% --- Called by action in RootFile_1 edit box
1178function RootFile_1_Callback(hObject, eventdata, handles)
1179% -----------------------------------------------------------------------
1180update_rootinfo_1(hObject,eventdata,handles)
1181
1182%------------------------------------------------------------------------
1183% --- Called by action in FileIndex_1 edit box
1184function FileIndex_1_Callback(hObject, eventdata, handles)
1185%------------------------------------------------------------------------
1186run0_Callback(hObject, eventdata, handles)
1187
1188%------------------------------------------------------------------------
1189% --- Update information about a new second field series (indices to scan, timing,
1190%     calibration from an xml file, then refresh current plots
1191function update_rootinfo_1(hObject,eventdata,handles) %A REVOIR
1192% -----------------------------------------------------------------------
1193set(handles.RootPath_1,'BackgroundColor',[1 1 0])% indicate active program by yellow color
1194drawnow
1195UvData=get(handles.uvmat,'UserData');%huvmat=handles of the uvmat interface
1196UvData.NewSeries=1; %flag for run0: begin a new series
1197
1198[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes_1(handles);
1199if ~exist(FileName,'file')
1200    msgbox_uvmat('ERROR',['input file ' FileName ' not found']);
1201end
1202set(handles.FixVelType,'Value',0); %desactivate fixed veltype
1203nbfield_1=[];%default
1204nburst_1=[];%default
1205XmlData.Time=[];
1206XmlData.GeometryCalib=[];%default
1207TimeUnit=[];
1208if isfield(UvData,'TimeUnit')
1209    TimeUnit=UvData.TimeUnit;
1210end
1211TimeUnit_1=[];
1212hhh='';%default, test for  movie reading with mmreader
1213imainfo=[];
1214if isequal(lower(FileExt),'.avi') %.avi file
1215    imainfo=aviinfo([FileBase FileIndices FileExt]);
1216    nbfield_1=imainfo.NumFrames;
1217    nburst_1=1;
1218    set(handles.Dt_txt,'String',['Dt=' num2str(1000/info.FramesPerSecond) 'ms']);%display the elementary time interval in millisec
1219    time=(0:1/imainfo.FramesPerSecond:(imainfo.NumFrames-1)/imainfo.FramesPerSecond)';
1220    ColorType=imainfo.ImageType;%='truecolor' for color images
1221    hhh=which('mmreader');
1222elseif ~isempty(imformats(FileExt(2:end)))|| isequal(FileExt,'.vol')
1223    if ~isequal(SubDir,'')
1224        RootFile=get(handles.RootFile,'String');
1225        imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]);
1226    else
1227        imainfo=imfinfo([FileBase FileIndices FileExt]);
1228    end
1229    ColorType=imainfo.ColorType;%='truecolor' for color images
1230    if length(imainfo) >1 %case of image with multiple frames
1231        nbfield_1=length(imainfo);
1232        nburst_1=1;
1233    end
1234end
1235if ~strcmp(hhh,'')&& mmreader.isPlatformSupported()% if the function is found (recent version of matlab)
1236    UvData.MovieObject_1=mmreader([FileBase FileIndices FileExt]);
1237elseif isfield(UvData,'MovieObject_1')
1238    UvData=rmfield(UvData,'MovieObject_1');
1239end
1240if ~isempty(imainfo)% (an image has been introduced as second fierld input)
1241    if strcmp(get(handles.npx,'String'),'') || strcmp(get(handles.npy,'String'),'')%update npx and npy if it is not already filled by the first input field
1242        if  isfield(imainfo,'Width') && isfield(imainfo,'Height')
1243            set(handles.npx,'String',num2str(imainfo.Width));%fills nbre of pixels x box
1244            set(handles.npy,'String',num2str(imainfo.Height));%fills nbre of pixels x box
1245        else
1246            set(handles.npx,'String','');%fills nbre of pixels x box
1247            set(handles.npy,'String','');%fills nbre of pixels x box
1248        end
1249        set(handles.BW,'Value',strcmp(ColorType,'grayscale'))% select handles.BW if grayscale image
1250    end
1251end
1252% find scaling parameters
1253filexml=[FileBase '.xml'];
1254fileciv=[FileBase '.civ'];
1255warntext='';%default warning text
1256if exist(filexml,'file')
1257    [XmlData,warntext]=imadoc2struct(filexml);
1258    if ~isempty(warntext)
1259        msgbox_uvmat('WARNING',warntext)
1260    end
1261    if isfield(XmlData,'Camera')
1262        if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
1263            TimeUnit=XmlData.Camera.TimeUnit;
1264        end
1265    end
1266elseif exist(fileciv,'file')% if .civ file found
1267    [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']);
1268    GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
1269    GeometryCalib.Tx=0;
1270    GeometryCalib.Ty=0;
1271    GeometryCalib.Tz=1;
1272    GeometryCalib.dpx=1;
1273    GeometryCalib.dpy=1;
1274    GeometryCalib.sx=1;
1275    GeometryCalib.Cx=0;
1276    GeometryCalib.Cy=0;
1277    GeometryCalib.f=1;
1278    GeometryCalib.kappa1=0;
1279    GeometryCalib.CoordUnit='cm';
1280    XmlData.GeometryCalib=GeometryCalib;
1281    if error==2, warntext=['no file ' FileBase '.civ'];
1282    elseif error==1, warntext='inconsistent number of fields in the .civ file';
1283    end
1284   
1285    set(handles.npx,'String',num2str(npx));%fills nbre of pixels x box
1286    set(handles.npy,'String',num2str(npy));%fills nbre of pixels y box
1287    set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box
1288    set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box
1289    set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box
1290    set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box
1291end   
1292if ~isempty(TimeUnit_1) && ~isequal(TimeUnit_1,TimeUnit)
1293        msgbox_uvmat('WARNING','the time units for the second series differs from the first one')
1294end
1295       
1296% store last index in handles.lat_i and .last_j
1297if ~isempty(XmlData.Time)
1298    nbfield_1=size(XmlData.Time,1);
1299    nburst_1=size(XmlData.Time,2);   
1300end
1301last_i_cell=get(handles.last_i,'String');
1302if isempty(nbfield_1)
1303    last_i_cell{2}='';
1304else
1305    last_i_cell{2}=num2str(nbfield_1);
1306end
1307set(handles.last_i,'String',last_i_cell)
1308last_j_cell=get(handles.last_j,'String');
1309if isempty(nburst_1)
1310     last_j_cell{2}='';
1311else
1312     last_j_cell{2}=num2str(nburst_1);
1313end
1314set(handles.last_j,'String',last_j_cell);
1315if ~isequal(last_i_cell{1},last_i_cell{2}) || ~isequal(last_j_cell{1},last_j_cell{2})
1316        msgbox_uvmat('WARNING','the numbers of input file of the second series differs from the first one')
1317end
1318
1319% store calibration data
1320GeometryCalib=XmlData.GeometryCalib;
1321if isempty(GeometryCalib)
1322    if isfield(UvData, 'GeometryCalib_1')
1323        UvData=rmfield(UvData,'GeometryCalib_1');
1324    end
1325else
1326    UvData.GeometryCalib_1=GeometryCalib;
1327    if (isfield(GeometryCalib,'R')&& ~isequal(GeometryCalib.R(2,1),0) && ~isequal(GeometryCalib.R(1,2),0)) ||...
1328        (isfield(GeometryCalib,'kappa1')&& ~isequal(GeometryCalib.kappa1,0))
1329        set(handles.pxcm,'String','var')
1330        set(handles.pycm,'String','var')
1331    else
1332        if isfield(GeometryCalib,'fx_fy')
1333            pixcmx=GeometryCalib.fx_fy(1);
1334            pixcmy=GeometryCalib.fx_fy(2);
1335            set(handles.pxcm,'String',num2str(pixcmx))
1336            set(handles.pycm,'String',num2str(pixcmy))
1337        end
1338    end
1339end
1340UvData.XmlData_1=XmlData;
1341set(handles.uvmat,'UserData',UvData)%update the data attached to the uvmat interface
1342
1343if ~isequal(warntext,'')
1344    msgbox_uvmat('WARNING',warntext)
1345end
1346
1347set(handles.RootPath_1,'BackgroundColor',[1 1 1])% signa the end the input operation
1348drawnow
1349
1350set_scan_options(hObject, eventdata, handles)
1351
1352%---------------------------------------------------
1353% switch file index scanning options scan_i and scan_j in an exclusive way
1354function scan_i_Callback(hObject, eventdata, handles)
1355%---------------------------------------------------
1356if get(handles.scan_i,'Value')==1
1357    set(handles.scan_i,'BackgroundColor',[1 1 0])
1358    set(handles.scan_j,'Value',0)
1359%     set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
1360else
1361    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1362    set(handles.scan_j,'Value',1)
1363%     set(handles.scan_j,'BackgroundColor',[1 1 0])
1364end
1365scan_j_Callback(hObject, eventdata, handles)
1366
1367%-------------------------------------------------------------------
1368% switch file index scanning options scan_i and scan_j in an exclusive way
1369function scan_j_Callback(hObject, eventdata, handles)
1370%-------------------------------------------------------------------
1371if get(handles.scan_j,'Value')==1
1372    set(handles.scan_j,'BackgroundColor',[1 1 0])
1373    set(handles.scan_i,'Value',0)
1374    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1375    NomType=get(handles.FileIndex,'UserData');
1376    switch NomType
1377    case {'_i_j1-j2','#_ab','%3dab'},% pair with j index
1378        set(handles.fix_pair,'Visible','on')% option fixed pair on/off made visible (choice of avaible pair with buttons + and - if ='off')
1379    otherwise
1380        set(handles.fix_pair,'Visible','off')
1381    end
1382else
1383    set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
1384    set(handles.scan_i,'Value',1)
1385    set(handles.scan_i,'BackgroundColor',[1 1 0])
1386    set(handles.fix_pair,'Visible','off')
1387end
1388
1389%-------------------------------------------------------------------
1390function i1_Callback(hObject, eventdata, handles)
1391%-------------------------------------------------------------------
1392set(handles.i1,'BackgroundColor',[0.7 0.7 0.7])
1393NomType=get(handles.FileIndex,'UserData');
1394num1=stra2num(get(handles.i1,'String'));
1395num2=stra2num(get(handles.i2,'String'));
1396num_a=stra2num(get(handles.j1,'String'));
1397num_b=stra2num(get(handles.j2,'String'));
1398indices=name_generator('',num1,num_a,'',NomType,1,num2,num_b,'');
1399set(handles.FileIndex,'String',indices)
1400set(handles.FileIndex,'BackgroundColor',[0.7 0.7 0.7])
1401if get(handles.SubField,'Value')==1
1402    NomType_1=get(handles.FileIndex_1,'String');
1403     FileExt_1=get(handles.FileExt_1,'String');
1404    [P,F,str1,str2,str_a,str_b,Ext,NomType_1]=name2display(['xx' NomType_1 FileExt_1]);
1405     indices=name_generator('',num1,num_a,'',NomType_1,1,num2,num_b,'');
1406     set(handles.FileIndex_1,'String',indices)
1407     set(handles.FileIndex_1,'BackgroundColor',[0.7 0.7 0.7])
1408end
1409%Run0_Callback(hObject, eventdata, handles)
1410
1411%-------------------------------------------------------------------
1412function i2_Callback(hObject, eventdata, handles)
1413set(handles.i2,'BackgroundColor',[0.7 0.7 0.7])
1414i1_Callback(hObject, eventdata, handles)
1415%-------------------------------------------------------------------
1416
1417%-------------------------------------------------------------------
1418function j1_Callback(hObject, eventdata, handles)
1419set(handles.j1,'BackgroundColor',[0.7 0.7 0.7])
1420i1_Callback(hObject, eventdata, handles)
1421%-------------------------------------------------------------------
1422
1423%-------------------------------------------------------------------
1424function j2_Callback(hObject, eventdata, handles)
1425set(handles.j2,'BackgroundColor',[0.7 0.7 0.7])
1426i1_Callback(hObject, eventdata, handles)
1427%-------------------------------------------------------------------
1428
1429%-------------------------------------------------------------------
1430function slices_Callback(hObject, eventdata, handles)
1431%-------------------------------------------------------------------
1432if get(handles.slices,'Value')==1
1433    set(handles.slices,'BackgroundColor',[1 1 0])
1434    set(handles.nb_slice,'Visible','on')
1435    set(handles.z_text,'Visible','on')
1436    set(handles.z_index,'Visible','on')
1437    nb_slice_Callback(hObject, eventdata, handles)
1438else
1439    set(handles.nb_slice,'Visible','off')
1440    set(handles.slices,'BackgroundColor',[0.7 0.7 0.7])
1441    set(handles.z_text,'Visible','off')
1442    set(handles.z_index,'Visible','off')
1443    set(handles.masklevel,'Value',1)
1444    set(handles.masklevel,'String',{'1'})
1445end
1446
1447%-------------------------------------------------------------------
1448function nb_slice_Callback(hObject, eventdata, handles)
1449%-------------------------------------------------------------------
1450nb_slice_str=get(handles.nb_slice,'String');
1451if isequal(nb_slice_str,'volume')
1452    num=stra2num(get(handles.j1,'String'));
1453    last_j=get(handles.last_j,'String');
1454    nbslice=str2double(last_j{1});
1455else
1456    num=str2double(get(handles.i1,'String'));
1457    nbslice=str2double(get(handles.nb_slice,'String'));
1458end
1459z=mod(num-1,nbslice)+1;
1460set(handles.z_index,'String',num2str(z))
1461for ilist=1:nbslice
1462    list_index{ilist,1}=num2str(ilist);
1463end   
1464set(handles.masklevel,'String',list_index)
1465set(handles.masklevel,'Value',z)
1466
1467%------------------------------------------------------------------------
1468% --- Executes on button press in view_xml.
1469function view_xml_Callback(hObject, eventdata, handles)
1470%------------------------------------------------------------------------
1471[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles);
1472option=get(handles.view_xml,'String');
1473if isequal(option,'view .xml')
1474    FileXml=[FileBase '.xml'];
1475    heditxml=editxml(FileXml);
1476end
1477
1478%------------------------------------------------------------------------
1479% --- Executes on button press in mask_test.
1480function mask_test_Callback(hObject, eventdata, handles)
1481%------------------------------------------------------------------------
1482%case of view mask selection
1483if isequal(get(handles.mask_test,'Value'),1)
1484    [FF,RootPath,FileBase]=read_file_boxes(handles);
1485    num_i1=stra2num(get(handles.i1,'String'));
1486    num_j1=stra2num(get(handles.j1,'String'));
1487    currentdir=pwd; 
1488    cd(RootPath);
1489    maskfiles=dir('*_*mask_*.png');%look for a mask file
1490    cd(currentdir);%come back to the working directory
1491    mdetect=0;
1492    if ~isempty(maskfiles)
1493        for ilist=1:length(maskfiles)
1494            maskname=maskfiles(ilist).name;% take the first mask file in the list
1495            [rr,ff,x1,x2,xa,xb,xext,Mask_NomType{ilist}]=name2display(maskname);
1496            if ~strcmp(Mask_NomType{ilist},Mask_NomType{1})
1497                msgbox_uvmat('ERROR',['inconsistent mask types ' Mask_NomType{1} Mask_NomType{ilist } ' coexist in the current image directory'])
1498                return
1499            end
1500            [Path2,Name,ext]=fileparts(maskname);
1501            Namedouble=double(Name);
1502            val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1503            ind_mask=findstr('mask',Name);
1504            i=ind_mask-1;
1505            while val(i)==0 && i>0
1506                i=i-1;
1507            end
1508            nbmask_str=str2num(Name(i+1:ind_mask-1));
1509            if ~isempty(nbmask_str)
1510                nbslice(ilist)=nbmask_str; % number of different masks (slices)
1511            end
1512        end
1513        if isequal(min(nbslice),max(nbslice))
1514            nbslice=nbslice(1);
1515        else
1516            msgbox_uvmat('ERROR','several inconsistent mask sets coexist in the current image directory')
1517            return
1518        end
1519        if ~isempty(nbslice) && Name(i)=='_'
1520            Mask.Base=[FileBase Name(i:ind_mask+3)];
1521            Mask.NbSlice=nbslice;
1522            num_i1=mod(num_i1-1,nbslice)+1;
1523            Mask.NomType=Mask_NomType{1};
1524            [maskname,mdetect]=name_generator(Mask.Base,num_i1,num_j1,'.png',Mask.NomType);%
1525            mdetect=exist(maskname,'file');
1526            if mdetect
1527                set(handles.nb_slice,'String',Name(i+1:ind_mask-1));
1528                set(handles.nb_slice,'BackgroundColor',[1 1 0])
1529                set(handles.mask_test,'UserData',Mask);
1530                set(handles.mask_test,'BackgroundColor',[1 1 0])
1531                if nbslice > 1
1532                    set(handles.slices,'value',1)
1533                    slices_Callback(hObject, eventdata, handles)
1534                end
1535            end
1536        end
1537    end
1538    errormsg=[];%default
1539    if mdetect==0
1540        [FileName, PathName, filterindex] = uigetfile( ...
1541            {'*.png', ' (*.png)';
1542            '*.png',  '.png files '; ...
1543            '*.*', 'All Files (*.*)'}, ...
1544            'Pick a mask file *.png',FileBase);
1545        maskname=fullfile(PathName,FileName);
1546        if ~exist(maskname,'file')
1547            errormsg='no file browsed';
1548        end
1549        [RootDir,RootFile,x1,x2,xa,xb,xext,Mask.NomType]=name2display(maskname);
1550        Mask.Base=fullfile(RootDir,RootFile);
1551        Mask.NbSlice=1;
1552        set(handles.mask_test,'UserData',Mask);
1553        set(handles.mask_test,'BackgroundColor',[1 1 0])
1554    end
1555    if isempty(errormsg)
1556        errormsg=update_mask(handles,num_i1,num_j1);
1557    end
1558    if ~isempty(errormsg)
1559            set(handles.mask_test,'Value',0)
1560            set(handles.mask_test,'BackgroundColor',[0.7 0.7 0.7])
1561     end
1562else
1563    MaskData=get(handles.mask_test,'UserData');
1564    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1565          delete(MaskData.maskhandle)   
1566    end
1567    set(handles.mask_test,'UserData',[])   
1568    %huvmat=get(handles.mask_test,'parent');
1569    UvData=get(handles.uvmat,'UserData');
1570    if isfield(UvData,'MaskName')
1571        UvData=rmfield(UvData,'MaskName');
1572        set(handles.uvmat,'UserData',UvData)
1573    end
1574    set(handles.mask_test,'BackgroundColor',[0.7 0.7 0.7])
1575end
1576
1577%-------------------------------------------------------------------
1578function errormsg=update_mask(handles,num_i1,num_j1)
1579%-------------------------------------------------------------------
1580errormsg=[];%default
1581MaskData=get(handles.mask_test,'UserData');
1582if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1583    uistack(MaskData.maskhandle,'top');
1584end
1585num_i1_mask=mod(num_i1-1,MaskData.NbSlice)+1;
1586MaskName=name_generator(MaskData.Base,num_i1_mask,num_j1,'.png',MaskData.NomType);
1587huvmat=get(handles.mask_test,'parent');
1588UvData=get(huvmat,'UserData');
1589
1590%update mask image if the mask is new
1591if ~ (isfield(UvData,'MaskName') && isequal(UvData.MaskName,MaskName))
1592    UvData.MaskName=MaskName; %update the recorded name on UvData
1593    set(huvmat,'UserData',UvData);
1594    if ~exist(MaskName,'file')
1595        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1596            delete(MaskData.maskhandle)   
1597        end
1598    else
1599        %read mask image
1600        Mask.AName='image';
1601        Mask.A=imread(MaskName);
1602        npxy=size(Mask.A);
1603        test_error=0;
1604        if length(npxy)>2
1605            errormsg=[MaskName ' is not a grey scale image'];
1606            return
1607        elseif ~isa(Mask.A,'uint8')
1608            errormsg=[MaskName ' is not a 8 bit grey level image'];
1609            return
1610        end
1611        Mask.AX=[0.5 npxy(2)-0.5];
1612        Mask.AY=[npxy(1)-0.5 0.5 ];
1613        Mask.CoordUnit='pixel';
1614        if isequal(get(handles.slices,'Value'),1)
1615           NbSlice=str2num(get(handles.nb_slice,'String'));
1616           num_i1=str2num(get(handles.i1,'String'));
1617           Mask.ZIndex=mod(num_i1-1,NbSlice)+1;
1618        end
1619        %px to phys or other transform on field
1620         menu_transform=get(handles.transform_fct,'String');
1621        choice_value=get(handles.transform_fct,'Value');
1622        transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1623        transform_list=get(handles.transform_fct,'UserData');
1624        transform=transform_list{choice_value};
1625        if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
1626            if isfield(UvData,'XmlData') && isfield(UvData.XmlData,'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
1627                Calib=UvData.XmlData.GeometryCalib;
1628                Mask=transform(Mask,UvData.XmlData);
1629            end
1630        end
1631        flagmask=Mask.A < 200;
1632       
1633        %make brown color image
1634        imflag(:,:,1)=0.9*flagmask;
1635        imflag(:,:,2)=0.7*flagmask;
1636        imflag(:,:,3)=zeros(size(flagmask));
1637       
1638        %update mask image
1639        hmask=[]; %default
1640        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1641            hmask=MaskData.maskhandle;
1642        end
1643        if ~isempty(hmask)
1644            set(hmask,'CData',imflag)   
1645            set(hmask,'AlphaData',flagmask*0.6)
1646            set(hmask,'XData',Mask.AX);
1647            set(hmask,'YData',Mask.AY);
1648%             uistack(hmask,'top')
1649        else
1650            axes(handles.axes3)
1651            hold on   
1652            MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*flagmask);
1653%             set(MaskData.maskhandle,'AlphaData',0.6*flagmask)
1654            set(handles.mask_test,'UserData',MaskData)
1655        end
1656    end
1657end
1658
1659
1660%-------------------------------------------------------------------
1661function MenuExportFigure_Callback(hObject, eventdata, handles)
1662%-------------------------------------------------------------------
1663huvmat=get(handles.MenuExport,'parent');
1664%UvData=get(huvmat,'UserData');
1665hfig=figure;
1666copyobj(handles.axes3,hfig);
1667map=colormap(handles.axes3);
1668colormap(map);%transmit the current colormap to the zoom fig
1669colorbar
1670
1671%-------------------------------------------------------------------
1672%-------------------------------------------------------------------
1673% III - MAIN REFRESH FUNCTIONS : 'FRAME PLOT'
1674%-------------------------------------------------------------------
1675
1676%-------------------------------------------------------------------
1677% --- Executes on button press in runplus: make one step forward and call
1678% --- run0. The step forward is along the fields series 1 or 2 depending on
1679% --- the scan_i and scan_j check box (exclusive each other)
1680function runplus_Callback(hObject, eventdata, handles)
1681%-------------------------------------------------------------------
1682set(handles.runplus,'BackgroundColor',[1 1 0])%paint the command button in yellow
1683drawnow
1684%TODO: introduce the option: increment ='*' to move to the next available view
1685increment=str2double(get(handles.increment_scan,'String')); %get the field increment d
1686if isnan(increment)
1687    set(handles.increment_scan,'String','1')%default value
1688    increment=1;
1689end
1690errormsg=runpm(hObject,eventdata,handles,increment);
1691if ~isempty(errormsg)
1692    msgbox_uvmat('ERROR',errormsg);
1693end
1694set(handles.runplus,'BackgroundColor',[1 0 0])%paint the command button back to red
1695
1696%-------------------------------------------------------------------
1697% --- Executes on button press in runmin: make one step backward and call
1698% --- run0. The step backward is along the fields series 1 or 2 depending on
1699% --- the scan_i and scan_j check box (exclusive each other)
1700function runmin_Callback(hObject, eventdata, handles)
1701%-------------------------------------------------------------------
1702set(handles.runmin,'BackgroundColor',[1 1 0])%paint the command button in yellow
1703drawnow
1704increment=-str2double(get(handles.increment_scan,'String')); %get the field increment d
1705if isnan(increment)
1706    set(handles.increment_scan,'String','1')%default value
1707    increment=1;
1708end
1709errormsg=runpm(hObject,eventdata,handles,increment);
1710if ~isempty(errormsg)
1711    msgbox_uvmat('ERROR',errormsg);
1712end
1713set(handles.runmin,'BackgroundColor',[1 0 0])%paint the command button back to red
1714
1715%-------------------------------------------------------------------
1716% -- Executes on button press in Movie: make a series of +> steps
1717function Movie_Callback(hObject, eventdata, handles)
1718%------------------------------------------------------------------
1719set(handles.Movie,'BackgroundColor',[1 1 0])%paint the command button in yellow
1720drawnow
1721increment=str2double(get(handles.increment_scan,'String')); %get the field increment d
1722if isnan(increment)
1723    set(handles.increment_scan,'String','1')%default value
1724    increment=1;
1725end
1726set(handles.STOP,'Visible','on')
1727set(handles.speed,'Visible','on')
1728set(handles.speed_txt,'Visible','on')
1729set(handles.Movie,'BusyAction','queue')
1730UvData=get(handles.uvmat,'UserData');
1731
1732while get(handles.speed,'Value')~=0 && isequal(get(handles.Movie,'BusyAction'),'queue') % enable STOP command
1733        errormsg=runpm(hObject,eventdata,handles,increment);
1734        if ~isempty(errormsg)
1735            set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1736            return
1737        end
1738        pause(1.02-get(handles.speed,'Value'))% wait for next image
1739end
1740if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1741    UvData.aviobj=close(UvData.aviobj);
1742   set(handles.uvmat,'UserData',UvData);
1743end
1744set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1745
1746%-------------------------------------------------------------------
1747% -- Executes on button press in Movie: make a series of <- steps
1748function MovieBackward_Callback(hObject, eventdata, handles)
1749%------------------------------------------------------------------
1750set(handles.MovieBackward,'BackgroundColor',[1 1 0])%paint the command button in yellow
1751drawnow
1752increment=-str2double(get(handles.increment_scan,'String')); %get the field increment d
1753if isnan(increment)
1754    set(handles.increment_scan,'String','1')%default value
1755    increment=1;
1756end
1757set(handles.STOP,'Visible','on')
1758set(handles.speed,'Visible','on')
1759set(handles.speed_txt,'Visible','on')
1760set(handles.MovieBackward,'BusyAction','queue')
1761UvData=get(handles.uvmat,'UserData');
1762
1763while get(handles.speed,'Value')~=0 && isequal(get(handles.MovieBackward,'BusyAction'),'queue') % enable STOP command
1764        errormsg=runpm(hObject,eventdata,handles,increment);
1765        if ~isempty(errormsg)
1766            set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1767            return
1768        end
1769        pause(1.02-get(handles.speed,'Value'))% wait for next image
1770end
1771if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1772    UvData.aviobj=close(UvData.aviobj);
1773   set(handles.uvmat,'UserData',UvData);
1774end
1775set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1776
1777%-------------------------------------------------------------------
1778function STOP_Callback(hObject, eventdata, handles)
1779%-------------------------------------------------------------------
1780set(handles.movie_pair,'BusyAction','Cancel')
1781set(handles.movie_pair,'value',0)
1782set(handles.Movie,'BusyAction','Cancel')
1783set(handles.MovieBackward,'BusyAction','Cancel')
1784set(handles.MenuExportMovie,'BusyAction','Cancel')
1785set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1786set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1787set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1788
1789%------------------------------------------------------------------
1790function errormsg=runpm(hObject,eventdata,handles,increment)
1791%------------------------------------------------------------------
1792%check for mï¿œovie pair status
1793movie_status=get(handles.movie_pair,'Value');
1794if isequal(movie_status,1)
1795    STOP_Callback(hObject, eventdata, handles)%interrupt movie pair if active
1796end
1797%read the data on the current input rootfile(s)
1798
1799[FileName,RootPath,filebase,FileIndices,FileExt,subdir]=read_file_boxes(handles);
1800NomType=get(handles.FileIndex,'UserData');
1801
1802num1=stra2num(get(handles.i1,'String'));
1803num2=stra2num(get(handles.i2,'String'));
1804num_a=stra2num(get(handles.j1,'String'));
1805num_b=stra2num(get(handles.j2,'String'));
1806
1807sub_value= get(handles.SubField,'Value');
1808if sub_value % a second input file has been entered
1809    [FileName_1,RootPath_1,filebase_1,FileIndices_1,FileExt_1,SubDir_1]=read_file_boxes_1(handles);
1810    [pp,ff,str1,str2,str_a,str_b]=name2display(FileIndices_1);
1811    num1_1=stra2num(str1);%current set of indices for the second field (may be set different than the main indices)
1812    num2_1=stra2num(str2);
1813    num_a_1=stra2num(str_a);
1814    num_b_1=stra2num(str_b);
1815    NomType_1=get(handles.FileIndex_1,'UserData');
1816else
1817    filename_1=[];
1818end   
1819
1820comp_input=get(handles.fix_pair,'Value');
1821
1822%case of scanning along the first direction (rootfile numbers)
1823if get(handles.scan_i,'Value')==1% case of scanning along index i   
1824     num1=num1+increment;
1825     num2=num2+increment;
1826     [filename,num1,num_a,num2,num_b]=name_generator(filebase,num1,num_a,FileExt,NomType,comp_input,num2,num_b,subdir);
1827     if sub_value% set the second field name and indices
1828        num1_1=num1_1+increment;
1829        num2_1=num2_1+increment;
1830        filename_1=name_generator(filebase_1,num1_1,num_a_1,FileExt_1,NomType_1,1,num2_1,num_b_1,SubDir_1);
1831     end   
1832else % case of scanning along index j (burst numbers)
1833    num_a=num_a+increment;
1834    num_b=num_b+increment;
1835    [filename,num1,num_a,num2,num_b]=name_generator(filebase,num1,num_a,FileExt,NomType,comp_input,num2,num_b,subdir);
1836    if sub_value
1837        num_a_1=num_a_1+increment;
1838        num_b_1=num_b_1+increment;
1839        filename_1=name_generator(filebase_1,num1_1,num_a_1,FileExt_1,NomType_1,1,num2_1,num_b_1,SubDir_1);
1840    end   
1841end
1842
1843% refresh plots
1844errormsg=refresh_field(handles,filename,filename_1,num1,num2,num_a,num_b);
1845if isempty(errormsg)  %update the index counters
1846    set(handles.i1,'String',num2stra(num1,NomType,1));
1847    if isequal(num2,num1)
1848         set(handles.i2,'String','');
1849    else
1850        set(handles.i2,'String',num2stra(num2,NomType,1));
1851    end
1852    set(handles.j1,'String',num2stra(num_a,NomType,2));
1853    if isequal(num_b,num_a)
1854         set(handles.j2,'String','');
1855    else
1856        set(handles.j2,'String',num2stra(num_b,NomType,2));
1857    end
1858    [indices]=name_generator('',num1,num_a,'',NomType,1,num2,num_b,'');
1859    set(handles.FileIndex,'String',indices);
1860    if ~isempty(filename_1)
1861         indices_1=name_generator('',num1_1,num_a_1,'',NomType_1,1,num2_1,num_b_1,'');
1862         set(handles.FileIndex_1,'String',indices_1);
1863    end
1864    if isequal(movie_status,1)
1865        set(handles.movie_pair,'Value',1)
1866        movie_pair_Callback(hObject, eventdata, handles); %reactivate moviepair if it was activated
1867    end
1868end
1869
1870
1871%-------------------------------------------------------
1872% --- Executes on button press in movie_pair: create an alternating movie with two view
1873%-------------------------------------------------------
1874function movie_pair_Callback(hObject, eventdata, handles)
1875status=get(handles.movie_pair,'value');
1876if isequal(status,0)
1877    set(handles.movie_pair,'BusyAction','Cancel')%stop movie pair if button is 'off'
1878    set(handles.i2,'String','')
1879    set(handles.j2,'String','')
1880    return
1881else
1882    set(handles.movie_pair,'BusyAction','queue')
1883end
1884%initialisation
1885set(handles.movie_pair,'BackgroundColor',[1 1 0])%paint the command button in yellow
1886drawnow
1887list_fields=get(handles.Fields,'String');% list menu fields
1888index_fields=get(handles.Fields,'Value');% selected string index
1889FieldName=list_fields{index_fields}; % selected field
1890UvData=get(handles.uvmat,'UserData');
1891if isequal(FieldName,'image')
1892    test_1=0;
1893    [ff,rr,filebase,xx,Ext,SubDir]=read_file_boxes(handles);
1894    NomType=get(handles.FileIndex,'UserData');
1895else
1896    list_fields=get(handles.Fields_1,'String');% list menu fields
1897    index_fields=get(handles.Fields_1,'Value');% selected string index
1898    FieldName=list_fields{index_fields}; % selected field
1899    if isequal(FieldName,'image')
1900        test_1=1;
1901        [ff,rr,filebase,xx,Ext,SubDir]=read_file_boxes_1(handles);
1902        NomType=get(handles.FileIndex_1,'UserData');
1903    else
1904        msgbox_uvmat('ERROR','an image or movie must be first introduced as input')
1905        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1906        return
1907    end
1908end
1909
1910num_i1=str2double(get(handles.i1,'String'));
1911num_j1=stra2num(get(handles.j1,'String'));
1912num_i2=str2double(get(handles.i2,'String'));
1913num_j2=stra2num(get(handles.j2,'String'));
1914if isnan(num_j2)
1915    if isempty(num_i2)   
1916        msgbox_uvmat('ERROR', 'a second image index i2 or j2 is needed to show the pair as a movie')
1917        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1918        return
1919    else
1920        num_j2=num_j1;%repeat the index i1 by default
1921    end
1922end
1923if isnan(num_i2)
1924    num_i2=num_i1;%repeat the index i1 by default
1925end
1926imaname_1=name_generator(filebase,num_i2,num_j2,Ext,NomType);
1927if ~exist(imaname_1,'file')
1928      msgbox_uvmat('ERROR',['second input open (-)  ' imaname_1 ' not found']);
1929      set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1930      return
1931end
1932
1933%read the second image
1934Field.AName='image';
1935if test_1
1936    Field_a=UvData.Field_1;
1937else
1938    Field_a=UvData.Field;
1939end
1940Field_b.AX=Field_a.AX;
1941Field_b.AY=Field_a.AY;
1942% z index
1943nbslice=str2double(get(handles.nb_slice,'String'));
1944if ~isempty(nbslice)
1945    Field_b.ZIndex=mod(num_i2-1,nbslice)+1;
1946end
1947Field_b.CoordUnit='pixel';
1948%determine the input file type
1949if (test_1 && isfield(UvData,'MovieObject_1'))||(~test_1 && isfield(UvData,'MovieObject'))
1950    FileType='movie';
1951elseif isequal(lower(Ext),'.avi')
1952    FileType='avi';
1953elseif isequal(lower(Ext),'.vol')
1954    FileType='vol';
1955else
1956   form=imformats(Ext(2:end));
1957   if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
1958       if isequal(NomType,'*');
1959           FileType='multimage';
1960       else
1961           FileType='image';
1962       end
1963   end
1964end
1965switch FileType
1966        case 'movie'
1967            if test_1
1968                Field_b.A=read(UvData.MovieObject_1,num_i2);
1969            else
1970                Field_b.A=read(UvData.MovieObject,num_i2);
1971            end
1972        case 'avi'
1973            mov=aviread(imaname_1,num_i2);
1974            Field_b.A=frame2im(mov(1));
1975        case 'vol'
1976            Field_b.A=imread(imaname_1);
1977        case 'multimage'
1978            Field_b.A=imread(imaname_1,num_i2);
1979        case 'image'
1980            Field_b.A=imread(imaname_1);
1981end
1982if get(handles.slices,'Value')
1983    Field.ZIndex=str2double(get(handles.z_index,'String'));
1984end
1985
1986%px to phys or other transform on field
1987menu_transform=get(handles.transform_fct,'String');
1988choice_value=get(handles.transform_fct,'Value');
1989transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1990transform_list=get(handles.transform_fct,'UserData');
1991transform=transform_list{choice_value};
1992if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
1993    if test_1 && isfield(UvData,'XmlData_1') && isfield(UvData.XmlData_1,'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
1994        Field_a=transform(Field_a,UvData.XmlData_1);%the first field has been stored without transform
1995        Field_b=transform(Field_b,UvData.XmlData_1);
1996    elseif ~test_1 && isfield(UvData,'XmlData') && isfield(UvData.XmlData,'GeometryCalib')%use geometry calib
1997        Field_b=transform(Field_b,UvData.XmlData);
1998    end
1999end
2000
2001 % make movie until movie speed is set to 0 or STOP is activated
2002hima=findobj(handles.axes3,'Tag','ima');% %handles.axes3 =main plotting window (A GENERALISER)
2003set(handles.STOP,'Visible','on')
2004set(handles.speed,'Visible','on')
2005set(handles.speed_txt,'Visible','on')
2006while get(handles.speed,'Value')~=0 && isequal(get(handles.movie_pair,'BusyAction'),'queue')%isequal(get(handles.run0,'BusyAction'),'queue'); % enable STOP command
2007    % read and plot the series of images in non erase mode
2008    set(hima,'CData',Field_b.A);
2009    pause(1.02-get(handles.speed,'Value'));% wait for next image
2010    set(hima,'CData',Field_a.A);
2011    pause(1.02-get(handles.speed,'Value'));% wait for next image
2012end
2013set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
2014
2015%------------------------------------------------------------------------
2016% --- Executes on button press in run0.
2017function run0_Callback(hObject, eventdata, handles)
2018%------------------------------------------------------------------------
2019set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
2020drawnow
2021filename=read_file_boxes(handles);
2022
2023filename_1=[];%default
2024if get(handles.SubField,'Value')
2025    filename_1=read_file_boxes_1(handles);
2026end
2027num_i1=stra2num(get(handles.i1,'String'));
2028num_i2=stra2num(get(handles.i2,'String'));
2029num_j1=stra2num(get(handles.j1,'String'));
2030num_j2=stra2num(get(handles.j2,'String'));
2031
2032errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2);
2033
2034if ~isempty(errormsg)
2035      msgbox_uvmat('ERROR',errormsg);
2036else
2037    set(handles.i1,'BackgroundColor',[1 1 1])
2038    set(handles.i2,'BackgroundColor',[1 1 1])
2039    set(handles.j1,'BackgroundColor',[1 1 1])
2040    set(handles.j2,'BackgroundColor',[1 1 1])
2041    set(handles.FileIndex,'BackgroundColor',[1 1 1])
2042    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
2043end   
2044set(handles.run0,'BackgroundColor',[1 0 0])
2045
2046
2047%------------------------------------------------------------------------
2048% --- read the input files and refresh all the plots, including projection.
2049% OUTPUT:
2050%  errormsg: error message char string  =[] by default
2051% INPUT:
2052% filename: first input file (=[] in the absence of input file)
2053% filename_1: second input file (=[] in the asbsenc of secodn input file)
2054% num_i1,num_i2,num_j1,num_j2; frame indices
2055% Field: structure describing an optional input field (then replace the input file)
2056function errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2,Field)
2057%------------------------------------------------------------------------
2058
2059%% initialisation
2060abstime=[];
2061abstime_1=[];
2062dt=[];
2063if ~exist('Field','var')
2064    Field={};
2065end
2066UvData=get(handles.uvmat,'UserData');
2067if ishandle(handles.UVMAT_title) %remove title panel on uvmat
2068    delete(handles.UVMAT_title)
2069end
2070
2071%% determine the main input file information for action
2072FileType=[];%default
2073if ~exist(filename,'file')
2074    errormsg=['input file ' filename ' does not exist'];
2075    return
2076end
2077%Ext=get(handles.FileExt,'String');
2078NomType=get(handles.FileIndex,'UserData');
2079%update the z position index
2080nbslice_str=get(handles.nb_slice,'String');
2081if isequal(nbslice_str,'volume')%NOT USED
2082    z_index=num_j1;
2083    set(handles.z_index,'String',num2str(z_index))
2084else
2085    nbslice=str2num(nbslice_str);
2086    z_index=mod(num_i1-1,nbslice)+1;
2087    set(handles.z_index,'String',num2str(z_index))
2088end
2089% refresh menu for save_mask if relevant
2090masknumber=get(handles.masklevel,'String');
2091if length(masknumber)>=z_index
2092    set(handles.masklevel,'Value',z_index)
2093end
2094
2095%% read the first input field if a filename has been introduced
2096if ~isempty(filename)
2097    ObjectName=filename;
2098    FieldName=[];%default
2099    VelType=[];%default
2100    Ext=get(handles.FileExt,'String');
2101    if strcmp(Ext,'.nc')||strcmp(Ext,'.cdf')
2102        FileType='netcdf';
2103        list_fields=get(handles.Fields,'String');% list menu fields
2104        index_fields=get(handles.Fields,'Value');% selected string index
2105        FieldName= list_fields{index_fields}; % selected field
2106        if ~strcmp(FieldName,'get_field...')
2107           TestVelType=get(handles.FixVelType,'Value');
2108           if TestVelType
2109               VelType=setfield(handles);% read the velocity type.
2110           end
2111        end
2112        if strcmp(FieldName,'velocity')
2113            list_code=get(handles.color_code,'String');% list menu fields
2114            index_code=get(handles.color_code,'Value');% selected string index
2115            if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2116                list_code=get(handles.col_vec,'String');% list menu fields
2117                index_code=get(handles.col_vec,'Value');% selected string index
2118                ParamIn.ColorVar= list_code{index_code}; % selected field
2119            end
2120        end
2121    elseif isfield(UvData,'MovieObject')
2122        ObjectName=UvData.MovieObject;
2123        FileType='movie';
2124    elseif isequal(lower(Ext),'.avi')
2125        FileType='avi';
2126    elseif isequal(lower(Ext),'.vol')
2127        FileType='vol';
2128        if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2129            ParamIn.Npy=UvData.XmlData.Npy;
2130            ParamIn.Npx=UvData.XmlData.Npx;
2131        else
2132            errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2133            return
2134        end
2135    else
2136       form=imformats(Ext(2:end));
2137       if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2138           if isequal(NomType,'*');
2139               FileType='multimage';
2140           else
2141               FileType='image';
2142           end
2143       end
2144    end
2145    ParamIn.FieldName=FieldName;
2146    ParamIn.VelType=VelType;
2147    ParamIn.GUIName='get_field';
2148    [Field{1},ParamOut,errormsg] = read_field(ObjectName,FileType,ParamIn,num_i1);
2149    if ~isempty(errormsg)
2150        errormsg=['error in reading ' filename ': ' errormsg];
2151        return
2152    end
2153       
2154    if isfield(ParamOut,'Npx')&& isfield(ParamOut,'Npy')
2155        set(handles.npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2156        set(handles.npy,'String',num2str(ParamOut.Npy));
2157    end
2158    if isfield(ParamOut,'TimeIndex')
2159        set(handles.i1,'String',num2str(ParamOut.TimeIndex))
2160    end
2161    if isfield(ParamOut,'TimeValue')
2162        Field{1}.Time=ParamOut.TimeValue;
2163    end
2164end
2165
2166%% choose a second field filename_1 if defined
2167VelType_1=[];%default
2168FieldName_1=[];
2169ParamOut_1=[];
2170if ~isempty(filename_1)
2171    if ~exist(filename_1,'file')
2172        errormsg=['second file ' filename_1 ' does not exist'];
2173        return
2174    else
2175        Name=filename_1;
2176        FieldName_1=[];%default
2177        VelType_1=[];%default
2178        if strcmp(get(handles.FileExt_1,'Visible'),'on')
2179            Ext_1=get(handles.FileExt_1,'String');
2180        else
2181            Ext_1=get(handles.FileExt,'String');%read the file extension for the first series (case of veltype comparison within a single file)
2182        end
2183        NomType_1=get(handles.FileIndex_1,'UserData');
2184        if isequal(Ext_1,'.nc')||isequal(Ext_1,'.cdf')
2185            FileType_1='netcdf';
2186        elseif isfield(UvData,'MovieObject_1')
2187            Name=UvData.MovieObject_1;
2188            FileType_1='movie';
2189        elseif isequal(lower(Ext_1),'.avi')
2190            FileType_1='avi';
2191        elseif isequal(lower(Ext_1),'.vol')
2192            FileType_1='vol';
2193            if isfield(UvData.XmlData_1,'Npy') && isfield(UvData.XmlData_1,'Npx')
2194                ParamIn.Npy=UvData.XmlData_1.Npy;
2195                ParamIn.Npx=UvData.XmlData_1.Npx;
2196            else
2197                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2198                return
2199            end
2200        else
2201           if length(Ext_1)>=2
2202           form=imformats(Ext_1(2:end));
2203           if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2204               if isequal(NomType_1,'*');
2205                   FileType_1='multimage';
2206               else
2207                   FileType_1='image';
2208               end
2209           end
2210           end
2211        end
2212        if strcmp(FileType_1,'netcdf')
2213            list_fields=get(handles.Fields_1,'String');% list menu fields
2214            index_fields=get(handles.Fields_1,'Value');% selected string index
2215            FieldName_1= list_fields{index_fields}; % selected field
2216            if ~isequal(FieldName_1,'get_field...')% read the field names on the interface get_field...
2217                VelType_1='';
2218                if get(handles.FixVelType,'Value')
2219                    VelTypeList=get(handles.VelType_1,'String');
2220                    index=get(handles.VelType_1,'Value');
2221                    VelType_1=VelTypeList{index};
2222                end
2223            end
2224            if strcmp(VelType_1,'*')% free veltype choice
2225                VelType_1=[];
2226            elseif strcmp(VelType_1,'"')% veltype the same as for the first field
2227                if isempty(VelType)
2228                    VelType_1=[];
2229                else
2230                    VelType_1=VelType;
2231                end
2232            end
2233            if strcmp(FieldName_1,'velocity')
2234                list_code=get(handles.color_code,'String');% list menu fields
2235                index_code=get(handles.color_code,'Value');% selected string index
2236                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2237                    list_code=get(handles.col_vec,'String');% list menu fields
2238                    index_code=get(handles.col_vec,'Value');% selected string index
2239                    ParamIn.ColorVar= list_code{index_code}; % selected field
2240                end
2241            end
2242        end
2243        test_keepdata_1=0;% test for keeping the previous stored data if the input files are unchanged
2244        if ~isequal(NomType_1,'*')%in case of a series of files (not avi movie)
2245            if isfield(UvData,'filename_1')&& isfield(UvData,'VelType_1') && isfield(UvData,'FieldName_1')
2246                test_keepdata_1= strcmp(filename_1,UvData.filename_1) && strcmp(VelType_1,UvData.VelType_1) && strcmp(FieldName_1,UvData.FieldName_1);
2247            end
2248        end
2249        if test_keepdata_1
2250            Field{2}=UvData.Field_1;
2251        else
2252            ParamIn.FieldName=FieldName_1;
2253            ParamIn.VelType=VelType_1;
2254            ParamIn.GUIName='get_field_1';
2255            [Field{2},ParamOut_1,errormsg] = read_field(Name,FileType_1,ParamIn,num_i1);
2256            if ~isempty(errormsg)
2257                errormsg=['error in reading ' FieldName_1 ' in ' filename_1 ': ' errormsg];
2258                return
2259            end
2260            UvData.Field_1=Field{2}; %store the second field for possible use at next RUN
2261        end
2262    end
2263end
2264
2265%% update uvmat interface
2266if isfield(ParamOut,'Npx')
2267    set(handles.npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2268    set(handles.npy,'String',num2str(ParamOut.Npy));
2269elseif isfield(ParamOut_1,'Npx')
2270    set(handles.npx,'String',num2str(ParamOut_1.Npx));% display image size on the interface
2271    set(handles.npy,'String',num2str(ParamOut_1.Npy));
2272end
2273
2274%% update the display menu for the first velocity type (first menuline)
2275% veltype_handles=[handles.VelType handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2];
2276% if ~isequal(FileType,'netcdf')|| isequal(FieldName,'get_field...')
2277%     set(veltype_handles,'Visible','off')
2278% else% if isempty(ParamOut.VelType) && ~isequal(FieldName,'get_field...')
2279%     set_veltype_display(veltype_handles,ParamOut.CivStage)%update the display of available velocity types for the first field
2280%     if isempty(ParamOut.VelType)
2281%         reset_vel_type(veltype_handles)
2282%     else
2283%         handle1=eval(['handles.' ParamOut.VelType]);
2284%         reset_vel_type(veltype_handles,handle1)
2285%     end
2286% end
2287test_veltype=0;
2288if ~isequal(FileType,'netcdf')|| isequal(FieldName,'get_field...')
2289    set(handles.VelType,'Visible','off')
2290else
2291    test_veltype=1;
2292    set(handles.VelType,'Visible','on')
2293    set(handles.VelType_1,'Visible','on')
2294    set(handles.FixVelType,'Visible','on')
2295    menu=set_veltype_display(ParamOut.CivStage);
2296    index_menu=strcmp(ParamOut.VelType,menu);
2297    set(handles.VelType,'Value',find(index_menu,1))
2298    set(handles.VelType,'String',menu)
2299%     set(handles.VelType_1,'Value',1)
2300%     set(handles.VelType_1,'String',[{''};menu])
2301end
2302field_index=strcmp(ParamOut.FieldName,ParamOut.FieldList);
2303set(handles.Fields,'String',ParamOut.FieldList); %update the field menu
2304set(handles.Fields,'Value',find(field_index,1))
2305
2306%% update the display menu for the second velocity type (second menuline)
2307% if ~isempty(filename_1)
2308%     veltype_handles_1=[handles.VelType_1 handles.interp1_1 handles.filter1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1];
2309%     if ~isequal(FileType_1,'netcdf')|| isequal(FieldName_1,'get_field...')
2310%         set(veltype_handles_1,'Visible','off')
2311%         %reset_vel_type(veltype_handles_1)
2312%     else %if isempty(VelType_1) && ~isequal(FieldName_1,'get_field...')
2313%         set_veltype_display(veltype_handles_1,ParamOut_1.CivStage)%update the display of available velocity types for the first field
2314%         if isempty(ParamOut_1.VelType)
2315%             reset_vel_type(veltype_handles_1)
2316%         else
2317%             handle1=eval(['handles.' ParamOut_1.VelType '_1']);
2318%             reset_vel_type(veltype_handles_1,handle1)
2319%         end
2320%     end
2321%     field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
2322%     set(handles.Fields_1,'String',ParamOut_1.FieldList); %update the field menu
2323%     set(handles.Fields_1,'Value',find(field_index,1))
2324% end
2325test_veltype_1=0;
2326if isempty(filename_1)
2327    set(handles.Fields_1,'Value',1); %update the field menu
2328    set(handles.Fields_1,'String',[{''};ParamOut.FieldList]); %update the field menu
2329else
2330    if ~isequal(FileType_1,'netcdf')|| isequal(FieldName_1,'get_field...')
2331        set(handles.VelType_1,'Visible','off')
2332    else
2333        test_veltype_1=1;
2334        set(handles.VelType_1,'Visible','on')
2335        if ~get(handles.FixVelType,'Value')
2336            menu=set_veltype_display(ParamOut_1.CivStage);
2337            index_menu=strcmp(ParamOut_1.VelType,menu);
2338            set(handles.VelType_1,'Value',1+find(index_menu,1))
2339            set(handles.VelType_1,'String',[{''};menu])
2340        end
2341    end
2342end
2343if test_veltype||test_veltype_1
2344     set(handles.FixVelType,'Visible','on')
2345else
2346     set(handles.FixVelType,'Visible','off')
2347end
2348   
2349%% introduce w as background image by default for a new series (only for nbdim=2)
2350if ~isfield(UvData,'NewSeries')
2351    UvData.NewSeries=1;
2352end
2353%put W as background image by default if NbDim=2:
2354if  UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W) && ~isequal(Field{1}.NbDim,3);
2355        set(handles.SubField,'Value',1);
2356        %menu=update_menu(handles.Fields_1,'w');%update the menu for the background scalar nd set the choice to 'w'
2357        set(handles.RootPath_1,'String','"')
2358        set(handles.RootFile_1,'String','"')
2359        set(handles.SubDir_1,'String','"');
2360        [indices]=name_generator('',num_i1,num_j1,'',NomType,1,num_i2,num_j2,'');
2361        set(handles.FileIndex_1,'String',indices)
2362        set(handles.FileExt_1,'String','"');
2363        set(handles.Fields_1,'Visible','on');
2364        set(handles.Fields_1,'Visible','on');
2365        set(handles.RootPath_1,'Visible','on')
2366        set(handles.RootFile_1,'Visible','on')
2367        set(handles.SubDir_1,'Visible','on');
2368        set(handles.FileIndex_1,'Visible','on');
2369        set(handles.FileExt_1,'Visible','on');
2370        set(handles.Fields_1,'Visible','on');
2371        Field{1}.AName='w';
2372end           
2373
2374%% store the current open names, fields and vel types in uvmat interface
2375UvData.filename_1=filename_1;
2376UvData.VelType_1=[];%default
2377UvData.FieldName_1=[];
2378if isfield(ParamOut_1,VelType)
2379    UvData.VelType_1=ParamOut_1.VelType;
2380end
2381if isfield(ParamOut_1,FieldName)
2382    UvData.FieldName_1=ParamOut_1.FieldName;
2383end
2384
2385%% apply coordinate transform or other user fct
2386XmlData=[];%default
2387if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority
2388    XmlData=UvData.XmlData;
2389end
2390XmlData_1=[];%default
2391if isfield(UvData,'XmlData_1')
2392   XmlData_1=UvData.XmlData_1;
2393end
2394% menu_transform=get(handles.transform_fct,'String');
2395choice_value=get(handles.transform_fct,'Value');
2396transform_list=get(handles.transform_fct,'UserData');
2397transform=transform_list{choice_value};%selected function handles
2398% z index
2399if ~isempty(filename)
2400    Field{1}.ZIndex=z_index;
2401end
2402%px to phys or other transform on field
2403if ~isempty(transform)
2404    if length(Field)>=2
2405        Field{2}.ZIndex=z_index;
2406        [Field{1},Field{2}]=transform(Field{1},XmlData,Field{2},XmlData_1);
2407        if isempty(Field{2})
2408            Field(2)=[];
2409        end
2410    else
2411        Field{1}=transform(Field{1},XmlData);
2412    end
2413end
2414
2415%% calculate scalar
2416if isequal(FileType,'netcdf') && ~isequal(ParamOut.CivStage,0)%&&~isempty(FieldName)%
2417    Field{1}=calc_field([{ParamOut.FieldName} {ParamOut.ColorVar}],Field{1});
2418end
2419if length(Field)==2 && ~test_keepdata_1 && isequal(FileType_1,'netcdf') && ~isequal(ParamOut_1.FieldName,'get_field...')%&&~isempty(FieldName_1)
2420    Field{2}=calc_field([{ParamOut_1.FieldName} {ParamOut_1.ColorVar}],Field{2});
2421end
2422
2423%% combine the two input fields (e.g. substract velocity fields)
2424if numel(Field)==2
2425   UvData.Field=sub_field(Field{1},Field{2}); 
2426else
2427   UvData.Field=Field{1};
2428end
2429
2430%% get bounds and mesh (needed for mouse action and to open set_object)
2431test_x=0;
2432test_z=0;% test for unstructured z coordinate
2433[UvData.Field,errormsg]=check_field_structure(UvData.Field);
2434if ~isempty(errormsg)
2435    errormsg=['error in uvmat/refresh_field/check_field_structure: ' errormsg];
2436    return
2437end
2438[CellVarIndex,NbDim,VarType,errormsg]=find_field_indices(UvData.Field);
2439if ~isempty(errormsg)
2440    errormsg=['error in uvmat/refresh_field/find_field_indices: ' errormsg];
2441    return
2442end
2443[NbDim,imax]=max(NbDim);
2444if isfield(UvData.Field,'NbDim')
2445    NbDim=UvData.Field.NbDim;% deal with plane fields containing z coordinates
2446end
2447if ~isempty(VarType{imax}.coord_x)  && ~isempty(VarType{imax}.coord_y)    %unstructured coordinates
2448    XName=UvData.Field.ListVarName{VarType{imax}.coord_x};
2449    YName=UvData.Field.ListVarName{VarType{imax}.coord_y};
2450    eval(['nbvec=length(UvData.Field.' XName ');'])%nbre of measurement points (e.g. vectors)
2451    test_x=1;%test for unstructured coordinates
2452    if ~isempty(VarType{imax}.coord_z)
2453        ZName=UvData.Field.ListVarName{VarType{imax}.coord_z};
2454    else
2455       NbDim=2;
2456    end
2457elseif numel(VarType)>=imax && numel(VarType{imax}.coord)>=NbDim && VarType{imax}.coord(NbDim)>0 %structured coordinate 
2458    XName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim)};
2459    if NbDim>1
2460        YName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim-1)}; %structured coordinates
2461    end
2462else
2463    errormsg='input field coordinates not defined';
2464    return
2465end
2466if NbDim==3
2467    if ~test_x
2468        ZName=UvData.Field.ListVarName{VarType{imax}.coord(1)};%structured coordinates in 3D
2469    end
2470    eval(['ZMax=max(UvData.Field.' ZName ');'])
2471    eval(['ZMin=min(UvData.Field.' ZName ');'])
2472    UvData.Field.ZMax=ZMax;
2473    UvData.Field.ZMin=ZMin;
2474    test_z=1;
2475    if isequal(ZMin,ZMax)%no z dependency
2476        NbDim=2;
2477        test_z=0;
2478    end
2479end
2480if exist('XName','var')
2481    eval(['XMax=max(max(UvData.Field.' XName '));'])
2482    eval(['XMin=min(min(UvData.Field.' XName '));'])
2483    UvData.Field.NbDim=NbDim;
2484    UvData.Field.XMax=XMax;
2485    UvData.Field.XMin=XMin;
2486    if NbDim >1
2487        eval(['YMax=max(max(UvData.Field.' YName '));'])
2488        eval(['YMin=min(min(UvData.Field.' YName '));'])
2489        UvData.Field.YMax=YMax;
2490        UvData.Field.YMin=YMin;
2491    end
2492    eval(['nbvec=length(UvData.Field.' XName ');'])
2493    if test_x %unstructured coordinates
2494        if test_z
2495            UvData.Field.Mesh=((XMax-XMin)*(YMax-YMin)*(ZMax-ZMin))/nbvec;% volume per vector
2496            UvData.Field.Mesh=(UvData.Field.Mesh)^(1/3);
2497        else
2498            UvData.Field.Mesh=sqrt((XMax-XMin)*(YMax-YMin)/nbvec);%2D
2499        end
2500    else
2501        VarIndex=CellVarIndex{imax}; % list of variable indices
2502        DimIndex=UvData.Field.VarDimIndex{VarIndex(1)}; %list of dim indices for the variable
2503        nbpoints_x=UvData.Field.DimValue(DimIndex(NbDim));
2504        DX=(XMax-XMin)/(nbpoints_x-1);
2505        if NbDim >1
2506            nbpoints_y=UvData.Field.DimValue(DimIndex(NbDim-1));
2507            DY=(YMax-YMin)/(nbpoints_y-1);
2508        end
2509        if NbDim==3
2510            nbpoints_z=UvData.Field.DimValue(DimIndex(1));
2511            DZ=(ZMax-ZMin)/(nbpoints_z-1);
2512            UvData.Field.Mesh=sqrt(DX*DY*DZ);
2513            UvData.Field.ZMax=ZMax;
2514            UvData.Field.ZMin=ZMin;
2515        else
2516            UvData.Field.Mesh=DX;%sqrt(DX*DY);
2517        end
2518    end
2519end
2520
2521%% 3D case (menuvolume)
2522if NbDim==3% && UvData.NewSeries
2523    test_set_object=1;
2524    hset_object=findobj(allchild(0),'tag','set_object');% look for the set_object GUI
2525    ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
2526    ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
2527    if ~isempty(hset_object) %if set_object is detected
2528%         hhset_object=guidata(hset_object);
2529% %         ZBounds_old(1)=get(hhset_object.z_slider,'Min');
2530% %         ZBounds_old(2)=get(hhset_object.z_slider,'Max');
2531% %         if isequal(ZBounds_old,ZBounds)
2532%             test_set_object=0;% do not refresh the GUI set_object
2533%         else
2534            delete(hset_object);% delete the GUI set_object if it does not fit
2535%         end
2536    end
2537    if test_set_object% reinitiate the GUI set_object
2538        delete_object(1);% delete the current projection object in the list UvData.Object, delete its graphic representations and update the list displayed in handles.list_object_1 and 2
2539        UvData.Object{1}.Style='plane';%main plotting plane
2540        UvData.Object{1}.ProjMode='projection';%main plotting plane
2541        UvData.Object{1}.DisplayHandle_uvmat=[]; %plane not visible in uvmat
2542        UvData.Object{1}.NbDim=NbDim;%test for 3D objects
2543        UvData.Object{1}.RangeZ=UvData.Field.Mesh;%main plotting plane
2544        UvData.Object{1}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen
2545        UvData.Object{1}.Angle=[0 0 0];
2546%         UvData.Object{1}.Theta=0;
2547%         UvData.Object{1}.Psi=0;
2548        UvData.Object{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR
2549%         PlotHandles=get_plot_handles(handles);
2550        UvData.Object{1}.Name='1-PLANE';
2551        UvData.Object{1}.enable_plot=1;
2552        set_object(UvData.Object{1},handles,ZBounds);
2553        set(handles.list_object_1,'Value',1);
2554        set(handles.list_object_1,'String',{'1-PLANE'});
2555        set(handles.edit_object,'Value',1)% put the plane in edit mode to enable the z cursor
2556        edit_object_Callback([],[], handles)
2557    end
2558    %multilevel case (single menuplane in a 3D space)
2559elseif isfield(UvData,'Z')
2560    if isfield(UvData,'CoordType')&& isequal(UvData.CoordType,'phys') && isfield(UvData,'XmlData')
2561        XmlData=UvData.XmlData;
2562        if isfield(XmlData,'PlanePos')
2563            UvData.Object{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:);
2564        end
2565        if isfield(XmlData,'PlaneAngle')
2566            siz=size(XmlData.PlaneAngle);
2567            indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning)
2568            UvData.Object{1}.PlaneAngle=XmlData.PlaneAngle(indangle,:);
2569        end
2570    elseif isfield(UvData,'ZIndex')
2571        UvData.Object{1}.ZObject=UvData.ZIndex;
2572    end
2573else
2574    % create a default projection
2575%     UvData.Object{1}.ProjMode='projection';%main plotting plane
2576%     UvData.Object{1}.DisplayHandle_uvmat=[]; %plane not visible in uvmat
2577%     set(handles.list_object_1,'Value',1);
2578%     set(handles.list_object_1,'String',{''});
2579end
2580% if ~isfield(UvData.Object{1},'plotaxes')
2581%     UvData.Object{1}.plotaxes=handles.axes3;%default plotting axis
2582% end
2583testnewseries=UvData.NewSeries;
2584UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback)
2585set(handles.uvmat,'UserData',UvData)
2586
2587%% reset the min and max of scalar if only the mask is displayed(TODO: check the need)
2588if isfield(UvData,'Mask')&& ~isfield(UvData,'A')
2589    set(handles.MinA,'String','0')
2590    set(handles.MaxA,'String','255')
2591end
2592
2593%% Plot the projections on the selected  projection objects
2594
2595% main projection object (uvmat display)
2596list_object=get(handles.list_object_1,'String');
2597if isequal(list_object,{''})%refresh list of objects if the menu is empty
2598    UvData.Object={[]};
2599    set(handles.list_object_1,'Value',1)
2600    set(handles.list_object_2,'Value',1)
2601    set(handles.list_object_2,'String',{''})
2602    set(handles.list_object_2,'Visible','off')
2603end
2604IndexObj(1)=get(handles.list_object_1,'Value');%selected projection object for main view
2605if IndexObj(1)> numel(UvData.Object)
2606    IndexObj(1)=1;%select the first object if the selected one does not exist
2607    set(handles.list_object_1,'Value',1)
2608end
2609plot_handles{1}=handles;
2610if isfield(UvData,'plotaxes')%case of movies
2611    haxes(1)=UvData.plotaxes;
2612else
2613    haxes(1)=handles.axes3;
2614end
2615PlotParam{1}=read_plot_param(handles);%read plotting parameters on the uvmat interfac
2616keeplim(1)=get(handles.FixLimits,'Value');% test for fixed graph limits
2617PosColorbar{1}=UvData.OpenParam.PosColorbar;%prescribe the colorbar position on the uvmat interface
2618
2619% second projection object (view_field display)
2620IndexObj_2=get(handles.list_object_2,'Value');%selected projection object for the second view
2621if IndexObj_2==0
2622    IndexObj_2=1;
2623end
2624if isequal(get(handles.list_object_2,'Visible'),'on') && IndexObj_2 <= numel(UvData.Object)&& ~isempty(UvData.Object{IndexObj_2})
2625    IndexObj(2)=IndexObj_2;
2626    view_field_handle=findobj(allchild(0),'tag','view_field');%handles of the view_field GUI
2627    if ~isempty(view_field_handle)
2628        plot_handles{2}=guidata(view_field_handle);
2629        haxes(2)=plot_handles{2}.axes3;
2630        PlotParam{2}=read_plot_param(plot_handles{2});%read plotting parameters on the uvmat interface
2631        keeplim(2)=get(plot_handles{2}.FixLimits,'Value');
2632        PosColorbar{2}='*'; %TODO: deal with colorbar position on view_field
2633    end
2634end
2635
2636%loop on the projection objects: one or two
2637for imap=1:numel(IndexObj)
2638    iobj=IndexObj(imap);
2639    [ObjectData,errormsg]=proj_field(UvData.Field,UvData.Object{iobj});% project field on the object
2640    if testnewseries && isfield(ObjectData,'CoordUnit')
2641        PlotParam{imap}=rmfield(PlotParam{imap},'FixEqual'); %set FixEqual to depend on the field (=1 if Data.CoordUnit=1 in plot_field)
2642    end
2643    if ~isempty(errormsg)
2644        return
2645    end
2646    %use of mask (TODO: check)
2647    if isfield(ObjectData,'NbDim') && isequal(ObjectData.NbDim,2) && isfield(ObjectData,'Mask') && isfield(ObjectData,'A')
2648        flag_mask=double(ObjectData.Mask>200);%=0 for masked regions
2649        AX=ObjectData.AX;%x coordiantes for the scalar field
2650        AY=ObjectData.AY;%y coordinates for the scalar field
2651        MaskX=ObjectData.MaskX;%x coordiantes for the mask
2652        MaskY=ObjectData.MaskY;%y coordiantes for the mask
2653        if ~isequal(MaskX,AX)||~isequal(MaskY,AY)
2654            nxy=size(flag_mask);
2655            sizpx=(ObjectData.MaskX(end)-ObjectData.MaskX(1))/(nxy(2)-1);%size of a mask pixel
2656            sizpy=(ObjectData.MaskY(1)-ObjectData.MaskY(end))/(nxy(1)-1);
2657            x_mask=ObjectData.MaskX(1):sizpx:ObjectData.MaskX(end); % pixel x coordinates for image display
2658            y_mask=ObjectData.MaskY(1):-sizpy:ObjectData.MaskY(end);% pixel x coordinates for image display
2659            %project on the positions of the scalar
2660            npxy=size(ObjectData.A);
2661            dxy(1)=(ObjectData.AY(end)-ObjectData.AY(1))/(npxy(1)-1);%grid mesh in y
2662            dxy(2)=(ObjectData.AX(end)-ObjectData.AX(1))/(npxy(2)-1);%grid mesh in x
2663            xi=ObjectData.AX(1):dxy(2):ObjectData.AX(end);
2664            yi=ObjectData.AY(1):dxy(1):ObjectData.AY(end);
2665            [XI,YI]=meshgrid(xi,yi);% creates the matrix of regular coordinates
2666            flag_mask = interp2(x_mask,y_mask,flag_mask,XI,YI);
2667        end
2668        AClass=class(ObjectData.A);
2669        ObjectData.A=flag_mask.*double(ObjectData.A);
2670        ObjectData.A=feval(AClass,ObjectData.A);
2671        ind_off=[];
2672        if isfield(ObjectData,'ListVarName')
2673            for ilist=1:length(ObjectData.ListVarName)
2674                if isequal(ObjectData.ListVarName{ilist},'Mask')||isequal(ObjectData.ListVarName{ilist},'MaskX')||isequal(ObjectData.ListVarName{ilist},'MaskY')
2675                    ind_off=[ind_off ilist];
2676                end
2677            end
2678            ObjectData.ListVarName(ind_off)=[];
2679            ObjectData.VarDimIndex(ind_off)=[];
2680            ind_off=[];
2681            for ilist=1:length(ObjectData.ListDimName)
2682                if isequal(ObjectData.ListDimName{ilist},'MaskX') || isequal(ObjectData.ListDimName{ilist},'MaskY')
2683                    ind_off=[ind_off ilist];
2684                end
2685            end
2686            ObjectData.ListDimName(ind_off)=[];
2687            ObjectData.DimValue(ind_off)=[];
2688        end
2689    end   
2690    if ~isempty(ObjectData)
2691        PlotType='none'; %default
2692        if imap==2 && isempty(view_field_handle)
2693            view_field(ObjectData)
2694        else
2695            [PlotType,PlotParamOut]=plot_field(ObjectData,haxes(imap),PlotParam{imap},PosColorbar{imap});
2696            write_plot_param(plot_handles{imap},PlotParamOut) %update the auto plot parameters
2697            if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
2698                ObjectData.Mesh=Field.Mesh; % gives an estimated mesh size (useful for mouse action on the plot)
2699            end
2700        end
2701        if isequal(PlotType,'none')
2702            hget_field=findobj(allchild(0),'name','get_field');
2703            if isempty(hget_field)
2704                get_field(filename)% the projected field cannot be automatically plotted: use get_field to specify the variablesdelete(hget_field)
2705            end
2706            errormsg='The field defined by get_field cannot be plotted';
2707            return
2708        end
2709    end
2710end
2711
2712%% update the mask
2713if isequal(get(handles.mask_test,'Value'),1)%if the mask option is on
2714   update_mask(handles,num_i1,num_i2);
2715end
2716
2717%% prepare the menus of histograms and plot them (histogram of the whole volume in 3D case)
2718menu_histo=(UvData.Field.ListVarName)';%list of field variables to be displayed for the menu of histogram display
2719ind_bad=[];
2720nb_histo=1;
2721
2722% suppress coordinates from the histogram menu
2723for ivar=1:numel(menu_histo)%l loop on field variables:
2724    if isfield(UvData.Field,'VarAttribute') && numel(UvData.Field.VarAttribute)>=ivar && isfield(UvData.Field.VarAttribute{ivar},'Role')
2725        Role=UvData.Field.VarAttribute{ivar}.Role;
2726        switch Role
2727            case {'coord_x','coord_y','coord_z','dimvar'}
2728                ind_bad=[ind_bad ivar];
2729            case {'vector_y'}
2730                nb_histo=nb_histo+1;
2731        end
2732    end
2733    DimCell=UvData.Field.VarDimName{ivar};
2734    DimName='';
2735    if ischar(DimCell)
2736        DimName=DimCell;
2737    elseif iscell(DimCell)&& numel(DimCell)==1
2738        DimName=DimCell{1};
2739    end
2740    if strcmp(DimName,menu_histo{ivar})
2741        ind_bad=[ind_bad ivar];
2742    end
2743end
2744menu_histo(ind_bad)=[];
2745
2746%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2747% display menus and plot histograms
2748test_v=0;
2749if ~isempty(menu_histo)
2750    set(handles.histo1_menu,'Value',1)
2751    set(handles.histo1_menu,'String',menu_histo)
2752    histo1_menu_Callback(handles.histo1_menu, [], handles)% plot first histogram
2753    % case of more than one variables (eg vector components)
2754    if nb_histo > 1
2755        test_v=1;
2756        set(handles.histo2_menu,'Visible','on')
2757        set(handles.histo_v,'Visible','on')
2758        set(handles.histo2_menu,'String',menu_histo)
2759        set(handles.histo2_menu,'Value',2)
2760        histo2_menu_Callback(handles.histo2_menu,[], handles)% plot second histogram
2761    end
2762end
2763if ~test_v
2764    set(handles.histo2_menu,'Visible','off')
2765    set(handles.histo_v,'Visible','off')
2766    cla(handles.histo_v)
2767    set(handles.histo2_menu,'Value',1)
2768end
2769%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2770
2771%% display time
2772testimedoc=0;
2773TimeUnit='';
2774if isfield(UvData.Field,'Time')
2775    abstime=UvData.Field.Time;%time read from the netcdf input file
2776end
2777if isfield(UvData,'Field_1') && isfield(UvData.Field_1,'Time')
2778    abstime_1=UvData.Field_1.Time;%time read from the netcdf input file
2779end
2780if isfield(UvData.Field,'dt')
2781    dt=UvData.Field.dt;%dt read from the netcdf input file
2782    if isfield(UvData.Field,'TimeUnit')
2783       TimeUnit=UvData.Field.TimeUnit;
2784    end
2785elseif isfield(UvData,'Field_1') && isfield(UvData.Field_1,'dt')%dt obtained from the second field if not defined in the first
2786    dt=UvData.Field_1.dt;%dt read from the netcdf input file
2787    if isfield(UvData.Field_1,'TimeUnit')
2788       TimeUnit=UvData.Field_1.TimeUnit;
2789    end
2790end
2791% time from xml file overset previous result
2792if isfield(UvData,'XmlData') && isfield(UvData.XmlData,'Time')
2793    if isempty(num_i2)||isnan(num_i2)
2794        num_i2=num_i1;
2795    end
2796    if isempty(num_j1)||isnan(num_j1)
2797        num_j1=1;
2798    end
2799    if isempty(num_j2)||isnan(num_j2)
2800        num_j2=num_j1;
2801    end
2802    siz=size(UvData.XmlData.Time);
2803    if siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2804        abstime=(UvData.XmlData.Time(num_i1,num_j1)+UvData.XmlData.Time(num_i2,num_j2))/2;%overset the time read from files
2805        dt=(UvData.XmlData.Time(num_i2,num_j2)-UvData.XmlData.Time(num_i1,num_j1));
2806        testimedoc=1;
2807        if isfield(UvData.XmlData,'TimeUnit')
2808            TimeUnit=UvData.XmlData.TimeUnit;
2809        end
2810    end
2811end
2812if isfield(UvData,'XmlData_1') && isfield(UvData.XmlData_1,'Time')
2813    [P,F,str1,str2,str_a,str_b,E]=name2display(['xx' get(handles.FileIndex_1,'String') get(handles.FileExt_1,'String')]);
2814    num_i2=str2double(str2);
2815    if isnan(num_i2)
2816        num_i2=num_i1;
2817    end
2818    num_j1=str2double(str_a);
2819    if isnan(num_j1)
2820        num_j1=1;
2821    end
2822    num_j2=str2double(str_b);
2823    if isnan(num_j2)
2824        num_j2=num_j1;
2825    end
2826    num_i1=str2double(str1);
2827    siz=size(UvData.XmlData_1.Time);
2828    if siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2829        abstime_1=(UvData.XmlData_1.Time(num_i1,num_j1)+UvData.XmlData_1.Time(num_i2,num_j2))/2;%overset the time read from files
2830    end
2831end
2832set(handles.abs_time,'String',num2str(abstime,4))
2833set(handles.abs_time_1,'String',num2str(abstime_1,4))
2834if testimedoc && isfield(UvData,'dt')
2835    dt=UvData.dt;
2836end
2837if isempty(dt)||isequal(dt,0)
2838    set(handles.Dt_txt,'String','')
2839else
2840    if  isempty(TimeUnit)
2841        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  10^(-3)'] )
2842    else
2843        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  m' TimeUnit] )
2844    end
2845end
2846
2847
2848%-------------------------------------------------------------------
2849% --- translate coordinate to matrix index
2850%-------------------------------------------------------------------
2851function [indx,indy]=pos2ind(x0,rangx0,nxy)
2852indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel 
2853indy=1+round((nxy(1)-1)*(y12-rangy0(1))/(rangy0(2)-rangy0(1)));% index y of pixel
2854
2855%-------------------------------------------------------------------
2856% --- Executes on button press in 'FixLimits'.
2857%-------------------------------------------------------------------
2858function FixLimits_Callback(hObject, eventdata, handles)
2859test=get(handles.FixLimits,'Value');
2860if test
2861    set(handles.FixLimits,'BackgroundColor',[1 1 0])
2862else
2863    set(handles.FixLimits,'BackgroundColor',[0.7 0.7 0.7])
2864    update_plot(handles);
2865end
2866
2867%-------------------------------------------------------------------
2868% --- Executes on button press in FixEqual.
2869function FixEqual_Callback(hObject, eventdata, handles)
2870test=get(handles.FixEqual,'Value');
2871if test
2872    set(handles.FixEqual,'BackgroundColor',[1 1 0])
2873    cla(handles.axes3)
2874    update_plot(handles);
2875else
2876    set(handles.FixEqual,'BackgroundColor',[0.7 0.7 0.7])
2877    update_plot(handles);
2878%     axis(handles.axes3,'image')
2879end
2880
2881
2882%-------------------------------------------------------------------
2883
2884%-------------------------------------------------------------------
2885% --- Executes on button press in 'zoom'.
2886%-------------------------------------------------------------------
2887function zoom_Callback(hObject, eventdata, handles)
2888
2889if (get(handles.zoom,'Value') == 1);
2890    set(handles.zoom,'BackgroundColor',[1 1 0])
2891    set(handles.FixLimits,'Value',1)% propose by default fixed limits for the plotting axes
2892    set(handles.FixLimits,'BackgroundColor',[1 1 0])
2893else
2894    set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
2895end
2896
2897
2898%-------------------------------------------------------------------
2899%----Executes on button press in 'record': records the current flags of manual correction.
2900%-------------------------------------------------------------------
2901function record_Callback(hObject, eventdata, handles)
2902% [filebase,num_i1,num_j1,num_i2,num_j2,Ext,NomType,SubDir]=read_input_file(handles);
2903filename=read_file_boxes(handles);
2904[erread,message]=fileattrib(filename);
2905if ~isempty(message) && ~isequal(message.UserWrite,1)
2906     msgbox_uvmat('ERROR',['no writting access to ' filename])
2907     return
2908end
2909test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
2910test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
2911if ~test_civ2 && ~test_civ1
2912    msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
2913end
2914if test_civ2
2915    nbname='nb_vectors2';
2916   flagname='vec2_FixFlag';
2917   attrname='fix2';
2918end
2919if test_civ1
2920    nbname='nb_vectors';
2921   flagname='vec_FixFlag';
2922   attrname='fix';
2923end
2924%write fix flags in the netcdf file
2925UvData=get(handles.uvmat,'UserData');
2926hhh=which('netcdf.open');% look for built-in matlab netcdf library
2927if ~isequal(hhh,'')% case of new builtin Matlab netcdf library
2928    nc=netcdf.open(filename,'NC_WRITE');
2929    netcdf.reDef(nc);
2930    netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),attrname,1);
2931    dimid = netcdf.inqDimID(nc,nbname);
2932    try
2933        varid = netcdf.inqVarID(nc,flagname);% look for already existing fixflag variable
2934    catch
2935        varid=netcdf.defVar(nc,flagname,'double',dimid);%create fixflag variable if it does not exist
2936    end
2937    netcdf.endDef(nc);
2938    netcdf.putVar(nc,varid,UvData.axes3.FF);
2939    netcdf.close(nc); 
2940else %old netcdf library
2941    netcdf_toolbox(filename,AxeData,attrname,nbname,flagname)
2942end
2943
2944%-------------------------------------------------------------------
2945%----Correct the netcdf file, using toolbox (old versions of Matlab).
2946%-------------------------------------------------------------------
2947function netcdf_toolbox(filename,AxeData,attrname,nbname,flagname)
2948nc=netcdf(filename,'write'); %open netcdf file
2949result=redef(nc);
2950eval(['nc.' attrname '=1;']);
2951theDim=nc(nbname) ;% get the number of velocity vectors
2952nb_vectors=size(theDim);
2953var_FixFlag=ncvar(flagname,nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag
2954var_FixFlag(1:nb_vectors)=AxeData.FF;%
2955fin=close(nc);
2956
2957
2958%-------------------------------------------------------------------
2959%determines the fields to read from the interface
2960%------------------------------------------------------------------
2961function VelType=setfield(handles)
2962VelTypeList=get(handles.VelType,'String');
2963index=get(handles.VelType,'Value');
2964VelType=VelTypeList{index};
2965
2966% VelType=[]; %default
2967% if (get(handles.VelType,'Value') == 1);
2968%         VelType='civ1';
2969% % interp1   
2970% elseif (get(handles.interp1,'Value') == 1);
2971%     VelType='interp1';
2972% % filter1   
2973% elseif (get(handles.filter1,'Value') == 1);
2974%     VelType='filter1'; 
2975% % CIV2
2976% elseif (get(handles.civ2,'Value') == 1);
2977%     VelType='civ2';
2978% % interp2   
2979% elseif (get(handles.interp2,'Value') == 1);
2980%     VelType='interp2';
2981% % filter2   
2982% elseif (get(handles.filter2,'Value') == 1); 
2983%     VelType='filter2';
2984% end
2985%
2986% if isequal(get(handles.filter2,'Visible'),'on');
2987%     civ=6;
2988% % interp1   
2989% elseif isequal(get(handles.interp2,'Visible'),'on');
2990%     civ=5;
2991% % filter1   
2992% elseif isequal(get(handles.civ2,'Visible'),'on');
2993%     civ=4; 
2994% % CIV2
2995% elseif isequal(get(handles.filter1,'Visible'),'on');
2996%    civ=3;
2997% % interp2   
2998% elseif isequal(get(handles.interp1,'Visible'),'on');
2999%     civ=2;
3000% % filter2   
3001% elseif isequal(get(handles.VelType,'Visible'),'on'); 
3002%     civ=1;
3003% else
3004%     civ=0;
3005% end
3006
3007%-------------------------------------------------------------------
3008%determines the veltype of the second field to read from the iinterface
3009%------------------------------------------------------------------
3010function VelType=setfield_1(handles)
3011VelTypeList=get(handles.VelType_1,'String');
3012index=get(handles.VelType_1,'Value');
3013VelType=VelTypeList{index};
3014% VelType=[]; %default
3015% if (get(handles.VelType_1,'Value') == 1);
3016%     VelType='civ1';
3017% % interp1   
3018% elseif (get(handles.interp1_1,'Value') == 1);
3019%     VelType='interp1';
3020% % filter1   
3021% elseif (get(handles.filter1_1,'Value') == 1);
3022%     VelType='filter1'; 
3023% % CIV2
3024% elseif (get(handles.civ2_1,'Value') == 1);
3025%     VelType='civ2';
3026% % interp2   
3027% elseif (get(handles.interp2_1,'Value') == 1);
3028%     VelType='interp2';
3029% % filter2   
3030% elseif (get(handles.filter2_1,'Value') == 1); 
3031%     VelType='filter2';
3032% end
3033
3034
3035%---------------------------------------------------
3036% --- Executes on button press in SubField
3037function SubField_Callback(hObject, eventdata, handles)
3038% huvmat=get(handles.run0,'parent');
3039UvData=get(handles.uvmat,'UserData');
3040if get(handles.SubField,'Value')==0% if the subfield button is desactivated   
3041    set(handles.RootPath_1,'String','')
3042    set(handles.RootFile_1,'String','')
3043    set(handles.SubDir_1,'String','');
3044    set(handles.FileIndex_1,'String','');
3045    set(handles.FileExt_1,'String','');
3046    set(handles.RootPath_1,'Visible','off')
3047    set(handles.RootFile_1,'Visible','off')
3048    set(handles.SubDir_1,'Visible','off');
3049    set(handles.FileIndex_1,'Visible','off');
3050    set(handles.FileExt_1,'Visible','off');
3051    set(handles.Fields_1,'Value',1);%set to blank state
3052    set(handles.VelType_1,'Value',1);%set to blank state
3053    if ~strcmp(get(handles.VelType,'Visible'),'on')
3054        set(handles.VelType_1,'Visible','off')
3055    end
3056%     set_veltype_display([handles.VelType_1 handles.interp1_1 handles.filter1_1 ...
3057%             handles.civ2_1 handles.interp2_1 handles.filter2_1],0)
3058    if isfield(UvData,'XmlData_1')
3059        UvData=rmfield(UvData,'XmlData_1');
3060    end
3061    set(handles.uvmat,'UserData',UvData);
3062    run0_Callback(hObject, eventdata, handles); %run
3063else
3064    MenuBrowse_1_Callback(hObject, eventdata, handles)
3065end
3066
3067%------------------------------------------------------------------------
3068% --- read the data displayed for the input rootfile windows (new)
3069function [FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles)
3070%------------------------------------------------------------------------
3071RootPath=get(handles.RootPath,'String');
3072FileName=RootPath; %default
3073SubDir=get(handles.SubDir,'String');
3074if ~isempty(SubDir) && ~isequal(SubDir,'')
3075    if (isequal(SubDir(1),'/')|| isequal(SubDir(1),'\'))
3076        SubDir(1)=[]; %suppress possible / or \ separator
3077    end
3078    FileName=fullfile(RootPath,SubDir);
3079end
3080RootFile=get(handles.RootFile,'String');
3081if ~isempty(RootFile) && ~isequal(RootFile,'')
3082    if (isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
3083        RootFile(1)=[]; %suppress possible / or \ separator
3084    end
3085    FileName=fullfile(FileName,RootFile);
3086end
3087FileBase=fullfile(RootPath,RootFile);
3088FileIndices=get(handles.FileIndex,'String');
3089FileExt=get(handles.FileExt,'String');
3090FileName=[FileName FileIndices FileExt];
3091
3092%------------------------------------------------------------------------
3093% ---- read the data displayed for the second input rootfile windows
3094function [FileName_1,RootPath_1,FileBase_1,FileIndices_1,FileExt_1,SubDir_1]=read_file_boxes_1(handles)
3095%------------------------------------------------------------------------
3096RootPath_1=get(handles.RootPath_1,'String'); % read the data from the file1_input window
3097if isequal(get(handles.RootPath_1,'Visible'),'off') || isequal(RootPath_1,'"')
3098    RootPath_1=get(handles.RootPath,'String');
3099end;
3100FileName_1=RootPath_1; %default
3101SubDir_1=get(handles.SubDir_1,'String');
3102if isequal(get(handles.SubDir_1,'Visible'),'off')|| isequal(SubDir_1,'"')
3103    SubDir_1=get(handles.SubDir,'String');
3104end
3105if numel(SubDir_1)>=1
3106    if (isequal(SubDir_1(1),'/')|| isequal(SubDir_1(1),'\'))
3107        SubDir_1(1)=[]; %suppress possible / or \ separator
3108    end
3109    FileName_1=fullfile(RootPath_1,SubDir_1);
3110end
3111RootFile_1=get(handles.RootFile_1,'String');
3112if isequal(get(handles.RootFile_1,'Visible'),'off') || isequal(RootFile_1,'"')
3113    RootFile_1=get(handles.RootFile,'String');
3114end
3115if numel(RootFile_1)>=1
3116    if ~(isequal(RootFile_1(1),'/')||isequal(RootFile_1(1),'\'))
3117        RootFile_1(1)=[];%suppress possible / or \ separator
3118    end
3119    FileName_1=fullfile(FileName_1,RootFile_1);
3120end
3121FileBase_1=fullfile(RootPath_1,RootFile_1);
3122if isequal(get(handles.FileIndex_1,'Visible'),'off')
3123    FileIndices_1=get(handles.FileIndex,'String');
3124else
3125    FileIndices_1=get(handles.FileIndex_1,'String');
3126end
3127FileExt_1=get(handles.FileExt_1,'String');
3128if isequal(FileExt_1,'"'),FileExt_1=get(handles.FileExt,'String'); end;
3129FileName_1=[FileName_1 FileIndices_1 FileExt_1];
3130
3131%------------------------------------------------------------------------
3132% --- Executes on menu selection Fields
3133function Fields_Callback(hObject, eventdata, handles)
3134%------------------------------------------------------------------------
3135list_fields=get(handles.Fields,'String');% list menu fields
3136index_fields=get(handles.Fields,'Value');% selected string index
3137field= list_fields{index_fields(1)}; % selected string
3138if isequal(field,'get_field...')
3139     set(handles.FixVelType,'visible','off')
3140      set(handles.VelType,'visible','off')
3141       set(handles.VelType_1,'visible','off')
3142%      veltype_handles=[handles.VelType handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2];
3143%      set_veltype_display(veltype_handles,0) % unvisible civ buttons
3144     filename=read_file_boxes(handles);
3145     hget_field=findobj(allchild(0),'name','get_field');
3146     if ~isempty(hget_field)
3147         delete(hget_field)
3148     end
3149     hget_field=get_field(filename);
3150     set(hget_field,'Name','get_field')       
3151     hhget_field=guidata(hget_field);
3152     set(hhget_field.list_fig,'Value',1)
3153     set(hhget_field.list_fig,'String',{'uvmat'})
3154     set(handles.transform_fct,'Value',1)% no transform by default
3155     set(handles.path_transform,'String','')
3156    return %no action
3157end
3158list_fields=get(handles.Fields_1,'String');% list menu fields
3159index_fields=get(handles.Fields_1,'Value');% selected string index
3160field_1= list_fields{index_fields(1)}; % selected string
3161UvData=get(handles.uvmat,'UserData');
3162
3163%read the rootfile input display
3164[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles);
3165[P,F,str1,str2,str_a,str_b,E,NomType]=name2display(['xxx' get(handles.FileIndex,'String') FileExt]);
3166NomTypeNew=NomType;%default
3167if isequal(field,'image')
3168    % transform netc type to the corresponding image type
3169%     if isequal(NomType,'_i1-i2_j')||isequal(NomType,'_i_j1-j2')|| isequal(NomType,'#_ab')|| isequal(NomType,'_i1-i2')
3170%         UvData.SubDir=get(handles.SubDir,'String'); %preserve the subdir in memory
3171%         if ~isempty(UvData.SubDir) && (isequal(UvData.SubDir(1),'/')||isequal(UvData.SubDir(1),'/'))
3172%             UvData.SubDir(1)=[];
3173%         end
3174%         set(handles.SubDir,'String','')
3175%         set(handles.FileExt,'String','.png');
3176        if isequal(NomType,'_i1-i2_j')||isequal(NomType,'_i_j1-j2')
3177            NomTypeNew='_i_j';
3178        elseif isequal(NomType,'#_ab')
3179            NomTypeNew='#a';
3180        elseif isequal(NomType,'_i1-i2')
3181            NomTypeNew='_i';
3182        end 
3183        imagename=name_generator(FileBase,str2double(str1),str2double(str_a),'.png',NomTypeNew,1,str2double(str2),str2double(str_b),'');
3184        if ~exist(imagename,'file')
3185                [FileName,PathName] = uigetfile( ...
3186           {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3187            '*.jpg',' jpeg image files'; ...
3188            '*.png','.png image files'; ...
3189            '*.tif','.tif image files'; ...
3190            '*.avi;*.AVI','.avi movie files'; ...
3191            '*.vol','.volume images (png)'; ...
3192            '*.*',  'All Files (*.*)'}, ...
3193            'Pick an image',imagename);           
3194            % display the selected field and related information
3195           imagename=[PathName FileName];
3196        end
3197        display_file_name(hObject, eventdata, handles,imagename)%display the image
3198        return
3199%     end
3200%     veltype_handles=[handles.VelType handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2];
3201%     set_veltype_display(veltype_handles,0) % unvisible civ buttons
3202else
3203    ext=get(handles.FileExt,'String');
3204    if ~isequal(ext,'.nc') %find the new NomType if the previous display was not already a netcdf file
3205                [FileName,PathName] = uigetfile( ...
3206           {'*.nc', ' (*.nc)';
3207            '*.nc',' netcdf files'; ...
3208            '*.*',  'All Files (*.*)'}, ...
3209            'Pick a netcdf file',FileBase);           
3210            % display the selected field and related information
3211           filename=[PathName FileName];
3212        display_file_name(hObject, eventdata, handles,filename)
3213        return
3214       %  MenuBrowse_Callback(hObject, eventdata, handles)
3215    end
3216%     if isequal(field,'vort') || isequal(field,'div') || isequal(field,'strain')
3217% %         set(handles.VelType,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey
3218% %         set(handles.civ2,'BackgroundColor',[0.702 0.702 0.702])
3219% %         set(handles.interp1,'BackgroundColor',[0.702 0.702 0.702])
3220% %         set(handles.interp2,'BackgroundColor',[0.702 0.702 0.702])
3221%     elseif isequal(field,'more...');
3222%         set(handles.VelType,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey
3223%         set(handles.civ2,'BackgroundColor',[0.702 0.702 0.702])
3224%         str=calc_field;%get the list of available scalars by the function calc_scal
3225%         [ind_answer] = listdlg('PromptString','Select a file:',...
3226%                 'SelectionMode','single',...
3227%                 'ListString',str);
3228%        % edit the choice in the field and action menu
3229%         scalar=cell2mat(str(ind_answer));
3230%         menu=update_menu(handles.Fields,scalar);
3231%         menu=[{''};menu];
3232%         set(handles.Fields_1,'String',menu);% store the selected scalar type
3233%     end
3234end
3235indices=name_generator('',str2double(str1),str2double(str_a),'',NomTypeNew,1,str2double(str2),str2double(str_b),'');
3236set(handles.FileIndex,'String',indices)
3237set(handles.FileIndex,'UserData',NomTypeNew)
3238%common to Fields_1_Callback
3239if isequal(field,'image')||isequal(field_1,'image')
3240    set(handles.npx_title,'Visible','on')% visible npx,pxcm... buttons
3241    set(handles.npy_title,'Visible','on')
3242    set(handles.npx,'Visible','on')
3243    set(handles.npy,'Visible','on')
3244else
3245    set(handles.npx_title,'Visible','off')% visible npx,pxcm... buttons
3246    set(handles.npy_title,'Visible','off')
3247    set(handles.npx,'Visible','off')
3248    set(handles.npy,'Visible','off')
3249end
3250setfield(handles);% update the field structure ('civ1'....)
3251
3252if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3253    run0_Callback(hObject, eventdata, handles)
3254end
3255
3256%---------------------------------------------------
3257% --- Executes on menu selection Fields
3258function Fields_1_Callback(hObject, eventdata, handles)
3259%-------------------------------------------------
3260list_fields=get(handles.Fields,'String');% list menu fields
3261index_fields=get(handles.Fields,'Value');% selected string index
3262field= list_fields{index_fields(1)}; % selected string
3263list_fields=get(handles.Fields_1,'String');% list menu fields
3264index_fields=get(handles.Fields_1,'Value');% selected string index
3265field_1= list_fields{index_fields(1)}; % selected string for the second field
3266if isequal(field_1,'') %remove second field if 'blank' field is selected
3267    set(handles.SubField,'Value',0)
3268    SubField_Callback(hObject, eventdata, handles)
3269    return
3270end
3271UvData=get(handles.uvmat,'UserData');
3272
3273%read the rootfile input display
3274[FileName,RootPath,FileBase,FileIndices,FileExt_prev]=read_file_boxes_1(handles);
3275[P,F,str1,str2,str_a,str_b,E,NomType]=name2display(['xxx' get(handles.FileIndex,'String') FileExt_prev]);
3276if isempty(FileExt_prev)|| strcmp(FileExt_prev,'')
3277    FileExt_1=get(handles.FileExt,'String');
3278else
3279    FileExt_1=FileExt_prev;
3280end
3281NomType_1=get(handles.FileIndex_1,'UserData');
3282if isempty(NomType_1)|| strcmp(NomType_1,'')
3283    NomType_1=get(handles.FileIndex,'UserData');
3284end
3285NomTypeNew=NomType_1;%default
3286
3287set(handles.SubField,'Value',1)%introduce second field
3288if isfield(UvData,'XmlData')
3289    UvData.XmlData_1=UvData.XmlData;
3290end
3291set(handles.FileIndex_1,'Visible','on')
3292set(handles.FileExt_1,'Visible','on')
3293RootPath_1=get(handles.RootPath_1,'String');
3294RootFile_1=get(handles.RootFile_1,'String');
3295if isempty(RootPath_1)||isequal(RootPath_1,'')
3296    set(handles.RootPath_1,'String','"')
3297end
3298if isempty(RootFile_1) || isequal(RootFile_1,'')
3299    set(handles.RootFile_1,'String','"')
3300end
3301if ~isempty(RootFile_1)&&(isequal(RootFile_1(1),'/')||isequal(RootFile_1(1),'\'))
3302    RootFile_1(1)=[];
3303end
3304
3305if isequal(field_1,'get_field...')
3306     veltype_handles=[handles.VelType handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2];
3307     set_veltype_display(veltype_handles,0) % unvisible civ buttons
3308     filename=read_file_boxes_1(handles);
3309     hget_field=findobj(allchild(0),'name','get_field_1');
3310     if ~isempty(hget_field)
3311         delete(hget_field)
3312     end
3313     hget_field=get_field(filename);
3314     set(hget_field,'name','get_field_1')
3315     hhget_field=guidata(hget_field);
3316     set(hhget_field.list_fig,'Value',1)
3317     set(hhget_field.list_fig,'String',{'uvmat'})
3318     set(handles.transform_fct,'Value',1)% no transform by default
3319     set(handles.path_transform,'String','')
3320    return %no action
3321end
3322if isequal(field_1,'image')
3323    % transform netc type to the corresponding image type
3324    if isequal(NomType_1,'_i1-i2_j')||isequal(NomType_1,'_i_j1-j2')|| isequal(NomType_1,'#_ab')|| isequal(NomType_1,'_i1-i2')
3325        UvData.SubDir_1=get(handles.SubDir_1,'String'); %preserve the subdir in memory   
3326        if isequal(NomType_1,'_i1-i2_j')||isequal(NomType_1,'_i_j1-j2')
3327            NomTypeNew='_i_j';
3328        elseif isequal(NomType_1,'#_ab')
3329            NomTypeNew='#a';
3330        elseif isequal(NomType_1,'_i1-i2')
3331            NomTypeNew='_i';
3332        end 
3333    end
3334    imagename=name_generator(FileBase,str2double(str1),str2double(str_a),'.png',NomTypeNew,1,str2double(str2),str2double(str_b),'');
3335    if ~exist(imagename,'file')
3336        [FileName,PathName] = uigetfile( ...
3337            {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3338            '*.jpg',' jpeg image files'; ...
3339            '*.png','.png image files'; ...
3340            '*.tif','.tif image files'; ...
3341            '*.avi;*.AVI','.avi movie files'; ...
3342            '*.vol','.volume images (png)'; ...
3343            '*.*',  'All Files (*.*)'}, ...
3344            'Pick an image',imagename);
3345        % display the selected field and related information
3346        imagename=[PathName FileName];
3347    end
3348    display_file_name_1(hObject, eventdata, handles,imagename)%display the image
3349    return
3350else
3351    set(handles.SubDir_1,'Visible','on')
3352    if ~isequal(FileExt_prev,'.nc') %find the new NomType if the previous display was not already a netcdf file
3353%         veltype_handles=[handles.VelType_1 handles.interp1_1 handles.filter1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1];
3354%         set_veltype_display(veltype_handles,6); % make all civ buttons visible
3355        RootPath_1=get(handles.RootPath_1,'String');
3356        RootFile_1=get(handles.RootFile_1,'String');
3357        if isempty(RootPath_1)||isequal(RootPath_1,'')
3358            set(handles.RootPath_1,'String','"')
3359        end
3360        if isempty(RootFile_1) || isequal(RootFile_1,'')
3361            set(handles.RootFile_1,'String','"')
3362        end
3363        if ~isempty(RootFile_1)&&(isequal(RootFile_1(1),'/')||isequal(RootFile_1(1),'\'))
3364            RootFile_1(1)=[];
3365        end
3366        filebase_1=fullfile(RootPath_1,RootFile_1);
3367        SubDir_1=get(handles.SubDir,'String');
3368        if isempty(SubDir_1)||isequal(SubDir_1,'')
3369            if isfield(UvData,'SubDir_1')
3370                SubDir_1=UvData.SubDir_1;%retrieve previous subdir
3371            else
3372                SubDir_1='?';
3373            end
3374        end
3375        str1=get(handles.i1,'String');
3376        str_a=get(handles.j1,'String');
3377        if isequal(NomType_1,'#_ab')||isequal(NomType_1,'_i1-i2_j')||isequal(NomType_1,'_i_j1-j2')||isequal(NomType_1,'_i1-i2')
3378            NomTypeNew=NomType_1;
3379        elseif isequal(NomType_1,'#a')
3380             [filename, n1,na,n2,nb,SubDir_1]=name_generator(filebase_1, str2num(str1),stra2num(str_a),'.nc','#_ab',0,[],[],SubDir_1);
3381             NomTypeNew='#_ab';
3382        elseif isequal(NomType_1,'_i_j')
3383             [filename,n1,na,n2,nb,SubDir_1]=name_generator(filebase_1,str2num(str1),stra2num(str_a),'.nc','_i1-i2_j',0,str2num(str1),[],SubDir_1);
3384            if idetect==1
3385                NomTypeNew='_i1-i2_j';
3386            else
3387                NomTypeNew='_i_j1-j2';
3388            end
3389        else %for instance avi files or any ima_num series
3390            [filename,n1,na,n2,nb,SubDir_1]=name_generator(filebase_1,str2num(str1),stra2num(str_a),'.nc','_i1-i2',0,str2num(str1),[],SubDir_1);
3391            NomTypeNew='_i1-i2';
3392        end           
3393        [Path,Name]=fileparts(filebase_1);
3394        set(handles.FileExt_1,'String','.nc');
3395        if ~isempty(SubDir_1) && ~strcmp(SubDir_1,'''')&& ~strcmp(SubDir_1,'"')&& ~strcmp(SubDir_1(1),'/')
3396            SubDir_1=['/' SubDir_1];
3397        end
3398        set(handles.SubDir_1,'String',SubDir_1);
3399    end
3400    if isequal(field,'vort') || isequal(field,'div') || isequal(field,'strain')
3401        set(handles.VelType_1,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey
3402        set(handles.civ2_1,'BackgroundColor',[0.702 0.702 0.702])
3403        set(handles.interp1_1,'BackgroundColor',[0.702 0.702 0.702])
3404        set(handles.interp2_1,'BackgroundColor',[0.702 0.702 0.702])
3405    elseif isequal(field_1,'more...'); %add new item to the menu
3406        set(handles.VelType_1,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey
3407        set(handles.civ2_1,'BackgroundColor',[0.702 0.702 0.702])
3408        str=calc_field;%get the list of available scalars by the function calc_scal
3409        [ind_answer,v] = listdlg('PromptString','Select a file:',...
3410                'SelectionMode','single',...
3411                'ListString',str);
3412       % edit the choice in the field and action menu
3413        scalar=cell2mat(str(ind_answer));
3414        menu=update_menu(handles.Fields_1,scalar);
3415        set(handles.Fields_1,'String',menu);% store the selected scalar type
3416    end
3417end
3418str1=get(handles.i1,'String');
3419str2=get(handles.i2,'String');
3420str_a=get(handles.j1,'String');
3421str_b=get(handles.j2,'String');
3422indices=name_generator('',str2num(str1),stra2num(str_a),'',NomTypeNew,1,str2num(str2),stra2num(str_b),'');
3423set(handles.FileIndex_1,'String',indices)
3424set(handles.FileIndex_1,'UserData',NomTypeNew)
3425
3426%common to Fields_Callback
3427if isequal(field,'image')||isequal(field_1,'image')
3428    set(handles.npx_title,'Visible','on')% visible npx,pxcm... buttons
3429    set(handles.npy_title,'Visible','on')
3430    set(handles.npx,'Visible','on')
3431    set(handles.npy,'Visible','on')
3432%     set(handles.fix_pair,'Value',0)
3433else
3434    set(handles.npx_title,'Visible','off')% visible npx,pxcm... buttons
3435    set(handles.npy_title,'Visible','off')
3436    set(handles.npx,'Visible','off')
3437    set(handles.npy,'Visible','off')
3438%     set(handles.fix_pair,'Value',1)
3439end
3440if isequal(field,'velocity')||isequal(field_1,'velocity');
3441    state_vect='on';
3442else
3443    state_vect='off';
3444end
3445if ~isequal(field,'velocity')||(~isequal(field_1,'velocity')&~isequal(field_1,''));
3446    state_scal='on';
3447else
3448    state_scal='off';
3449end
3450set(handles.uvmat,'UserData',UvData)
3451setfield(handles);% update the field structure ('civ1'....)
3452if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3453    run0_Callback(hObject, eventdata, handles)
3454end
3455
3456%------------------------------------------------------------------------
3457% --- set the visibility of relevant velocity type menus:
3458function menu=set_veltype_display(Civ)
3459%------------------------------------------------------------------------
3460if isequal(Civ,0)
3461    imax=0;
3462elseif isequal(Civ,1) || isequal(Civ,2)
3463   imax=1;
3464elseif isequal(Civ,3)
3465    imax=3;
3466elseif isequal(Civ,4) || isequal(Civ,5)
3467    imax=4;
3468elseif isequal(Civ,6) %patch2
3469    imax=6;
3470end
3471menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3472menu=menu(1:imax);
3473% for ibutton=1:imax;
3474%     set(handles(ibutton),'Visible','on')  % unvisible civ buttons
3475% end
3476% % for ibutton=max(imax+1,2):6;
3477% for ibutton=imax+1:6;
3478%     set(handles(ibutton),'Visible','off')  % unvisible civ buttons
3479%     set(handles(ibutton),'Value',0)%unactivate unvisible buttons
3480% end
3481
3482%-------------------------------------------------------------------
3483% --- Executes on button press in VelType.
3484function VelType_Callback(hObject, eventdata, handles)
3485%-------------------------------------------------------------------
3486% if get(handles.VelType,'Value')==1
3487%     reset_vel_type([handles.interp1 handles.civ2 handles.filter1 handles.interp1 handles.interp2 handles.filter2],handles.VelType)
3488% else
3489%     reset_vel_type([handles.VelType handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3490% end
3491set(handles.FixVelType,'Value',1)
3492run0_Callback(hObject, eventdata, handles)
3493
3494%---------------------------------------------
3495function VelType_1_Callback(hObject, eventdata, handles)
3496%---------------------------------------------
3497 
3498set(handles.FixVelType,'Value',1)
3499%refresh field with a second filename=first fiel name
3500set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
3501drawnow
3502filename=read_file_boxes(handles);
3503if get(handles.SubField,'Value')
3504    filename_1=read_file_boxes_1(handles);
3505else
3506    index=get(handles.VelType_1,'Value');
3507    if index==1
3508        filename_1='';% we plot the current field without the second field
3509    else
3510        filename_1=filename;
3511    end
3512end
3513num_i1=stra2num(get(handles.i1,'String'));
3514num_i2=stra2num(get(handles.i2,'String'));
3515num_j1=stra2num(get(handles.j1,'String'));
3516num_j2=stra2num(get(handles.j2,'String'));
3517
3518errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2);
3519
3520if ~isempty(errormsg)
3521    msgbox_uvmat('ERROR',errormsg);
3522else
3523    set(handles.i1,'BackgroundColor',[1 1 1])
3524    set(handles.i2,'BackgroundColor',[1 1 1])
3525    set(handles.j1,'BackgroundColor',[1 1 1])
3526    set(handles.j2,'BackgroundColor',[1 1 1])
3527    set(handles.FileIndex,'BackgroundColor',[1 1 1])
3528    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
3529end
3530set(handles.run0,'BackgroundColor',[1 0 0])
3531
3532%-----------------------------------------------
3533% --- reset civ buttons
3534function reset_vel_type(handles_civ0,handle1)
3535for ibutton=1:length(handles_civ0)
3536    set(handles_civ0(ibutton),'BackgroundColor',[0.831 0.816 0.784])
3537    set(handles_civ0(ibutton),'Value',0)
3538end
3539if exist('handle1','var')%handles of selected button
3540        set(handle1,'BackgroundColor',[1 1 0]) 
3541end
3542
3543%-------------------------------------------------------
3544% --- Executes on button press in MENUVOLUME.
3545%-------------------------------------------------------
3546function VOLUME_Callback(hObject, eventdata, handles)
3547%errordlg('command VOL not implemented yet')
3548if ishandle(handles.UVMAT_title)
3549    delete(handles.UVMAT_title)
3550end
3551UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3552if isequal(get(handles.VOLUME,'Value'),1)
3553    set(handles.zoom,'Value',0)
3554    set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
3555    set(handles.edit_vect,'Value',0)
3556    edit_vect_Callback(hObject, eventdata, handles)
3557    set(handles.edit_object,'Value',0)
3558    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3559%     set(handles.cal,'Value',0)
3560%     set(handles.cal,'BackgroundColor',[0 1 0])
3561    set(handles.edit_vect,'Value',0)
3562    edit_vect_Callback(hObject, eventdata, handles)
3563    %initiate set_object GUI
3564    data.TITLE='VOLUME';
3565    if isfield(UvData,'CoordType')
3566        data.CoordType=UvData.CoordType;
3567    end
3568    if isfield(UvData,'Mesh')&~isempty(UvData.Mesh)
3569        data.RangeY=UvData.Mesh;
3570        data.RangeX=UvData.Mesh;
3571        data.DX=UvData.Mesh;
3572        data.DY=UvData.Mesh;
3573    elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3574        np=size(UvData.Field.A);
3575        meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
3576        meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
3577        data.RangeY=max(meshx,meshy);
3578        data.RangeX=max(meshx,meshy);
3579        data.DX=max(meshx,meshy);
3580    end
3581    data.ParentButton=handles.VOLUME;
3582    PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
3583    [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes,
3584                                                      % associate the set_object interface handle to the plotting axes
3585    if isfield(UvData.OpenParam,'SetObjectOrigin')                                               
3586    pos_uvmat=get(huvmat,'Position');
3587    pos_set_object(1:2)=UvData.OpenParam.SetObjectOrigin + pos_uvmat(1:2);
3588    pos_set_object(3:4)=UvData.OpenParam.SetObjectSize .* pos_uvmat(3:4); 
3589    set(hset_object,'Position',pos_set_object)
3590    end
3591    UvData.MouseAction='create_object';
3592else
3593    set(handles.VOLUME,'BackgroundColor',[0 1 0])
3594    UvData.MouseAction='none';
3595end
3596set(huvmat,'UserData',UvData)
3597
3598%-------------------------------------------------------
3599function edit_vect_Callback(hObject, eventdata, handles)
3600%-------------------------------------------------------
3601%
3602% UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3603if isequal(get(handles.edit_vect,'Value'),1)
3604    test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
3605    test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
3606    if ~test_civ2 && ~test_civ1
3607        msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
3608    end
3609    set(handles.record,'Visible','on')
3610    set(handles.edit_vect,'BackgroundColor',[1 1 0])
3611    set(handles.edit_object,'Value',0)
3612    set(handles.zoom,'Value',0)
3613    set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
3614%     set(handles.create,'Value',0)
3615%     set(handles.create,'BackgroundColor',[0 1 0])
3616    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3617    set(gcf,'Pointer','arrow')
3618%     UvData.MouseAction='edit_vect';
3619else
3620    set(handles.record,'Visible','off')
3621    set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7])
3622%     UvData.MouseAction='none';
3623end
3624% set(handles.uvmat,'UserData',UvData)
3625
3626%----------------------------------------------
3627function save_mask_Callback(hObject, eventdata, handles)
3628%-----------------------------------------------------------------------
3629UvData=get(handles.uvmat,'UserData');
3630
3631flag=1;
3632npx=size(UvData.Field.A,2);
3633npy=size(UvData.Field.A,1);
3634xi=0.5:npx-0.5;
3635yi=0.5:npy-0.5;
3636[Xi,Yi]=meshgrid(xi,yi);
3637if isfield(UvData,'Object')
3638    for iobj=1:length(UvData.Object)
3639        ObjectData=UvData.Object{iobj};
3640        if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
3641            flagobj=1;
3642            testphys=0; %coordinates in pixels by default
3643            if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys')
3644                if isfield(UvData,'XmlData')&& isfield(UvData.XmlData,'GeometryCalib')
3645                    Calib=UvData.XmlData.GeometryCalib;
3646                    testphys=1;
3647                end
3648            end
3649            if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style')
3650                if isequal(ObjectData.Style,'polygon')
3651                    X=ObjectData.Coord(:,1);
3652                    Y=ObjectData.Coord(:,2);
3653                    if testphys
3654                        [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
3655                    end
3656                    flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside                 
3657                elseif isequal(ObjectData.Style,'ellipse')
3658                    if testphys
3659                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3660                    end
3661                    RangeX=max(ObjectData.RangeX);
3662                    RangeY=max(ObjectData.RangeY);
3663                    X2Max=RangeX*RangeX;
3664                    Y2Max=RangeY*RangeY;
3665                    distX=(Xi-ObjectData.Coord(1,1));
3666                    distY=(Yi-ObjectData.Coord(1,2));
3667                    flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
3668                elseif isequal(ObjectData.Style,'rectangle')
3669                    if testphys
3670                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3671                    end
3672                    distX=abs(Xi-ObjectData.Coord(1,1));
3673                    distY=abs(Yi-ObjectData.Coord(1,2));
3674                    flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
3675                end
3676                if isequal(ObjectData.ProjMode,'mask_outside')
3677                    flagobj=~flagobj;
3678                end
3679                flag=flag & flagobj;
3680            end
3681        end
3682    end
3683end
3684% flag=~flag;
3685%mask name
3686RootPath=get(handles.RootPath,'String');
3687RootFile=get(handles.RootFile,'String');
3688if ~isempty(RootFile)&&(isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
3689        RootFile(1)=[];
3690end
3691filebase=fullfile(RootPath,RootFile);
3692list=get(handles.masklevel,'String');
3693masknumber=num2str(length(list));
3694maskindex=get(handles.masklevel,'Value');
3695mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
3696imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
3697imflag=flipdim(imflag,1);
3698% imflag=uint8(255*flag);% =0 for flag=0 (vectors=0 when 20<imflag<200)
3699msgbox_uvmat('CONFIRMATION',[mask_name ' saved'])
3700imwrite(imflag,mask_name,'BitDepth',8);
3701
3702%display the mask
3703%update_mask(handles,num_i1,num_j1)
3704figure;
3705vec=linspace(0,1,256);%define a linear greyscale colormap
3706map=[vec' vec' vec'];
3707colormap(map)
3708
3709image(imflag);
3710
3711%-------------------------------------------------------------------
3712%-------------------------------------------------------------------
3713%  - FUNCTIONS FOR SETTING PLOTTING PARAMETERS
3714
3715%------------------------------------------------------------------
3716
3717
3718
3719%------------------------------------------------------------------
3720% --- Executes on selection change in col_vec: choice of the color code.
3721%
3722function col_vec_Callback(hObject, eventdata, handles)
3723%------------------------------------------------------------------
3724% edit the choice for color code
3725list_code=get(handles.col_vec,'String');% list menu fields
3726index_code=get(handles.col_vec,'Value');% selected string index
3727col_code= list_code{index_code(1)}; % selected field
3728if isequal(col_code,'black') || isequal(col_code,'white')
3729   set(handles.slider1,'Visible','off')
3730   set(handles.slider2,'Visible','off')
3731   set(handles.colcode1,'Visible','off')
3732   set(handles.colcode2,'Visible','off')
3733   set(handles.AutoVecColor,'Visible','off')
3734   set_vec_col_bar(handles)
3735else
3736   set(handles.slider1,'Visible','on')
3737   set(handles.slider2,'Visible','on')
3738   set(handles.colcode1,'Visible','on')
3739   set(handles.colcode2,'Visible','on')
3740   set(handles.AutoVecColor,'Visible','on') 
3741   if isequal(col_code,'ima_cor')
3742       set(handles.AutoVecColor,'Value',0)%fixed scale by default
3743       set(handles.vec_col_bar,'Value',0)% 3 colors r,g,b by default
3744       set(handles.slider1,'Min',0);
3745       set(handles.slider1,'Max',1);
3746       set(handles.slider2,'Min',0);
3747       set(handles.slider2,'Max',1);
3748 %      set(handles.min_title_vec,'String','0')
3749       set(handles.max_vec,'String','1')
3750       set(handles.colcode1,'String','0.333')
3751       colcode1_Callback(hObject, eventdata, handles)
3752       set(handles.colcode2,'String','0.666')
3753       colcode2_Callback(hObject, eventdata, handles)
3754   else
3755       set(handles.AutoVecColor,'Value',1)%auto scale between min,max by default
3756       set(handles.vec_col_bar,'Value',1)% colormap 'jet' by default
3757       minval=get(handles.slider1,'Min');
3758       maxval=get(handles.slider1,'Max');
3759       set(handles.slider1,'Value',minval)
3760       set(handles.slider2,'Value',maxval)
3761       set_vec_col_bar(handles)
3762   end
3763%    slider_update(handles)
3764end
3765%replot the current graph
3766run0_Callback(hObject, eventdata, handles)
3767
3768
3769%----------------------------------------------------------------
3770% -- Executes on slider movement to set the color code
3771%
3772function slider1_Callback(hObject, eventdata, handles)
3773%------------------------------------------------------------------
3774slider1=get(handles.slider1,'Value');
3775min_val=str2num(get(handles.min_vec,'String'));
3776max_val=str2num(get(handles.max_vec,'String'));
3777col=min_val+(max_val-min_val)*slider1;
3778set(handles.colcode1,'String',num2str(col))
3779if(get(handles.slider2,'Value') < col)%move also the second slider at the same value if needed
3780    set(handles.slider2,'Value',col)
3781    set(handles.colcode2,'String',num2str(col))
3782end
3783colcode1_Callback(hObject, eventdata, handles)
3784
3785%----------------------------------------------------------------
3786% Executes on slider movement to set the color code
3787%----------------------------------------------------------------
3788function slider2_Callback(hObject, eventdata, handles)
3789slider2=get(handles.slider2,'Value');
3790min_val=str2num(get(handles.min_vec,'String'));
3791max_val=str2num(get(handles.max_vec,'String'));
3792col=min_val+(max_val-min_val)*slider2;
3793set(handles.colcode2,'String',num2str(col))
3794if(get(handles.slider1,'Value') > col)%move also the first slider at the same value if needed
3795    set(handles.slider1,'Value',col)
3796    set(handles.colcode1,'String',num2str(col))
3797end
3798colcode2_Callback(hObject, eventdata, handles)
3799
3800%----------------------------------------------------------------
3801%execute on return carriage on the edit box corresponding to slider 1
3802%----------------------------------------------------------------
3803function colcode1_Callback(hObject, eventdata, handles)
3804% col=str2num(get(handles.colcode1,'String'));
3805% set(handles.slider1,'Value',col)
3806set_vec_col_bar(handles)
3807update_plot(handles);
3808
3809%----------------------------------------------------------------
3810%execute on return carriage on the edit box corresponding to slider 2
3811%----------------------------------------------------------------
3812function colcode2_Callback(hObject, eventdata, handles)
3813% col=str2num(get(handles.colcode2,'String'));
3814% set(handles.slider2,'Value',col)
3815% slider2_Callback(hObject, eventdata, handles)
3816set_vec_col_bar(handles)
3817update_plot(handles);
3818%------------------------------------------------------------
3819%update the slider values after displaying vectors
3820%--------------------------------------------------------
3821% function slider_update(handles,auto,minC,colcode1,colcode2,maxC)
3822% set(handles.slider1,'Min',minC)
3823% set(handles.slider1,'Max',maxC)
3824% set(handles.slider2,'Min',minC)
3825% set(handles.slider2,'Max',maxC)
3826% set(handles.min_title_vec,'String',num2str(minC))
3827% set(handles.max_vec,'String',num2str(maxC))
3828% if auto
3829%         set(handles.colcode1,'String',num2str(colcode1,3))%update display
3830%         set(handles.colcode2,'String',num2str(colcode2,3))
3831% end
3832% set(handles.slider1,'Value',colcode1)%update slider with constant display
3833% set(handles.slider2,'Value',colcode2)
3834% set_vec_col_bar(handles)
3835
3836
3837%-------------------------------------------------------
3838% --- Executes on button press in AutoVecColor.
3839%-------------------------------------------------------
3840function vec_col_bar_Callback(hObject, eventdata, handles)
3841set_vec_col_bar(handles)
3842
3843%-------------------------------------------------------------
3844% --- Executes on selection change in transform_fct.
3845function transform_fct_Callback(hObject, eventdata, handles)
3846%-------------------------------------------------------------
3847
3848UvData=get(handles.uvmat,'UserData');
3849menu=get(handles.transform_fct,'String');
3850ind_coord=get(handles.transform_fct,'Value');
3851coord_option=menu{ind_coord};
3852list_transform=get(handles.transform_fct,'UserData');
3853ff=functions(list_transform{end}); 
3854if isequal(coord_option,'more...');
3855    coord_fct='';
3856    prompt = {'Enter the name of the transform function'};
3857    dlg_title = 'user defined transform';
3858    num_lines= 1;
3859    [FileName, PathName] = uigetfile( ...
3860       {'*.m', ' (*.m)';
3861        '*.m',  '.m files '; ...
3862        '*.*', 'All Files (*.*)'}, ...
3863        'Pick a file', ff.file);
3864    if isequal(PathName(end),'/')||isequal(PathName(end),'\')
3865        PathName(end)=[];
3866    end
3867    transform_selected =fullfile(PathName,FileName);
3868    if ~exist(transform_selected,'file')
3869           return
3870    end
3871   [ppp,transform,ext_fct]=fileparts(FileName);% removes extension .m
3872   if ~isequal(ext_fct,'.m')
3873        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3874        return
3875   end
3876   menu=update_menu(handles.transform_fct,transform);%add the selected fct to the menu
3877   ind_coord=get(handles.transform_fct,'Value');
3878   addpath(PathName)
3879   list_transform{ind_coord}=str2func(transform);% create the function handle corresponding to the newly seleced function
3880   set(handles.transform_fct,'UserData',list_transform)
3881   rmpath(PathName)
3882   % save the new menu in the personal file 'uvmat_perso.mat'
3883   dir_perso=prefdir;%personal Matalb directory
3884   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3885   if exist(profil_perso,'file')
3886       nb_builtin=UvData.OpenParam.NbBuiltin;
3887       for ilist=nb_builtin+1:numel(list_transform)
3888           ff=functions(list_transform{ilist});
3889           transform_fct{ilist-nb_builtin}=ff.file;
3890       end
3891        save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
3892   end   
3893end
3894
3895%check the current path to the selected function
3896if isa(list_transform{ind_coord},'function_handle')
3897    func=functions(list_transform{ind_coord});
3898    set(handles.path_transform,'String',fileparts(func.file)); %show the path to the senlected function
3899else
3900    set(handles.path_transform,'String','')
3901end
3902
3903set(handles.FixLimits,'Value',0)
3904set(handles.FixLimits,'BackgroundColor',[0.7 0.7 0.7])
3905
3906%delete drawn objects
3907hother=findobj('Tag','proj_object');%find all the proj objects
3908for iobj=1:length(hother)
3909    delete_object(hother(iobj))
3910end
3911hother=findobj('Tag','DeformPoint');%find all the proj objects
3912for iobj=1:length(hother)
3913    delete_object(hother(iobj))
3914end
3915hh=findobj('Tag','calib_points');
3916if ~isempty(hh)
3917    delete(hh)
3918end
3919hhh=findobj('Tag','calib_marker');
3920if ~isempty(hhh)
3921    delete(hhh)
3922end
3923if isfield(UvData,'Object')
3924     UvData.Object=UvData.Object(1);
3925end
3926list_object=get(handles.list_object_1,'String');
3927set(handles.list_object_1,'Value',1)
3928set(handles.list_object_1,'String',{''})
3929set(handles.list_object_2,'Value',1)
3930set(handles.list_object_2,'String',{''})
3931list_object_2_Callback(hObject, eventdata, handles)
3932
3933%delete mask if it is displayed
3934if isequal(get(handles.mask_test,'Value'),1)%if the mask option is on
3935   UvData=rmfield(UvData,'MaskName'); %will impose mask refresh 
3936end
3937set(handles.uvmat,'UserData',UvData)
3938run0_Callback(hObject, eventdata, handles)
3939
3940%--------------------------------------------
3941function histo1_menu_Callback(hObject, eventdata, handles)
3942%--------------------------------------------
3943%plot first histo
3944huvmat=get(handles.histo1_menu,'parent');
3945histo_menu=get(handles.histo1_menu,'String');
3946histo_value=get(handles.histo1_menu,'Value');
3947FieldName=histo_menu{histo_value};
3948update_histo(handles.histo_u,huvmat,FieldName)
3949
3950%----------------------------------------------
3951function histo2_menu_Callback(hObject, eventdata, handles)
3952%----------------------------------------------
3953%plot second histo
3954huvmat=get(handles.histo2_menu,'parent');
3955histo_menu=get(handles.histo2_menu,'String');
3956histo_value=get(handles.histo2_menu,'Value');
3957FieldName=histo_menu{histo_value};
3958update_histo(handles.histo_v,huvmat,FieldName)
3959
3960
3961%--------------------------------------------
3962%read the field .Fieldname stored in UvData and plot its histogram
3963function update_histo(haxes,huvmat,FieldName)
3964UvData=get(huvmat,'UserData');
3965if ~isfield(UvData.Field,FieldName)
3966    msgbox_uvmat('ERROR',['no field  ' FieldName ' for histogram'])
3967    return
3968end
3969Field=UvData.Field;
3970FieldHisto=eval(['Field.' FieldName]);
3971if isfield(Field,'FF') && ~isempty(Field.FF) && isequal(size(Field.FF),size(FieldHisto))
3972    indsel=find(Field.FF==0);%find values marked as false
3973    if ~isempty(indsel)
3974        FieldHisto=FieldHisto(indsel);
3975    end
3976end
3977if isempty(Field)
3978    msgbox_uvmat('ERROR',['empty field ' FieldName])
3979else
3980    nxy=size(FieldHisto);
3981    Amin=double(min(min(min(FieldHisto))));%min of image
3982    Amax=double(max(max(max(FieldHisto))));%max of image
3983    if isequal(Amin,Amax)
3984        msgbox_uvmat('WARNING',['uniform field =' num2str(Amin)]);
3985    else
3986        Histo.ListVarName={FieldName,'histo'};
3987        if isequal(Field.NbDim,3)
3988            Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
3989        else
3990            if numel(nxy)==2
3991                Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
3992            else
3993                Histo.VarDimName={FieldName,{FieldName,'rgb'}}; %dimensions for the histogram
3994            end
3995        end
3996        %unit
3997        units=[]; %default
3998        for ivar=1:numel(Field.ListVarName)
3999            if strcmp(Field.ListVarName{ivar},FieldName)
4000                if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'units')
4001                    units=Field.VarAttribute{ivar}.units;
4002                    break
4003                end
4004            end
4005        end
4006        if ~isempty(units)
4007            Histo.VarAttribute{1}.units=units;
4008        end
4009        eval(['Histo.' FieldName '=linspace(Amin,Amax,50);'])%absissa values for histo
4010        if isequal(Field.NbDim,3)
4011            C=reshape(double(FieldHisto),1,[]);% reshape in a vector
4012            eval(['Histo.histo(:,1)=hist(C, Histo.' FieldName ');']);  %calculate histogram
4013        else
4014            for col=1:size(FieldHisto,3)
4015                B=FieldHisto(:,:,col);
4016                C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector
4017                eval(['Histo.histo(:,col)=hist(C, Histo.' FieldName ');']);  %calculate histogram
4018            end
4019        end
4020%         set(haxes,'XLimMode','auto')%reset auto mode (after zoom effect)
4021%         set(haxes,'YLimMode','auto')
4022%         PlotParam.Auto_xy=1;
4023        plot_field(Histo,haxes);
4024    end
4025end
4026
4027%------------------------------------------------
4028%CALLBACKS FOR PLOTTING PARAMETERS
4029%-------------------------------------------------
4030
4031%------------------------------------------------------------------------
4032function MinX_Callback(hObject, eventdata, handles)
4033%------------------------------------------------------------------------
4034set(handles.FixLimits,'Value',1) %suppress auto mode
4035set(handles.FixLimits,'BackgroundColor',[1 1 0])
4036update_plot(handles);
4037
4038%------------------------------------------------------------------------
4039function MaxX_Callback(hObject, eventdata, handles)
4040%------------------------------------------------------------------------
4041set(handles.FixLimits,'Value',1) %suppress auto mode
4042set(handles.FixLimits,'BackgroundColor',[1 1 0])
4043update_plot(handles);
4044
4045%------------------------------------------------------------------------
4046function MinY_Callback(hObject, eventdata, handles)
4047%------------------------------------------
4048set(handles.FixLimits,'Value',1) %suppress auto mode
4049set(handles.FixLimits,'BackgroundColor',[1 1 0])
4050update_plot(handles);
4051
4052%------------------------------------------------------------------------
4053function MaxY_Callback(hObject, eventdata, handles)
4054%------------------------------------------------------------------------
4055set(handles.FixLimits,'Value',1) %suppress auto mode
4056set(handles.FixLimits,'BackgroundColor',[1 1 0])
4057update_plot(handles);
4058
4059%------------------------------------------------------------------------
4060function MinA_Callback(hObject, eventdata, handles)
4061%------------------------------------------
4062set(handles.FixScal,'Value',1) %suppress auto mode
4063set(handles.FixScal,'BackgroundColor',[1 1 0])
4064MinA=str2double(get(handles.MinA,'String'));
4065MaxA=str2double(get(handles.MaxA,'String'));
4066if MinA>MaxA% switch minA and maxA in case of error
4067    MinA_old=MinA;
4068    MinA=MaxA;
4069    MaxA=MinA_old;
4070    set(handles.MinA,'String',num2str(MinA,5));
4071    set(handles.MaxA,'String',num2str(MaxA,5));
4072end
4073update_plot(handles);
4074
4075%------------------------------------------------------------------------
4076function MaxA_Callback(hObject, eventdata, handles)
4077%------------------------------------------------------------------------
4078set(handles.FixScal,'Value',1) %suppress auto mode
4079set(handles.FixScal,'BackgroundColor',[1 1 0])
4080MinA=str2double(get(handles.MinA,'String'));
4081MaxA=str2double(get(handles.MaxA,'String'));
4082if MinA>MaxA% switch minA and maxA in case of error
4083        MinA_old=MinA;
4084    MinA=MaxA;
4085    MaxA=MinA_old;
4086    set(handles.MinA,'String',num2str(MinA,5));
4087    set(handles.MaxA,'String',num2str(MaxA,5));
4088end
4089update_plot(handles);
4090
4091%------------------------------------------------------------------------
4092function FixScal_Callback(hObject, eventdata, handles)
4093%------------------------------------------------------------------------
4094test=get(handles.FixScal,'Value');
4095if test
4096    set(handles.FixScal,'BackgroundColor',[1 1 0])
4097else
4098    set(handles.FixScal,'BackgroundColor',[0.7 0.7 0.7])
4099    update_plot(handles);
4100end
4101
4102%-------------------------------------------------------------------
4103function BW_Callback(hObject, eventdata, handles)
4104%-------------------------------------------------------------------
4105update_plot(handles);
4106
4107%-------------------------------------------------------------------
4108function Contours_Callback(hObject, eventdata, handles)
4109%-------------------------------------------------------------------
4110val=get(handles.Contours,'Value');
4111if val==2
4112    set(handles.interval_txt,'Visible','on')
4113    set(handles.IncrA,'Visible','on')
4114else
4115    set(handles.interval_txt,'Visible','off')
4116    set(handles.IncrA,'Visible','off')
4117end
4118update_plot(handles);
4119
4120%-------------------------------------------------------------------
4121function IncrA_Callback(hObject, eventdata, handles)
4122%-------------------------------------------------------------------
4123update_plot(handles);
4124
4125%-------------------------------------------------------------------
4126function HideWarning_Callback(hObject, eventdata, handles)
4127%-------------------------------------------------------------------
4128update_plot(handles);
4129
4130%-------------------------------------------------------------------
4131function HideFalse_Callback(hObject, eventdata, handles)
4132%-------------------------------------------------------------------
4133update_plot(handles);
4134
4135%-------------------------------------------------------------------
4136function VecScale_Callback(hObject, eventdata, handles)
4137%-------------------------------------------------------------------
4138set(handles.FixVec,'Value',1);
4139set(handles.FixVec,'BackgroundColor',[1 1 0])
4140update_plot(handles);
4141
4142%-------------------------------------------------------------------
4143function FixVec_Callback(hObject, eventdata, handles)
4144%-------------------------------------------------------------------
4145test=get(handles.FixVec,'Value');
4146if test
4147    set(handles.FixVec,'BackgroundColor',[1 1 0])
4148else
4149    update_plot(handles);
4150    %set(handles.VecScale,'String',num2str(ScalOut.VecScale,3))
4151    set(handles.FixVec,'BackgroundColor',[0.7 0.7 0.7])
4152end
4153
4154%------------------------------------------------------------------------
4155% --- Executes on selection change in decimate4 (nb_vec/4).
4156function decimate4_Callback(hObject, eventdata, handles)
4157%------------------------------------------------------------------------
4158update_plot(handles);
4159
4160%------------------------------------------------------------------------
4161% --- Executes on selection change in color_code menu
4162function color_code_Callback(hObject, eventdata, handles)
4163%------------------------------------------------------------------------
4164set_vec_col_bar(handles)
4165update_plot(handles);
4166
4167%------------------------------------------------------------------------
4168% --- Executes on button press in AutoVecColor.
4169function AutoVecColor_Callback(hObject, eventdata, handles)
4170%------------------------------------------------------------------------
4171test=get(handles.AutoVecColor,'Value');
4172if test
4173    set(handles.AutoVecColor,'BackgroundColor',[1 1 0])
4174else
4175    update_plot(handles);
4176    %set(handles.VecScale,'String',num2str(ScalOut.VecScale,3))
4177    set(handles.AutoVecColor,'BackgroundColor',[0.7 0.7 0.7])
4178end
4179
4180%------------------------------------------------------------------------
4181% --- Executes on selection change in max_vec.
4182function min_vec_Callback(hObject, eventdata, handles)
4183%------------------------------------------------------------------------
4184max_vec_Callback(hObject, eventdata, handles)
4185
4186%------------------------------------------------------------------------
4187% --- Executes on selection change in max_vec.
4188function max_vec_Callback(hObject, eventdata, handles)
4189%------------------------------------------------------------------------
4190set(handles.AutoVecColor,'Value',1)
4191AutoVecColor_Callback(hObject, eventdata, handles)
4192min_val=str2num(get(handles.min_vec,'String'));
4193max_val=str2num(get(handles.max_vec,'String'));
4194slider1=get(handles.slider1,'Value');
4195slider2=get(handles.slider2,'Value');
4196colcode1=min_val+(max_val-min_val)*slider1;
4197colcode2=min_val+(max_val-min_val)*slider2;
4198set(handles.colcode1,'String',num2str(colcode1))
4199set(handles.colcode2,'String',num2str(colcode2))
4200update_plot(handles);
4201
4202%------------------------------------------------------------------------
4203% --- update the display of color code for vectors
4204function set_vec_col_bar(handles)
4205%------------------------------------------------------------------------
4206%get the image of the color display button 'vec_col_bar' in pixels
4207set(handles.vec_col_bar,'Unit','pixel');
4208pos_vert=get(handles.vec_col_bar,'Position');
4209set(handles.vec_col_bar,'Unit','Normalized');
4210width=ceil(pos_vert(3));
4211height=ceil(pos_vert(4));
4212
4213%get slider indications
4214list=get(handles.color_code,'String');
4215ichoice=get(handles.color_code,'Value');
4216colcode.ColorCode=list{ichoice};
4217colcode.MinC=str2num(get(handles.min_vec,'String'));
4218colcode.MaxC=str2num(get(handles.max_vec,'String'));
4219test3color=strcmp(colcode.ColorCode,'rgb') || strcmp(colcode.ColorCode,'bgr');
4220if test3color
4221    colcode.colcode1=str2num(get(handles.colcode1,'String'));
4222    colcode.colcode2=str2num(get(handles.colcode2,'String'));
4223end
4224colcode.FixedCbounds=0;
4225colcode.FixedCbounds=1;
4226vec_C=colcode.MinC+(colcode.MaxC-colcode.MinC)*(0.5:width-0.5)/width;%sample of vec_C values from min to max
4227[colorlist,col_vec]=set_col_vec(colcode,vec_C);
4228oneheight=ones(1,height);
4229A1=colorlist(col_vec,1)*oneheight;
4230A2=colorlist(col_vec,2)*oneheight;
4231A3=colorlist(col_vec,3)*oneheight;
4232A(:,:,1)=A1';
4233A(:,:,2)=A2';
4234A(:,:,3)=A3';
4235set(handles.vec_col_bar,'Cdata',A)
4236
4237
4238%-------------------------------------------------------------------
4239function update_plot(handles)
4240%-------------------------------------------------------------------
4241haxes= handles.axes3;
4242UvData=get(handles.uvmat,'UserData');
4243AxeData=UvData.axes3;
4244PlotParam=read_plot_param(handles);
4245[PP,PlotParamOut]= plot_field(AxeData,haxes,PlotParam);
4246write_plot_param(handles,PlotParamOut); %update the auto plot parameters
4247
4248%-------------------------------------------------------------------
4249% --- Executes on button press in grid.
4250function grid_Callback(hObject, eventdata, handles)
4251
4252
4253%-------------------------------------------------------------------
4254% --- Executes on selection change in edit_object.
4255function edit_object_Callback(hObject, eventdata, handles)
4256%-------------------------------------------------------------------
4257UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4258test=get(handles.edit_object,'Value');
4259if test
4260    set(handles.edit_object,'BackgroundColor',[1,1,0]) 
4261    %suppress the other options
4262    set(handles.zoom,'Value',0)
4263    zoom_Callback(hObject, eventdata, handles)
4264    hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4265    if ishandle(hgeometry_calib)
4266        hhgeometry_calib=guidata(hgeometry_calib);
4267        set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4268        set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4269    end
4270else
4271    UvData.MouseAction='none';
4272    set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])   
4273    hset_object=findobj(allchild(0),'tag','set_object');% look for the set_object GUI
4274    if ~isempty(hset_object)
4275        delete(hset_object)% delete the current GUI set_object
4276    end
4277end
4278set(handles.uvmat,'UserData',UvData);
4279hset_object=findobj(allchild(0),'Tag','set_object');
4280if ~isempty(hset_object)
4281    hhset_object=guidata(hset_object);
4282    if test
4283        set(hhset_object.PLOT,'enable','on');
4284    else
4285       set(hhset_object.PLOT,'enable','off');
4286    end
4287end
4288
4289%------------------------------------------------------------------------
4290% --- Executes on selection change in list_object_1.
4291function list_object_1_Callback(hObject, eventdata, handles)
4292%------------------------------------------------------------------------
4293list_str=get(handles.list_object_1,'String');
4294IndexObj=get(handles.list_object_1,'Value');
4295str_1=list_str{IndexObj};
4296% val_2=get(handles.list_object_2,'Value');
4297% str_2=get(handles.list_object_2,'String');
4298% if isequal(val_2,IndexObj)% if the first selection is equal to the second, it will suppress the second
4299%     set(handles.list_object_2,'Value',numel(str_2))%select the end of the list ('...')
4300%     list_object_2_Callback(hObject, eventdata, handles)
4301% end
4302update_object(handles,IndexObj,1,str_1)
4303
4304%------------------------------------------------------------------------
4305% --- Executes on selection change in list_object_1.
4306function list_object_2_Callback(hObject, eventdata, handles)
4307%------------------------------------------------------------------------
4308list_str=get(handles.list_object_2,'String');
4309IndexObj=get(handles.list_object_2,'Value');
4310if ischar(list_str) || isempty(list_str{IndexObj})% || strcmp(list_str{IndexObj},'...')
4311    hview_field=findobj(allchild(0),'Tag','view_field');
4312    if ~isempty(hview_field)
4313        delete(hview_field)
4314    end
4315    hset_object=findobj(allchild(0),'Tag','set_object');
4316    if ~isempty(hset_object)
4317        delete(hset_object)
4318    end
4319else
4320    update_object(handles,IndexObj,2,list_str{IndexObj})
4321end
4322
4323%------------------------------------------------------------------------
4324function update_object(handles,IndexObj,option,ObjectName)
4325%------------------------------------------------------------------------
4326UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4327if numel(UvData.Object)<IndexObj;
4328    return
4329end
4330ObjectData=UvData.Object{IndexObj};
4331ObjectData.Name=ObjectName;
4332if isequal(get(handles.edit_object,'Value'),1)
4333    ObjectData.enable_plot=1; % desable the PLOT option in the set_object GUI (editing mode
4334end
4335ZBounds=0; % default
4336if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4337    ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4338    ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4339end
4340hset_object=findobj(allchild(0),'tag','set_object');
4341if ~isempty(hset_object)
4342    delete(hset_object)% delete existing version of set_object
4343end
4344edit_test=get(handles.edit_object,'Value');
4345if edit_test
4346    ObjectData.enable_plot=1;
4347else
4348    if isfield(ObjectData,'enable_plot')
4349        ObjectData=rmfield(ObjectData,'enable_plot');
4350    end
4351end
4352hset_object=set_object(ObjectData,[],ZBounds);% call the set_object interface,
4353
4354% %project the current field on the object and plot it
4355ProjData= proj_field(UvData.Field,ObjectData);%project the current interface field on ObjectData
4356if option==1%length(UvData.Object)>= IndexObj && isfield(UvData.Object{IndexObj},'plotaxes')&& ishandle(UvData.Object{IndexObj}.plotaxes)
4357    PlotHandles=handles;
4358else
4359    hview_field=findobj(allchild(0),'tag','view_field');
4360    if isempty(hview_field)
4361        hview_field=view_field;
4362    end
4363    PlotHandles=guidata(hview_field);
4364end
4365%plot_field(ProjData,PlotHandles.axes3,PlotHandles);
4366set(handles.uvmat,'UserData',UvData)
4367hother=findobj('Tag','proj_object');%find all the proj objects
4368for iobj=1:length(hother)
4369    if isequal(get(hother(iobj),'Type'),'rectangle')||isequal(get(hother(iobj),'Type'),'patch')
4370        set(hother(iobj),'EdgeColor','b')
4371        if isequal(get(hother(iobj),'FaceColor'),'m')
4372            set(hother(iobj),'FaceColor','b')
4373        end
4374    elseif isequal(get(hother(iobj),'Type'),'image')
4375        Acolor=get(hother(iobj),'CData');
4376        Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2));
4377        set(hother(iobj),'CData',Acolor);
4378    else
4379        set(hother(iobj),'Color','b')
4380    end
4381    set(hother(iobj),'Selected','off')
4382end
4383hother=findobj('Tag','DeformPoint');
4384set(hother,'Color','b');
4385set(hother,'Selected','off')
4386if isfield(ObjectData,'DisplayHandle_uvmat')
4387    if ishandle(ObjectData.DisplayHandle_uvmat)
4388        uistack(ObjectData.DisplayHandle_uvmat,'top')
4389        linetype=get(ObjectData.DisplayHandle_uvmat,'Type');
4390        if isequal(linetype,'line')
4391            set(ObjectData.DisplayHandle_uvmat,'Color','m'); %set the selected object to magenta color
4392        elseif isequal(linetype,'rectangle')
4393            set(ObjectData.DisplayHandle_uvmat,'EdgeColor','m'); %set the selected object to magenta color
4394        elseif isequal(linetype,'patch')
4395            set(ObjectData.DisplayHandle_uvmat,'FaceColor','m'); %set the selected object to magenta color
4396        end
4397        SubObjectData=get(ObjectData.DisplayHandle_uvmat,'UserData');
4398        if isfield(SubObjectData,'SubObject') & ishandle(SubObjectData.SubObject)
4399            uistack(SubObjectData.SubObject,'top')
4400            for iobj=1:length(SubObjectData.SubObject)
4401                hsub=SubObjectData.SubObject(iobj);
4402                if isequal(get(hsub,'Type'),'rectangle')
4403                    set(hsub,'EdgeColor','m'); %set the selected object to magenta color
4404                elseif isequal(get(hsub,'Type'),'image')
4405                    Acolor=get(hsub,'CData');
4406                    Acolor(:,:,1)=Acolor(:,:,3);
4407                    set(hsub,'CData',Acolor);
4408                else
4409                    set(hsub,'Color','m')
4410                end
4411            end
4412        end
4413        if isfield(SubObjectData,'DeformPoint') & ishandle(SubObjectData.DeformPoint)
4414            set(SubObjectData.DeformPoint,'Color','m')
4415        end
4416    end
4417    %     end
4418end
4419% pause(0.1)
4420figure(hset_object)%put set_object in front
4421
4422%------------------------------------------------------
4423% --- Executes on button press in Menu/Export/field in workspace.
4424%------------------------------------------------------
4425function MenuExportField_Callback(hObject, eventdata, handles)
4426global Data_uvmat
4427Data_uvmat=get(handles.uvmat,'UserData');
4428evalin('base','global Data_uvmat')%make CurData global in the workspace
4429display('current field :')
4430evalin('base','Data_uvmat') %display CurData in the workspace
4431commandwindow; %brings the Matlab command window to the front
4432
4433%------------------------------------------------------
4434% --- Executes on button press in Menu/Export/extract figure.
4435%------------------------------------------------------
4436function MenuExport_plot_Callback(hObject, eventdata, handles)
4437huvmat=get(handles.MenuExport_plot,'parent');
4438UvData=get(huvmat,'UserData');
4439hfig=figure;
4440newaxes=copyobj(handles.axes3,hfig);
4441map=colormap(handles.axes3);
4442colormap(map);%transmit the current colormap to the zoom fig
4443colorbar
4444
4445
4446% --------------------------------------------------------------------
4447function Insert_Callback(hObject, eventdata, handles)
4448
4449
4450% --------------------------------------------------------------------
4451function MenuHelp_Callback(hObject, eventdata, handles)
4452% --------------------------------------------------------------------
4453path_to_uvmat=which ('uvmat');% check the path of uvmat
4454pathelp=fileparts(path_to_uvmat);
4455helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
4456if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
4457else
4458    addpath (fullfile(pathelp,'uvmat_doc'))
4459    web(helpfile);
4460end
4461
4462%------------------------------------------------------------------------
4463% --------------------------------------------------------------------
4464function MenuExportMovie_Callback(hObject, eventdata, handles)
4465% --------------------------------------------------------------------
4466set(handles.MenuExportMovie,'BusyAction','queue')% activate the button
4467huvmat=get(handles.run0,'parent');
4468UvData=get(huvmat,'UserData');
4469[xx,xx,FileBase]=read_file_boxes(handles);
4470 %read the current input file name
4471prompt = {'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)'};
4472dlg_title = 'select properties of the output avi movie';
4473num_lines= 1;
4474% nbfield_cell=get(handles.last_i,'String');
4475def     = {[FileBase '_out.avi'];'10';'1';'[0.03 0.05 0.95 0.92]';'10'};
4476answer = inputdlg(prompt,dlg_title,num_lines,def,'on');
4477aviname=answer{1};
4478fps=str2double(answer{2});
4479% check for existing file with output name aviname
4480if exist(aviname,'file')
4481    backup=aviname;
4482    testexist=2;
4483    while testexist==2
4484        backup=[backup '~'];
4485        testexist=exist(backup,'file');     
4486    end
4487    [success,message]=copyfile(aviname,backup);%make backup of the existing file
4488    if isequal(success,1)
4489        delete(aviname)%delete existing file
4490    else
4491        msgbox_uvmat('ERROR',message)
4492        return
4493    end
4494end
4495%create avi open
4496aviobj=avifile(aviname,'Compression','None','fps',fps);
4497
4498%display first view for tests
4499newfig=figure;
4500newaxes=copyobj(handles.axes3,newfig);%new plotting axes in the new figure
4501set(newaxes,'Tag','movieaxes')
4502nbpix=[512 384]*str2double(answer{3});
4503set(gcf,'Position',[1 1 nbpix])% resolution XVGA
4504set(newaxes,'Position',eval(answer{4}));
4505map=colormap(handles.axes3);
4506colormap(map);%transmit the current colormap to the zoom fig
4507msgbox_uvmat('INPUT_Y-N',{['adjust figure ' num2str(newfig) ' with its matlab edit menu '] ;...
4508        ['then press OK to get the avi movie as a copy of figure ' num2str(newfig) ' display']});
4509UvData.plotaxes=newaxes;% the axis in the new figure becomes the current main plotting axes
4510set(huvmat,'UserData',UvData);
4511increment=str2double(get(handles.increment_scan,'String')); %get the field increment d
4512if isnan(increment)
4513    set(handles.increment_scan,'String','1')%default value
4514    increment=1;
4515end
4516set(handles.STOP,'Visible','on')
4517set(handles.speed,'Visible','on')
4518set(handles.speed_txt,'Visible','on')
4519set(handles.Movie,'BusyAction','queue')
4520
4521%imin=str2double(get(handles.i1,'String'));
4522imax=str2double(answer{5});
4523% if isfield(UvData,'Time')
4524htitle=get(newaxes,'Title');
4525xlim=get(newaxes,'XLim');
4526ylim=get(newaxes,'YLim');
4527set(htitle,'Position',[xlim(2)+0.07*(xlim(2)-xlim(1)) ylim(2)-0.05*(ylim(2)-ylim(1)) 0])
4528time_str=get(handles.abs_time,'String');
4529set(htitle,'String',['t=' time_str])
4530set(handles.speed,'Value',1)
4531for i=1:imax
4532    if get(handles.speed,'Value')~=0 && isequal(get(handles.MenuExportMovie,'BusyAction'),'queue') % enable STOP command
4533            runpm(hObject,eventdata,handles,increment)% run plus
4534            drawnow
4535            time_str=get(handles.abs_time,'String');
4536            if ishandle(htitle)
4537             set(htitle,'String',['t=' time_str])
4538            end
4539            mov=getframe(newfig);
4540            aviobj=addframe(aviobj,mov);
4541    end
4542end
4543aviobj=close(aviobj);
4544UvData=rmfield(UvData,'plotaxes');
4545%UvData.Object{1}.plotaxes=handles.axes3;
4546set(huvmat,'UserData',UvData);
4547msgbox_uvmat('CONFIRMATION',{['movie ' aviname ' created '];['with ' num2str(imax) ' frames']})
4548
4549%------------------------------------------------------------------------
4550function MenuCalib_Callback(hObject, eventdata, handles)
4551%------------------------------------------------------------------------
4552
4553UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4554
4555%suppress competing options
4556set(handles.zoom,'Value',0)
4557set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
4558set(handles.list_object_1,'Value',1)     
4559% initiate display of GUI geometry_calib
4560data=[]; %default
4561if isfield(UvData,'CoordType')
4562    data.CoordType=UvData.CoordType;
4563end
4564pos=get(handles.uvmat,'Position');
4565pos(1)=pos(1)+pos(3)-0.311+0.04; %0.311= width of the geometry_calib interface (units relative to the srcreen)
4566pos(2)=pos(2)-0.02;
4567[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles);
4568set(handles.view_xml,'Backgroundcolor',[1 1 0])%indicate the reading of the current xml file by geometry_calib
4569if isfield(UvData.OpenParam,'CalOrigin')
4570    pos_uvmat=get(handles.uvmat,'Position');
4571    pos_cal(1)=pos_uvmat(1)+UvData.OpenParam.CalOrigin(1)*pos_uvmat(3);
4572    pos_cal(2)=pos_uvmat(2)+UvData.OpenParam.CalOrigin(2)*pos_uvmat(4);
4573    pos_cal(3:4)=UvData.OpenParam.CalSize .* pos_uvmat(3:4);
4574end
4575geometry_calib(FileName,pos_cal);% call the geometry_calib interface   
4576set(handles.view_xml,'Backgroundcolor',[1 1 1])%indicate the end of reading of the current xml file by geometry_calib
4577set(handles.MenuCalib,'checked','on')% indicate that MenuCalib is activated, test used by mouse action
4578
4579%------------------------------------------------------------------------
4580function MenuMask_Callback(hObject, eventdata, handles)
4581%------------------------------------------------------------------------
4582UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4583ListObj=UvData.Object;
4584select=zeros(1,numel(ListObj));
4585for iobj=1:numel(ListObj);
4586    if strcmp(ListObj{iobj}.ProjMode,'mask_inside')||strcmp(ListObj{iobj}.ProjMode,'mask_outside')
4587        select(iobj)=1;
4588    end
4589end
4590val=find(select);
4591if isempty(val)
4592    msgbox_uvmat('ERROR','polygons must be first created by Projection object/mask polygon in the menu bar');
4593    return
4594else
4595    set(handles.list_object_1,'Max',2);%allow multiple selection
4596    set(handles.list_object_1,'Value',val);
4597    flag=1;
4598    npx=size(UvData.Field.A,2);
4599    npy=size(UvData.Field.A,1);
4600    xi=0.5:npx-0.5;
4601    yi=0.5:npy-0.5;
4602    [Xi,Yi]=meshgrid(xi,yi);
4603    if isfield(UvData,'Object')
4604        for iobj=1:length(UvData.Object)
4605            ObjectData=UvData.Object{iobj};
4606            if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
4607                flagobj=1;
4608                testphys=0; %coordinates in pixels by default
4609                if isfield(ObjectData,'CoordUnit') && ~isequal(ObjectData.CoordUnit,'pixel')
4610                    if isfield(UvData,'XmlData')&& isfield(UvData.XmlData,'GeometryCalib')
4611                        Calib=UvData.XmlData.GeometryCalib;
4612                        testphys=1;
4613                    end
4614                end
4615                if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style')
4616                    if isequal(ObjectData.Style,'polygon')
4617                        X=ObjectData.Coord(:,1);
4618                        Y=ObjectData.Coord(:,2);
4619                        if testphys
4620                            [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
4621                        end
4622                        flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside
4623                    elseif isequal(ObjectData.Style,'ellipse')
4624                        if testphys
4625                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4626                        end
4627                        RangeX=max(ObjectData.RangeX);
4628                        RangeY=max(ObjectData.RangeY);
4629                        X2Max=RangeX*RangeX;
4630                        Y2Max=RangeY*RangeY;
4631                        distX=(Xi-ObjectData.Coord(1,1));
4632                        distY=(Yi-ObjectData.Coord(1,2));
4633                        flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
4634                    elseif isequal(ObjectData.Style,'rectangle')
4635                        if testphys
4636                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4637                        end
4638                        distX=abs(Xi-ObjectData.Coord(1,1));
4639                        distY=abs(Yi-ObjectData.Coord(1,2));
4640                        flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
4641                    end
4642                    if isequal(ObjectData.ProjMode,'mask_outside')
4643                        flagobj=~flagobj;
4644                    end
4645                    flag=flag & flagobj;
4646                end
4647            end
4648        end
4649    end
4650    %mask name
4651    RootPath=get(handles.RootPath,'String');
4652    RootFile=get(handles.RootFile,'String');
4653    if ~isempty(RootFile)&&(isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
4654        RootFile(1)=[];
4655    end
4656    filebase=fullfile(RootPath,RootFile);
4657    list=get(handles.masklevel,'String');
4658    masknumber=num2str(length(list));
4659    maskindex=get(handles.masklevel,'Value');
4660    mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
4661    imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
4662    imflag=flipdim(imflag,1);
4663
4664    %display the mask
4665    hfigmask=figure;
4666    set(hfigmask,'Name','mask image')
4667    vec=linspace(0,1,256);%define a linear greyscale colormap
4668    map=[vec' vec' vec'];
4669    colormap(map)
4670    image(imflag);
4671    answer=msgbox_uvmat('INPUT_TXT','mask file name:', mask_name);
4672    if ~strcmp(answer,'Cancel')
4673        mask_dir=fileparts(answer);
4674        if ~exist(mask_dir,'dir')
4675            msgbox_uvmat('ERROR',['directory ' mask_dir ' does not exist'])
4676            return
4677        end
4678        imwrite(imflag,answer,'BitDepth',8);
4679    end
4680    set(handles.list_object_1,'Value',1)
4681    set(handles.list_object_1,'Max',1)
4682end
4683
4684%------------------------------------------------------------------------
4685%-- open the GUI set_grid.fig to create grid
4686function MenuGrid_Callback(hObject, eventdata, handles)
4687%------------------------------------------------------------------------
4688%UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4689
4690%suppress the other options if grid is chosen
4691set(handles.edit_vect,'Value',0)
4692edit_vect_Callback(hObject, eventdata, handles)
4693set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
4694set(handles.list_object_1,'Value',1)     
4695
4696%prepare display of the set_grid GUI
4697FileName=read_file_boxes(handles);
4698CoordList=get(handles.transform_fct,'String');
4699val=get(handles.transform_fct,'Value');
4700set_grid(FileName,CoordList{val});% call the set_object interface
4701%set(handles.uvmat,'UserData',UvData);
4702
4703%------------------------------------------------------------------------
4704% open the GUI 'series'
4705function MenuSeries_Callback(hObject, eventdata, handles)
4706%------------------------------------------------------------------------
4707series; %first display of the GUI to fill waiting time
4708[param.FileName]=read_file_boxes(handles);
4709if isequal(get(handles.SubField,'Value'),1)
4710    FileName_1=read_file_boxes_1(handles);%
4711    if ~isequal(FileName_1,param.FileName)
4712        param.FileName_1=FileName_1;
4713    end
4714end
4715param.NomType=get(handles.FileIndex,'UserData');
4716param.NomType_1=get(handles.FileIndex_1,'UserData');
4717param.comp_input=get(handles.fix_pair,'Value');
4718huvmat=get(handles.MenuSeries,'parent');
4719UvData=get(huvmat,'UserData');
4720if isfield(UvData,'Time')
4721    param.Time=UvData.XmlData.Time;
4722end
4723if isequal(get(handles.scan_i,'Value'),1)
4724    param.incr_i=str2double(get(handles.increment_scan,'String'));
4725elseif isequal(get(handles.scan_j,'Value'),1)
4726    param.incr_j=str2double(get(handles.increment_scan,'String'));
4727end
4728param.list_fields=get(handles.Fields,'String');% list menu fields
4729param.list_fields(1)=[]; %suppress  'image' option
4730param.index_fields=get(handles.Fields,'Value');% selected string index
4731if param.index_fields>1
4732    param.index_fields=param.index_fields-1;
4733end
4734param.list_fields_1=get(handles.Fields_1,'String');% list menu fields
4735param.list_fields_1(1)=[]; %suppress  'image' option
4736param.index_fields_1=get(handles.Fields_1,'Value')-1;% selected string index
4737if param.index_fields_1>1
4738    param.index_fields_1=param.index_fields_1-1;
4739end
4740% if isequal(get(handles.VelType,'Visible'),'on')
4741%     param.VelTypeMenu=get(handles.VelType,'String');
4742%     param.VelTypeIndex=get(handles.VelType,'Value');
4743% end
4744% param.civ1=get(handles.VelType,'Value');
4745% param.civ2=get(handles.civ2,'Value');
4746% param.interp1=get(handles.interp1,'Value');
4747% param.interp2=get(handles.interp2,'Value');
4748% param.filter1=get(handles.filter1,'Value');
4749% param.filter2=get(handles.filter2,'Value');
4750param.menu_coord_str=get(handles.transform_fct,'String');
4751param.menu_coord_val=get(handles.transform_fct,'Value');
4752
4753series(param); %run the series interface
4754
4755%------------------------------------------------------------------------
4756% -- open the GUI civ.fig for civx (PIV)
4757function MenuPIV_Callback(hObject, eventdata, handles)
4758%------------------------------------------------------------------------
4759 
4760[FileName,RootPath,filebase,FileIndices,ext,SubDir]=read_file_boxes(handles);
4761num1=stra2num(get(handles.i1,'String'));
4762num2=stra2num(get(handles.i2,'String'));
4763num_a=stra2num(get(handles.j1,'String'));
4764num_b=stra2num(get(handles.j2,'String'));
4765NomType=get(handles.FileIndex,'UserData');
4766ind_opening=1; % default (images): will advice civ1 option by default in the civ interface
4767if isequal(ext,'.nc') ||  isequal(ext,'.cdf')% netcdf files
4768    ind_opening=2;% propose 'fix' as the default option
4769% +read the current netcdf rootfile
4770    Data=nc2struct(FileName,'ListGlobalAttribute','fix','patch','civ2','fix2');
4771    if isfield(Data,'fix') && isequal(Data.fix,1)
4772        ind_opening=3;
4773    end
4774    if isfield(Data,'patch') && isequal(Data.patch,1)
4775        ind_opening=4;
4776    end
4777    if isfield(Data,'civ2') && isequal(Data.civ2,1)
4778        ind_opening=5;
4779    end
4780    if isfield(Data,'fix2') && isequal(Data.fix2,1)
4781        ind_opening=6;
4782    end
4783end     
4784param.RootName=filebase;
4785param.NomType=NomType;
4786param.num1=num1;
4787param.num2=num2;
4788param.num_a=num_a;
4789param.num_b=num_b;
4790param.SubDir=SubDir;
4791param.IndOpening=ind_opening;% A REVOIR +TRANSMETTRE IMADOC INFO
4792param.ImaExt=ext;
4793civ(param);% interface de civ(not in the uvmat file)
4794
4795%------------------------------------------------------------------------
4796function MenuTools_Callback(hObject, eventdata, handles)
4797%------------------------------------------------------------------------
4798
4799%------------------------------------------------------------------------
4800function MenuEditObject_Callback(hObject, eventdata, handles)
4801%------------------------------------------------------------------------
4802set(handles.edit_object,'Value',1)
4803edit_Callback(hObject, eventdata, handles)
4804
4805%------------------------------------------------------------------------
4806function enable_transform(handles,state)
4807%------------------------------------------------------------------------
4808set(handles.transform_fct,'Visible',state)
4809set(handles.TRANSFORM_txt,'Visible',state)   
4810set(handles.transform_fct,'Visible',state) 
4811set(handles.path_transform,'Visible',state)
4812set(handles.pxcmx_txt,'Visible',state)
4813set(handles.pxcmy_txt,'Visible',state)
4814set(handles.pxcm,'Visible',state)
4815set(handles.pycm,'Visible',state)
4816
4817%------------------------------------------------------------------------
4818function MenuEditVectors_Callback(hObject, eventdata, handles)
4819%------------------------------------------------------------------------
4820set(handles.edit_vect,'Visible','on')
4821set(handles.edit_vect,'Value',1)
4822edit_vect_Callback(hObject, eventdata, handles)
4823
4824% -----------------------------------------------------------------------
4825function Menupoints_Callback(hObject, eventdata, handles)
4826%------------------------------------------------------------------------
4827data.Style='points';
4828data.ProjMode='projection';%default
4829create_object(data,handles)
4830
4831% -----------------------------------------------------------------------
4832function Menuline_Callback(hObject, eventdata, handles)
4833%------------------------------------------------------------------------
4834data.Style='line';
4835data.ProjMode='projection';%default
4836create_object(data,handles)
4837
4838%------------------------------------------------------------------------
4839function Menupolyline_Callback(hObject, eventdata, handles)
4840%------------------------------------------------------------------------
4841data.Style='polyline';
4842data.ProjMode='projection';%default
4843create_object(data,handles)
4844
4845%------------------------------------------------------------------------
4846function Menupolygon_Callback(hObject, eventdata, handles)
4847%------------------------------------------------------------------------
4848data.Style='polygon';
4849data.ProjMode='inside';%default
4850create_object(data,handles)
4851
4852%------------------------------------------------------------------------
4853function Menurectangle_Callback(hObject, eventdata, handles)
4854%------------------------------------------------------------------------
4855data.Style='rectangle';
4856data.ProjMode='inside';%default
4857create_object(data,handles)
4858
4859%------------------------------------------------------------------------
4860function Menuellipse_Callback(hObject, eventdata, handles)
4861%------------------------------------------------------------------------
4862data.Style='ellipse';
4863data.ProjMode='inside';%default
4864create_object(data,handles)
4865
4866%------------------------------------------------------------------------
4867function MenuMaskObject_Callback(hObject, eventdata, handles)
4868%------------------------------------------------------------------------
4869data.Style='polygon';
4870data.StyleMenu={'polygon'};
4871data.ProjMode='mask_inside';%default
4872data.ProjMenu={'mask_inside';'mask_outside'};
4873create_object(data,handles)
4874
4875%------------------------------------------------------------------------
4876function Menuplane_Callback(hObject, eventdata, handles)
4877%------------------------------------------------------------------------
4878data.Style='plane';
4879data.ProjMode='projection';%default
4880
4881create_object(data,handles)
4882
4883%------------------------------------------------------------------------
4884function Menuvolume_Callback(hObject, eventdata, handles)
4885%------------------------------------------------------------------------
4886data.Style='volume';
4887data.ProjMode='interp';%default
4888% set(handles.create,'Visible','on')
4889% set(handles.create,'Value',1)
4890% VOLUME_Callback(hObject,eventdata,handles)
4891create_object(data,handles)
4892
4893%------------------------------------------------------------------------
4894function MenuBrowseObject_Callback(hObject, eventdata, handles)
4895%------------------------------------------------------------------------
4896%get the object file
4897[FileName, PathName, filterindex] = uigetfile( ...
4898       {'*.xml;*.mat', ' (*.xml,*.mat)';
4899       '*.xml',  '.xml files '; ...
4900        '*.mat',  '.mat matlab files '}, ...
4901        'Pick an xml Object file',get(handles.RootPath,'String'));
4902fileinput=[PathName FileName];%complete file name
4903% testblank=findstr(fileinput,' ');%look for blanks
4904% if ~isempty(testblank)
4905%     msgbox_uvmat('ERROR','forbidden input file name: contain blanks')
4906%     return
4907% end
4908sizf=size(fileinput);
4909if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
4910
4911%read the file
4912t=xmltree(fileinput);
4913data=convert(t);
4914data.enable_plot=1;
4915[pp,data.Name]=fileparts(FileName);
4916%PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
4917hset_object=findobj(allchild(0),'tag','set_object');
4918if ~isempty(hset_object)
4919    delete(hset_object)% delete existing version of set_object
4920end
4921% UvData=get(handles.uvmat,'UserData');
4922set_object(data);% call the set_object interface
4923% %position the set_object GUI with respect to uvmat
4924% pos_uvmat=get(handles.uvmat,'Position');
4925% if isfield(UvData,'SetObjectOrigin')
4926%     pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2);
4927%     pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4);
4928%     set(hset_object,'Position',pos_set_object)
4929% end
4930set(handles.edit_object,'Value',0); %suppress the object edit mode
4931set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4932set(handles.MenuObject,'checked','on')
4933%UvData.MouseAction='create_object';
4934% set(handles.uvmat,'UserData',UvData)
4935set(handles.delete_object,'Visible','on')
4936set(handles.uvmat_title,'Visible','on')
4937set(handles.view_field_title,'Visible','on')
4938
4939%------------------------------------------------------------------------
4940% --- generic function used for the creation of a projection object
4941function create_object(data,handles)
4942%------------------------------------------------------------------------
4943hset_object=findobj(allchild(0),'tag','set_object');
4944if ~isempty(hset_object)
4945    delete(hset_object)% delete existing version of set_object
4946end
4947hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4948if ishandle(hgeometry_calib)
4949    hhgeometry_calib=guidata(hgeometry_calib);
4950    set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4951    set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4952end
4953UvData=get(handles.uvmat,'UserData');
4954set(handles.edit_object,'Value',0); %suppress the object edit mode
4955set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4956data.enable_plot=1;
4957transform_list=get(handles.transform_fct,'String');
4958val=get(handles.transform_fct,'Value');
4959%data.CoordType=transform_list{val};
4960if isfield(UvData,'Field')
4961    Field=UvData.Field;
4962    if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
4963        data.RangeX=Field.Mesh;
4964        data.RangeY=Field.Mesh;
4965        data.DX=Field.Mesh;
4966        data.DY=Field.Mesh;
4967    elseif isfield(Field,'AX')&& isfield(Field,'AY')&& isfield(Field,'A')%only image
4968        np=size(Field.A);
4969        meshx=(Field.AX(end)-Field.AX(1))/np(2);
4970        meshy=abs(Field.AY(end)-Field.AY(1))/np(1);
4971        data.RangeY=max(meshx,meshy);
4972        data.RangeX=max(meshx,meshy);
4973        data.DX=max(meshx,meshy);
4974    end
4975    if isfield(Field,'NbDim')
4976        data.NbDim=Field.NbDim;
4977    end
4978    if isfield(Field,'CoordUnit')
4979        data.CoordUnit=Field.CoordUnit;
4980    end
4981end
4982data.Coord=[0 0 0]; %default
4983if isfield(data,'Style') && isequal(data.Style,'line')
4984    if isfield(data,'DX')
4985        data.Coord=[[0 0 0];[data.DX 0 0]]; %default
4986    else
4987        data.Coord=[[0 0 0];[1 0 0]]; %default
4988    end
4989end
4990if ishandle(handles.UVMAT_title)
4991    delete(handles.UVMAT_title)%delete the initial display of uvmat if no field has been entered
4992end
4993%PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
4994set_object(data,handles);% call the set_object interface
4995set(handles.MenuObject,'checked','on')
4996set(handles.uvmat,'UserData',UvData)
4997set(handles.zoom,'Value',0)
4998zoom_Callback(handles.uvmat, [], handles)
4999set(handles.delete_object,'Visible','on')
5000set(handles.uvmat_title,'Visible','on')
5001set(handles.view_field_title,'Visible','on')
5002
5003%------------------------------------------------------------------------
5004function MenuRuler_Callback(hObject, eventdata, handles)
5005%------------------------------------------------------------------------
5006set(handles.zoom,'Value',0)
5007zoom_Callback(handles.uvmat, [], handles)
5008set(handles.MenuRuler,'checked','on')
5009UvData=get(handles.uvmat,'UserData');
5010UvData.MouseAction='ruler';
5011set(handles.uvmat,'UserData',UvData);
5012
5013%------------------------------------------------------------------------
5014% --- executed when closing: set the parent interface button to value 0
5015function closefcn(gcbo,eventdata)
5016%------------------------------------------------------------------------
5017%delete all the associated figures if exist
5018hh=findobj(allchild(0),'tag','view_field');
5019if ~isempty(hh)
5020    delete(hh)
5021end
5022hh=findobj(allchild(0),'tag','geometry_calib');
5023if ~isempty(hh)
5024    delete(hh)
5025end
5026hh=findobj(allchild(0),'tag','set_object');
5027if ~isempty(hh)
5028    hhh=findobj(hh,'tag','PLOT');
5029    set(hhh,'enable','off')
5030end
5031
5032%------------------------------------------------------------------------
5033% --- Executes on button press in delete_object.
5034function delete_object_Callback(hObject, eventdata, handles)
5035%------------------------------------------------------------------------
5036IndexObj=get(handles.list_object_2,'Value');
5037if IndexObj>1
5038    delete_object(IndexObj)
5039end
5040
5041% --- Executes on button press in FixVelType.
5042function FixVelType_Callback(hObject, eventdata, handles)
5043val=get(handles.FixVelType,'Value');
5044if ~val
5045    run0_Callback(hObject, eventdata, handles)
5046end
5047
5048
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