source: trunk/src/uvmat.m @ 199

Last change on this file since 199 was 199, checked in by sommeria, 13 years ago

bug corrections. Introduction of water wheight in calibration

File size: 212.2 KB
Line 
1%'uvmat': function associated with the GUI 'uvmat.fig' for images and data field visualization
2%------------------------------------------------------------------------
3% function huvmat=uvmat(input)
4%
5%OUTPUT
6% huvmat=current handles of the GUI uvmat.fig
7%%
8%
9%INPUT:
10% input: input file name (if character chain), or input image matrix to
11% visualize, or Matlab structure representing  netcdf 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 (civ1, 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
234%UvData.Object{1}.Style='plane';%main plotting plane
235UvData.Object{1}.ProjMode='projection';%main plotting plane
236if ~isfield(UvData.Object{1},'plotaxes')
237    UvData.Object{1}.plotaxes=handles.axes3;%default plotting axis
238    set(handles.list_object_1,'Value',1);
239   % set(handles.list_object_1,'String',{'1-PLANE'});
240   set(handles.list_object_1,'String',{''});
241end
242set(handles.Fields,'Value',1)
243set(handles.Fields,'string',{''})
244
245%% TRANSFORM menu: builtin fcts
246menu_str={'';'phys';'px';'phys_polar'};
247UvData.OpenParam.NbBuiltin=numel(menu_str); %number of functions
248path_uvmat=fileparts(which('uvmat'));
249addpath(fullfile(path_uvmat,'transform_field'))
250fct_handle{1,1}=[];
251testexist=zeros(size(menu_str'));%default
252testexist(1)=1;
253for ilist=2:length(menu_str)
254    if exist(menu_str{ilist},'file')
255        fct_handle{ilist,1}=str2func(menu_str{ilist});
256        testexist(ilist)=1;
257    else
258        testexist(ilist)=0;
259    end
260end
261rmpath(fullfile(path_uvmat,'transform_field'))
262
263%% load the list of previously browsed files in menus Open and Open_1
264 dir_perso=prefdir; % path to the directory .matlab for personal data
265 profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmauvmat_perso.mat' in .matlab
266 if exist(profil_perso,'file')
267      h=load (profil_perso);
268      if isfield(h,'MenuFile_1')
269          set(handles.MenuFile_1,'Label',h.MenuFile_1);
270          set(handles.MenuFile_1_1,'Label',h.MenuFile_1);
271      end
272      if isfield(h,'MenuFile_2')
273          set(handles.MenuFile_2,'Label',h.MenuFile_2);
274          set(handles.MenuFile_2_1,'Label',h.MenuFile_2);
275      end
276      if isfield(h,'MenuFile_3')
277          set(handles.MenuFile_3,'Label',h.MenuFile_3);
278          set(handles.MenuFile_3_1,'Label',h.MenuFile_3);
279      end
280      if isfield(h,'MenuFile_4')
281          set(handles.MenuFile_4,'Label',h.MenuFile_4);
282          set(handles.MenuFile_4_1,'Label',h.MenuFile_4);
283      end
284      if isfield(h,'MenuFile_5')
285          set(handles.MenuFile_5,'Label',h.MenuFile_5);
286          set(handles.MenuFile_5_1,'Label',h.MenuFile_5);
287      end
288      if isfield(h,'transform_fct') && iscell(h.transform_fct)
289         for ilist=1:length(h.transform_fct);
290             if exist(h.transform_fct{ilist},'file')
291                [path,file]=fileparts(h.transform_fct{ilist});
292                addpath(path)
293                h_func=str2func(file);
294                rmpath(path)
295                testexist=[testexist 1];
296             else
297                file='';
298                h_func=[];
299                testexist=[testexist 0];
300             end
301             fct_handle=[fct_handle; {h_func}]; %concatene the list of paths
302             menu_str=[menu_str; {file}];
303         end
304      end
305 end
306menu_str=menu_str(testexist==1);%=menu_str(testexist~=0)
307fct_handle=fct_handle(testexist==1);
308menu_str=[menu_str;{'more...'}];
309set(handles.transform_fct,'String',menu_str)
310set(handles.transform_fct,'UserData',fct_handle)% store the list of path in UserData of ACTION
311set(handles.uvmat,'UserData',UvData)
312
313%% check the path and date of modification of all functions in uvmat
314path_to_uvmat=which ('uvmat');% check the path detected for source file uvmat
315[errormsg,date_str]=check_functions;%check the path of the functions called by uvmat.m
316date_str=['last modification: ' date_str];
317
318%% case of an input argument for uvmat
319testinputfield=0;
320inputfile=[];
321Field=[];
322if exist('input','var')
323    if ~isempty(errormsg)
324        msgbox_uvmat('WARNING',errormsg)
325    end
326    if ishandle(handles.UVMAT_title)
327        delete(handles.UVMAT_title)
328    end   
329    if isstruct(input)
330        if isfield(input,'InputFile')
331            inputfile=input.InputFile;
332        end
333        Field=input;
334    elseif ischar(input)% file name introduced as input
335           inputfile=input;
336    elseif isnumeric(input)%simple matrix introduced as input
337        sizinput=size(input);
338        if sizinput(1)<=1 || sizinput(2)<=1
339            msgbox_uvmat('ERROR','bad input for uvmat: file name, structure or numerical matrix accepted')
340            return
341        end
342        Field.ListVarName={'A','coord_y','coord_x'};
343        Field.VarDimName={{'coord_y','coord_x'},'cord_y','coord_x'};
344        Field.A=input;
345        Field.coord_x=[0.5 size(input,2)-0.5];
346        Field.coord_y=[size(input,1)-0.5 0.5];
347    end
348    if ~isempty(inputfile)
349        %%%%% display the indput field %%%%%%%
350        display_file_name(hObject, eventdata, handles,inputfile)
351        %%%%%%%
352        testinputfield=1;
353    end
354else
355   if ishandle(handles.UVMAT_title)
356       fid=fopen('revision.log');
357       if fid~=-1
358         a=textscan(fid,'%s%s%s',1,'HeaderLines',1,'Delimiter','|');
359         set(handles.UVMAT_title,'String',[{'Copyright Joel Sommeria, 2008, Coriolis/ LEGI / CNRS-UJF-INPG'};{'GNU General Public License'}; {path_to_uvmat}; ...
360           {['at revision ' a{1}{1}]};a{3}(1);{date_str};errormsg]);
361         fclose(fid);
362       else
363          set(handles.UVMAT_title,'String',[{'Copyright Joel Sommeria, 2008, Coriolis/ LEGI / CNRS-UJF-INPG'};{'GNU General Public License'};{path_to_uvmat};...
364               {date_str};errormsg]);
365       end
366   end
367end
368% set(handles.uvmat,'UserData',UvData)
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
389set_vec_col_bar(handles) %update the display of color code for vectors
390
391%------------------------------------------------------------------------
392% --- Outputs from this function are returned to the command menuline.
393function varargout = uvmat_OutputFcn(hObject, eventdata, handles)
394varargout{1} = handles.output;% the only output argument is the handle to the GUI figure
395
396%------------------------------------------------------------------------
397%------------------------------------------------------------------------
398%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
399% automatically sets the global properties when the rootfile name is introduced
400% then activate the view-field action if selected
401% it is activated either by clicking on the RootPath window or by the
402% browser
403%------------------------------------------------------------------------
404%------------------------------------------------------------------------
405% --- Executes on the menu Open/Browse...
406% search the files, recognize their type according to their name and fill the rootfile input windows
407function MenuBrowse_Callback(hObject, eventdata, handles)
408oldfile=read_file_boxes(handles);
409
410if isempty(oldfile)||isequal(oldfile,'') %loads the previously stored file name and set it as default in the file_input box
411         dir_perso=prefdir;
412         profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
413         if exist(profil_perso,'file')
414              h=load (profil_perso);
415             if isfield(h,'MenuFile_1')
416                  oldfile=h.MenuFile_1;
417             end
418         end
419end
420[FileName, PathName] = uigetfile( ...
421       {'*.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)';
422       '*.xml',  '.xml files '; ...
423        '*.xls',  '.xls files '; ...
424        '*.civ',  '.civ files '; ...
425        '*.jpg',' jpeg image files'; ...
426        '*.png','.png image files'; ...
427        '*.tif','.tif image files'; ...
428        '*.avi;*.AVI','.avi movie files'; ...
429        '*.vol','.volume images (png)'; ...
430        '*.nc','.netcdf files'; ...
431        '*.cdf','.netcdf files'; ...
432        '*.cmx','.cmx text files ';...
433        '*.fig','.fig files (matlab fig)';...
434        '*.log','.log text files ';...
435        '*.dat','.dat text files ';...
436        '*.bat','.bat system command text files';...
437        '*.*',  'All Files (*.*)'}, ...
438        'Pick a file',oldfile);
439%global filebase
440fileinput=[PathName FileName];%complete file name
441% testblank=findstr(fileinput,' ');%look for blanks
442% if ~isempty(testblank)
443%     msgbox_uvmat('ERROR',['The input file name ' fileinput ' contains blank character : This is not allowed. Please change name'])
444%     return
445% end
446sizf=size(fileinput);
447if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
448
449% display the selected field and related information
450display_file_name(hObject, eventdata, handles,fileinput)
451
452%update list of recent files in the menubar
453MenuFile_1=fileinput;
454MenuFile_2=get(handles.MenuFile_1,'Label');
455MenuFile_3=get(handles.MenuFile_2,'Label');
456MenuFile_4=get(handles.MenuFile_3,'Label');
457MenuFile_5=get(handles.MenuFile_4,'Label');
458set(handles.MenuFile_1,'Label',MenuFile_1)
459set(handles.MenuFile_2,'Label',MenuFile_2)
460set(handles.MenuFile_3,'Label',MenuFile_3)
461set(handles.MenuFile_4,'Label',MenuFile_4)
462set(handles.MenuFile_5,'Label',MenuFile_5)
463set(handles.MenuFile_1_1,'Label',MenuFile_1)
464set(handles.MenuFile_2_1,'Label',MenuFile_2)
465set(handles.MenuFile_3_1,'Label',MenuFile_3)
466set(handles.MenuFile_4_1,'Label',MenuFile_4)
467set(handles.MenuFile_5_1,'Label',MenuFile_5)
468dir_perso=prefdir;
469profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
470if exist(profil_perso,'file')
471    save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
472else
473    txt=ver('MATLAB');
474    Release=txt.Release;
475    relnumb=str2double(Release(3:4));
476    if relnumb >= 14
477        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
478    else
479        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
480    end
481end
482
483% -----------------------------------------------------------------------
484% --- Open again the file whose name has been recorded in MenuFile_1
485function MenuFile_1_Callback(hObject, eventdata, handles)
486fileinput=get(handles.MenuFile_1,'Label');
487display_file_name(hObject, eventdata, handles,fileinput)
488
489% -----------------------------------------------------------------------
490% --- Open again the file whose name has been recorded in MenuFile_2
491function MenuFile_2_Callback(hObject, eventdata, handles)
492fileinput=get(handles.MenuFile_2,'Label');
493display_file_name(hObject, eventdata, handles,fileinput)
494
495% -----------------------------------------------------------------------
496% --- Open again the file whose name has been recorded in MenuFile_3
497function MenuFile_3_Callback(hObject, eventdata, handles)
498fileinput=get(handles.MenuFile_3,'Label');
499display_file_name(hObject, eventdata, handles,fileinput)
500
501% -----------------------------------------------------------------------
502% --- Open again the file whose name has been recorded in MenuFile_4
503function MenuFile_4_Callback(hObject, eventdata, handles)
504fileinput=get(handles.MenuFile_4,'Label');
505display_file_name(hObject, eventdata, handles,fileinput)
506
507% -----------------------------------------------------------------------
508% --- Open again the file whose name has been recorded in MenuFile_5
509function MenuFile_5_Callback(hObject, eventdata, handles)
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)
516if ~exist(fileinput,'file')
517    msgbox_uvmat('ERROR',['input file ' fileinput  ' does not exist'])
518    return
519end
520[RootPath,RootFile,i1,i2,str_a,str_b,ext,NomType,SubDir]=name2display(fileinput);
521ext_test=''; %default
522if ~isempty(ext)
523    form=imformats(ext(2:end));%test valid Matlab image formats
524    if ~isempty(form)
525        ext_test='.image';
526        imainfo=imfinfo(fileinput); 
527        if length(imainfo) >1 %case of image with multiple frames
528            i1='1'; % set the frame counter to 1 by default
529            i2='';
530            str_a='';
531            str_b='';
532            NomType='*'; %indicate a set of indexed frames within a single file
533            [RootPath,RootFile]=fileparts(fileinput); %include the indices in the root file
534        end
535    elseif isequal(lower(ext),'.avi')
536        ext_test='.image';
537        i1='1'; % set the frame counter to 1 by default
538        i2='';
539        str_a='';
540        str_b='';
541        NomType='*'; %indicate a set of indexed frames within a single file
542        [RootPath,RootFile]=fileparts(fileinput); %include the indices in the root file
543    else
544        ext_test=lower(ext);
545    end
546end
547switch ext_test
548    case {'.civ','.log','.cmx','.cmx2','.txt','.bat'}  %display text file
549        edit(fileinput) 
550    case '.fig'                           %display matlab figure
551        hfig=open(fileinput);
552        set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
553        set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
554        set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
555    case {'.xml','.xls'}                % edit xml or Excel files
556       editxml(fileinput);
557    case {'.avi','.image','.vol','.nc','.cdf'}   
558        set(handles.RootPath,'String',RootPath);
559        if  isequal(SubDir,'')
560            rootname=fullfile(RootPath,RootFile);
561        else
562            rootname=fullfile(RootPath,SubDir,RootFile);
563            SubDir=['/' SubDir]; %display the separator
564        end
565        set(handles.SubDir,'String',SubDir);
566        set(handles.RootFile,'String',['/' RootFile]); %display the separator
567        indices=fileinput(length(rootname)+1:end);
568        indices(end-length(ext)+1:end)=[]; %remove extension
569        set(handles.FileIndex,'String',indices);       
570        set(handles.FileIndex,'UserData',NomType);
571        set(handles.FileExt,'String',ext);
572        % fill file index counters
573        set(handles.i1,'String',i1);   
574        set(handles.i2,'String',i2);
575        set(handles.j1,'String',str_a);
576        set(handles.j2,'String',str_b);
577       
578        % synchronise indices of the second  input file if it exists
579        if get(handles.SubField,'Value')==1% if the subfield button is activated, update the field numbers
580            [ff,rr,FileBase_1,ii,FileExt_1,SubDir_1]=read_file_boxes_1(handles);
581            NomType_1=get(handles.FileIndex_1,'UserData');     
582            FileName_1=name_generator(FileBase_1,str2double(i1),str2double(i2),FileExt_1,NomType_1,1,stra2num(str_a),stra2num(str_b),SubDir_1);
583            if exist(FileName_1,'file')
584                FileIndex_1=name_generator('',str2double(i1),str2double(i2),'',NomType_1,1,stra2num(str_a),stra2num(str_b),'');
585                set(handles.FileIndex_1,'String',FileIndex_1)
586            else
587                set(handles.SubField,'Value',0)
588                SubField_Callback(hObject, eventdata, handles)
589            end
590        end 
591
592        %enable other menus
593        set(handles.MenuOpen_1,'Enable','on')
594        set(handles.MenuFile_1_1,'Enable','on')
595        set(handles.MenuFile_2_1,'Enable','on')
596        set(handles.MenuFile_3_1,'Enable','on')
597        set(handles.MenuFile_4_1,'Enable','on')
598        set(handles.MenuFile_5_1,'Enable','on')
599        set(handles.MenuExport,'Enable','on')
600        set(handles.MenuExportFigure,'Enable','on')
601        set(handles.MenuExportMovie,'Enable','on')
602        set(handles.MenuTools,'Enable','on')
603        set(handles.OBJECT_txt,'Visible','on')
604        set(handles.edit_object,'Visible','on')
605        set(handles.list_object_1,'Visible','on')
606        set(handles.frame_object,'Visible','on')
607         %%%%%% initiate input file:
608        update_rootinfo(hObject,eventdata,handles); 
609    otherwise
610       msgbox_uvmat('ERROR',['invalid input file extension' ext])
611end
612
613%------------------------------------------------------------------------
614% --- Called by action in RootPath edit box
615function RootPath_Callback(hObject,eventdata,handles)
616%------------------------------------------------------------------------
617update_rootinfo(hObject,eventdata,handles);
618
619%------------------------------------------------------------------------
620% --- Called by action in RootFile edit box
621function SubDir_Callback(hObject, eventdata, handles)
622%------------------------------------------------------------------------
623%refresh the menu of input fields
624Fields_Callback(hObject, eventdata, handles);
625% refresh the current field
626run0_Callback(hObject, eventdata, handles);
627
628%------------------------------------------------------------------------
629% --- Called by action in RootFile edit box
630function RootFile_Callback(hObject, eventdata, handles)
631%------------------------------------------------------------------------
632update_rootinfo(hObject,eventdata,handles)
633
634%------------------------------------------------------------------------
635% --- Called by action in FileIndex edit box
636function FileIndex_Callback(hObject, eventdata, handles)
637%------------------------------------------------------------------------
638FileIndices=get(handles.FileIndex,'String');
639if isempty(str2num(FileIndices))
640    [pp,ff,str1,str2,str_a,str_b]=name2display(FileIndices);
641else
642    str1=FileIndices;
643    str2='';
644    str_a='';
645    str_b='';
646end
647set(handles.i1,'String',str1);
648set(handles.i2,'String',str2);
649set(handles.j1,'String',str_a);
650set(handles.j2,'String',str_b);
651run0_Callback(hObject, eventdata, handles)
652
653%------------------------------------------------------------------------
654% --- Update information about a new field series (indices to scan, timing,
655%     calibration from an xml file, then refresh current plots
656function update_rootinfo(hObject,eventdata,handles)
657%------------------------------------------------------------------------
658set(handles.RootPath,'BackgroundColor',[1 1 0])
659drawnow
660set(handles.Fields,'UserData',[])% reinialize data from uvmat opening
661UvData=get(handles.uvmat,'UserData');%huvmat=handles of the uvmat interface
662UvData.NewSeries=1; %flag for run0: begin a new series
663UvData.TestInputFile=1;
664set(handles.fix_pair,'Value',1) % activate by default the comp_input '-'input window
665
666[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles);
667if ~exist(FileName,'file')
668   msgbox_uvmat('ERROR',['input file ' FileName ' not found']);
669    return
670end
671nbfield=[];%default
672nburst=[];%default
673
674% read timing and total frame number from the current file (movie files) !! may be overrid by xml file
675XmlData.Time=[];%default
676XmlData.GeometryCalib=[];%default
677TimeUnit=[];%default
678testima=0; %test for image input
679imainfo=[];
680ColorType='falsecolor'; %default
681hhh='';
682if isequal(lower(FileExt),'.avi') %.avi file
683    testima=1;
684    imainfo=aviinfo([FileBase FileIndices FileExt]);
685    nbfield=imainfo.NumFrames;
686    nburst=1;
687    set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FramesPerSecond) 'ms']);%display the elementary time interval in millisec
688    XmlData.Time=(0:1/imainfo.FramesPerSecond:(imainfo.NumFrames-1)/imainfo.FramesPerSecond)';
689    TimeUnit='s';
690    hhh=which('mmreader');
691    ColorType=imainfo.ImageType;%='truecolor' for color images
692elseif ~isempty(FileExt(2:end))&&(~isempty(imformats(FileExt(2:end))) || isequal(FileExt,'.vol'))%&& isequal(NomType,'*')% multi-frame image
693    testima=1;
694    if ~isequal(SubDir,'')
695       RootFile=get(handles.RootFile,'String');
696        imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]);
697    else
698        imainfo=imfinfo([FileBase FileIndices FileExt]);
699    end
700    ColorType=imainfo.ColorType;%='truecolor' for color images
701    if length(imainfo) >1 %case of image with multiple frames
702        nbfield=length(imainfo);
703        nburst=1;
704    end
705end
706if ~strcmp(hhh,'')&& mmreader.isPlatformSupported()% if the function is found (recent version of matlab)
707    UvData.MovieObject=mmreader([FileBase FileIndices FileExt]);
708elseif isfield(UvData,'MovieObject')
709    UvData=rmfield(UvData,'MovieObject');
710end
711if isfield(imainfo,'Width') && isfield(imainfo,'Height')
712    set(handles.npx,'String',num2str(imainfo.Width));%fills nbre of pixels x box
713    set(handles.npy,'String',num2str(imainfo.Height));%fills nbre of pixels x box
714else
715    set(handles.npx,'String','');%fills nbre of pixels x box
716    set(handles.npy,'String','');%fills nbre of pixels x box
717end
718set(handles.BW,'Value',strcmp(ColorType,'grayscale'))% select handles.BW if grayscale image
719
720% read parameters (time, geometric calibration..) from a documentation file (.xml advised)
721filexml=[FileBase '.xml'];
722fileciv=[FileBase '.civ'];
723warntext='';%default warning message
724NbSlice=1;%default
725
726if exist(filexml,'file')
727    set(handles.view_xml,'Visible','on')
728    set(handles.view_xml,'BackgroundColor',[1 1 0])
729    set(handles.RootPath,'BackgroundColor',[1 1 1])
730    set(handles.view_xml,'String','view .xml')
731    drawnow
732    [XmlData,warntext]=imadoc2struct(filexml);
733    if ~isempty(warntext)
734        msgbox_uvmat('WARNING',warntext)
735    end
736    if isfield(XmlData,'TimeUnit')
737        if isfield(XmlData,'TimeUnit')&& ~isempty(XmlData.TimeUnit)
738            TimeUnit=XmlData.TimeUnit;
739        end
740    end
741    set(handles.view_xml,'BackgroundColor',[1 1 1])
742    drawnow
743    if isfield(XmlData, 'GeometryCalib') && ~isempty(XmlData.GeometryCalib)
744        XmlData.GeometryCalib
745        if isfield(XmlData.GeometryCalib,'VolumeScan') && isequal(XmlData.GeometryCalib.VolumeScan,'y')
746            set (handles.nb_slice,'String','volume')
747        end
748        hgeometry_calib=findobj('tag','geometry_calib');
749        if ~isempty(hgeometry_calib)
750            GUserData=get(hgeometry_calib,'UserData');
751            if ~(isfield(GUserData,'XmlInputFile') && strcmp(GUserData.XmlInputFile,filexml))
752                answer=msgbox_uvmat('INPUT_Y-N','replace the display of geometry_calib with the new input data?');
753                if strcmp(answer,'Yes')
754                    geometry_calib(filexml);%diplay the new calibration points and parameters in geometry_calib
755                end
756            end
757        end
758    end 
759elseif exist(fileciv,'file')% if .civ file found
760    [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']);
761    GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
762    GeometryCalib.Tx=0;
763    GeometryCalib.Ty=0;
764    GeometryCalib.Tz=1;
765    GeometryCalib.dpx=1;
766    GeometryCalib.dpy=1;
767    GeometryCalib.sx=1;
768    GeometryCalib.Cx=0;
769    GeometryCalib.Cy=0;
770    GeometryCalib.f=1;
771    GeometryCalib.kappa1=0;
772    GeometryCalib.CoordUnit='cm';
773    XmlData.GeometryCalib=GeometryCalib;
774    if error==2, warntext=['no file ' FileBase '.civ'];
775    elseif error==1, warntext='inconsistent number of fields in the .civ file';
776    end 
777    set(handles.npx,'String',num2str(npx));%fills nbre of pixels x box
778    set(handles.npy,'String',num2str(npy));%fills nbre of pixels y box
779    set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box
780    set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box
781    set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box
782    set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box
783    set(handles.view_xml,'Visible','on')   
784    set(handles.view_xml,'String','view .civ')
785else
786    set(handles.view_xml,'Visible','off')
787end
788
789% store last index in handles.lat_i and .last_j
790if ~isempty(XmlData.Time)
791    nbfield=size(XmlData.Time,1);
792    nburst=size(XmlData.Time,2);
793    %transform .Time to a column vector if it is a line vector the nomenclature uses a single index
794    if isequal(nbfield,1) && ~isequal(nburst,1)% .Time is a line vector
795        NomType=get(handles.FileIndex,'UserData');
796        if numel(NomType)>=2 &&(strcmp(NomType,'_i')||strcmp(NomType(1:2),'%0')||strcmp(NomType(1:2),'_%'))
797            XmlData.Time=(XmlData.Time)';
798            nbfield=nburst;
799            nburst=1;
800        end
801    end
802end
803last_i_cell=get(handles.last_i,'String');
804if isempty(nbfield)
805    last_i_cell{1}='';
806else
807    last_i_cell{1}=num2str(nbfield);
808end
809set(handles.last_i,'String',last_i_cell)
810last_j_cell=get(handles.last_j,'String');
811if isempty(nburst)
812     last_j_cell{1}='';
813else
814     last_j_cell{1}=num2str(nburst);
815end
816set(handles.last_j,'String',last_j_cell);
817
818% store geometric calibration in UvData
819if isfield(XmlData,'GeometryCalib')
820    GeometryCalib=XmlData.GeometryCalib;
821    if isempty(GeometryCalib)
822        set(handles.pxcm,'String','')
823        set(handles.pycm,'String','')
824        set(handles.transform_fct,'Value',1); %  no transform by default
825    else
826        if (isfield(GeometryCalib,'R')&& ~isequal(GeometryCalib.R(2,1),0) && ~isequal(GeometryCalib.R(1,2),0)) ||...
827            (isfield(GeometryCalib,'kappa1')&& ~isequal(GeometryCalib.kappa1,0))
828            set(handles.pxcm,'String','var')
829            set(handles.pycm,'String','var')
830        elseif isfield(GeometryCalib,'fx_fy')
831            pixcmx=GeometryCalib.fx_fy(1);%*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx);
832            pixcmy=GeometryCalib.fx_fy(2);%*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy);
833            set(handles.pxcm,'String',num2str(pixcmx))
834            set(handles.pycm,'String',num2str(pixcmy))
835        end
836        if ~get(handles.FixLimits,'Value')
837            set(handles.transform_fct,'Value',2); % phys transform by default if fixedLimits is off
838        end
839        if isfield(GeometryCalib,'SliceCoord')
840           
841           siz=size(GeometryCalib.SliceCoord);
842           if siz(1)>1
843               NbSlice=siz(1);
844               set(handles.slices,'Visible','on')
845               set(handles.slices,'Value',1)
846           end
847           if isfield(GeometryCalib,'VolumeScan') && isequal(GeometryCalib.VolumeScan,'y')
848               set(handles.nb_slice,'String','volume')
849           else
850               set(handles.nb_slice,'String',num2str(NbSlice))
851           end
852           slices_Callback(hObject, eventdata, handles)
853        end           
854    end
855end
856
857%update the data attached to the uvmat interface
858if ~isempty(TimeUnit)
859    set(handles.time_txt,'String',['time (' TimeUnit ')'])
860end
861UvData.TimeUnit=TimeUnit;
862UvData.XmlData=XmlData;
863UvData.NewSeries=1;
864set(handles.uvmat,'UserData',UvData)
865
866%display warning message
867if ~isequal(warntext,'')
868    msgbox_uvmat('WARNING',warntext);
869end
870
871% set default options in menu 'Fields'
872
873if testima
874elseif isequal(FileExt,'.nc')||isequal(FileExt,'.cdf')
875   Data=nc2struct(FileName,'ListGlobalAttribute','absolut_time_T0','civ');
876   %col_vec=get(handles.col_vec,'String');
877   if ~isempty(Data.absolut_time_T0)&& ~isequal(Data.civ,0)%if the new input is Civx
878       FieldList=calc_field;
879       set(handles.Fields,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data
880       set(handles.Fields,'Value',2) % set menu to 'velocity'
881       col_vec=FieldList;
882       col_vec(1)=[];%remove 'velocity' option for vector color (must be a scalar)
883   else %general netcdf file (not civx)
884       set(handles.Fields,'Value',1) % set menu to 'get_field...
885       set(handles.Fields,'String',{'get_field...'})
886       col_vec={'get_field...'};
887       hget_field=findobj('Name','get_field');
888       if ~isempty(hget_field)%delete any existing get_field GUI for reinitialisation withthe new file series
889           hhget_field=guidata(hget_field);
890           if ~strcmp(get(hhget_field.inputfile,'String'),FileName)%delete any existing get_field GUI with file name different than the input
891                delete(hget_field)
892           end
893       end
894   end
895   set(handles.col_vec,'String',col_vec)
896else
897    msgbox_uvmat('ERROR',['invalid input file extension ' FileExt])
898    return
899end 
900
901%% set index navigation options and refresh plots
902set(handles.RootPath,'BackgroundColor',[1 1 1])
903drawnow
904set_scan_options(hObject, eventdata, handles)
905
906%------------------------------------------------------------------------
907%--- Set index navigation options for new series input and refresh plot
908%------------------------------------------------------------------------
909function set_scan_options(hObject, eventdata, handles)
910
911%  set the corresponding index navigation options
912NomType=get(handles.FileIndex,'UserData');       
913NomType_1=get(handles.FileIndex_1,'UserData');
914last_i_str=get(handles.last_i,'String');
915nbfield=str2num(last_i_str{1});
916if numel(last_i_str)==2
917    nbfield=min(nbfield,str2num(last_i_str{2}));
918end 
919state_j='off'; %default
920scan_option='i';%default
921NomTypeRaw=regexprep(NomType(2:end), '-', '');
922if numel(regexp(NomTypeRaw,'\D'))>=1
923        state_j='on';
924        if isequal(nbfield,1)
925            scan_option='j'; %scan j index by default if nbfield=1               
926        end
927end
928if ~isempty(NomType_1)
929    NomTypeRaw=regexprep(NomType_1(2:end), '-', '');
930    if numel(regexp(NomTypeRaw,'\D'))>=1
931            state_j='on';
932            if isequal(nbfield,1)
933                scan_option='j';                 
934            end           
935    end
936end
937if isequal(scan_option,'i')
938     set(handles.scan_i,'Value',1)
939     scan_i_Callback(hObject, eventdata, handles);
940else
941     set(handles.scan_j,'Value',1)
942     scan_j_Callback(hObject, eventdata, handles);
943end
944set(handles.scan_j,'Visible',state_j)
945set(handles.j1,'Visible',state_j)
946set(handles.j2,'Visible',state_j)
947set(handles.last_j,'Visible',state_j);
948set(handles.frame_j,'Visible',state_j);
949set(handles.j_text,'Visible',state_j);
950
951%% view the field 
952run0_Callback(hObject, eventdata, handles); %view field
953mask_test=get(handles.mask_test,'value');
954if mask_test
955    MaskData=get(handles.mask_test,'UserData');
956    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
957          delete(MaskData.maskhandle)    %delete old mask
958    end
959    mask_test_Callback(hObject, eventdata, handles)
960end
961
962%------------------------------------------------------------------------
963% --- Executes on the menu Open/Browse_1 for the second input field,
964%     search the files, recognize their type according to their name and fill the rootfile input windows
965function MenuBrowse_1_Callback(hObject, eventdata, handles)
966%------------------------------------------------------------------------
967% huvmat=get(handles.run0,'parent');
968UvData=get(handles.uvmat,'UserData');
969
970RootPath=get(handles.RootPath,'String');
971[FileName, PathName, filterindex] = uigetfile( ...
972       {'*.xml;*.xls;*.civ;*.jpg;*.png;*.avi;*.AVI;*.nc;*.cmx;*.fig;*.log;*.dat', ' (*.xml,*.xls,*.civ, *.jpg,*.png, *.avi,*.nc,*.cmx ,*.fig,*.log,*.dat)';
973       '*.xml',  '.xml files '; ...
974        '*.xls',  '.xls files '; ...
975        '*.civ',  '.civ files '; ...
976        '*.jpg','.jpg image files'; ...
977        '*.png','.png image files'; ...
978        '*.avi;*.AVI','.avi movie files'; ...
979        '*.nc','.netcdf files'; ...
980        '*.cdf','.netcdf files'; ...
981        '*.cmx','.cmx text files';...
982        '*.cmx2','.cmx2 text files';...
983        '*.fig','.fig files (matlab fig)';...
984        '*.log','.log text files ';...
985        '*.dat','.dat text files ';...
986        '*.*',  'All Files (*.*)'}, ...
987        'Pick a file',RootPath);
988fileinput_1=[PathName FileName];%complete file name
989% testblank=findstr(fileinput_1,' ');%look for blanks
990% if ~isempty(testblank)
991%     msgbox_uvmat('ERROR',['The input file name ' fileinput_1 ' contains blank character : This is not allowed. Please change name'])
992%     return
993% end
994sizf=size(fileinput_1);
995if (~ischar(fileinput_1)||~isequal(sizf(1),1)),return;end
996
997% refresh the current displayed field
998display_file_name_1(hObject,eventdata,handles,fileinput_1)
999
1000%update list of recent files in the menubar
1001MenuFile_1=fileinput_1;
1002MenuFile_2=get(handles.MenuFile_1,'Label');
1003MenuFile_3=get(handles.MenuFile_2,'Label');
1004MenuFile_4=get(handles.MenuFile_3,'Label');
1005MenuFile_5=get(handles.MenuFile_4,'Label');
1006set(handles.MenuFile_1,'Label',MenuFile_1)
1007set(handles.MenuFile_2,'Label',MenuFile_2)
1008set(handles.MenuFile_3,'Label',MenuFile_3)
1009set(handles.MenuFile_4,'Label',MenuFile_4)
1010set(handles.MenuFile_5,'Label',MenuFile_5)
1011set(handles.MenuFile_1_1,'Label',MenuFile_1)
1012set(handles.MenuFile_2_1,'Label',MenuFile_2)
1013set(handles.MenuFile_3_1,'Label',MenuFile_3)
1014set(handles.MenuFile_4_1,'Label',MenuFile_4)
1015set(handles.MenuFile_5_1,'Label',MenuFile_5)
1016dir_perso=prefdir;
1017profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1018if exist(profil_perso,'file')
1019    save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
1020else
1021    txt=ver('MATLAB');
1022    Release=txt.Release;
1023    relnumb=str2double(Release(3:4));
1024    if relnumb >= 14
1025        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
1026    else
1027        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
1028    end
1029end
1030
1031% -----------------------------------------------------------------------
1032% --- Open again as second field the file whose name has been recorded in MenuFile_1
1033function MenuFile_1_1_Callback(hObject, eventdata, handles)
1034% -----------------------------------------------------------------------
1035fileinput_1=get(handles.MenuFile_1_1,'Label');
1036display_file_name_1(hObject,eventdata,handles,fileinput_1)
1037
1038% -----------------------------------------------------------------------
1039% --- Open again as second field the file whose name has been recorded in MenuFile_2
1040function MenuFile_2_1_Callback(hObject, eventdata, handles)
1041% -----------------------------------------------------------------------
1042fileinput_1=get(handles.MenuFile_2_1,'Label');
1043display_file_name_1(hObject,eventdata,handles,fileinput_1)
1044
1045% -----------------------------------------------------------------------
1046% --- Open again as second field the file whose name has been recorded in MenuFile_3
1047function MenuFile_3_1_Callback(hObject, eventdata, handles)
1048% -----------------------------------------------------------------------
1049fileinput_1=get(handles.MenuFile_3_1,'Label');
1050display_file_name_1(hObject,eventdata,handles,fileinput_1)
1051
1052% -----------------------------------------------------------------------
1053% --- Open again as second field the file whose name has been recorded in MenuFile_4
1054function MenuFile_4_1_Callback(hObject, eventdata, handles)
1055% -----------------------------------------------------------------------
1056fileinput_1=get(handles.MenuFile_4_1,'Label');
1057display_file_name_1(hObject,eventdata,handles,fileinput_1)
1058
1059% -----------------------------------------------------------------------
1060% --- Open again as second field the file whose name has been recorded in MenuFile_5
1061function MenuFile_5_1_Callback(hObject, eventdata, handles)
1062% -----------------------------------------------------------------------
1063fileinput_1=get(handles.MenuFile_5_1,'Label');
1064display_file_name_1(hObject,eventdata,handles,fileinput_1)
1065
1066%------------------------------------------------------------------------
1067% fills the edit boxes RootPath_1, RootFile_1,NomType_1...from an input file name 'fileinput_1'
1068%------------------------------------------------------------------------
1069function display_file_name_1(hObject,eventdata,handles,fileinput_1)
1070
1071%[path,name,ext]=fileparts(fileinput_1);
1072[RootPath_1,RootFile_1,field_count,str2,str_a,str_b,FileExt_1,NomType_1,SubDir_1]=name2display(fileinput_1);
1073nbfield_1=1; %default
1074ext_test=FileExt_1;%default
1075form=imformats(FileExt_1(2:end));
1076if ~isempty(form) % if the extension corresponds to an image format recognized by Matlab
1077    imainfo=imfinfo(fileinput_1); 
1078    nbfield_1=length(imainfo);
1079    ext_test='.image';
1080elseif isequal(lower(FileExt_1),'.avi')
1081    info=aviinfo(fileinput_1);
1082    nbfield_1=info.NumFrames;
1083    ext_test='.image';
1084end
1085
1086%open directly fig or text files
1087switch ext_test
1088    case {'.civ','.log','.cmx','.cmx2','.txt'}  %display text file
1089        edit(fileinput) 
1090        return
1091    case '.fig'                           %display matlab figure
1092        hfig=open(fileinput);
1093        set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
1094        set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
1095        set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
1096        return
1097    case {'.xml','.xls'}                % edit xml or Excel files
1098       heditxml=editxml(fileinput);
1099       return
1100    case {'.image','.nc','.cdf'}
1101%         set(handles.FileIndex,'UserData',NomType_1);
1102    otherwise
1103        msgbox_uvmat(['invalid input file extension ' FileExt_1 ' for uvmat'],'ERROR')
1104        return
1105end
1106
1107% test for image series in a single file and synchronise file indices of the two series
1108if nbfield_1 >1 %case of image with multiple frames
1109    if nbfield_1 < num_i1
1110        msgbox_uvmat('ERROR','current frame index beyond the input movie length')
1111        return
1112    else
1113        NomType_1='*'; %indicate a set of indexed frames within a single file
1114        filename_new=fileinput_1;
1115    end
1116else  % cases of data files   
1117    RootPath=get(handles.RootPath,'String');
1118    RootFile=get(handles.RootFile,'String');
1119    FileBase=fullfile(RootPath,RootFile);
1120    FileBase_1=fullfile(RootPath_1,RootFile_1);
1121    if isequal(FileBase,FileBase_1)
1122        filename_new=fileinput_1;
1123    else       
1124        num_i1=stra2num(get(handles.i1,'String'));%get the current file indices from counters
1125        num_j1=stra2num(get(handles.j1,'String'));
1126        num_i2=stra2num(get(handles.i2,'String'));
1127        num_j2=stra2num(get(handles.j2,'String'));
1128        [filename_new,idetect]=...
1129           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
1130        indices=''; %default
1131        if ~idetect
1132            msgbox_uvmat('ERROR','second input file with indices corresponding to the first one does not exist')
1133            return
1134        end
1135    end
1136end
1137set(handles.FileIndex_1,'UserData',NomType_1);
1138
1139% make visible and fill the second raw of edit boxes
1140set(handles.RootPath_1,'Visible','on')
1141set(handles.RootFile_1,'Visible','on')
1142set(handles.SubDir_1,'Visible','on');
1143set(handles.FileIndex_1,'Visible','on');
1144set(handles.FileExt_1,'Visible','on');
1145[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles);
1146if isequal(FileBase,FileBase_1)
1147    set(handles.RootPath_1,'String','"')
1148    set(handles.RootFile_1,'String','"');
1149else
1150    set(handles.RootPath_1,'String',RootPath_1)
1151    set(handles.RootFile_1,'String',['/' RootFile_1]);
1152end
1153if  isequal(SubDir_1,'')
1154     set(handles.SubDir_1,'String','');
1155     FileBaseSub_1=FileBase_1;
1156else 
1157    set(handles.SubDir_1,'String',['/' SubDir_1]);
1158    FileBaseSub_1=fullfile(FileBase_1,SubDir_1);
1159end
1160indices=filename_new(length(FileBaseSub_1)+1:end);
1161indices(end-length(FileExt_1)+1:end)=[]; %remove extension
1162set(handles.FileIndex_1,'String',indices)
1163set(handles.FileIndex_1,'UserData',NomType_1)
1164set(handles.FileExt_1,'String',FileExt_1);
1165
1166% % default choice of fields
1167% if isequal(ext_test,'.image')
1168% %    set(handles.Fields_1,'String',{'';'image';'get_field...';'velocity';'vort';'div';'more...'})
1169% %    set(handles.Fields_1,'Value',2) % set menu to 'image'
1170% elseif strcmp(FileExt_1,'.nc')||strcmp(FileExt_1,'.cdf')
1171%    Data=nc2struct(fileinput_1,[]);
1172% %    if isfield(Data,'absolut_time_T0')
1173% %        set(handles.Fields_1,'String',{'';'image';'get_field...';'velocity';'vort';'div';'more...'})
1174% %        set(handles.Fields_1,'Value',4) % set menu to 'velocity'
1175% %    else   
1176% %        set(handles.Fields_1,'Value',2) % set menu to 'get_field...'
1177% %        set(handles.Fields_1,'String',{'';'get_field...'});
1178% %    end
1179% end 
1180set(handles.SubField,'Visible','on')
1181set(handles.SubField,'Value',1)
1182RootPath_1_Callback(hObject,eventdata,handles); 
1183
1184%-----------------------------------------------------------------------
1185% --- Called by action in RootPath_1 edit box
1186function RootPath_1_Callback(hObject,eventdata,handles)
1187% -----------------------------------------------------------------------
1188update_rootinfo_1(hObject,eventdata,handles)
1189
1190%-----------------------------------------------------------------------
1191% --- Called by action in RootFile_1 edit box
1192function RootFile_1_Callback(hObject, eventdata, handles)
1193% -----------------------------------------------------------------------
1194update_rootinfo_1(hObject,eventdata,handles)
1195
1196%------------------------------------------------------------------------
1197% --- Called by action in FileIndex_1 edit box
1198function FileIndex_1_Callback(hObject, eventdata, handles)
1199%------------------------------------------------------------------------
1200run0_Callback(hObject, eventdata, handles)
1201
1202%------------------------------------------------------------------------
1203% --- Update information about a new second field series (indices to scan, timing,
1204%     calibration from an xml file, then refresh current plots
1205function update_rootinfo_1(hObject,eventdata,handles) %A REVOIR
1206% -----------------------------------------------------------------------
1207set(handles.RootPath_1,'BackgroundColor',[1 1 0])% indicate active program by yellow color
1208drawnow
1209UvData=get(handles.uvmat,'UserData');%huvmat=handles of the uvmat interface
1210UvData.NewSeries=1; %flag for run0: begin a new series
1211
1212[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes_1(handles);
1213if ~exist(FileName,'file')
1214    msgbox_uvmat('ERROR',['input file ' FileName ' not found']);
1215end
1216nbfield_1=[];%default
1217nburst_1=[];%default
1218XmlData.Time=[];
1219XmlData.GeometryCalib=[];%default
1220TimeUnit=[];
1221if isfield(UvData,'TimeUnit')
1222    TimeUnit=UvData.TimeUnit;
1223end
1224TimeUnit_1=[];
1225hhh='';%default, test for  movie reading with mmreader
1226imainfo=[];
1227if isequal(lower(FileExt),'.avi') %.avi file
1228    imainfo=aviinfo([FileBase FileIndices FileExt]);
1229    nbfield_1=imainfo.NumFrames;
1230    nburst_1=1;
1231    set(handles.Dt_txt,'String',['Dt=' num2str(1000/info.FramesPerSecond) 'ms']);%display the elementary time interval in millisec
1232    time=(0:1/imainfo.FramesPerSecond:(imainfo.NumFrames-1)/imainfo.FramesPerSecond)';
1233    ColorType=imainfo.ImageType;%='truecolor' for color images
1234    hhh=which('mmreader');
1235elseif ~isempty(imformats(FileExt(2:end)))|| isequal(FileExt,'.vol')
1236    if ~isequal(SubDir,'')
1237        RootFile=get(handles.RootFile,'String');
1238        imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]);
1239    else
1240        imainfo=imfinfo([FileBase FileIndices FileExt]);
1241    end
1242    ColorType=imainfo.ColorType;%='truecolor' for color images
1243    if length(imainfo) >1 %case of image with multiple frames
1244        nbfield_1=length(imainfo);
1245        nburst_1=1;
1246    end
1247end
1248if ~strcmp(hhh,'')&& mmreader.isPlatformSupported()% if the function is found (recent version of matlab)
1249    UvData.MovieObject_1=mmreader([FileBase FileIndices FileExt]);
1250elseif isfield(UvData,'MovieObject_1')
1251    UvData=rmfield(UvData,'MovieObject_1');
1252end
1253if ~isempty(imainfo)% (an image has been introduced as second fierld input)
1254    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
1255        if  isfield(imainfo,'Width') && isfield(imainfo,'Height')
1256            set(handles.npx,'String',num2str(imainfo.Width));%fills nbre of pixels x box
1257            set(handles.npy,'String',num2str(imainfo.Height));%fills nbre of pixels x box
1258        else
1259            set(handles.npx,'String','');%fills nbre of pixels x box
1260            set(handles.npy,'String','');%fills nbre of pixels x box
1261        end
1262        set(handles.BW,'Value',strcmp(ColorType,'grayscale'))% select handles.BW if grayscale image
1263    end
1264end
1265% find scaling parameters
1266filexml=[FileBase '.xml'];
1267fileciv=[FileBase '.civ'];
1268warntext='';%default warning text
1269if exist(filexml,'file')
1270    [XmlData,warntext]=imadoc2struct(filexml);
1271    if ~isempty(warntext)
1272        msgbox_uvmat('WARNING',warntext)
1273    end
1274    if isfield(XmlData,'Camera')
1275        if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
1276            TimeUnit=XmlData.Camera.TimeUnit;
1277        end
1278    end
1279elseif exist(fileciv,'file')% if .civ file found
1280    [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']);
1281    GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
1282    GeometryCalib.Tx=0;
1283    GeometryCalib.Ty=0;
1284    GeometryCalib.Tz=1;
1285    GeometryCalib.dpx=1;
1286    GeometryCalib.dpy=1;
1287    GeometryCalib.sx=1;
1288    GeometryCalib.Cx=0;
1289    GeometryCalib.Cy=0;
1290    GeometryCalib.f=1;
1291    GeometryCalib.kappa1=0;
1292    GeometryCalib.CoordUnit='cm';
1293    XmlData.GeometryCalib=GeometryCalib;
1294    if error==2, warntext=['no file ' FileBase '.civ'];
1295    elseif error==1, warntext='inconsistent number of fields in the .civ file';
1296    end
1297   
1298    set(handles.npx,'String',num2str(npx));%fills nbre of pixels x box
1299    set(handles.npy,'String',num2str(npy));%fills nbre of pixels y box
1300    set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box
1301    set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box
1302    set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box
1303    set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box
1304end   
1305if ~isempty(TimeUnit_1) && ~isequal(TimeUnit_1,TimeUnit)
1306        msgbox_uvmat('WARNING','the time units for the second series differs from the first one')
1307end
1308       
1309% store last index in handles.lat_i and .last_j
1310if ~isempty(XmlData.Time)
1311    nbfield_1=size(XmlData.Time,1);
1312    nburst_1=size(XmlData.Time,2);   
1313end
1314last_i_cell=get(handles.last_i,'String');
1315if isempty(nbfield_1)
1316    last_i_cell{2}='';
1317else
1318    last_i_cell{2}=num2str(nbfield_1);
1319end
1320set(handles.last_i,'String',last_i_cell)
1321last_j_cell=get(handles.last_j,'String');
1322if isempty(nburst_1)
1323     last_j_cell{2}='';
1324else
1325     last_j_cell{2}=num2str(nburst_1);
1326end
1327set(handles.last_j,'String',last_j_cell);
1328if ~isequal(last_i_cell{1},last_i_cell{2}) || ~isequal(last_j_cell{1},last_j_cell{2})
1329        msgbox_uvmat('WARNING','the numbers of input file of the second series differs from the first one')
1330end
1331
1332% store calibration data
1333GeometryCalib=XmlData.GeometryCalib;
1334if isempty(GeometryCalib)
1335    if isfield(UvData, 'GeometryCalib_1')
1336        UvData=rmfield(UvData,'GeometryCalib_1');
1337    end
1338else
1339    UvData.GeometryCalib_1=GeometryCalib;
1340    if (isfield(GeometryCalib,'R')&& ~isequal(GeometryCalib.R(2,1),0) && ~isequal(GeometryCalib.R(1,2),0)) ||...
1341        (isfield(GeometryCalib,'kappa1')&& ~isequal(GeometryCalib.kappa1,0))
1342        set(handles.pxcm,'String','var')
1343        set(handles.pycm,'String','var')
1344    else
1345        if isfield(GeometryCalib,'fx_fy')
1346            pixcmx=GeometryCalib.fx_fy(1);
1347            pixcmy=GeometryCalib.fx_fy(2);
1348            set(handles.pxcm,'String',num2str(pixcmx))
1349            set(handles.pycm,'String',num2str(pixcmy))
1350        end
1351    end
1352end
1353UvData.XmlData_1=XmlData;
1354set(handles.uvmat,'UserData',UvData)%update the data attached to the uvmat interface
1355
1356if ~isequal(warntext,'')
1357    msgbox_uvmat('WARNING',warntext)
1358end
1359
1360set(handles.RootPath_1,'BackgroundColor',[1 1 1])% signa the end the input operation
1361drawnow
1362
1363set_scan_options(hObject, eventdata, handles)
1364
1365%---------------------------------------------------
1366% switch file index scanning options scan_i and scan_j in an exclusive way
1367function scan_i_Callback(hObject, eventdata, handles)
1368%---------------------------------------------------
1369if get(handles.scan_i,'Value')==1
1370    set(handles.scan_i,'BackgroundColor',[1 1 0])
1371    set(handles.scan_j,'Value',0)
1372%     set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
1373else
1374    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1375    set(handles.scan_j,'Value',1)
1376%     set(handles.scan_j,'BackgroundColor',[1 1 0])
1377end
1378scan_j_Callback(hObject, eventdata, handles)
1379
1380%-------------------------------------------------------------------
1381% switch file index scanning options scan_i and scan_j in an exclusive way
1382function scan_j_Callback(hObject, eventdata, handles)
1383%-------------------------------------------------------------------
1384if get(handles.scan_j,'Value')==1
1385    set(handles.scan_j,'BackgroundColor',[1 1 0])
1386    set(handles.scan_i,'Value',0)
1387    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1388    NomType=get(handles.FileIndex,'UserData');
1389    switch NomType
1390    case {'_i_j1-j2','#_ab','%3dab'},% pair with j index
1391        set(handles.fix_pair,'Visible','on')% option fixed pair on/off made visible (choice of avaible pair with buttons + and - if ='off')
1392    otherwise
1393        set(handles.fix_pair,'Visible','off')
1394    end
1395else
1396    set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
1397    set(handles.scan_i,'Value',1)
1398    set(handles.scan_i,'BackgroundColor',[1 1 0])
1399    set(handles.fix_pair,'Visible','off')
1400end
1401
1402%-------------------------------------------------------------------
1403function i1_Callback(hObject, eventdata, handles)
1404%-------------------------------------------------------------------
1405set(handles.i1,'BackgroundColor',[0.7 0.7 0.7])
1406NomType=get(handles.FileIndex,'UserData');
1407num1=stra2num(get(handles.i1,'String'));
1408num2=stra2num(get(handles.i2,'String'));
1409num_a=stra2num(get(handles.j1,'String'));
1410num_b=stra2num(get(handles.j2,'String'));
1411indices=name_generator('',num1,num_a,'',NomType,1,num2,num_b,'');
1412set(handles.FileIndex,'String',indices)
1413set(handles.FileIndex,'BackgroundColor',[0.7 0.7 0.7])
1414if get(handles.SubField,'Value')==1
1415    NomType_1=get(handles.FileIndex_1,'String');
1416     FileExt_1=get(handles.FileExt_1,'String');
1417    [P,F,str1,str2,str_a,str_b,Ext,NomType_1]=name2display(['xx' NomType_1 FileExt_1]);
1418     indices=name_generator('',num1,num_a,'',NomType_1,1,num2,num_b,'');
1419     set(handles.FileIndex_1,'String',indices)
1420     set(handles.FileIndex_1,'BackgroundColor',[0.7 0.7 0.7])
1421end
1422%Run0_Callback(hObject, eventdata, handles)
1423
1424%-------------------------------------------------------------------
1425function i2_Callback(hObject, eventdata, handles)
1426set(handles.i2,'BackgroundColor',[0.7 0.7 0.7])
1427i1_Callback(hObject, eventdata, handles)
1428%-------------------------------------------------------------------
1429
1430%-------------------------------------------------------------------
1431function j1_Callback(hObject, eventdata, handles)
1432set(handles.j1,'BackgroundColor',[0.7 0.7 0.7])
1433i1_Callback(hObject, eventdata, handles)
1434%-------------------------------------------------------------------
1435
1436%-------------------------------------------------------------------
1437function j2_Callback(hObject, eventdata, handles)
1438set(handles.j2,'BackgroundColor',[0.7 0.7 0.7])
1439i1_Callback(hObject, eventdata, handles)
1440%-------------------------------------------------------------------
1441
1442%-------------------------------------------------------------------
1443function slices_Callback(hObject, eventdata, handles)
1444%-------------------------------------------------------------------
1445if get(handles.slices,'Value')==1
1446    set(handles.slices,'BackgroundColor',[1 1 0])
1447    set(handles.nb_slice,'Visible','on')
1448    set(handles.z_text,'Visible','on')
1449    set(handles.z_index,'Visible','on')
1450    nb_slice_Callback(hObject, eventdata, handles)
1451else
1452    set(handles.nb_slice,'Visible','off')
1453    set(handles.slices,'BackgroundColor',[0.7 0.7 0.7])
1454    set(handles.z_text,'Visible','off')
1455    set(handles.z_index,'Visible','off')
1456    set(handles.masklevel,'Value',1)
1457    set(handles.masklevel,'String',{'1'})
1458end
1459
1460%-------------------------------------------------------------------
1461function nb_slice_Callback(hObject, eventdata, handles)
1462%-------------------------------------------------------------------
1463nb_slice_str=get(handles.nb_slice,'String');
1464if isequal(nb_slice_str,'volume')
1465    num=stra2num(get(handles.j1,'String'));
1466    last_j=get(handles.last_j,'String');
1467    nbslice=str2double(last_j{1});
1468else
1469    num=str2double(get(handles.i1,'String'));
1470    nbslice=str2double(get(handles.nb_slice,'String'));
1471end
1472z=mod(num-1,nbslice)+1;
1473set(handles.z_index,'String',num2str(z))
1474for ilist=1:nbslice
1475    list_index{ilist,1}=num2str(ilist);
1476end   
1477set(handles.masklevel,'String',list_index)
1478set(handles.masklevel,'Value',z)
1479
1480%------------------------------------------------------------------------
1481% --- Executes on button press in view_xml.
1482function view_xml_Callback(hObject, eventdata, handles)
1483%------------------------------------------------------------------------
1484[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles);
1485option=get(handles.view_xml,'String');
1486if isequal(option,'view .xml')
1487    FileXml=[FileBase '.xml'];
1488    heditxml=editxml(FileXml);
1489end
1490
1491%------------------------------------------------------------------------
1492% --- Executes on button press in mask_test.
1493function mask_test_Callback(hObject, eventdata, handles)
1494%------------------------------------------------------------------------
1495%case of view mask selection
1496if isequal(get(handles.mask_test,'Value'),1)
1497    [FF,RootPath,FileBase]=read_file_boxes(handles);
1498    num_i1=stra2num(get(handles.i1,'String'));
1499    num_j1=stra2num(get(handles.j1,'String'));
1500    currentdir=pwd; 
1501    cd(RootPath);
1502    maskfiles=dir('*_*mask_*.png');%look for a mask file
1503    cd(currentdir);%come back to the working directory
1504    mdetect=0;
1505    if ~isempty(maskfiles)
1506        for ilist=1:length(maskfiles)
1507            maskname=maskfiles(ilist).name;% take the first mask file in the list
1508            [rr,ff,x1,x2,xa,xb,xext,Mask_NomType{ilist}]=name2display(maskname);
1509            if ~strcmp(Mask_NomType{ilist},Mask_NomType{1})
1510                msgbox_uvmat('ERROR',['inconsistent mask types ' Mask_NomType{1} Mask_NomType{ilist } ' coexist in the current image directory'])
1511                return
1512            end
1513            [Path2,Name,ext]=fileparts(maskname);
1514            Namedouble=double(Name);
1515            val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1516            ind_mask=findstr('mask',Name);
1517            i=ind_mask-1;
1518            while val(i)==0 && i>0
1519                i=i-1;
1520            end
1521            nbmask_str=str2num(Name(i+1:ind_mask-1));
1522            if ~isempty(nbmask_str)
1523                nbslice(ilist)=nbmask_str; % number of different masks (slices)
1524            end
1525        end
1526        if isequal(min(nbslice),max(nbslice))
1527            nbslice=nbslice(1);
1528        else
1529            msgbox_uvmat('ERROR','several inconsistent mask sets coexist in the current image directory')
1530            return
1531        end
1532        if ~isempty(nbslice) && Name(i)=='_'
1533            Mask.Base=[FileBase Name(i:ind_mask+3)];
1534            Mask.NbSlice=nbslice;
1535            num_i1=mod(num_i1-1,nbslice)+1;
1536            Mask.NomType=Mask_NomType{1};
1537            [maskname,mdetect]=name_generator(Mask.Base,num_i1,num_j1,'.png',Mask.NomType);%
1538            mdetect=exist(maskname,'file');
1539            if mdetect
1540                set(handles.nb_slice,'String',Name(i+1:ind_mask-1));
1541                set(handles.nb_slice,'BackgroundColor',[1 1 0])
1542                set(handles.mask_test,'UserData',Mask);
1543                set(handles.mask_test,'BackgroundColor',[1 1 0])
1544                if nbslice > 1
1545                    set(handles.slices,'value',1)
1546                    slices_Callback(hObject, eventdata, handles)
1547                end
1548            end
1549        end
1550    end
1551    errormsg=[];%default
1552    if mdetect==0
1553        [FileName, PathName, filterindex] = uigetfile( ...
1554            {'*.png', ' (*.png)';
1555            '*.png',  '.png files '; ...
1556            '*.*', 'All Files (*.*)'}, ...
1557            'Pick a mask file *.png',FileBase);
1558        maskname=fullfile(PathName,FileName);
1559        if ~exist(maskname,'file')
1560            errormsg='no file browsed';
1561        end
1562        [RootDir,RootFile,x1,x2,xa,xb,xext,Mask.NomType]=name2display(maskname);
1563        Mask.Base=fullfile(RootDir,RootFile);
1564        Mask.NbSlice=1;
1565        set(handles.mask_test,'UserData',Mask);
1566        set(handles.mask_test,'BackgroundColor',[1 1 0])
1567    end
1568    if isempty(errormsg)
1569        errormsg=update_mask(handles,num_i1,num_j1);
1570    end
1571    if ~isempty(errormsg)
1572            set(handles.mask_test,'Value',0)
1573            set(handles.mask_test,'BackgroundColor',[0.7 0.7 0.7])
1574     end
1575else
1576    MaskData=get(handles.mask_test,'UserData');
1577    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1578          delete(MaskData.maskhandle)   
1579    end
1580    set(handles.mask_test,'UserData',[])   
1581    %huvmat=get(handles.mask_test,'parent');
1582    UvData=get(handles.uvmat,'UserData');
1583    if isfield(UvData,'MaskName')
1584        UvData=rmfield(UvData,'MaskName');
1585        set(handles.uvmat,'UserData',UvData)
1586    end
1587    set(handles.mask_test,'BackgroundColor',[0.7 0.7 0.7])
1588end
1589
1590%-------------------------------------------------------------------
1591function errormsg=update_mask(handles,num_i1,num_j1)
1592%-------------------------------------------------------------------
1593errormsg=[];%default
1594MaskData=get(handles.mask_test,'UserData');
1595if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1596    uistack(MaskData.maskhandle,'top');
1597end
1598num_i1_mask=mod(num_i1-1,MaskData.NbSlice)+1;
1599MaskName=name_generator(MaskData.Base,num_i1_mask,num_j1,'.png',MaskData.NomType);
1600huvmat=get(handles.mask_test,'parent');
1601UvData=get(huvmat,'UserData');
1602
1603%update mask image if the mask is new
1604if ~ (isfield(UvData,'MaskName') && isequal(UvData.MaskName,MaskName))
1605    UvData.MaskName=MaskName; %update the recorded name on UvData
1606    set(huvmat,'UserData',UvData);
1607    if ~exist(MaskName,'file')
1608        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1609            delete(MaskData.maskhandle)   
1610        end
1611    else
1612        %read mask image
1613        Mask.AName='image';
1614        Mask.A=imread(MaskName);
1615        npxy=size(Mask.A);
1616        test_error=0;
1617        if length(npxy)>2
1618            errormsg=[MaskName ' is not a grey scale image'];
1619            return
1620        elseif ~isa(Mask.A,'uint8')
1621            errormsg=[MaskName ' is not a 8 bit grey level image'];
1622            return
1623        end
1624        Mask.AX=[0.5 npxy(2)-0.5];
1625        Mask.AY=[npxy(1)-0.5 0.5 ];
1626        Mask.CoordUnit='pixel';
1627        if isequal(get(handles.slices,'Value'),1)
1628           NbSlice=str2num(get(handles.nb_slice,'String'));
1629           num_i1=str2num(get(handles.i1,'String'));
1630           Mask.ZIndex=mod(num_i1-1,NbSlice)+1;
1631        end
1632        %px to phys or other transform on field
1633         menu_transform=get(handles.transform_fct,'String');
1634        choice_value=get(handles.transform_fct,'Value');
1635        transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1636        transform_list=get(handles.transform_fct,'UserData');
1637        transform=transform_list{choice_value};
1638        if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
1639            if isfield(UvData,'XmlData') && isfield(UvData.XmlData,'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
1640                Calib=UvData.XmlData.GeometryCalib;
1641                Mask=transform(Mask,UvData.XmlData);
1642            end
1643        end
1644        flagmask=Mask.A < 200;
1645       
1646        %make brown color image
1647        imflag(:,:,1)=0.9*flagmask;
1648        imflag(:,:,2)=0.7*flagmask;
1649        imflag(:,:,3)=zeros(size(flagmask));
1650       
1651        %update mask image
1652        hmask=[]; %default
1653        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1654            hmask=MaskData.maskhandle;
1655        end
1656        if ~isempty(hmask)
1657            set(hmask,'CData',imflag)   
1658            set(hmask,'AlphaData',flagmask*0.6)
1659            set(hmask,'XData',Mask.AX);
1660            set(hmask,'YData',Mask.AY);
1661%             uistack(hmask,'top')
1662        else
1663            axes(handles.axes3)
1664            hold on   
1665            MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*flagmask);
1666%             set(MaskData.maskhandle,'AlphaData',0.6*flagmask)
1667            set(handles.mask_test,'UserData',MaskData)
1668        end
1669    end
1670end
1671
1672
1673%-------------------------------------------------------------------
1674function MenuExportFigure_Callback(hObject, eventdata, handles)
1675%-------------------------------------------------------------------
1676huvmat=get(handles.MenuExport,'parent');
1677%UvData=get(huvmat,'UserData');
1678hfig=figure;
1679copyobj(handles.axes3,hfig);
1680map=colormap(handles.axes3);
1681colormap(map);%transmit the current colormap to the zoom fig
1682colorbar
1683
1684%-------------------------------------------------------------------
1685%-------------------------------------------------------------------
1686% III - MAIN REFRESH FUNCTIONS : 'FRAME PLOT'
1687%-------------------------------------------------------------------
1688
1689%-------------------------------------------------------------------
1690% --- Executes on button press in runplus: make one step forward and call
1691% --- run0. The step forward is along the fields series 1 or 2 depending on
1692% --- the scan_i and scan_j check box (exclusive each other)
1693function runplus_Callback(hObject, eventdata, handles)
1694%-------------------------------------------------------------------
1695set(handles.runplus,'BackgroundColor',[1 1 0])%paint the command button in yellow
1696drawnow
1697%TODO: introduce the option: increment ='*' to move to the next available view
1698increment=str2double(get(handles.increment_scan,'String')); %get the field increment d
1699if isnan(increment)
1700    set(handles.increment_scan,'String','1')%default value
1701    increment=1;
1702end
1703errormsg=runpm(hObject,eventdata,handles,increment);
1704if ~isempty(errormsg)
1705    msgbox_uvmat('ERROR',errormsg);
1706end
1707set(handles.runplus,'BackgroundColor',[1 0 0])%paint the command button back to red
1708
1709%-------------------------------------------------------------------
1710% --- Executes on button press in runmin: make one step backward and call
1711% --- run0. The step backward is along the fields series 1 or 2 depending on
1712% --- the scan_i and scan_j check box (exclusive each other)
1713function runmin_Callback(hObject, eventdata, handles)
1714%-------------------------------------------------------------------
1715set(handles.runmin,'BackgroundColor',[1 1 0])%paint the command button in yellow
1716drawnow
1717increment=-str2double(get(handles.increment_scan,'String')); %get the field increment d
1718if isnan(increment)
1719    set(handles.increment_scan,'String','1')%default value
1720    increment=1;
1721end
1722errormsg=runpm(hObject,eventdata,handles,increment);
1723if ~isempty(errormsg)
1724    msgbox_uvmat('ERROR',errormsg);
1725end
1726set(handles.runmin,'BackgroundColor',[1 0 0])%paint the command button back to red
1727
1728%-------------------------------------------------------------------
1729% -- Executes on button press in Movie: make a series of +> steps
1730function Movie_Callback(hObject, eventdata, handles)
1731%------------------------------------------------------------------
1732set(handles.Movie,'BackgroundColor',[1 1 0])%paint the command button in yellow
1733drawnow
1734increment=str2double(get(handles.increment_scan,'String')); %get the field increment d
1735if isnan(increment)
1736    set(handles.increment_scan,'String','1')%default value
1737    increment=1;
1738end
1739set(handles.STOP,'Visible','on')
1740set(handles.speed,'Visible','on')
1741set(handles.speed_txt,'Visible','on')
1742set(handles.Movie,'BusyAction','queue')
1743UvData=get(handles.uvmat,'UserData');
1744
1745while get(handles.speed,'Value')~=0 && isequal(get(handles.Movie,'BusyAction'),'queue') % enable STOP command
1746        errormsg=runpm(hObject,eventdata,handles,increment);
1747        if ~isempty(errormsg)
1748            set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1749            return
1750        end
1751        pause(1.02-get(handles.speed,'Value'))% wait for next image
1752end
1753if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1754    UvData.aviobj=close(UvData.aviobj);
1755   set(handles.uvmat,'UserData',UvData);
1756end
1757set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1758
1759%-------------------------------------------------------------------
1760% -- Executes on button press in Movie: make a series of <- steps
1761function MovieBackward_Callback(hObject, eventdata, handles)
1762%------------------------------------------------------------------
1763set(handles.MovieBackward,'BackgroundColor',[1 1 0])%paint the command button in yellow
1764drawnow
1765increment=-str2double(get(handles.increment_scan,'String')); %get the field increment d
1766if isnan(increment)
1767    set(handles.increment_scan,'String','1')%default value
1768    increment=1;
1769end
1770set(handles.STOP,'Visible','on')
1771set(handles.speed,'Visible','on')
1772set(handles.speed_txt,'Visible','on')
1773set(handles.MovieBackward,'BusyAction','queue')
1774UvData=get(handles.uvmat,'UserData');
1775
1776while get(handles.speed,'Value')~=0 && isequal(get(handles.MovieBackward,'BusyAction'),'queue') % enable STOP command
1777        errormsg=runpm(hObject,eventdata,handles,increment);
1778        if ~isempty(errormsg)
1779            set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1780            return
1781        end
1782        pause(1.02-get(handles.speed,'Value'))% wait for next image
1783end
1784if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1785    UvData.aviobj=close(UvData.aviobj);
1786   set(handles.uvmat,'UserData',UvData);
1787end
1788set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1789
1790%-------------------------------------------------------------------
1791function STOP_Callback(hObject, eventdata, handles)
1792%-------------------------------------------------------------------
1793set(handles.movie_pair,'BusyAction','Cancel')
1794set(handles.movie_pair,'value',0)
1795set(handles.Movie,'BusyAction','Cancel')
1796set(handles.MovieBackward,'BusyAction','Cancel')
1797set(handles.MenuExportMovie,'BusyAction','Cancel')
1798set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1799set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1800set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1801
1802%------------------------------------------------------------------
1803function errormsg=runpm(hObject,eventdata,handles,increment)
1804%------------------------------------------------------------------
1805%check for mï¿œovie pair status
1806movie_status=get(handles.movie_pair,'Value');
1807if isequal(movie_status,1)
1808    STOP_Callback(hObject, eventdata, handles)%interrupt movie pair if active
1809end
1810%read the data on the current input rootfile(s)
1811
1812[FileName,RootPath,filebase,FileIndices,FileExt,subdir]=read_file_boxes(handles);
1813NomType=get(handles.FileIndex,'UserData');
1814
1815num1=stra2num(get(handles.i1,'String'));
1816num2=stra2num(get(handles.i2,'String'));
1817num_a=stra2num(get(handles.j1,'String'));
1818num_b=stra2num(get(handles.j2,'String'));
1819
1820sub_value= get(handles.SubField,'Value');
1821if sub_value % a second input file has been entered
1822    [FileName_1,RootPath_1,filebase_1,FileIndices_1,FileExt_1,SubDir_1]=read_file_boxes_1(handles);
1823    [pp,ff,str1,str2,str_a,str_b]=name2display(FileIndices_1);
1824    num1_1=stra2num(str1);%current set of indices for the second field (may be set different than the main indices)
1825    num2_1=stra2num(str2);
1826    num_a_1=stra2num(str_a);
1827    num_b_1=stra2num(str_b);
1828    NomType_1=get(handles.FileIndex_1,'UserData');
1829else
1830    filename_1=[];
1831end   
1832
1833comp_input=get(handles.fix_pair,'Value');
1834
1835%case of scanning along the first direction (rootfile numbers)
1836if get(handles.scan_i,'Value')==1% case of scanning along index i   
1837     num1=num1+increment;
1838     num2=num2+increment;
1839     [filename,num1,num_a,num2,num_b]=name_generator(filebase,num1,num_a,FileExt,NomType,comp_input,num2,num_b,subdir);
1840     if sub_value% set the second field name and indices
1841        num1_1=num1_1+increment;
1842        num2_1=num2_1+increment;
1843        filename_1=name_generator(filebase_1,num1_1,num_a_1,FileExt_1,NomType_1,1,num2_1,num_b_1,SubDir_1);
1844     end   
1845else % case of scanning along index j (burst numbers)
1846    num_a=num_a+increment;
1847    num_b=num_b+increment;
1848    [filename,num1,num_a,num2,num_b]=name_generator(filebase,num1,num_a,FileExt,NomType,comp_input,num2,num_b,subdir);
1849    if sub_value
1850        num_a_1=num_a_1+increment;
1851        num_b_1=num_b_1+increment;
1852        filename_1=name_generator(filebase_1,num1_1,num_a_1,FileExt_1,NomType_1,1,num2_1,num_b_1,SubDir_1);
1853    end   
1854end
1855
1856% refresh plots
1857errormsg=refresh_field(handles,filename,filename_1,num1,num2,num_a,num_b);
1858if isempty(errormsg)  %update the index counters
1859    set(handles.i1,'String',num2stra(num1,NomType,1));
1860    if isequal(num2,num1)
1861         set(handles.i2,'String','');
1862    else
1863        set(handles.i2,'String',num2stra(num2,NomType,1));
1864    end
1865    set(handles.j1,'String',num2stra(num_a,NomType,2));
1866    if isequal(num_b,num_a)
1867         set(handles.j2,'String','');
1868    else
1869        set(handles.j2,'String',num2stra(num_b,NomType,2));
1870    end
1871    [indices]=name_generator('',num1,num_a,'',NomType,1,num2,num_b,'');
1872    set(handles.FileIndex,'String',indices);
1873    if ~isempty(filename_1)
1874         indices_1=name_generator('',num1_1,num_a_1,'',NomType_1,1,num2_1,num_b_1,'');
1875         set(handles.FileIndex_1,'String',indices_1);
1876    end
1877    if isequal(movie_status,1)
1878        set(handles.movie_pair,'Value',1)
1879        movie_pair_Callback(hObject, eventdata, handles); %reactivate moviepair if it was activated
1880    end
1881end
1882
1883
1884%-------------------------------------------------------
1885% --- Executes on button press in movie_pair: create an alternating movie with two view
1886%-------------------------------------------------------
1887function movie_pair_Callback(hObject, eventdata, handles)
1888status=get(handles.movie_pair,'value');
1889if isequal(status,0)
1890    set(handles.movie_pair,'BusyAction','Cancel')%stop movie pair if button is 'off'
1891    set(handles.i2,'String','')
1892    set(handles.j2,'String','')
1893    return
1894else
1895    set(handles.movie_pair,'BusyAction','queue')
1896end
1897%initialisation
1898set(handles.movie_pair,'BackgroundColor',[1 1 0])%paint the command button in yellow
1899drawnow
1900list_fields=get(handles.Fields,'String');% list menu fields
1901index_fields=get(handles.Fields,'Value');% selected string index
1902FieldName=list_fields{index_fields}; % selected field
1903UvData=get(handles.uvmat,'UserData');
1904if isequal(FieldName,'image')
1905    test_1=0;
1906    [ff,rr,filebase,xx,Ext,SubDir]=read_file_boxes(handles);
1907    NomType=get(handles.FileIndex,'UserData');
1908else
1909    list_fields=get(handles.Fields_1,'String');% list menu fields
1910    index_fields=get(handles.Fields_1,'Value');% selected string index
1911    FieldName=list_fields{index_fields}; % selected field
1912    if isequal(FieldName,'image')
1913        test_1=1;
1914        [ff,rr,filebase,xx,Ext,SubDir]=read_file_boxes_1(handles);
1915        NomType=get(handles.FileIndex_1,'UserData');
1916    else
1917        msgbox_uvmat('ERROR','an image or movie must be first introduced as input')
1918        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1919        return
1920    end
1921end
1922
1923num_i1=str2double(get(handles.i1,'String'));
1924num_j1=stra2num(get(handles.j1,'String'));
1925num_i2=str2double(get(handles.i2,'String'));
1926num_j2=stra2num(get(handles.j2,'String'));
1927if isnan(num_j2)
1928    if isempty(num_i2)   
1929        msgbox_uvmat('ERROR', 'a second image index i2 or j2 is needed to show the pair as a movie')
1930        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1931        return
1932    else
1933        num_j2=num_j1;%repeat the index i1 by default
1934    end
1935end
1936if isnan(num_i2)
1937    num_i2=num_i1;%repeat the index i1 by default
1938end
1939imaname_1=name_generator(filebase,num_i2,num_j2,Ext,NomType);
1940if ~exist(imaname_1,'file')
1941      msgbox_uvmat('ERROR',['second input open (-)  ' imaname_1 ' not found']);
1942      set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1943      return
1944end
1945
1946%read the second image
1947Field.AName='image';
1948if test_1
1949    Field_a=UvData.Field_1;
1950else
1951    Field_a=UvData.Field;
1952end
1953Field_b.AX=Field_a.AX;
1954Field_b.AY=Field_a.AY;
1955% z index
1956nbslice=str2double(get(handles.nb_slice,'String'));
1957if ~isempty(nbslice)
1958    Field_b.ZIndex=mod(num_i2-1,nbslice)+1;
1959end
1960Field_b.CoordUnit='pixel';
1961%determine the input file type
1962if (test_1 && isfield(UvData,'MovieObject_1'))||(~test_1 && isfield(UvData,'MovieObject'))
1963    FileType='movie';
1964elseif isequal(lower(Ext),'.avi')
1965    FileType='avi';
1966elseif isequal(lower(Ext),'.vol')
1967    FileType='vol';
1968else
1969   form=imformats(Ext(2:end));
1970   if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
1971       if isequal(NomType,'*');
1972           FileType='multimage';
1973       else
1974           FileType='image';
1975       end
1976   end
1977end
1978switch FileType
1979        case 'movie'
1980            if test_1
1981                Field_b.A=read(UvData.MovieObject_1,num_i2);
1982            else
1983                Field_b.A=read(UvData.MovieObject,num_i2);
1984            end
1985        case 'avi'
1986            mov=aviread(imaname_1,num_i2);
1987            Field_b.A=frame2im(mov(1));
1988        case 'vol'
1989            Field_b.A=imread(imaname_1);
1990        case 'multimage'
1991            Field_b.A=imread(imaname_1,num_i2);
1992        case 'image'
1993            Field_b.A=imread(imaname_1);
1994end
1995if get(handles.slices,'Value')
1996    Field.ZIndex=str2double(get(handles.z_index,'String'));
1997end
1998
1999%px to phys or other transform on field
2000menu_transform=get(handles.transform_fct,'String');
2001choice_value=get(handles.transform_fct,'Value');
2002transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
2003transform_list=get(handles.transform_fct,'UserData');
2004transform=transform_list{choice_value};
2005if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
2006    if test_1 && isfield(UvData,'XmlData_1') && isfield(UvData.XmlData_1,'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
2007        Field_a=transform(Field_a,UvData.XmlData_1);%the first field has been stored without transform
2008        Field_b=transform(Field_b,UvData.XmlData_1);
2009    elseif ~test_1 && isfield(UvData,'XmlData') && isfield(UvData.XmlData,'GeometryCalib')%use geometry calib
2010        Field_b=transform(Field_b,UvData.XmlData);
2011    end
2012end
2013
2014 % make movie until movie speed is set to 0 or STOP is activated
2015hima=findobj(handles.axes3,'Tag','ima');% %handles.axes3 =main plotting window (A GENERALISER)
2016set(handles.STOP,'Visible','on')
2017set(handles.speed,'Visible','on')
2018set(handles.speed_txt,'Visible','on')
2019while get(handles.speed,'Value')~=0 && isequal(get(handles.movie_pair,'BusyAction'),'queue')%isequal(get(handles.run0,'BusyAction'),'queue'); % enable STOP command
2020    % read and plot the series of images in non erase mode
2021    set(hima,'CData',Field_b.A);
2022    pause(1.02-get(handles.speed,'Value'));% wait for next image
2023    set(hima,'CData',Field_a.A);
2024    pause(1.02-get(handles.speed,'Value'));% wait for next image
2025end
2026set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
2027
2028%------------------------------------------------------------------------
2029% --- Executes on button press in run0.
2030function run0_Callback(hObject, eventdata, handles)
2031%------------------------------------------------------------------------
2032set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
2033drawnow
2034filename=read_file_boxes(handles);
2035
2036filename_1=[];%default
2037if get(handles.SubField,'Value')
2038    filename_1=read_file_boxes_1(handles);
2039end
2040num_i1=stra2num(get(handles.i1,'String'));
2041num_i2=stra2num(get(handles.i2,'String'));
2042num_j1=stra2num(get(handles.j1,'String'));
2043num_j2=stra2num(get(handles.j2,'String'));
2044errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2);
2045if ~isempty(errormsg)
2046      msgbox_uvmat('ERROR',errormsg);
2047else
2048    set(handles.i1,'BackgroundColor',[1 1 1])
2049    set(handles.i2,'BackgroundColor',[1 1 1])
2050    set(handles.j1,'BackgroundColor',[1 1 1])
2051    set(handles.j2,'BackgroundColor',[1 1 1])
2052    set(handles.FileIndex,'BackgroundColor',[1 1 1])
2053    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
2054end   
2055set(handles.run0,'BackgroundColor',[1 0 0])
2056
2057
2058%------------------------------------------------------------------------
2059% --- read the input files and refresh all the plots, including projection.
2060% OUTPUT:
2061%  errormsg: error message char string  =[] by default
2062% INPUT:
2063% filename: first input file (=[] in the absence of input file)
2064% filename_1: second input file (=[] in the asbsenc of secodn input file)
2065% num_i1,num_i2,num_j1,num_j2; frame indices
2066% Field: structure describing an optional input field (then replace the input file)
2067function errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2,Field)
2068%------------------------------------------------------------------------
2069
2070%% initialisation
2071abstime=[];
2072abstime_1=[];
2073dt=[];
2074if ~exist('Field','var')
2075    Field={};
2076end
2077UvData=get(handles.uvmat,'UserData');
2078if ishandle(handles.UVMAT_title) %remove title panel on uvmat
2079    delete(handles.UVMAT_title)
2080end
2081
2082%% determine the main input file information for action
2083FileType=[];%default
2084if ~exist(filename,'file')
2085    errormsg=['input file ' filename ' does not exist'];
2086    return
2087end
2088%Ext=get(handles.FileExt,'String');
2089NomType=get(handles.FileIndex,'UserData');
2090%update the z position index
2091nbslice_str=get(handles.nb_slice,'String');
2092if isequal(nbslice_str,'volume')%NOT USED
2093    z_index=num_j1;
2094    set(handles.z_index,'String',num2str(z_index))
2095else
2096    nbslice=str2num(nbslice_str);
2097    z_index=mod(num_i1-1,nbslice)+1;
2098    set(handles.z_index,'String',num2str(z_index))
2099end
2100% refresh menu for save_mask if relevant
2101masknumber=get(handles.masklevel,'String');
2102if length(masknumber)>=z_index
2103    set(handles.masklevel,'Value',z_index)
2104end
2105
2106%% read the first input field if a filename has been introduced
2107if ~isempty(filename)
2108    ObjectName=filename;
2109    FieldName=[];%default
2110    VelType=[];%default
2111    Ext=get(handles.FileExt,'String');
2112    if strcmp(Ext,'.nc')||strcmp(Ext,'.cdf')
2113        FileType='netcdf';
2114        list_fields=get(handles.Fields,'String');% list menu fields
2115        index_fields=get(handles.Fields,'Value');% selected string index
2116        FieldName= list_fields{index_fields}; % selected field
2117        if ~strcmp(FieldName,'get_field...')% read the field names on the interface get_field...
2118           VelType=setfield(handles);
2119        end
2120        if strcmp(FieldName,'velocity')
2121            list_code=get(handles.color_code,'String');% list menu fields
2122            index_code=get(handles.color_code,'Value');% selected string index
2123            if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2124                list_code=get(handles.col_vec,'String');% list menu fields
2125                index_code=get(handles.col_vec,'Value');% selected string index
2126                ParamIn.ColorVar= list_code{index_code}; % selected field
2127            end
2128        end
2129    elseif isfield(UvData,'MovieObject')
2130        ObjectName=UvData.MovieObject;
2131        FileType='movie';
2132    elseif isequal(lower(Ext),'.avi')
2133        FileType='avi';
2134    elseif isequal(lower(Ext),'.vol')
2135        FileType='vol';
2136        if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2137            ParamIn.Npy=UvData.XmlData.Npy;
2138            ParamIn.Npx=UvData.XmlData.Npx;
2139        else
2140            errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2141            return
2142        end
2143    else
2144       form=imformats(Ext(2:end));
2145       if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2146           if isequal(NomType,'*');
2147               FileType='multimage';
2148           else
2149               FileType='image';
2150           end
2151       end
2152    end
2153    ParamIn.FieldName=FieldName;
2154    ParamIn.VelType=VelType;
2155    ParamIn.GUIName='get_field';
2156    [Field{1},ParamOut,errormsg] = read_field(ObjectName,FileType,ParamIn,num_i1);
2157    if ~isempty(errormsg)
2158        errormsg=['error in reading ' filename ': ' errormsg];
2159        return
2160    end
2161    if isfield(ParamOut,'Npx')&& isfield(ParamOut,'Npy')
2162        set(handles.npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2163        set(handles.npy,'String',num2str(ParamOut.Npy));
2164    end
2165end
2166
2167%% choose a second field if Subfield option is 'on', and if the field has changed
2168VelType_1=[];%default
2169FieldName_1=[];
2170ParamOut_1=[];
2171if ~isempty(filename_1)
2172    if ~exist(filename_1,'file')
2173        errormsg=['second file ' filename_1 ' does not exist'];
2174        return
2175    else
2176        Name=filename_1;
2177        FieldName_1=[];%default
2178        VelType_1=[];%default
2179        Ext_1=get(handles.FileExt_1,'String');
2180        NomType_1=get(handles.FileIndex_1,'UserData');
2181        if isequal(Ext_1,'.nc')||isequal(Ext_1,'.cdf')
2182            FileType_1='netcdf';
2183        elseif isfield(UvData,'MovieObject_1')
2184            Name=UvData.MovieObject_1;
2185            FileType_1='movie';
2186        elseif isequal(lower(Ext_1),'.avi')
2187            FileType_1='avi';
2188        elseif isequal(lower(Ext_1),'.vol')
2189            FileType_1='vol';
2190            if isfield(UvData.XmlData_1,'Npy') && isfield(UvData.XmlData_1,'Npx')
2191                ParamIn.Npy=UvData.XmlData_1.Npy;
2192                ParamIn.Npx=UvData.XmlData_1.Npx;
2193            else
2194                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2195                return
2196            end
2197        else
2198           form=imformats(Ext_1(2:end));
2199           if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2200               if isequal(NomType_1,'*');
2201                   FileType_1='multimage';
2202               else
2203                   FileType_1='image';
2204               end
2205           end
2206        end
2207        if strcmp(FileType_1,'netcdf')
2208            list_fields=get(handles.Fields_1,'String');% list menu fields
2209            index_fields=get(handles.Fields_1,'Value');% selected string index
2210            FieldName_1= list_fields{index_fields}; % selected field
2211            if ~isequal(FieldName_1,'get_field...')% read the field names on the interface get_field...
2212                VelType_1=setfield_1(handles);
2213            end
2214            if strcmp(VelType_1,'*')% free veltype choice
2215                VelType_1=[];
2216            elseif strcmp(VelType_1,'"')% veltype the same as for the first field
2217                if isempty(VelType)
2218                    VelType_1=[];
2219                else
2220                    VelType_1=VelType;
2221                end
2222            end
2223            if strcmp(FieldName_1,'velocity')
2224                list_code=get(handles.color_code,'String');% list menu fields
2225                index_code=get(handles.color_code,'Value');% selected string index
2226                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2227                    list_code=get(handles.col_vec,'String');% list menu fields
2228                    index_code=get(handles.col_vec,'Value');% selected string index
2229                    ParamIn.ColorVar= list_code{index_code}; % selected field
2230                end
2231            end
2232        end
2233        test_keepdata_1=0;% test for keeping the previous stored data if the input files are unchanged
2234        if ~isequal(NomType_1,'*')%in case of a series of files (not avi movie)
2235            if isfield(UvData,'filename_1')&& isfield(UvData,'VelType_1') && isfield(UvData,'FieldName_1')
2236                test_keepdata_1= strcmp(filename_1,UvData.filename_1) && strcmp(VelType_1,UvData.VelType_1) && strcmp(FieldName_1,UvData.FieldName_1);
2237            end
2238        end
2239        if test_keepdata_1
2240            Field{2}=UvData.Field_1;
2241        else
2242            ParamIn.FieldName=FieldName_1;
2243            ParamIn.VelType=VelType_1;
2244            ParamIn.GUIName='get_field_1';
2245            [Field{2},ParamOut_1,errormsg] = read_field(Name,FileType_1,ParamIn,num_i1);
2246            if ~isempty(errormsg)
2247                errormsg=['error in reading ' filename_1 ': ' errormsg];
2248                return
2249            end
2250            UvData.Field_1=Field{2}; %store the second field for possible use at next RUN
2251        end
2252    end
2253end
2254
2255%% update uvmat interface
2256if isfield(ParamOut,'Npx')
2257    set(handles.npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2258    set(handles.npy,'String',num2str(ParamOut.Npy));
2259elseif isfield(ParamOut_1,'Npx')
2260    set(handles.npx,'String',num2str(ParamOut_1.Npx));% display image size on the interface
2261    set(handles.npy,'String',num2str(ParamOut_1.Npy));
2262end
2263
2264%% update the display buttons for the first velocity type (first menuline)
2265veltype_handles=[handles.civ1 handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2];
2266if ~isequal(FileType,'netcdf')|| isequal(FieldName,'get_field...')
2267%     reset_vel_type(veltype_handles)
2268    set(veltype_handles,'Visible','off')
2269else% if isempty(ParamOut.VelType) && ~isequal(FieldName,'get_field...')
2270    set_veltype_display(veltype_handles,ParamOut.CivStage)%update the display of available velocity types for the first field
2271    if isempty(ParamOut.VelType)
2272        reset_vel_type(veltype_handles)
2273    else
2274        handle1=eval(['handles.' ParamOut.VelType]);
2275        reset_vel_type(veltype_handles,handle1)
2276    end
2277end
2278field_index=strcmp(ParamOut.FieldName,ParamOut.FieldList);
2279set(handles.Fields,'String',ParamOut.FieldList); %update the field menu
2280set(handles.Fields,'Value',find(field_index,1))
2281
2282%% update the display buttons for the second velocity type (second menuline)
2283if ~isempty(filename_1)
2284    veltype_handles_1=[handles.civ1_1 handles.interp1_1 handles.filter1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1];
2285    if ~isequal(FileType_1,'netcdf')|| isequal(FieldName_1,'get_field...')
2286        set(veltype_handles_1,'Visible','off')
2287        %reset_vel_type(veltype_handles_1)
2288    else %if isempty(VelType_1) && ~isequal(FieldName_1,'get_field...')
2289        set_veltype_display(veltype_handles_1,ParamOut_1.CivStage)%update the display of available velocity types for the first field
2290        if isempty(ParamOut_1.VelType)
2291            reset_vel_type(veltype_handles_1)
2292        else
2293            handle1=eval(['handles.' ParamOut_1.VelType '_1']);
2294            reset_vel_type(veltype_handles_1,handle1)
2295        end
2296    end
2297    field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
2298    set(handles.Fields_1,'String',ParamOut_1.FieldList); %update the field menu
2299    set(handles.Fields_1,'Value',find(field_index,1))
2300end
2301
2302%% introduce w as background image by default for a new series (only for nbdim=2)
2303if ~isfield(UvData,'NewSeries')
2304    UvData.NewSeries=1;
2305end
2306%put W as background image by default if NbDim=2:
2307if  UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W) && ~isequal(Field{1}.NbDim,3);
2308        set(handles.SubField,'Value',1);
2309        %menu=update_menu(handles.Fields_1,'w');%update the menu for the background scalar nd set the choice to 'w'
2310        set(handles.RootPath_1,'String','"')
2311        set(handles.RootFile_1,'String','"')
2312        set(handles.SubDir_1,'String','"');
2313        [indices]=name_generator('',num_i1,num_j1,'',NomType,1,num_i2,num_j2,'');
2314        set(handles.FileIndex_1,'String',indices)
2315        set(handles.FileExt_1,'String','"');
2316        set(handles.Fields_1,'Visible','on');
2317        set(handles.Fields_1,'Visible','on');
2318        set(handles.RootPath_1,'Visible','on')
2319        set(handles.RootFile_1,'Visible','on')
2320        set(handles.SubDir_1,'Visible','on');
2321        set(handles.FileIndex_1,'Visible','on');
2322        set(handles.FileExt_1,'Visible','on');
2323        set(handles.Fields_1,'Visible','on');
2324        Field{1}.AName='w';
2325end           
2326
2327%% store the current open names, fields and vel types in uvmat interface
2328UvData.filename_1=filename_1;
2329UvData.VelType_1=[];%default
2330UvData.FieldName_1=[];
2331if isfield(ParamOut_1,VelType)
2332    UvData.VelType_1=ParamOut_1.VelType;
2333end
2334if isfield(ParamOut_1,FieldName)
2335    UvData.FieldName_1=ParamOut_1.FieldName;
2336end
2337
2338%% apply coordinate transform or other user fct
2339XmlData=[];%default
2340if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority
2341    XmlData=UvData.XmlData;
2342end
2343XmlData_1=[];%default
2344if isfield(UvData,'XmlData_1')
2345   XmlData_1=UvData.XmlData_1;
2346end
2347% menu_transform=get(handles.transform_fct,'String');
2348choice_value=get(handles.transform_fct,'Value');
2349transform_list=get(handles.transform_fct,'UserData');
2350transform=transform_list{choice_value};%selected function handles
2351% z index
2352if ~isempty(filename)
2353    Field{1}.ZIndex=z_index;
2354end
2355%px to phys or other transform on field
2356if ~isempty(transform)
2357    if length(Field)>=2
2358        Field{2}.ZIndex=z_index;
2359        [Field{1},Field{2}]=transform(Field{1},XmlData,Field{2},XmlData_1);
2360        if isempty(Field{2})
2361            Field(2)=[];
2362        end
2363    else
2364        Field{1}=transform(Field{1},XmlData);
2365    end
2366end
2367
2368%% calculate scalar
2369if isequal(FileType,'netcdf') && ~isequal(ParamOut.CivStage,0)%&&~isempty(FieldName)%
2370    Field{1}=calc_field([{ParamOut.FieldName} {ParamOut.ColorVar}],Field{1});
2371end
2372if length(Field)==2 && ~test_keepdata_1 && isequal(FileType_1,'netcdf') && ~isequal(ParamOut_1.FieldName,'get_field...')%&&~isempty(FieldName_1)
2373    Field{2}=calc_field([{ParamOut_1.FieldName} {ParamOut_1.ColorVar}],Field{2});
2374end
2375
2376%% combine the two input fields (e.g. substract velocity fields)
2377if numel(Field)==2
2378   UvData.Field=sub_field(Field{1},Field{2}); 
2379else
2380   UvData.Field=Field{1};
2381end
2382
2383%% get bounds and mesh (needed for mouse action and to open set_object)
2384test_x=0;
2385test_z=0;% test for unstructured z coordinate
2386[UvData.Field,errormsg]=check_field_structure(UvData.Field);
2387if ~isempty(errormsg)
2388    errormsg=['error in uvmat/refresh_field/check_field_structure: ' errormsg];
2389    return
2390end
2391[CellVarIndex,NbDim,VarType,errormsg]=find_field_indices(UvData.Field);
2392if ~isempty(errormsg)
2393    errormsg=['error in uvmat/refresh_field/find_field_indices: ' errormsg];
2394    return
2395end
2396[NbDim,imax]=max(NbDim);
2397if ~isempty(VarType{imax}.coord_x)  && ~isempty(VarType{imax}.coord_y)    %unstructured coordinates
2398    XName=UvData.Field.ListVarName{VarType{imax}.coord_x};
2399    YName=UvData.Field.ListVarName{VarType{imax}.coord_y};
2400    eval(['nbvec=length(UvData.Field.' XName ');'])%nbre of measurement points (e.g. vectors)
2401    test_x=1;%test for unstructured coordinates
2402elseif VarType{imax}.coord(NbDim)>0 %structured coordinate 
2403    XName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim)};
2404    if NbDim>1
2405        YName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim-1)}; %structured coordinates
2406    end
2407end
2408if NbDim==3
2409    ZName=UvData.Field.ListVarName{VarType{imax}.coord(1)};%structured coordinates in 3D
2410    eval(['ZMax=max(UvData.Field.' ZName ');'])
2411    eval(['ZMin=min(UvData.Field.' ZName ');'])
2412    test_z=1;
2413    if isequal(ZMin,ZMax)%no z dependency
2414        NbDim=2;
2415        test_z=0;
2416    end
2417end
2418if exist('XName','var')
2419eval(['XMax=max(UvData.Field.' XName ');'])
2420eval(['XMin=min(UvData.Field.' XName ');'])
2421UvData.Field.NbDim=NbDim;
2422UvData.Field.XMax=XMax;
2423UvData.Field.XMin=XMin;
2424if NbDim >1
2425    eval(['YMax=max(UvData.Field.' YName ');'])
2426    eval(['YMin=min(UvData.Field.' YName ');'])
2427    UvData.Field.YMax=YMax;
2428    UvData.Field.YMin=YMin;
2429end
2430eval(['nbvec=length(UvData.Field.' XName ');'])
2431if test_x %unstructured coordinates
2432    if test_z
2433        UvData.Field.Mesh=((XMax-XMin)*(YMax-YMin)*(ZMax-ZMin))/nbvec;% volume per vector
2434        UvData.Field.Mesh=(UvData.Field.Mesh)^(1/3);
2435    else
2436        UvData.Field.Mesh=sqrt((XMax-XMin)*(YMax-YMin)/nbvec);%2D
2437    end
2438else
2439    VarIndex=CellVarIndex{imax}; % list of variable indices
2440    DimIndex=UvData.Field.VarDimIndex{VarIndex(1)}; %list of dim indices for the variable
2441    nbpoints_x=UvData.Field.DimValue(DimIndex(NbDim));
2442    DX=(XMax-XMin)/(nbpoints_x-1);
2443    if NbDim >1
2444        nbpoints_y=UvData.Field.DimValue(DimIndex(NbDim-1));
2445        DY=(YMax-YMin)/(nbpoints_y-1);
2446    end
2447    if NbDim==3
2448        nbpoints_z=UvData.Field.DimValue(DimIndex(1));
2449        DZ=(ZMax-ZMin)/(nbpoints_z-1);
2450        UvData.Field.Mesh=sqrt(DX*DY*DZ);
2451        UvData.Field.ZMax=ZMax;
2452        UvData.Field.ZMin=ZMin;
2453    else
2454        UvData.Field.Mesh=sqrt(DX*DY);
2455    end
2456end
2457end
2458
2459%% 3D case (menuvolume)
2460if NbDim==3% && UvData.NewSeries
2461    test_set_object=1;
2462    hset_object=findobj(allchild(0),'tag','set_object');% look for the set_object GUI
2463    ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
2464    ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
2465    if ~isempty(hset_object) %if set_object is detected
2466%         hhset_object=guidata(hset_object);
2467% %         ZBounds_old(1)=get(hhset_object.z_slider,'Min');
2468% %         ZBounds_old(2)=get(hhset_object.z_slider,'Max');
2469% %         if isequal(ZBounds_old,ZBounds)
2470%             test_set_object=0;% do not refresh the GUI set_object
2471%         else
2472            delete(hset_object);% delete the GUI set_object if it does not fit
2473%         end
2474    end
2475    if test_set_object% reinitiate the GUI set_object
2476        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
2477        UvData.Object{1}.Style='plane';%main plotting plane
2478        UvData.Object{1}.ProjMode='projection';%main plotting plane
2479        UvData.Object{1}.DisplayHandle_uvmat=[]; %plane not visible in uvmat
2480        UvData.Object{1}.NbDim=NbDim;%test for 3D objects
2481        UvData.Object{1}.RangeZ=UvData.Field.Mesh;%main plotting plane
2482        UvData.Object{1}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen
2483        UvData.Object{1}.Phi=0;
2484        UvData.Object{1}.Theta=0;
2485        UvData.Object{1}.Psi=0;
2486        UvData.Object{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR
2487        PlotHandles=get_plot_handles(handles);
2488        UvData.Object{1}.Name='1-PLANE';
2489        UvData.Object{1}.enable_plot=1;
2490        set_object(UvData.Object{1},PlotHandles,ZBounds);
2491        set(handles.list_object_1,'Value',1);
2492        set(handles.list_object_1,'String',{'1-PLANE'});
2493        set(handles.edit_object,'Value',1)% put the plane in edit mode to enable the z cursor
2494        edit_object_Callback([],[], handles)
2495    end
2496    %multilevel case (single menuplane in a 3D space)
2497elseif isfield(UvData,'Z')
2498    if isfield(UvData,'CoordType')&& isequal(UvData.CoordType,'phys') && isfield(UvData,'XmlData')
2499        XmlData=UvData.XmlData;
2500        if isfield(XmlData,'PlanePos')
2501            UvData.Object{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:);
2502        end
2503        if isfield(XmlData,'PlaneAngle')
2504            siz=size(XmlData.PlaneAngle);
2505            indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning)
2506            UvData.Object{1}.Phi=XmlData.PlaneAngle(indangle,1);
2507            UvData.Object{1}.Theta=XmlData.PlaneAngle(indangle,2);
2508            UvData.Object{1}.Psi=XmlData.PlaneAngle(indangle,3);
2509        end
2510    elseif isfield(UvData,'ZIndex')
2511        UvData.Object{1}.ZObject=UvData.ZIndex;
2512    end
2513else
2514    % create a default projection menuplane
2515    %UvData.Object{1}.Style='none';%main plotting plane
2516    UvData.Object{1}.ProjMode='projection';%main plotting plane
2517    UvData.Object{1}.DisplayHandle_uvmat=[]; %plane not visible in uvmat
2518    set(handles.list_object_1,'Value',1);
2519    set(handles.list_object_1,'String',{''});
2520end
2521if ~isfield(UvData.Object{1},'plotaxes')
2522    UvData.Object{1}.plotaxes=handles.axes3;%default plotting axis
2523end
2524testnewseries=UvData.NewSeries;
2525UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback)
2526set(handles.uvmat,'UserData',UvData)
2527
2528%% reset the min and max of scalar if only the mask is displayed(TODO: check the need)
2529if isfield(UvData,'Mask')&& ~isfield(UvData,'A')
2530    set(handles.MinA,'String','0')
2531    set(handles.MaxA,'String','255')
2532end
2533
2534%% Plot the projections on the selected  projection objects
2535
2536% main projection object (uvmat display)
2537IndexObj(1)=get(handles.list_object_1,'Value');%selected projection object for main view
2538if IndexObj(1)> numel(UvData.Object)
2539    IndexObj(1)=1;%select the first object if the selected one does not exist
2540    set(handles.list_object_1,'Value',1)
2541end
2542plot_handles{1}=handles;
2543haxes(1)=handles.axes3;
2544PlotParam{1}=read_plot_param(handles);%read plotting parameters on the uvmat interfac
2545keeplim(1)=get(handles.FixLimits,'Value');% test for fixed graph limits
2546PosColorbar{1}=UvData.OpenParam.PosColorbar;%prescribe the colorbar position on the uvmat interface
2547
2548% second projection object (view_field display)
2549IndexObj_2=get(handles.list_object_2,'Value');%selected projection object for the second view
2550if isequal(get(handles.list_object_2,'Visible'),'on') && IndexObj_2 <= numel(UvData.Object)&& ~isempty(UvData.Object{IndexObj_2})
2551    IndexObj(2)=IndexObj_2;
2552    view_field_handle=findobj(allchild(0),'tag','view_field');%handles of the view_field GUI
2553    if ~isempty(view_field_handle)
2554        plot_handles{2}=guidata(view_field_handle);
2555        haxes(2)=plot_handles{2}.axes3;
2556        PlotParam{2}=read_plot_param(plot_handles{2});%read plotting parameters on the uvmat interface
2557        keeplim(2)=get(plot_handles{2}.FixLimits,'Value');
2558        PosColorbar{2}='*'; %TODO: deal with colorbar position on view_field
2559    end
2560end
2561
2562%loop on the projection objects: one or two
2563for imap=1:numel(IndexObj)
2564    iobj=IndexObj(imap);   
2565    [ObjectData,errormsg]=proj_field(UvData.Field,UvData.Object{iobj});% project field on the object
2566    if testnewseries && isfield(ObjectData,'CoordUnit')
2567        PlotParam{imap}=rmfield(PlotParam{imap},'FixEqual'); %set FixEqual to depend on the field (=1 if Data.CoordUnit=1 in plot_field)
2568    end
2569    if ~isempty(errormsg)
2570        return
2571    end
2572    %use of mask (TODO: check)
2573    if isfield(ObjectData,'NbDim') && isequal(ObjectData.NbDim,2) && isfield(ObjectData,'Mask') && isfield(ObjectData,'A')
2574        flag_mask=double(ObjectData.Mask>200);%=0 for masked regions
2575        AX=ObjectData.AX;%x coordiantes for the scalar field
2576        AY=ObjectData.AY;%y coordinates for the scalar field
2577        MaskX=ObjectData.MaskX;%x coordiantes for the mask
2578        MaskY=ObjectData.MaskY;%y coordiantes for the mask
2579        if ~isequal(MaskX,AX)||~isequal(MaskY,AY)
2580            nxy=size(flag_mask);
2581            sizpx=(ObjectData.MaskX(end)-ObjectData.MaskX(1))/(nxy(2)-1);%size of a mask pixel
2582            sizpy=(ObjectData.MaskY(1)-ObjectData.MaskY(end))/(nxy(1)-1);
2583            x_mask=ObjectData.MaskX(1):sizpx:ObjectData.MaskX(end); % pixel x coordinates for image display
2584            y_mask=ObjectData.MaskY(1):-sizpy:ObjectData.MaskY(end);% pixel x coordinates for image display
2585            %project on the positions of the scalar
2586            npxy=size(ObjectData.A);
2587            dxy(1)=(ObjectData.AY(end)-ObjectData.AY(1))/(npxy(1)-1);%grid mesh in y
2588            dxy(2)=(ObjectData.AX(end)-ObjectData.AX(1))/(npxy(2)-1);%grid mesh in x
2589            xi=ObjectData.AX(1):dxy(2):ObjectData.AX(end);
2590            yi=ObjectData.AY(1):dxy(1):ObjectData.AY(end);
2591            [XI,YI]=meshgrid(xi,yi);% creates the matrix of regular coordinates
2592            flag_mask = interp2(x_mask,y_mask,flag_mask,XI,YI);
2593        end
2594        AClass=class(ObjectData.A);
2595        ObjectData.A=flag_mask.*double(ObjectData.A);
2596        ObjectData.A=feval(AClass,ObjectData.A);
2597        ind_off=[];
2598        if isfield(ObjectData,'ListVarName')
2599            for ilist=1:length(ObjectData.ListVarName)
2600                if isequal(ObjectData.ListVarName{ilist},'Mask')||isequal(ObjectData.ListVarName{ilist},'MaskX')||isequal(ObjectData.ListVarName{ilist},'MaskY')
2601                    ind_off=[ind_off ilist];
2602                end
2603            end
2604            ObjectData.ListVarName(ind_off)=[];
2605            ObjectData.VarDimIndex(ind_off)=[];
2606            ind_off=[];
2607            for ilist=1:length(ObjectData.ListDimName)
2608                if isequal(ObjectData.ListDimName{ilist},'MaskX') || isequal(ObjectData.ListDimName{ilist},'MaskY')
2609                    ind_off=[ind_off ilist];
2610                end
2611            end
2612            ObjectData.ListDimName(ind_off)=[];
2613            ObjectData.DimValue(ind_off)=[];
2614        end
2615    end   
2616    if ~isempty(ObjectData)
2617        PlotType='none'; %default
2618        if imap==2 && isempty(view_field_handle)
2619            view_field(ObjectData)
2620        else
2621            [PlotType,PlotParamOut]=plot_field(ObjectData,haxes(imap),PlotParam{imap},PosColorbar{imap});
2622            write_plot_param(plot_handles{imap},PlotParamOut) %update the auto plot parameters
2623            if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
2624                ObjectData.Mesh=Field.Mesh; % gives an estimated mesh size (useful for mouse action on the plot)
2625            end
2626        end
2627        if isequal(PlotType,'none')
2628            hget_field=findobj(allchild(0),'name','get_field');
2629            if isempty(hget_field)
2630                get_field(filename)% the projected field cannot be automatically plotted: use get_field to specify the variablesdelete(hget_field)
2631            end
2632            errormsg='The field defined by get_field cannot be plotted';
2633            return
2634        end
2635    end
2636end
2637
2638%% update the mask
2639if isequal(get(handles.mask_test,'Value'),1)%if the mask option is on
2640   update_mask(handles,num_i1,num_i2);
2641end
2642
2643%% prepare the menus of histograms and plot them (histogram of the whole volume in 3D case)
2644menu_histo=(UvData.Field.ListVarName)';%list of field variables to be displayed for the menu of histogram display
2645ind_bad=[];
2646nb_histo=1;
2647
2648% suppress coordinates from the histogram menu
2649for ivar=1:numel(menu_histo)%l loop on field variables:
2650    if isfield(UvData.Field,'VarAttribute') && numel(UvData.Field.VarAttribute)>=ivar && isfield(UvData.Field.VarAttribute{ivar},'Role')
2651        Role=UvData.Field.VarAttribute{ivar}.Role;
2652        switch Role
2653            case {'coord_x','coord_y','coord_z','dimvar'}
2654                ind_bad=[ind_bad ivar];
2655            case {'vector_y'}
2656                nb_histo=nb_histo+1;
2657        end
2658    end
2659    DimCell=UvData.Field.VarDimName{ivar};
2660    DimName='';
2661    if ischar(DimCell)
2662        DimName=DimCell;
2663    elseif iscell(DimCell)&& numel(DimCell)==1
2664        DimName=DimCell{1};
2665    end
2666    if strcmp(DimName,menu_histo{ivar})
2667        ind_bad=[ind_bad ivar];
2668    end
2669end
2670menu_histo(ind_bad)=[];
2671
2672%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2673% display menus and plot histograms
2674test_v=0;
2675if ~isempty(menu_histo)
2676    set(handles.histo1_menu,'Value',1)
2677    set(handles.histo1_menu,'String',menu_histo)
2678    histo1_menu_Callback(handles.histo1_menu, [], handles)% plot first histogram
2679    % case of more than one variables (eg vector components)
2680    if nb_histo > 1
2681        test_v=1;
2682        set(handles.histo2_menu,'Visible','on')
2683        set(handles.histo_v,'Visible','on')
2684        set(handles.histo2_menu,'String',menu_histo)
2685        set(handles.histo2_menu,'Value',2)
2686        histo2_menu_Callback(handles.histo2_menu,[], handles)% plot second histogram
2687    end
2688end
2689if ~test_v
2690    set(handles.histo2_menu,'Visible','off')
2691    set(handles.histo_v,'Visible','off')
2692    cla(handles.histo_v)
2693    set(handles.histo2_menu,'Value',1)
2694end
2695%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2696
2697%% display time
2698testimedoc=0;
2699if isfield(UvData,'XmlData') && isfield(UvData.XmlData,'Time')
2700    if isempty(num_i2)||isnan(num_i2)
2701        num_i2=num_i1;
2702    end
2703    if isempty(num_j1)||isnan(num_j1)
2704        num_j1=1;
2705    end
2706    if isempty(num_j2)||isnan(num_j2)
2707        num_j2=num_j1;
2708    end
2709    siz=size(UvData.XmlData.Time);
2710    if siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2711        abstime=(UvData.XmlData.Time(num_i1,num_j1)+UvData.XmlData.Time(num_i2,num_j2))/2;%overset the time read from files
2712        dt=(UvData.XmlData.Time(num_i2,num_j2)-UvData.XmlData.Time(num_i1,num_j1));
2713        testimedoc=1;
2714    end
2715end
2716if isfield(UvData,'XmlData_1') && isfield(UvData.XmlData_1,'Time')
2717    [P,F,str1,str2,str_a,str_b,E]=name2display(['xx' get(handles.FileIndex_1,'String') get(handles.FileExt_1,'String')]);
2718    num_i2=str2double(str2);
2719    if isnan(num_i2)
2720        num_i2=num_i1;
2721    end
2722    num_j1=str2double(str_a);
2723    if isnan(num_j1)
2724        num_j1=1;
2725    end
2726    num_j2=str2double(str_b);
2727    if isnan(num_j2)
2728        num_j2=num_j1;
2729    end
2730    num_i1=str2double(str1);
2731    siz=size(UvData.XmlData_1.Time);
2732    if siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2733        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
2734    end
2735end
2736set(handles.abs_time,'String',num2str(abstime,4))
2737set(handles.abs_time_1,'String',num2str(abstime_1,4))
2738if testimedoc && isfield(UvData,'dt')
2739    dt=UvData.dt;
2740end
2741if isempty(dt)||isequal(dt,0)
2742    set(handles.Dt_txt,'String','')
2743else
2744    if ~(isfield(UvData,'TimeUnit') && ~isempty(UvData.TimeUnit))
2745        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  10^(-3)'] )
2746    else
2747        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  m' UvData.TimeUnit] )
2748    end
2749end
2750
2751
2752%-------------------------------------------------------------------
2753% --- translate coordinate to matrix index
2754%-------------------------------------------------------------------
2755function [indx,indy]=pos2ind(x0,rangx0,nxy)
2756indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel 
2757indy=1+round((nxy(1)-1)*(y12-rangy0(1))/(rangy0(2)-rangy0(1)));% index y of pixel
2758
2759%-------------------------------------------------------------------
2760% --- Executes on button press in 'FixLimits'.
2761%-------------------------------------------------------------------
2762function FixLimits_Callback(hObject, eventdata, handles)
2763test=get(handles.FixLimits,'Value');
2764if test
2765    set(handles.FixLimits,'BackgroundColor',[1 1 0])
2766else
2767    set(handles.FixLimits,'BackgroundColor',[0.7 0.7 0.7])
2768    update_plot(handles);
2769end
2770
2771%-------------------------------------------------------------------
2772% --- Executes on button press in FixEqual.
2773function FixEqual_Callback(hObject, eventdata, handles)
2774test=get(handles.FixEqual,'Value');
2775if test
2776    set(handles.FixEqual,'BackgroundColor',[1 1 0])
2777    cla(handles.axes3)
2778    update_plot(handles);
2779else
2780    set(handles.FixEqual,'BackgroundColor',[0.7 0.7 0.7])
2781    update_plot(handles);
2782%     axis(handles.axes3,'image')
2783end
2784
2785
2786%-------------------------------------------------------------------
2787
2788%-------------------------------------------------------------------
2789% --- Executes on button press in 'zoom'.
2790%-------------------------------------------------------------------
2791function zoom_Callback(hObject, eventdata, handles)
2792
2793if (get(handles.zoom,'Value') == 1);
2794    set(handles.zoom,'BackgroundColor',[1 1 0])
2795    set(handles.FixLimits,'Value',1)% propose by default fixed limits for the plotting axes
2796    set(handles.FixLimits,'BackgroundColor',[1 1 0])
2797else
2798    set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
2799end
2800
2801
2802%-------------------------------------------------------------------
2803%----Executes on button press in 'record': records the current flags of manual correction.
2804%-------------------------------------------------------------------
2805function record_Callback(hObject, eventdata, handles)
2806% [filebase,num_i1,num_j1,num_i2,num_j2,Ext,NomType,SubDir]=read_input_file(handles);
2807filename=read_file_boxes(handles);
2808[erread,message]=fileattrib(filename);
2809if ~isempty(message) && ~isequal(message.UserWrite,1)
2810     msgbox_uvmat('ERROR',['no writting access to ' filename])
2811     return
2812end
2813test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
2814test_civ1=isequal(get(handles.civ1,'BackgroundColor'),[1 1 0]);
2815if ~test_civ2 && ~test_civ1
2816    msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
2817end
2818if test_civ2
2819    nbname='nb_vectors2';
2820   flagname='vec2_FixFlag';
2821   attrname='fix2';
2822end
2823if test_civ1
2824    nbname='nb_vectors';
2825   flagname='vec_FixFlag';
2826   attrname='fix';
2827end
2828%write fix flags in the netcdf file
2829UvData=get(handles.uvmat,'UserData');
2830hhh=which('netcdf.open');% look for built-in matlab netcdf library
2831if ~isequal(hhh,'')% case of new builtin Matlab netcdf library
2832    nc=netcdf.open(filename,'NC_WRITE');
2833    netcdf.reDef(nc);
2834    netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),attrname,1);
2835    dimid = netcdf.inqDimID(nc,nbname);
2836    try
2837        varid = netcdf.inqVarID(nc,flagname);% look for already existing fixflag variable
2838    catch
2839        varid=netcdf.defVar(nc,flagname,'double',dimid);%create fixflag variable if it does not exist
2840    end
2841    netcdf.endDef(nc);
2842    netcdf.putVar(nc,varid,UvData.axes3.FF);
2843    netcdf.close(nc); 
2844else %old netcdf library
2845    netcdf_toolbox(filename,AxeData,attrname,nbname,flagname)
2846end
2847
2848%-------------------------------------------------------------------
2849%----Correct the netcdf file, using toolbox (old versions of Matlab).
2850%-------------------------------------------------------------------
2851function netcdf_toolbox(filename,AxeData,attrname,nbname,flagname)
2852nc=netcdf(filename,'write'); %open netcdf file
2853result=redef(nc);
2854eval(['nc.' attrname '=1;']);
2855theDim=nc(nbname) ;% get the number of velocity vectors
2856nb_vectors=size(theDim);
2857var_FixFlag=ncvar(flagname,nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag
2858var_FixFlag(1:nb_vectors)=AxeData.FF;%
2859fin=close(nc);
2860
2861
2862%-------------------------------------------------------------------
2863%determines the fields to read from the interface
2864%------------------------------------------------------------------
2865function [VelType,civ]=setfield(handles)
2866
2867VelType=[]; %default
2868if (get(handles.civ1,'Value') == 1);
2869        VelType='civ1';
2870% interp1   
2871elseif (get(handles.interp1,'Value') == 1);
2872    VelType='interp1';
2873% filter1   
2874elseif (get(handles.filter1,'Value') == 1);
2875    VelType='filter1'; 
2876% CIV2
2877elseif (get(handles.civ2,'Value') == 1);
2878    VelType='civ2';
2879% interp2   
2880elseif (get(handles.interp2,'Value') == 1);
2881    VelType='interp2';
2882% filter2   
2883elseif (get(handles.filter2,'Value') == 1); 
2884    VelType='filter2';
2885end
2886
2887if isequal(get(handles.filter2,'Visible'),'on');
2888    civ=6;
2889% interp1   
2890elseif isequal(get(handles.interp2,'Visible'),'on');
2891    civ=5;
2892% filter1   
2893elseif isequal(get(handles.civ2,'Visible'),'on');
2894    civ=4; 
2895% CIV2
2896elseif isequal(get(handles.filter1,'Visible'),'on');
2897   civ=3;
2898% interp2   
2899elseif isequal(get(handles.interp1,'Visible'),'on');
2900    civ=2;
2901% filter2   
2902elseif isequal(get(handles.civ1,'Visible'),'on'); 
2903    civ=1;
2904else
2905    civ=0;
2906end
2907
2908%-------------------------------------------------------------------
2909%determines the veltype of the second field to read from the iinterface
2910%------------------------------------------------------------------
2911function VelType=setfield_1(handles)
2912
2913VelType=[]; %default
2914if (get(handles.civ1_1,'Value') == 1);
2915    VelType='civ1';
2916% interp1   
2917elseif (get(handles.interp1_1,'Value') == 1);
2918    VelType='interp1';
2919% filter1   
2920elseif (get(handles.filter1_1,'Value') == 1);
2921    VelType='filter1'; 
2922% CIV2
2923elseif (get(handles.civ2_1,'Value') == 1);
2924    VelType='civ2';
2925% interp2   
2926elseif (get(handles.interp2_1,'Value') == 1);
2927    VelType='interp2';
2928% filter2   
2929elseif (get(handles.filter2_1,'Value') == 1); 
2930    VelType='filter2';
2931end
2932
2933
2934%---------------------------------------------------
2935% --- Executes on button press in SubField
2936function SubField_Callback(hObject, eventdata, handles)
2937huvmat=get(handles.run0,'parent');
2938UvData=get(huvmat,'UserData');
2939if get(handles.SubField,'Value')==0% if the subfield button is desactivated   
2940    set(handles.RootPath_1,'String','')
2941    set(handles.RootFile_1,'String','')
2942    set(handles.SubDir_1,'String','');
2943    set(handles.FileIndex_1,'String','');
2944    set(handles.FileExt_1,'String','');
2945    set(handles.RootPath_1,'Visible','off')
2946    set(handles.RootFile_1,'Visible','off')
2947    set(handles.SubDir_1,'Visible','off');
2948    set(handles.FileIndex_1,'Visible','off');
2949    set(handles.FileExt_1,'Visible','off');
2950    set(handles.Fields_1,'Value',1);%set to blank state
2951    set_veltype_display([handles.civ1_1 handles.interp1_1 handles.filter1_1 ...
2952            handles.civ2_1 handles.interp2_1 handles.filter2_1],0)
2953    if isfield(UvData,'XmlData_1')
2954        UvData=rmfield(UvData,'XmlData_1');
2955    end
2956    set(huvmat,'UserData',UvData);
2957    run0_Callback(hObject, eventdata, handles); %run
2958else
2959    MenuBrowse_1_Callback(hObject, eventdata, handles)
2960end
2961
2962%------------------------------------------------------------------------
2963% --- read the data displayed for the input rootfile windows (new)
2964function [FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles)
2965%------------------------------------------------------------------------
2966RootPath=get(handles.RootPath,'String');
2967FileName=RootPath; %default
2968SubDir=get(handles.SubDir,'String');
2969if ~isempty(SubDir) && ~isequal(SubDir,'')
2970    if (isequal(SubDir(1),'/')|| isequal(SubDir(1),'\'))
2971        SubDir(1)=[]; %suppress possible / or \ separator
2972    end
2973    FileName=fullfile(RootPath,SubDir);
2974end
2975RootFile=get(handles.RootFile,'String');
2976if ~isempty(RootFile) && ~isequal(RootFile,'')
2977    if (isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
2978        RootFile(1)=[]; %suppress possible / or \ separator
2979    end
2980    FileName=fullfile(FileName,RootFile);
2981end
2982FileBase=fullfile(RootPath,RootFile);
2983FileIndices=get(handles.FileIndex,'String');
2984FileExt=get(handles.FileExt,'String');
2985FileName=[FileName FileIndices FileExt];
2986
2987%------------------------------------------------------------------------
2988% ---- read the data displayed for the second input rootfile windows
2989function [FileName_1,RootPath_1,FileBase_1,FileIndices_1,FileExt_1,SubDir_1]=read_file_boxes_1(handles)
2990%------------------------------------------------------------------------
2991RootPath_1=get(handles.RootPath_1,'String'); % read the data from the file1_input window
2992if isequal(get(handles.RootPath_1,'Visible'),'off') || isequal(RootPath_1,'"')
2993    RootPath_1=get(handles.RootPath,'String');
2994end;
2995FileName_1=RootPath_1; %default
2996SubDir_1=get(handles.SubDir_1,'String');
2997if isequal(get(handles.SubDir_1,'Visible'),'off')|| isequal(SubDir_1,'"')
2998    SubDir_1=get(handles.SubDir,'String');
2999end
3000if numel(SubDir_1)>=1
3001    if (isequal(SubDir_1(1),'/')|| isequal(SubDir_1(1),'\'))
3002        SubDir_1(1)=[]; %suppress possible / or \ separator
3003    end
3004    FileName_1=fullfile(RootPath_1,SubDir_1);
3005end
3006RootFile_1=get(handles.RootFile_1,'String');
3007if isequal(get(handles.RootFile_1,'Visible'),'off') || isequal(RootFile_1,'"')
3008    RootFile_1=get(handles.RootFile,'String');
3009end
3010if numel(RootFile_1)>=1
3011    if ~(isequal(RootFile_1(1),'/')|isequal(RootFile_1(1),'\'))
3012        RootFile_1(1)=[];%suppress possible / or \ separator
3013    end
3014    FileName_1=fullfile(FileName_1,RootFile_1);
3015end
3016FileBase_1=fullfile(RootPath_1,RootFile_1);
3017if isequal(get(handles.FileIndex_1,'Visible'),'off')
3018    FileIndices_1=get(handles.FileIndex,'String');
3019else
3020    FileIndices_1=get(handles.FileIndex_1,'String');
3021end
3022FileExt_1=get(handles.FileExt_1,'String');
3023if isequal(FileExt_1,'"'),FileExt_1=get(handles.FileExt,'String'); end;
3024FileName_1=[FileName_1 FileIndices_1 FileExt_1];
3025
3026%------------------------------------------------------------------------
3027% --- Executes on menu selection Fields
3028function Fields_Callback(hObject, eventdata, handles)
3029%------------------------------------------------------------------------
3030list_fields=get(handles.Fields,'String');% list menu fields
3031index_fields=get(handles.Fields,'Value');% selected string index
3032field= list_fields{index_fields(1)}; % selected string
3033if isequal(field,'get_field...')
3034     veltype_handles=[handles.civ1 handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2];
3035     set_veltype_display(veltype_handles,0) % unvisible civ buttons
3036     filename=read_file_boxes(handles);
3037     hget_field=findobj(allchild(0),'name','get_field');
3038     if ~isempty(hget_field)
3039         delete(hget_field)
3040     end
3041     hget_field=get_field(filename);
3042     set(hget_field,'Name','get_field')       
3043     hhget_field=guidata(hget_field);
3044     set(hhget_field.list_fig,'Value',1)
3045     set(hhget_field.list_fig,'String',{'uvmat'})
3046     set(handles.transform_fct,'Value',1)% no transform by default
3047     set(handles.path_transform,'String','')
3048    return %no action
3049end
3050list_fields=get(handles.Fields_1,'String');% list menu fields
3051index_fields=get(handles.Fields_1,'Value');% selected string index
3052field_1= list_fields{index_fields(1)}; % selected string
3053UvData=get(handles.uvmat,'UserData');
3054
3055%read the rootfile input display
3056[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles);
3057[P,F,str1,str2,str_a,str_b,E,NomType]=name2display(['xxx' get(handles.FileIndex,'String') FileExt]);
3058NomTypeNew=NomType;%default
3059if isequal(field,'image')
3060    % transform netc type to the corresponding image type
3061%     if isequal(NomType,'_i1-i2_j')||isequal(NomType,'_i_j1-j2')|| isequal(NomType,'#_ab')|| isequal(NomType,'_i1-i2')
3062%         UvData.SubDir=get(handles.SubDir,'String'); %preserve the subdir in memory
3063%         if ~isempty(UvData.SubDir) && (isequal(UvData.SubDir(1),'/')||isequal(UvData.SubDir(1),'/'))
3064%             UvData.SubDir(1)=[];
3065%         end
3066%         set(handles.SubDir,'String','')
3067%         set(handles.FileExt,'String','.png');
3068        if isequal(NomType,'_i1-i2_j')||isequal(NomType,'_i_j1-j2')
3069            NomTypeNew='_i_j';
3070        elseif isequal(NomType,'#_ab')
3071            NomTypeNew='#a';
3072        elseif isequal(NomType,'_i1-i2')
3073            NomTypeNew='_i';
3074        end 
3075        imagename=name_generator(FileBase,str2double(str1),str2double(str_a),'.png',NomTypeNew,1,str2double(str2),str2double(str_b),'');
3076        if ~exist(imagename,'file')
3077                [FileName,PathName] = uigetfile( ...
3078           {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3079            '*.jpg',' jpeg image files'; ...
3080            '*.png','.png image files'; ...
3081            '*.tif','.tif image files'; ...
3082            '*.avi;*.AVI','.avi movie files'; ...
3083            '*.vol','.volume images (png)'; ...
3084            '*.*',  'All Files (*.*)'}, ...
3085            'Pick an image',imagename);           
3086            % display the selected field and related information
3087           imagename=[PathName FileName];
3088        end
3089        display_file_name(hObject, eventdata, handles,imagename)%display the image
3090        return
3091%     end
3092%     veltype_handles=[handles.civ1 handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2];
3093%     set_veltype_display(veltype_handles,0) % unvisible civ buttons
3094else
3095    ext=get(handles.FileExt,'String');
3096    if ~isequal(ext,'.nc') %find the new NomType if the previous display was not already a netcdf file
3097                [FileName,PathName] = uigetfile( ...
3098           {'*.nc', ' (*.nc)';
3099            '*.nc',' netcdf files'; ...
3100            '*.*',  'All Files (*.*)'}, ...
3101            'Pick a netcdf file',FileBase);           
3102            % display the selected field and related information
3103           filename=[PathName FileName];
3104        display_file_name(hObject, eventdata, handles,filename)
3105        return
3106       %  MenuBrowse_Callback(hObject, eventdata, handles)
3107    end
3108    if isequal(field,'vort') || isequal(field,'div') || isequal(field,'strain')
3109        set(handles.civ1,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey
3110        set(handles.civ2,'BackgroundColor',[0.702 0.702 0.702])
3111        set(handles.interp1,'BackgroundColor',[0.702 0.702 0.702])
3112        set(handles.interp2,'BackgroundColor',[0.702 0.702 0.702])
3113    elseif isequal(field,'more...');
3114        set(handles.civ1,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey
3115        set(handles.civ2,'BackgroundColor',[0.702 0.702 0.702])
3116        str=calc_field;%get the list of available scalars by the function calc_scal
3117        [ind_answer] = listdlg('PromptString','Select a file:',...
3118                'SelectionMode','single',...
3119                'ListString',str);
3120       % edit the choice in the field and action menu
3121        scalar=cell2mat(str(ind_answer));
3122        menu=update_menu(handles.Fields,scalar);
3123        menu=[{''};menu];
3124        set(handles.Fields_1,'String',menu);% store the selected scalar type
3125    end
3126end
3127indices=name_generator('',str2double(str1),str2double(str_a),'',NomTypeNew,1,str2double(str2),str2double(str_b),'');
3128set(handles.FileIndex,'String',indices)
3129set(handles.FileIndex,'UserData',NomTypeNew)
3130%common to Fields_1_Callback
3131if isequal(field,'image')||isequal(field_1,'image')
3132    set(handles.npx_title,'Visible','on')% visible npx,pxcm... buttons
3133    set(handles.npy_title,'Visible','on')
3134    set(handles.npx,'Visible','on')
3135    set(handles.npy,'Visible','on')
3136else
3137    set(handles.npx_title,'Visible','off')% visible npx,pxcm... buttons
3138    set(handles.npy_title,'Visible','off')
3139    set(handles.npx,'Visible','off')
3140    set(handles.npy,'Visible','off')
3141end
3142setfield(handles);% update the field structure ('civ1'....)
3143
3144if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3145    run0_Callback(hObject, eventdata, handles)
3146end
3147
3148%---------------------------------------------------
3149% --- Executes on menu selection Fields
3150function Fields_1_Callback(hObject, eventdata, handles)
3151%-------------------------------------------------
3152list_fields=get(handles.Fields,'String');% list menu fields
3153index_fields=get(handles.Fields,'Value');% selected string index
3154field= list_fields{index_fields(1)}; % selected string
3155list_fields=get(handles.Fields_1,'String');% list menu fields
3156index_fields=get(handles.Fields_1,'Value');% selected string index
3157field_1= list_fields{index_fields(1)}; % selected string for the second field
3158if isequal(field_1,'') %remove second field if 'blank' field is selected
3159    set(handles.SubField,'Value',0)
3160    SubField_Callback(hObject, eventdata, handles)
3161    return
3162end
3163UvData=get(handles.uvmat,'UserData');
3164
3165%read the rootfile input display
3166[FileName,RootPath,FileBase,FileIndices,FileExt_prev]=read_file_boxes_1(handles);
3167[P,F,str1,str2,str_a,str_b,E,NomType]=name2display(['xxx' get(handles.FileIndex,'String') FileExt_prev]);
3168if isempty(FileExt_prev)|isequal(FileExt_prev,'')
3169    FileExt_1=get(handles.FileExt,'String');
3170else
3171    FileExt_1=FileExt_prev;
3172end
3173NomType_1=get(handles.FileIndex_1,'UserData');
3174if isempty(NomType_1)|isequal(NomType_1,'')
3175    NomType_1=get(handles.FileIndex,'UserData');
3176end
3177NomTypeNew=NomType_1;%default
3178
3179set(handles.SubField,'Value',1)%introduce second field
3180if isfield(UvData,'XmlData')
3181    UvData.XmlData_1=UvData.XmlData;
3182end
3183set(handles.FileIndex_1,'Visible','on')
3184set(handles.FileExt_1,'Visible','on')
3185RootPath_1=get(handles.RootPath_1,'String');
3186RootFile_1=get(handles.RootFile_1,'String');
3187if isempty(RootPath_1)||isequal(RootPath_1,'')
3188    set(handles.RootPath_1,'String','"')
3189end
3190if isempty(RootFile_1) || isequal(RootFile_1,'')
3191    set(handles.RootFile_1,'String','"')
3192end
3193if ~isempty(RootFile_1)&&(isequal(RootFile_1(1),'/')||isequal(RootFile_1(1),'\'))
3194    RootFile_1(1)=[];
3195end
3196
3197if isequal(field_1,'get_field...')
3198     veltype_handles=[handles.civ1 handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2];
3199     set_veltype_display(veltype_handles,0) % unvisible civ buttons
3200     filename=read_file_boxes_1(handles);
3201     hget_field=findobj(allchild(0),'name','get_field_1');
3202     if ~isempty(hget_field)
3203         delete(hget_field)
3204     end
3205     hget_field=get_field(filename);
3206     set(hget_field,'name','get_field_1')
3207     hhget_field=guidata(hget_field);
3208     set(hhget_field.list_fig,'Value',1)
3209     set(hhget_field.list_fig,'String',{'uvmat'})
3210     set(handles.transform_fct,'Value',1)% no transform by default
3211     set(handles.path_transform,'String','')
3212    return %no action
3213end
3214if isequal(field_1,'image')
3215    % transform netc type to the corresponding image type
3216%     set(handles.FileExt_1,'String','.png');
3217    if isequal(NomType_1,'_i1-i2_j')|isequal(NomType_1,'_i_j1-j2')| isequal(NomType_1,'#_ab')| isequal(NomType_1,'_i1-i2')
3218        UvData.SubDir_1=get(handles.SubDir_1,'String'); %preserve the subdir in memory
3219%         set(handles.SubDir_1,'String','')
3220%         set(handles.FileExt_1,'String','.png');       
3221        if isequal(NomType_1,'_i1-i2_j')|isequal(NomType_1,'_i_j1-j2')
3222            NomTypeNew='_i_j';
3223        elseif isequal(NomType_1,'#_ab')
3224            NomTypeNew='#a';
3225        elseif isequal(NomType_1,'_i1-i2')
3226            NomTypeNew='_i';
3227        end 
3228    end
3229    imagename=name_generator(FileBase,str2double(str1),str2double(str_a),'.png',NomTypeNew,1,str2double(str2),str2double(str_b),'');
3230    if ~exist(imagename,'file')
3231        [FileName,PathName] = uigetfile( ...
3232            {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3233            '*.jpg',' jpeg image files'; ...
3234            '*.png','.png image files'; ...
3235            '*.tif','.tif image files'; ...
3236            '*.avi;*.AVI','.avi movie files'; ...
3237            '*.vol','.volume images (png)'; ...
3238            '*.*',  'All Files (*.*)'}, ...
3239            'Pick an image',imagename);
3240        % display the selected field and related information
3241        imagename=[PathName FileName];
3242    end
3243    display_file_name_1(hObject, eventdata, handles,imagename)%display the image
3244    return
3245%     veltype_handles=[handles.civ1_1 handles.interp1_1 handles.filter1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1];
3246%     set_veltype_display(veltype_handles,0) % unvisible civ buttons
3247else
3248    set(handles.SubDir_1,'Visible','on')
3249    if ~isequal(FileExt_prev,'.nc') %find the new NomType if the previous display was not already a netcdf file
3250        veltype_handles=[handles.civ1_1 handles.interp1_1 handles.filter1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1];
3251        set_veltype_display(veltype_handles,6); % make all civ buttons visible
3252        RootPath_1=get(handles.RootPath_1,'String');
3253        RootFile_1=get(handles.RootFile_1,'String');
3254        if isempty(RootPath_1)|isequal(RootPath_1,'')
3255            set(handles.RootPath_1,'String','"')
3256        end
3257        if isempty(RootFile_1) | isequal(RootFile_1,'')
3258            set(handles.RootFile_1,'String','"')
3259        end
3260        if ~isempty(RootFile_1)&(isequal(RootFile_1(1),'/')|isequal(RootFile_1(1),'\'))
3261            RootFile_1(1)=[];
3262        end
3263        filebase_1=fullfile(RootPath_1,RootFile_1);
3264        SubDir_1=get(handles.SubDir,'String');
3265        if isempty(SubDir_1)||isequal(SubDir_1,'')
3266            if isfield(UvData,'SubDir_1')
3267                SubDir_1=UvData.SubDir_1;%retrieve previous subdir
3268            else
3269                SubDir_1='?';
3270            end
3271        end
3272        str1=get(handles.i1,'String');
3273        str_a=get(handles.j1,'String');
3274        if isequal(NomType_1,'#_ab')||isequal(NomType_1,'_i1-i2_j')||isequal(NomType_1,'_i_j1-j2')||isequal(NomType_1,'_i1-i2')
3275            NomTypeNew=NomType_1;
3276        elseif isequal(NomType_1,'#a')
3277             [filename, n1,na,n2,nb,SubDir_1]=name_generator(filebase_1, str2num(str1),stra2num(str_a),'.nc','#_ab',0,[],[],SubDir_1);
3278             NomTypeNew='#_ab';
3279        elseif isequal(NomType_1,'_i_j')
3280             [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);
3281            if idetect==1
3282                NomTypeNew='_i1-i2_j';
3283            else
3284                NomTypeNew='_i_j1-j2';
3285            end
3286        else %for instance avi files or any ima_num series
3287            [filename,n1,na,n2,nb,SubDir_1]=name_generator(filebase_1,str2num(str1),stra2num(str_a),'.nc','_i1-i2',0,str2num(str1),[],SubDir_1);
3288            NomTypeNew='_i1-i2';
3289        end           
3290        [Path,Name]=fileparts(filebase_1);
3291        set(handles.FileExt_1,'String','.nc');
3292        if ~isempty(SubDir_1) && ~strcmp(SubDir_1,'''')&& ~strcmp(SubDir_1,'"')&& ~strcmp(SubDir_1(1),'/')
3293            SubDir_1=['/' SubDir_1];
3294        end
3295        set(handles.SubDir_1,'String',SubDir_1);
3296    end
3297    if isequal(field,'vort') | isequal(field,'div') | isequal(field,'strain')
3298        set(handles.civ1_1,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey
3299        set(handles.civ2_1,'BackgroundColor',[0.702 0.702 0.702])
3300        set(handles.interp1_1,'BackgroundColor',[0.702 0.702 0.702])
3301        set(handles.interp2_1,'BackgroundColor',[0.702 0.702 0.702])
3302    elseif isequal(field_1,'more...'); %add new item to the menu
3303        set(handles.civ1_1,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey
3304        set(handles.civ2_1,'BackgroundColor',[0.702 0.702 0.702])
3305        str=calc_field;%get the list of available scalars by the function calc_scal
3306        [ind_answer,v] = listdlg('PromptString','Select a file:',...
3307                'SelectionMode','single',...
3308                'ListString',str);
3309       % edit the choice in the field and action menu
3310        scalar=cell2mat(str(ind_answer));
3311        menu=update_menu(handles.Fields_1,scalar);
3312        set(handles.Fields_1,'String',menu);% store the selected scalar type
3313    end
3314end
3315str1=get(handles.i1,'String');
3316str2=get(handles.i2,'String');
3317str_a=get(handles.j1,'String');
3318str_b=get(handles.j2,'String');
3319indices=name_generator('',str2num(str1),stra2num(str_a),'',NomTypeNew,1,str2num(str2),stra2num(str_b),'');
3320set(handles.FileIndex_1,'String',indices)
3321set(handles.FileIndex_1,'UserData',NomTypeNew)
3322
3323%common to Fields_Callback
3324if isequal(field,'image')|isequal(field_1,'image')
3325    set(handles.npx_title,'Visible','on')% visible npx,pxcm... buttons
3326    set(handles.npy_title,'Visible','on')
3327    set(handles.npx,'Visible','on')
3328    set(handles.npy,'Visible','on')
3329%     set(handles.fix_pair,'Value',0)
3330else
3331    set(handles.npx_title,'Visible','off')% visible npx,pxcm... buttons
3332    set(handles.npy_title,'Visible','off')
3333    set(handles.npx,'Visible','off')
3334    set(handles.npy,'Visible','off')
3335%     set(handles.fix_pair,'Value',1)
3336end
3337if isequal(field,'velocity')|isequal(field_1,'velocity');
3338    state_vect='on';
3339else
3340    state_vect='off';
3341end
3342if ~isequal(field,'velocity')|(~isequal(field_1,'velocity')&~isequal(field_1,''));
3343    state_scal='on';
3344else
3345    state_scal='off';
3346end
3347set(handles.uvmat,'UserData',UvData)
3348setfield(handles);% update the field structure ('civ1'....)
3349if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3350    run0_Callback(hObject, eventdata, handles)
3351end
3352
3353%------------------------------------------------------------------------
3354% --- set the visibility of relevant velocity type menus:
3355function set_veltype_display(handles,Civ)
3356%------------------------------------------------------------------------
3357%Civ=0; all states 'off'
3358%Civ=6; all states 'on'
3359if isequal(Civ,0)
3360    imax=0;
3361%    set(handles(1),'Visible','on')  % unvisible civ buttons
3362% else
3363%    set(handles(1),'String','civ1')
3364% end
3365elseif isequal(Civ,1) || isequal(Civ,2)
3366   imax=1;
3367elseif isequal(Civ,3)
3368    imax=3;
3369elseif isequal(Civ,4) || isequal(Civ,5)
3370    imax=4;
3371elseif isequal(Civ,6) %patch2
3372    imax=6;
3373end
3374for ibutton=1:imax;
3375    set(handles(ibutton),'Visible','on')  % unvisible civ buttons
3376end
3377% for ibutton=max(imax+1,2):6;
3378for ibutton=imax+1:6;
3379    set(handles(ibutton),'Visible','off')  % unvisible civ buttons
3380    set(handles(ibutton),'Value',0)%unactivate unvisible buttons
3381end
3382
3383%-------------------------------------------------------------------
3384% --- Executes on button press in civ1.
3385function civ1_Callback(hObject, eventdata, handles)
3386%-------------------------------------------------------------------
3387if get(handles.civ1,'Value')==1
3388    reset_vel_type([handles.interp1 handles.civ2 handles.filter1 handles.interp1 handles.interp2 handles.filter2],handles.civ1)
3389else
3390    reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3391end
3392run0_Callback(hObject, eventdata, handles)
3393
3394%-------------------------------------------------------------------
3395% --- Executes on button press in interp1.
3396function interp1_Callback(hObject, eventdata, handles)
3397%-------------------------------------------------------------------
3398if get(handles.interp1,'Value')==1
3399    reset_vel_type([handles.civ1 handles.civ2 handles.filter1 handles.interp2 handles.filter2],handles.interp1)
3400else
3401     reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3402end
3403run0_Callback(hObject, eventdata, handles)
3404
3405%-------------------------------------------------------------------
3406% --- Executes on button press in filter1.
3407function filter1_Callback(hObject, eventdata, handles)
3408%-------------------------------------------------------------------
3409if get(handles.filter1,'Value')==1
3410    reset_vel_type([handles.civ1 handles.civ2 handles.interp1 handles.interp2 handles.filter2],handles.filter1)
3411else
3412     reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3413end
3414run0_Callback(hObject, eventdata, handles)
3415
3416%-------------------------------------------------------------------
3417% --- Executes on button press in civ2.
3418function civ2_Callback(hObject, eventdata, handles)
3419%-------------------------------------------------------------------
3420if get(handles.civ2,'Value')==1
3421    reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.interp2 handles.filter2],handles.civ2)
3422else
3423     reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3424end
3425run0_Callback(hObject, eventdata, handles)
3426
3427%-----------------------------------------
3428% --- Executes on button press in interp2.
3429%-------------------------------------------
3430function interp2_Callback(hObject, eventdata, handles)
3431if get(handles.interp2,'Value')==1
3432    reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.filter2],handles.interp2)
3433else
3434     reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3435end
3436run0_Callback(hObject, eventdata, handles)
3437%---------------------------------------------
3438% --- Executes on button press in filter2.
3439%-------------------------------------------
3440function filter2_Callback(hObject, eventdata, handles)
3441if get(handles.filter2,'Value')==1
3442    reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2],handles.filter2)
3443else
3444     reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3445end
3446run0_Callback(hObject, eventdata, handles)
3447
3448%---------------------------------------------
3449function civ1_1_Callback(hObject, eventdata, handles)
3450%---------------------------------------------
3451if get(handles.civ1_1,'Value')==1
3452    reset_vel_type([handles.interp1_1 handles.civ2_1 handles.filter1_1 handles.interp1_1 handles.interp2_1 handles.filter2_1],handles.civ1_1)
3453else
3454     reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3455end
3456run0_Callback(hObject, eventdata, handles)
3457
3458%--------------------------------------------
3459function interp1_1_Callback(hObject, eventdata, handles)
3460%--------------------------------------------
3461if get(handles.interp1_1,'Value')==1
3462    reset_vel_type([handles.civ1_1 handles.civ2_1 handles.filter1_1 handles.interp2_1 handles.filter2_1],handles.interp1_1)
3463else
3464    reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3465end
3466run0_Callback(hObject, eventdata, handles)
3467
3468%--------------------------------------------
3469function filter1_1_Callback(hObject, eventdata, handles)
3470%--------------------------------------------
3471if get(handles.filter1_1,'Value')==1
3472    reset_vel_type([handles.interp1_1 handles.civ2_1 handles.interp1_1 handles.interp2_1 handles.filter2_1],handles.filter1_1)
3473else
3474    reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3475end
3476run0_Callback(hObject, eventdata, handles)
3477
3478%--------------------------------------------
3479function civ2_1_Callback(hObject, eventdata, handles)
3480%--------------------------------------------
3481if get(handles.civ2_1,'Value')==1
3482    reset_vel_type([handles.civ1_1 handles.interp1_1  handles.filter1_1 handles.interp2_1 handles.filter2_1],handles.civ2_1)
3483else
3484    reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3485end
3486run0_Callback(hObject, eventdata, handles)
3487
3488%--------------------------------------------
3489function interp2_1_Callback(hObject, eventdata, handles)
3490%--------------------------------------------
3491if get(handles.interp2_1,'Value')==1
3492    reset_vel_type([handles.civ1_1 handles.civ2_1 handles.filter1_1 handles.interp1_1 handles.filter2_1],handles.interp2_1)
3493else
3494    reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3495end
3496run0_Callback(hObject, eventdata, handles)
3497
3498%--------------------------------------------
3499function filter2_1_Callback(hObject, eventdata, handles)
3500%--------------------------------------------
3501if get(handles.filter2_1,'Value')==1
3502    reset_vel_type([handles.civ1_1 handles.interp1_1 handles.civ2_1 handles.filter1_1 handles.interp1_1 handles.interp2_1],handles.filter2_1)
3503else
3504    reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3505end
3506run0_Callback(hObject, eventdata, handles)
3507
3508%-----------------------------------------------
3509% --- reset civ buttons
3510function reset_vel_type(handles_civ0,handle1)
3511for ibutton=1:length(handles_civ0)
3512    set(handles_civ0(ibutton),'BackgroundColor',[0.831 0.816 0.784])
3513    set(handles_civ0(ibutton),'Value',0)
3514end
3515if exist('handle1','var')%handles of selected button
3516        set(handle1,'BackgroundColor',[1 1 0]) 
3517end
3518
3519%-------------------------------------------------------
3520% --- Executes on button press in MENUVOLUME.
3521%-------------------------------------------------------
3522function VOLUME_Callback(hObject, eventdata, handles)
3523%errordlg('command VOL not implemented yet')
3524if ishandle(handles.UVMAT_title)
3525    delete(handles.UVMAT_title)
3526end
3527UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3528if isequal(get(handles.VOLUME,'Value'),1)
3529    set(handles.zoom,'Value',0)
3530    set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
3531    set(handles.edit_vect,'Value',0)
3532    edit_vect_Callback(hObject, eventdata, handles)
3533    set(handles.edit_object,'Value',0)
3534    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3535%     set(handles.cal,'Value',0)
3536%     set(handles.cal,'BackgroundColor',[0 1 0])
3537    set(handles.edit_vect,'Value',0)
3538    edit_vect_Callback(hObject, eventdata, handles)
3539    %initiate set_object GUI
3540    data.TITLE='VOLUME';
3541    if isfield(UvData,'CoordType')
3542        data.CoordType=UvData.CoordType;
3543    end
3544    if isfield(UvData,'Mesh')&~isempty(UvData.Mesh)
3545        data.RangeY=UvData.Mesh;
3546        data.RangeX=UvData.Mesh;
3547        data.DX=UvData.Mesh;
3548        data.DY=UvData.Mesh;
3549    elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3550        np=size(UvData.Field.A);
3551        meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
3552        meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
3553        data.RangeY=max(meshx,meshy);
3554        data.RangeX=max(meshx,meshy);
3555        data.DX=max(meshx,meshy);
3556    end
3557    data.ParentButton=handles.VOLUME;
3558    PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
3559    [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes,
3560                                                      % associate the set_object interface handle to the plotting axes
3561    if isfield(UvData.OpenParam,'SetObjectOrigin')                                               
3562    pos_uvmat=get(huvmat,'Position');
3563    pos_set_object(1:2)=UvData.OpenParam.SetObjectOrigin + pos_uvmat(1:2);
3564    pos_set_object(3:4)=UvData.OpenParam.SetObjectSize .* pos_uvmat(3:4); 
3565    set(hset_object,'Position',pos_set_object)
3566    end
3567    UvData.MouseAction='create_object';
3568else
3569    set(handles.VOLUME,'BackgroundColor',[0 1 0])
3570    UvData.MouseAction='none';
3571end
3572set(huvmat,'UserData',UvData)
3573
3574%-------------------------------------------------------
3575function edit_vect_Callback(hObject, eventdata, handles)
3576%-------------------------------------------------------
3577%
3578% UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3579if isequal(get(handles.edit_vect,'Value'),1)
3580    test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
3581    test_civ1=isequal(get(handles.civ1,'BackgroundColor'),[1 1 0]);
3582    if ~test_civ2 && ~test_civ1
3583        msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
3584    end
3585    set(handles.record,'Visible','on')
3586    set(handles.edit_vect,'BackgroundColor',[1 1 0])
3587    set(handles.edit_object,'Value',0)
3588    set(handles.zoom,'Value',0)
3589    set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
3590%     set(handles.create,'Value',0)
3591%     set(handles.create,'BackgroundColor',[0 1 0])
3592    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3593    set(gcf,'Pointer','arrow')
3594%     UvData.MouseAction='edit_vect';
3595else
3596    set(handles.record,'Visible','off')
3597    set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7])
3598%     UvData.MouseAction='none';
3599end
3600% set(handles.uvmat,'UserData',UvData)
3601
3602%----------------------------------------------
3603function save_mask_Callback(hObject, eventdata, handles)
3604%-----------------------------------------------------------------------
3605UvData=get(handles.uvmat,'UserData');
3606
3607flag=1;
3608npx=size(UvData.Field.A,2);
3609npy=size(UvData.Field.A,1);
3610xi=0.5:npx-0.5;
3611yi=0.5:npy-0.5;
3612[Xi,Yi]=meshgrid(xi,yi);
3613if isfield(UvData,'Object')
3614    for iobj=1:length(UvData.Object)
3615        ObjectData=UvData.Object{iobj};
3616        if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
3617            flagobj=1;
3618            testphys=0; %coordinates in pixels by default
3619            if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys')
3620                if isfield(UvData,'XmlData')&& isfield(UvData.XmlData,'GeometryCalib')
3621                    Calib=UvData.XmlData.GeometryCalib;
3622                    testphys=1;
3623                end
3624            end
3625            if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style')
3626                if isequal(ObjectData.Style,'polygon')
3627                    X=ObjectData.Coord(:,1);
3628                    Y=ObjectData.Coord(:,2);
3629                    if testphys
3630                        [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
3631                    end
3632                    flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside                 
3633                elseif isequal(ObjectData.Style,'ellipse')
3634                    if testphys
3635                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3636                    end
3637                    RangeX=max(ObjectData.RangeX);
3638                    RangeY=max(ObjectData.RangeY);
3639                    X2Max=RangeX*RangeX;
3640                    Y2Max=RangeY*RangeY;
3641                    distX=(Xi-ObjectData.Coord(1,1));
3642                    distY=(Yi-ObjectData.Coord(1,2));
3643                    flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
3644                elseif isequal(ObjectData.Style,'rectangle')
3645                    if testphys
3646                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3647                    end
3648                    distX=abs(Xi-ObjectData.Coord(1,1));
3649                    distY=abs(Yi-ObjectData.Coord(1,2));
3650                    flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
3651                end
3652                if isequal(ObjectData.ProjMode,'mask_outside')
3653                    flagobj=~flagobj;
3654                end
3655                flag=flag & flagobj;
3656            end
3657        end
3658    end
3659end
3660% flag=~flag;
3661%mask name
3662RootPath=get(handles.RootPath,'String');
3663RootFile=get(handles.RootFile,'String');
3664if ~isempty(RootFile)&&(isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
3665        RootFile(1)=[];
3666end
3667filebase=fullfile(RootPath,RootFile);
3668list=get(handles.masklevel,'String');
3669masknumber=num2str(length(list));
3670maskindex=get(handles.masklevel,'Value');
3671mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
3672imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
3673imflag=flipdim(imflag,1);
3674% imflag=uint8(255*flag);% =0 for flag=0 (vectors=0 when 20<imflag<200)
3675msgbox_uvmat('CONFIRMATION',[mask_name ' saved'])
3676imwrite(imflag,mask_name,'BitDepth',8);
3677
3678%display the mask
3679%update_mask(handles,num_i1,num_j1)
3680figure;
3681vec=linspace(0,1,256);%define a linear greyscale colormap
3682map=[vec' vec' vec'];
3683colormap(map)
3684
3685image(imflag);
3686
3687%-------------------------------------------------------------------
3688%-------------------------------------------------------------------
3689%  - FUNCTIONS FOR SETTING PLOTTING PARAMETERS
3690
3691%------------------------------------------------------------------
3692
3693
3694
3695%------------------------------------------------------------------
3696% --- Executes on selection change in col_vec: choice of the color code.
3697%
3698function col_vec_Callback(hObject, eventdata, handles)
3699%------------------------------------------------------------------
3700% edit the choice for color code
3701list_code=get(handles.col_vec,'String');% list menu fields
3702index_code=get(handles.col_vec,'Value');% selected string index
3703col_code= list_code{index_code(1)}; % selected field
3704if isequal(col_code,'black') || isequal(col_code,'white')
3705   set(handles.slider1,'Visible','off')
3706   set(handles.slider2,'Visible','off')
3707   set(handles.colcode1,'Visible','off')
3708   set(handles.colcode2,'Visible','off')
3709   set(handles.AutoVecColor,'Visible','off')
3710   set_vec_col_bar(handles)
3711else
3712   set(handles.slider1,'Visible','on')
3713   set(handles.slider2,'Visible','on')
3714   set(handles.colcode1,'Visible','on')
3715   set(handles.colcode2,'Visible','on')
3716   set(handles.AutoVecColor,'Visible','on') 
3717   if isequal(col_code,'ima_cor')
3718       set(handles.AutoVecColor,'Value',0)%fixed scale by default
3719       set(handles.vec_col_bar,'Value',0)% 3 colors r,g,b by default
3720       set(handles.slider1,'Min',0);
3721       set(handles.slider1,'Max',1);
3722       set(handles.slider2,'Min',0);
3723       set(handles.slider2,'Max',1);
3724 %      set(handles.min_title_vec,'String','0')
3725       set(handles.max_vec,'String','1')
3726       set(handles.colcode1,'String','0.333')
3727       colcode1_Callback(hObject, eventdata, handles)
3728       set(handles.colcode2,'String','0.666')
3729       colcode2_Callback(hObject, eventdata, handles)
3730   else
3731       set(handles.AutoVecColor,'Value',1)%auto scale between min,max by default
3732       set(handles.vec_col_bar,'Value',1)% colormap 'jet' by default
3733       minval=get(handles.slider1,'Min');
3734       maxval=get(handles.slider1,'Max');
3735       set(handles.slider1,'Value',minval)
3736       set(handles.slider2,'Value',maxval)
3737       set_vec_col_bar(handles)
3738   end
3739%    slider_update(handles)
3740end
3741%replot the current graph
3742run0_Callback(hObject, eventdata, handles)
3743
3744
3745%----------------------------------------------------------------
3746% -- Executes on slider movement to set the color code
3747%
3748function slider1_Callback(hObject, eventdata, handles)
3749%------------------------------------------------------------------
3750slider1=get(handles.slider1,'Value');
3751min_val=str2num(get(handles.min_vec,'String'));
3752max_val=str2num(get(handles.max_vec,'String'));
3753col=min_val+(max_val-min_val)*slider1;
3754set(handles.colcode1,'String',num2str(col))
3755if(get(handles.slider2,'Value') < col)%move also the second slider at the same value if needed
3756    set(handles.slider2,'Value',col)
3757    set(handles.colcode2,'String',num2str(col))
3758end
3759colcode1_Callback(hObject, eventdata, handles)
3760
3761%----------------------------------------------------------------
3762% Executes on slider movement to set the color code
3763%----------------------------------------------------------------
3764function slider2_Callback(hObject, eventdata, handles)
3765slider2=get(handles.slider2,'Value');
3766min_val=str2num(get(handles.min_vec,'String'));
3767max_val=str2num(get(handles.max_vec,'String'));
3768col=min_val+(max_val-min_val)*slider2;
3769set(handles.colcode2,'String',num2str(col))
3770if(get(handles.slider1,'Value') > col)%move also the first slider at the same value if needed
3771    set(handles.slider1,'Value',col)
3772    set(handles.colcode1,'String',num2str(col))
3773end
3774colcode2_Callback(hObject, eventdata, handles)
3775
3776%----------------------------------------------------------------
3777%execute on return carriage on the edit box corresponding to slider 1
3778%----------------------------------------------------------------
3779function colcode1_Callback(hObject, eventdata, handles)
3780% col=str2num(get(handles.colcode1,'String'));
3781% set(handles.slider1,'Value',col)
3782set_vec_col_bar(handles)
3783update_plot(handles);
3784
3785%----------------------------------------------------------------
3786%execute on return carriage on the edit box corresponding to slider 2
3787%----------------------------------------------------------------
3788function colcode2_Callback(hObject, eventdata, handles)
3789% col=str2num(get(handles.colcode2,'String'));
3790% set(handles.slider2,'Value',col)
3791% slider2_Callback(hObject, eventdata, handles)
3792set_vec_col_bar(handles)
3793update_plot(handles);
3794%------------------------------------------------------------
3795%update the slider values after displaying vectors
3796%--------------------------------------------------------
3797% function slider_update(handles,auto,minC,colcode1,colcode2,maxC)
3798% set(handles.slider1,'Min',minC)
3799% set(handles.slider1,'Max',maxC)
3800% set(handles.slider2,'Min',minC)
3801% set(handles.slider2,'Max',maxC)
3802% set(handles.min_title_vec,'String',num2str(minC))
3803% set(handles.max_vec,'String',num2str(maxC))
3804% if auto
3805%         set(handles.colcode1,'String',num2str(colcode1,3))%update display
3806%         set(handles.colcode2,'String',num2str(colcode2,3))
3807% end
3808% set(handles.slider1,'Value',colcode1)%update slider with constant display
3809% set(handles.slider2,'Value',colcode2)
3810% set_vec_col_bar(handles)
3811
3812
3813%-------------------------------------------------------
3814% --- Executes on button press in AutoVecColor.
3815%-------------------------------------------------------
3816function vec_col_bar_Callback(hObject, eventdata, handles)
3817set_vec_col_bar(handles)
3818
3819%-------------------------------------------------------------
3820% --- Executes on selection change in transform_fct.
3821function transform_fct_Callback(hObject, eventdata, handles)
3822%-------------------------------------------------------------
3823
3824UvData=get(handles.uvmat,'UserData');
3825menu=get(handles.transform_fct,'String');
3826ind_coord=get(handles.transform_fct,'Value');
3827coord_option=menu{ind_coord};
3828list_transform=get(handles.transform_fct,'UserData');
3829ff=functions(list_transform{end}); 
3830if isequal(coord_option,'more...');
3831    coord_fct='';
3832    prompt = {'Enter the name of the transform function'};
3833    dlg_title = 'user defined transform';
3834    num_lines= 1;
3835    [FileName, PathName] = uigetfile( ...
3836       {'*.m', ' (*.m)';
3837        '*.m',  '.m files '; ...
3838        '*.*', 'All Files (*.*)'}, ...
3839        'Pick a file', ff.file);
3840    if isequal(PathName(end),'/')||isequal(PathName(end),'\')
3841        PathName(end)=[];
3842    end
3843    transform_selected =fullfile(PathName,FileName);
3844    if ~exist(transform_selected,'file')
3845           return
3846    end
3847   [ppp,transform,ext_fct]=fileparts(FileName);% removes extension .m
3848   if ~isequal(ext_fct,'.m')
3849        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3850        return
3851   end
3852   menu=update_menu(handles.transform_fct,transform);%add the selected fct to the menu
3853   ind_coord=get(handles.transform_fct,'Value');
3854   addpath(PathName)
3855   list_transform{ind_coord}=str2func(transform);% create the function handle corresponding to the newly seleced function
3856   set(handles.transform_fct,'UserData',list_transform)
3857   rmpath(PathName)
3858   % save the new menu in the personal file 'uvmat_perso.mat'
3859   dir_perso=prefdir;%personal Matalb directory
3860   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3861   if exist(profil_perso,'file')
3862       nb_builtin=UvData.OpenParam.NbBuiltin;
3863       for ilist=nb_builtin+1:numel(list_transform)
3864           ff=functions(list_transform{ilist});
3865           transform_fct{ilist-nb_builtin}=ff.file;
3866       end
3867        save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
3868   end   
3869end
3870
3871%check the current path to the selected function
3872if isa(list_transform{ind_coord},'function_handle')
3873    func=functions(list_transform{ind_coord});
3874    set(handles.path_transform,'String',fileparts(func.file)); %show the path to the senlected function
3875else
3876    set(handles.path_transform,'String','')
3877end
3878
3879set(handles.FixLimits,'Value',0)
3880set(handles.FixLimits,'BackgroundColor',[0.7 0.7 0.7])
3881
3882%delete drawn objects
3883hother=findobj('Tag','proj_object');%find all the proj objects
3884for iobj=1:length(hother)
3885    delete_object(hother(iobj))
3886end
3887hother=findobj('Tag','DeformPoint');%find all the proj objects
3888for iobj=1:length(hother)
3889    delete_object(hother(iobj))
3890end
3891hh=findobj('Tag','calib_points');
3892if ~isempty(hh)
3893    delete(hh)
3894end
3895hhh=findobj('Tag','calib_marker');
3896if ~isempty(hhh)
3897    delete(hhh)
3898end
3899if isfield(UvData,'Object')
3900     UvData.Object=UvData.Object(1);
3901end
3902list_object=get(handles.list_object_1,'String');
3903set(handles.list_object_1,'Value',1)
3904set(handles.list_object_1,'String',list_object(1))
3905set(handles.list_object_2,'Value',2)
3906set(handles.list_object_2,'String',[list_object(1);{'...'}])
3907list_object_2_Callback(hObject, eventdata, handles)
3908
3909%delete mask if it is displayed
3910if isequal(get(handles.mask_test,'Value'),1)%if the mask option is on
3911   UvData=rmfield(UvData,'MaskName'); %will impose mask refresh 
3912end
3913set(handles.uvmat,'UserData',UvData)
3914run0_Callback(hObject, eventdata, handles)
3915
3916%--------------------------------------------
3917function histo1_menu_Callback(hObject, eventdata, handles)
3918%--------------------------------------------
3919%plot first histo
3920huvmat=get(handles.histo1_menu,'parent');
3921histo_menu=get(handles.histo1_menu,'String');
3922histo_value=get(handles.histo1_menu,'Value');
3923FieldName=histo_menu{histo_value};
3924update_histo(handles.histo_u,huvmat,FieldName)
3925
3926%----------------------------------------------
3927function histo2_menu_Callback(hObject, eventdata, handles)
3928%----------------------------------------------
3929%plot second histo
3930huvmat=get(handles.histo2_menu,'parent');
3931histo_menu=get(handles.histo2_menu,'String');
3932histo_value=get(handles.histo2_menu,'Value');
3933FieldName=histo_menu{histo_value};
3934update_histo(handles.histo_v,huvmat,FieldName)
3935
3936
3937%--------------------------------------------
3938%read the field .Fieldname stored in UvData and plot its histogram
3939function update_histo(haxes,huvmat,FieldName)
3940UvData=get(huvmat,'UserData');
3941if ~isfield(UvData.Field,FieldName)
3942    msgbox_uvmat('ERROR',['no field  ' FieldName ' for histogram'])
3943    return
3944end
3945Field=UvData.Field;
3946FieldHisto=eval(['Field.' FieldName]);
3947if isfield(Field,'FF') && ~isempty(Field.FF) && isequal(size(Field.FF),size(FieldHisto))
3948    indsel=find(Field.FF==0);%find values marked as false
3949    if ~isempty(indsel)
3950        FieldHisto=FieldHisto(indsel);
3951    end
3952end
3953if isempty(Field)
3954    msgbox_uvmat('ERROR',['empty field ' FieldName])
3955else
3956    nxy=size(FieldHisto);
3957    Amin=double(min(min(min(FieldHisto))));%min of image
3958    Amax=double(max(max(max(FieldHisto))));%max of image
3959    if isequal(Amin,Amax)
3960        msgbox_uvmat('WARNING',['uniform field =' num2str(Amin)]);
3961    else
3962        Histo.ListVarName={FieldName,'histo'};
3963        if isequal(Field.NbDim,3)
3964            Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
3965        else
3966            if numel(nxy)==2
3967                Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
3968            else
3969                Histo.VarDimName={FieldName,{FieldName,'rgb'}}; %dimensions for the histogram
3970            end
3971        end
3972        %unit
3973        units=[]; %default
3974        for ivar=1:numel(Field.ListVarName)
3975            if strcmp(Field.ListVarName{ivar},FieldName)
3976                if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'units')
3977                    units=Field.VarAttribute{ivar}.units;
3978                    break
3979                end
3980            end
3981        end
3982        if ~isempty(units)
3983            Histo.VarAttribute{1}.units=units;
3984        end
3985        eval(['Histo.' FieldName '=linspace(Amin,Amax,50);'])%absissa values for histo
3986        if isequal(Field.NbDim,3)
3987            C=reshape(double(FieldHisto),1,[]);% reshape in a vector
3988            eval(['Histo.histo(:,1)=hist(C, Histo.' FieldName ');']);  %calculate histogram
3989        else
3990            for col=1:size(FieldHisto,3)
3991                B=FieldHisto(:,:,col);
3992                C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector
3993                eval(['Histo.histo(:,col)=hist(C, Histo.' FieldName ');']);  %calculate histogram
3994            end
3995        end
3996%         set(haxes,'XLimMode','auto')%reset auto mode (after zoom effect)
3997%         set(haxes,'YLimMode','auto')
3998%         PlotParam.Auto_xy=1;
3999        plot_field(Histo,haxes);
4000    end
4001end
4002
4003%------------------------------------------------
4004%CALLBACKS FOR PLOTTING PARAMETERS
4005%-------------------------------------------------
4006
4007%------------------------------------------------------------------------
4008function MinX_Callback(hObject, eventdata, handles)
4009%------------------------------------------------------------------------
4010set(handles.FixLimits,'Value',1) %suppress auto mode
4011set(handles.FixLimits,'BackgroundColor',[1 1 0])
4012update_plot(handles);
4013
4014%------------------------------------------------------------------------
4015function MaxX_Callback(hObject, eventdata, handles)
4016%------------------------------------------------------------------------
4017set(handles.FixLimits,'Value',1) %suppress auto mode
4018set(handles.FixLimits,'BackgroundColor',[1 1 0])
4019update_plot(handles);
4020
4021%------------------------------------------------------------------------
4022function MinY_Callback(hObject, eventdata, handles)
4023%------------------------------------------
4024set(handles.FixLimits,'Value',1) %suppress auto mode
4025set(handles.FixLimits,'BackgroundColor',[1 1 0])
4026update_plot(handles);
4027
4028%------------------------------------------------------------------------
4029function MaxY_Callback(hObject, eventdata, handles)
4030%------------------------------------------------------------------------
4031set(handles.FixLimits,'Value',1) %suppress auto mode
4032set(handles.FixLimits,'BackgroundColor',[1 1 0])
4033update_plot(handles);
4034
4035%------------------------------------------------------------------------
4036function MinA_Callback(hObject, eventdata, handles)
4037%------------------------------------------
4038set(handles.FixScal,'Value',1) %suppress auto mode
4039set(handles.FixScal,'BackgroundColor',[1 1 0])
4040update_plot(handles);
4041
4042%------------------------------------------------------------------------
4043function MaxA_Callback(hObject, eventdata, handles)
4044%------------------------------------------------------------------------
4045set(handles.FixScal,'Value',1) %suppress auto mode
4046set(handles.FixScal,'BackgroundColor',[1 1 0])
4047update_plot(handles);
4048
4049%------------------------------------------------------------------------
4050function FixScal_Callback(hObject, eventdata, handles)
4051%------------------------------------------------------------------------
4052test=get(handles.FixScal,'Value');
4053if test
4054    set(handles.FixScal,'BackgroundColor',[1 1 0])
4055else
4056    set(handles.FixScal,'BackgroundColor',[0.7 0.7 0.7])
4057    update_plot(handles);
4058end
4059
4060%-------------------------------------------------------------------
4061function BW_Callback(hObject, eventdata, handles)
4062%-------------------------------------------------------------------
4063update_plot(handles);
4064
4065%-------------------------------------------------------------------
4066function Contours_Callback(hObject, eventdata, handles)
4067%-------------------------------------------------------------------
4068val=get(handles.Contours,'Value');
4069if val==2
4070    set(handles.interval_txt,'Visible','on')
4071    set(handles.IncrA,'Visible','on')
4072else
4073    set(handles.interval_txt,'Visible','off')
4074    set(handles.IncrA,'Visible','off')
4075end
4076update_plot(handles);
4077
4078%-------------------------------------------------------------------
4079function IncrA_Callback(hObject, eventdata, handles)
4080%-------------------------------------------------------------------
4081update_plot(handles);
4082
4083%-------------------------------------------------------------------
4084function HideWarning_Callback(hObject, eventdata, handles)
4085%-------------------------------------------------------------------
4086update_plot(handles);
4087
4088%-------------------------------------------------------------------
4089function HideFalse_Callback(hObject, eventdata, handles)
4090%-------------------------------------------------------------------
4091update_plot(handles);
4092
4093%-------------------------------------------------------------------
4094function VecScale_Callback(hObject, eventdata, handles)
4095%-------------------------------------------------------------------
4096set(handles.FixVec,'Value',1);
4097set(handles.FixVec,'BackgroundColor',[1 1 0])
4098update_plot(handles);
4099
4100%-------------------------------------------------------------------
4101function FixVec_Callback(hObject, eventdata, handles)
4102%-------------------------------------------------------------------
4103test=get(handles.FixVec,'Value');
4104if test
4105    set(handles.FixVec,'BackgroundColor',[1 1 0])
4106else
4107    update_plot(handles);
4108    %set(handles.VecScale,'String',num2str(ScalOut.VecScale,3))
4109    set(handles.FixVec,'BackgroundColor',[0.7 0.7 0.7])
4110end
4111
4112%------------------------------------------------------------------------
4113% --- Executes on selection change in decimate4 (nb_vec/4).
4114function decimate4_Callback(hObject, eventdata, handles)
4115%------------------------------------------------------------------------
4116update_plot(handles);
4117
4118%------------------------------------------------------------------------
4119% --- Executes on selection change in color_code menu
4120function color_code_Callback(hObject, eventdata, handles)
4121%------------------------------------------------------------------------
4122set_vec_col_bar(handles)
4123update_plot(handles);
4124
4125%------------------------------------------------------------------------
4126% --- Executes on button press in AutoVecColor.
4127function AutoVecColor_Callback(hObject, eventdata, handles)
4128%------------------------------------------------------------------------
4129test=get(handles.AutoVecColor,'Value');
4130if test
4131    set(handles.AutoVecColor,'BackgroundColor',[1 1 0])
4132else
4133    update_plot(handles);
4134    %set(handles.VecScale,'String',num2str(ScalOut.VecScale,3))
4135    set(handles.AutoVecColor,'BackgroundColor',[0.7 0.7 0.7])
4136end
4137
4138%------------------------------------------------------------------------
4139% --- Executes on selection change in max_vec.
4140function min_vec_Callback(hObject, eventdata, handles)
4141%------------------------------------------------------------------------
4142max_vec_Callback(hObject, eventdata, handles)
4143
4144%------------------------------------------------------------------------
4145% --- Executes on selection change in max_vec.
4146function max_vec_Callback(hObject, eventdata, handles)
4147%------------------------------------------------------------------------
4148set(handles.AutoVecColor,'Value',1)
4149AutoVecColor_Callback(hObject, eventdata, handles)
4150min_val=str2num(get(handles.min_vec,'String'));
4151max_val=str2num(get(handles.max_vec,'String'));
4152slider1=get(handles.slider1,'Value');
4153slider2=get(handles.slider2,'Value');
4154colcode1=min_val+(max_val-min_val)*slider1;
4155colcode2=min_val+(max_val-min_val)*slider2;
4156set(handles.colcode1,'String',num2str(colcode1))
4157set(handles.colcode2,'String',num2str(colcode2))
4158update_plot(handles);
4159
4160%------------------------------------------------------------------------
4161% --- update the display of color code for vectors
4162function set_vec_col_bar(handles)
4163%------------------------------------------------------------------------
4164%get the image of the color display button 'vec_col_bar' in pixels
4165set(handles.vec_col_bar,'Unit','pixel');
4166pos_vert=get(handles.vec_col_bar,'Position');
4167set(handles.vec_col_bar,'Unit','Normalized');
4168width=ceil(pos_vert(3));
4169height=ceil(pos_vert(4));
4170
4171%get slider indications
4172list=get(handles.color_code,'String');
4173ichoice=get(handles.color_code,'Value');
4174colcode.ColorCode=list{ichoice};
4175colcode.MinC=str2num(get(handles.min_vec,'String'));
4176colcode.MaxC=str2num(get(handles.max_vec,'String'));
4177test3color=strcmp(colcode.ColorCode,'rgb') || strcmp(colcode.ColorCode,'bgr');
4178if test3color
4179    colcode.colcode1=str2num(get(handles.colcode1,'String'));
4180    colcode.colcode2=str2num(get(handles.colcode2,'String'));
4181end
4182colcode.FixedCbounds=0;
4183colcode.FixedCbounds=1;
4184vec_C=colcode.MinC+(colcode.MaxC-colcode.MinC)*(0.5:width-0.5)/width;%sample of vec_C values from min to max
4185[colorlist,col_vec]=set_col_vec(colcode,vec_C);
4186oneheight=ones(1,height);
4187A1=colorlist(col_vec,1)*oneheight;
4188A2=colorlist(col_vec,2)*oneheight;
4189A3=colorlist(col_vec,3)*oneheight;
4190A(:,:,1)=A1';
4191A(:,:,2)=A2';
4192A(:,:,3)=A3';
4193set(handles.vec_col_bar,'Cdata',A)
4194
4195
4196%-------------------------------------------------------------------
4197function update_plot(handles)
4198%-------------------------------------------------------------------
4199haxes= handles.axes3;
4200UvData=get(handles.uvmat,'UserData');
4201AxeData=UvData.axes3;
4202PlotParam=read_plot_param(handles);
4203[PP,PlotParamOut]= plot_field(AxeData,haxes,PlotParam);
4204write_plot_param(handles,PlotParamOut); %update the auto plot parameters
4205
4206%-------------------------------------------------------------------
4207% --- Executes on button press in grid.
4208function grid_Callback(hObject, eventdata, handles)
4209
4210
4211%-------------------------------------------------------------------
4212% --- Executes on selection change in edit_object.
4213function edit_object_Callback(hObject, eventdata, handles)
4214%-------------------------------------------------------------------
4215UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4216test=get(handles.edit_object,'Value');
4217if test
4218    set(handles.edit_object,'BackgroundColor',[1,1,0]) 
4219    %suppress the other options
4220    set(handles.zoom,'Value',0)
4221    zoom_Callback(hObject, eventdata, handles)
4222    hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4223    if ishandle(hgeometry_calib)
4224        hhgeometry_calib=guidata(hgeometry_calib);
4225        set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4226        set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4227    end
4228else
4229    UvData.MouseAction='none';
4230    set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])   
4231    hset_object=findobj(allchild(0),'tag','set_object');% look for the set_object GUI
4232    if ~isempty(hset_object)
4233        delete(hset_object)% delete the current GUI set_object
4234    end
4235end
4236set(handles.uvmat,'UserData',UvData);
4237hset_object=findobj(allchild(0),'Tag','set_object');
4238if ~isempty(hset_object)
4239    hhset_object=guidata(hset_object);
4240    if test
4241        set(hhset_object.PLOT,'enable','on');
4242    else
4243       set(hhset_object.PLOT,'enable','off');
4244    end
4245end
4246
4247%------------------------------------------------------------------------
4248% --- Executes on selection change in list_object_1.
4249function list_object_1_Callback(hObject, eventdata, handles)
4250%------------------------------------------------------------------------
4251list_str=get(handles.list_object_1,'String');
4252IndexObj=get(handles.list_object_1,'Value');
4253str_1=list_str{IndexObj};
4254val_2=get(handles.list_object_2,'Value');
4255str_2=get(handles.list_object_2,'String');
4256if isequal(val_2,IndexObj)% if the first selection is equal to the second, it will suppress the second
4257    set(handles.list_object_2,'Value',numel(str_2))%select the end of the list ('...')
4258    list_object_2_Callback(hObject, eventdata, handles)
4259end
4260update_object(handles,IndexObj,1,str_1)
4261
4262%------------------------------------------------------------------------
4263% --- Executes on selection change in list_object_1.
4264function list_object_2_Callback(hObject, eventdata, handles)
4265%------------------------------------------------------------------------
4266list_str=get(handles.list_object_2,'String');
4267IndexObj=get(handles.list_object_2,'Value');
4268if ischar(list_str) || strcmp(list_str{IndexObj},'...')
4269    hview_field=findobj(allchild(0),'Tag','view_field');
4270    if ~isempty(hview_field)
4271        delete(hview_field)
4272    end
4273    hset_object=findobj(allchild(0),'Tag','set_object');
4274    if ~isempty(hset_object)
4275        delete(hset_object)
4276    end
4277else
4278    update_object(handles,IndexObj,2,list_str{IndexObj})
4279end
4280
4281%------------------------------------------------------------------------
4282function update_object(handles,IndexObj,option,ObjectName)
4283%------------------------------------------------------------------------
4284UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4285if numel(UvData.Object)<IndexObj;
4286    return
4287end
4288ObjectData=UvData.Object{IndexObj};
4289ObjectData.Name=ObjectName;
4290if isequal(get(handles.edit_object,'Value'),1)
4291    ObjectData.enable_plot=1; % desable the PLOT option in the set_object GUI (editing mode
4292end
4293ZBounds=0; % default
4294if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4295    ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4296    ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4297end
4298hset_object=findobj(allchild(0),'tag','set_object');
4299if ~isempty(hset_object)
4300    delete(hset_object)% delete existing version of set_object
4301end
4302edit_test=get(handles.edit_object,'Value');
4303if edit_test
4304    ObjectData.enable_plot=1;
4305else
4306        if isfield(ObjectData,'enable_plot')
4307        ObjectData=rmfield(ObjectData,'enable_plot');
4308    end
4309end
4310hset_object=set_object(ObjectData,[],ZBounds);% call the set_object interface,
4311
4312% %project the current field on the object and plot it
4313ProjData= proj_field(UvData.Field,ObjectData);%project the current interface field on ObjectData
4314if option==1%length(UvData.Object)>= IndexObj && isfield(UvData.Object{IndexObj},'plotaxes')&& ishandle(UvData.Object{IndexObj}.plotaxes)
4315    PlotHandles=handles;
4316else
4317    hview_field=findobj(allchild(0),'tag','view_field');
4318    if isempty(hview_field)
4319        hview_field=view_field;
4320    end
4321    PlotHandles=guidata(hview_field);
4322end
4323plot_field(ProjData,PlotHandles.axes3,PlotHandles);
4324set(handles.uvmat,'UserData',UvData)
4325hother=findobj('Tag','proj_object');%find all the proj objects
4326for iobj=1:length(hother)
4327    if isequal(get(hother(iobj),'Type'),'rectangle')||isequal(get(hother(iobj),'Type'),'patch')
4328        set(hother(iobj),'EdgeColor','b')
4329        if isequal(get(hother(iobj),'FaceColor'),'m')
4330            set(hother(iobj),'FaceColor','b')
4331        end
4332    elseif isequal(get(hother(iobj),'Type'),'image')
4333        Acolor=get(hother(iobj),'CData');
4334        Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2));
4335        set(hother(iobj),'CData',Acolor);
4336    else
4337        set(hother(iobj),'Color','b')
4338    end
4339    set(hother(iobj),'Selected','off')
4340end
4341hother=findobj('Tag','DeformPoint');
4342set(hother,'Color','b');
4343set(hother,'Selected','off')
4344if isfield(ObjectData,'DisplayHandle_uvmat')
4345    if ishandle(ObjectData.DisplayHandle_uvmat)
4346        uistack(ObjectData.DisplayHandle_uvmat,'top')
4347        linetype=get(ObjectData.DisplayHandle_uvmat,'Type');
4348        if isequal(linetype,'line')
4349            set(ObjectData.DisplayHandle_uvmat,'Color','m'); %set the selected object to magenta color
4350        elseif isequal(linetype,'rectangle')
4351            set(ObjectData.DisplayHandle_uvmat,'EdgeColor','m'); %set the selected object to magenta color
4352        elseif isequal(linetype,'patch')
4353            set(ObjectData.DisplayHandle_uvmat,'FaceColor','m'); %set the selected object to magenta color
4354        end
4355        SubObjectData=get(ObjectData.DisplayHandle_uvmat,'UserData');
4356        if isfield(SubObjectData,'SubObject') & ishandle(SubObjectData.SubObject)
4357            uistack(SubObjectData.SubObject,'top')
4358            for iobj=1:length(SubObjectData.SubObject)
4359                hsub=SubObjectData.SubObject(iobj);
4360                if isequal(get(hsub,'Type'),'rectangle')
4361                    set(hsub,'EdgeColor','m'); %set the selected object to magenta color
4362                elseif isequal(get(hsub,'Type'),'image')
4363                    Acolor=get(hsub,'CData');
4364                    Acolor(:,:,1)=Acolor(:,:,3);
4365                    set(hsub,'CData',Acolor);
4366                else
4367                    set(hsub,'Color','m')
4368                end
4369            end
4370        end
4371        if isfield(SubObjectData,'DeformPoint') & ishandle(SubObjectData.DeformPoint)
4372            set(SubObjectData.DeformPoint,'Color','m')
4373        end
4374    end
4375    %     end
4376end
4377% pause(0.1)
4378figure(hset_object)%put set_object in front
4379
4380%------------------------------------------------------
4381% --- Executes on button press in Menu/Export/field in workspace.
4382%------------------------------------------------------
4383function MenuExportField_Callback(hObject, eventdata, handles)
4384global Data_uvmat
4385Data_uvmat=get(handles.uvmat,'UserData');
4386evalin('base','global Data_uvmat')%make CurData global in the workspace
4387display('current field :')
4388evalin('base','Data_uvmat') %display CurData in the workspace
4389commandwindow; %brings the Matlab command window to the front
4390
4391%------------------------------------------------------
4392% --- Executes on button press in Menu/Export/extract figure.
4393%------------------------------------------------------
4394function MenuExport_plot_Callback(hObject, eventdata, handles)
4395huvmat=get(handles.MenuExport_plot,'parent');
4396UvData=get(huvmat,'UserData');
4397hfig=figure;
4398newaxes=copyobj(handles.axes3,hfig);
4399map=colormap(handles.axes3);
4400colormap(map);%transmit the current colormap to the zoom fig
4401colorbar
4402
4403
4404% --------------------------------------------------------------------
4405function Insert_Callback(hObject, eventdata, handles)
4406
4407
4408% --------------------------------------------------------------------
4409function MenuHelp_Callback(hObject, eventdata, handles)
4410% --------------------------------------------------------------------
4411path_to_uvmat=which ('uvmat');% check the path of uvmat
4412pathelp=fileparts(path_to_uvmat);
4413helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
4414if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
4415else
4416    addpath (fullfile(pathelp,'uvmat_doc'))
4417    web(helpfile);
4418end
4419
4420%------------------------------------------------------------------------
4421% --------------------------------------------------------------------
4422function MenuExportMovie_Callback(hObject, eventdata, handles)
4423% --------------------------------------------------------------------
4424set(handles.MenuExportMovie,'BusyAction','queue')% activate the button
4425huvmat=get(handles.run0,'parent');
4426UvData=get(huvmat,'UserData');
4427[xx,xx,FileBase]=read_file_boxes(handles);
4428 %read the current input file name
4429prompt = {'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)'};
4430dlg_title = 'select properties of the output avi movie';
4431num_lines= 1;
4432% nbfield_cell=get(handles.last_i,'String');
4433def     = {[FileBase '_out.avi'];'10';'1';'[0.03 0.05 0.95 0.92]';'10'};
4434answer = inputdlg(prompt,dlg_title,num_lines,def,'on');
4435aviname=answer{1};
4436fps=str2double(answer{2});
4437% check for existing file with output name aviname
4438if exist(aviname,'file')
4439    backup=aviname;
4440    testexist=2;
4441    while testexist==2
4442        backup=[backup '~'];
4443        testexist=exist(backup,'file');     
4444    end
4445    [success,message]=copyfile(aviname,backup);%make backup of the existing file
4446    if isequal(success,1)
4447        delete(aviname)%delete existing file
4448    else
4449        msgbox_uvmat('ERROR',message)
4450        return
4451    end
4452end
4453%create avi open
4454aviobj=avifile(aviname,'Compression','None','fps',fps);
4455
4456%display first view for tests
4457newfig=figure;
4458newaxes=copyobj(handles.axes3,newfig);%new plotting axes in the new figure
4459set(newaxes,'Tag','movieaxes')
4460nbpix=[512 384]*str2double(answer{3});
4461set(gcf,'Position',[1 1 nbpix])% resolution XVGA
4462set(newaxes,'Position',eval(answer{4}));
4463map=colormap(handles.axes3);
4464colormap(map);%transmit the current colormap to the zoom fig
4465msgbox_uvmat('INPUT_Y-N',{['adjust figure ' num2str(newfig) ' with its matlab edit menu '] ;...
4466        ['then press OK to get the avi movie as a copy of figure ' num2str(newfig) ' display']});
4467UvData.Object{1}.plotaxes=newaxes;% the axis in the new figure becomes the current main plotting axes
4468set(huvmat,'UserData',UvData);
4469increment=str2double(get(handles.increment_scan,'String')); %get the field increment d
4470if isnan(increment)
4471    set(handles.increment_scan,'String','1')%default value
4472    increment=1;
4473end
4474set(handles.STOP,'Visible','on')
4475set(handles.speed,'Visible','on')
4476set(handles.speed_txt,'Visible','on')
4477set(handles.Movie,'BusyAction','queue')
4478
4479%imin=str2double(get(handles.i1,'String'));
4480imax=str2double(answer{5});
4481% if isfield(UvData,'Time')
4482htitle=get(newaxes,'Title');
4483xlim=get(newaxes,'XLim');
4484ylim=get(newaxes,'YLim');
4485set(htitle,'Position',[xlim(2)+0.07*(xlim(2)-xlim(1)) ylim(2)-0.05*(ylim(2)-ylim(1)) 0])
4486time_str=get(handles.abs_time,'String');
4487set(htitle,'String',['t=' time_str])
4488set(handles.speed,'Value',1)
4489for i=1:imax
4490    if get(handles.speed,'Value')~=0 && isequal(get(handles.MenuExportMovie,'BusyAction'),'queue') % enable STOP command
4491            runpm(hObject,eventdata,handles,increment)% run plus
4492            drawnow
4493            time_str=get(handles.abs_time,'String');
4494            if ishandle(htitle)
4495             set(htitle,'String',['t=' time_str])
4496            end
4497            mov=getframe(newfig);
4498            aviobj=addframe(aviobj,mov);
4499    end
4500end
4501close(aviobj);
4502UvData.Object{1}.plotaxes=handles.axes3;
4503set(huvmat,'UserData',UvData);
4504msgbox_uvmat('CONFIRMATION',{['movie ' aviname ' created '];['with ' num2str(imax) ' frames']})
4505
4506%------------------------------------------------------------------------
4507function MenuCalib_Callback(hObject, eventdata, handles)
4508%------------------------------------------------------------------------
4509
4510UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4511
4512%suppress competing options
4513set(handles.zoom,'Value',0)
4514set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
4515set(handles.list_object_1,'Value',1)     
4516% initiate display of GUI geometry_calib
4517data=[]; %default
4518if isfield(UvData,'CoordType')
4519    data.CoordType=UvData.CoordType;
4520end
4521pos=get(handles.uvmat,'Position');
4522pos(1)=pos(1)+pos(3)-0.311+0.04; %0.311= width of the geometry_calib interface (units relative to the srcreen)
4523pos(2)=pos(2)-0.02;
4524[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles);
4525set(handles.view_xml,'Backgroundcolor',[1 1 0])%indicate the reading of the current xml file by geometry_calib
4526if isfield(UvData.OpenParam,'CalOrigin')
4527    pos_uvmat=get(handles.uvmat,'Position');
4528    pos_cal(1)=pos_uvmat(1)+UvData.OpenParam.CalOrigin(1)*pos_uvmat(3);
4529    pos_cal(2)=pos_uvmat(2)+UvData.OpenParam.CalOrigin(2)*pos_uvmat(4);
4530    pos_cal(3:4)=UvData.OpenParam.CalSize .* pos_uvmat(3:4);
4531end
4532geometry_calib(FileName,pos_cal);% call the geometry_calib interface   
4533set(handles.view_xml,'Backgroundcolor',[1 1 1])%indicate the end of reading of the current xml file by geometry_calib
4534set(handles.MenuCalib,'checked','on')% indicate that MenuCalib is activated, test used by mouse action
4535
4536%------------------------------------------------------------------------
4537function MenuMask_Callback(hObject, eventdata, handles)
4538%------------------------------------------------------------------------
4539UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4540ListObj=UvData.Object;
4541select=zeros(1,numel(ListObj));
4542for iobj=1:numel(ListObj);
4543    if strcmp(ListObj{iobj}.ProjMode,'mask_inside')||strcmp(ListObj{iobj}.ProjMode,'mask_outside')
4544        select(iobj)=1;
4545    end
4546end
4547val=find(select);
4548if isempty(val)
4549    msgbox_uvmat('ERROR','polygons must be first created by Projection object/mask polygon in the menu bar');
4550    return
4551else
4552    set(handles.list_object_1,'Max',2);%allow multiple selection
4553    set(handles.list_object_1,'Value',val);
4554    flag=1;
4555    npx=size(UvData.Field.A,2);
4556    npy=size(UvData.Field.A,1);
4557    xi=0.5:npx-0.5;
4558    yi=0.5:npy-0.5;
4559    [Xi,Yi]=meshgrid(xi,yi);
4560    if isfield(UvData,'Object')
4561        for iobj=1:length(UvData.Object)
4562            ObjectData=UvData.Object{iobj};
4563            if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
4564                flagobj=1;
4565                testphys=0; %coordinates in pixels by default
4566                if isfield(ObjectData,'CoordUnit') && ~isequal(ObjectData.CoordUnit,'pixel')
4567                    if isfield(UvData,'XmlData')&& isfield(UvData.XmlData,'GeometryCalib')
4568                        Calib=UvData.XmlData.GeometryCalib;
4569                        testphys=1;
4570                    end
4571                end
4572                if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style')
4573                    if isequal(ObjectData.Style,'polygon')
4574                        X=ObjectData.Coord(:,1);
4575                        Y=ObjectData.Coord(:,2);
4576                        if testphys
4577                            [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
4578                        end
4579                        flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside
4580                    elseif isequal(ObjectData.Style,'ellipse')
4581                        if testphys
4582                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4583                        end
4584                        RangeX=max(ObjectData.RangeX);
4585                        RangeY=max(ObjectData.RangeY);
4586                        X2Max=RangeX*RangeX;
4587                        Y2Max=RangeY*RangeY;
4588                        distX=(Xi-ObjectData.Coord(1,1));
4589                        distY=(Yi-ObjectData.Coord(1,2));
4590                        flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
4591                    elseif isequal(ObjectData.Style,'rectangle')
4592                        if testphys
4593                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4594                        end
4595                        distX=abs(Xi-ObjectData.Coord(1,1));
4596                        distY=abs(Yi-ObjectData.Coord(1,2));
4597                        flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
4598                    end
4599                    if isequal(ObjectData.ProjMode,'mask_outside')
4600                        flagobj=~flagobj;
4601                    end
4602                    flag=flag & flagobj;
4603                end
4604            end
4605        end
4606    end
4607   
4608    %mask name
4609    RootPath=get(handles.RootPath,'String');
4610    RootFile=get(handles.RootFile,'String');
4611    if ~isempty(RootFile)&&(isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
4612        RootFile(1)=[];
4613    end
4614    filebase=fullfile(RootPath,RootFile);
4615    list=get(handles.masklevel,'String');
4616    masknumber=num2str(length(list));
4617    maskindex=get(handles.masklevel,'Value');
4618    mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
4619    imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
4620    imflag=flipdim(imflag,1);
4621
4622    %display the mask
4623    figure;
4624    vec=linspace(0,1,256);%define a linear greyscale colormap
4625    map=[vec' vec' vec'];
4626    colormap(map)
4627    image(imflag);
4628    answer=msgbox_uvmat('INPUT_TXT','mask file name:', mask_name);
4629    if ~strcmp(answer,'Cancel')
4630        mask_dir=fileparts(answer);
4631        if ~exist(mask_dir,'dir')
4632            msgbox_uvmat('ERROR',['directory ' mask_dir ' does not exist'])
4633            return
4634        end
4635        imwrite(imflag,answer,'BitDepth',8);
4636    end
4637    set(handles.list_object_1,'Value',1)
4638    set(handles.list_object_1,'Max',1)
4639end
4640
4641%------------------------------------------------------------------------
4642%-- open the GUI set_grid.fig to create grid
4643function MenuGrid_Callback(hObject, eventdata, handles)
4644%------------------------------------------------------------------------
4645%UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4646
4647%suppress the other options if grid is chosen
4648set(handles.edit_vect,'Value',0)
4649edit_vect_Callback(hObject, eventdata, handles)
4650set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
4651set(handles.list_object_1,'Value',1)     
4652
4653%prepare display of the set_grid GUI
4654FileName=read_file_boxes(handles);
4655CoordList=get(handles.transform_fct,'String');
4656val=get(handles.transform_fct,'Value');
4657set_grid(FileName,CoordList{val});% call the set_object interface
4658%set(handles.uvmat,'UserData',UvData);
4659
4660%------------------------------------------------------------------------
4661% open the GUI 'series'
4662function MenuSeries_Callback(hObject, eventdata, handles)
4663%------------------------------------------------------------------------
4664series; %first display of the GUI to fill waiting time
4665[param.FileName]=read_file_boxes(handles);
4666if isequal(get(handles.SubField,'Value'),1)
4667    FileName_1=read_file_boxes_1(handles);%
4668    if ~isequal(FileName_1,param.FileName)
4669        param.FileName_1=FileName_1;
4670    end
4671end
4672param.NomType=get(handles.FileIndex,'UserData');
4673param.NomType_1=get(handles.FileIndex_1,'UserData');
4674param.comp_input=get(handles.fix_pair,'Value');
4675huvmat=get(handles.MenuSeries,'parent');
4676UvData=get(huvmat,'UserData');
4677if isfield(UvData,'Time')
4678    param.Time=UvData.XmlData.Time;
4679end
4680if isequal(get(handles.scan_i,'Value'),1)
4681    param.incr_i=str2double(get(handles.increment_scan,'String'));
4682elseif isequal(get(handles.scan_j,'Value'),1)
4683    param.incr_j=str2double(get(handles.increment_scan,'String'));
4684end
4685param.list_fields=get(handles.Fields,'String');% list menu fields
4686param.list_fields(1)=[]; %suppress  'image' option
4687param.index_fields=get(handles.Fields,'Value');% selected string index
4688if param.index_fields>1
4689    param.index_fields=param.index_fields-1;
4690end
4691param.list_fields_1=get(handles.Fields_1,'String');% list menu fields
4692param.list_fields_1(1)=[]; %suppress  'image' option
4693param.index_fields_1=get(handles.Fields_1,'Value')-1;% selected string index
4694if param.index_fields_1>1
4695    param.index_fields_1=param.index_fields_1-1;
4696end
4697param.civ1=get(handles.civ1,'Value');
4698param.civ2=get(handles.civ2,'Value');
4699param.interp1=get(handles.interp1,'Value');
4700param.interp2=get(handles.interp2,'Value');
4701param.filter1=get(handles.filter1,'Value');
4702param.filter2=get(handles.filter2,'Value');
4703param.menu_coord_str=get(handles.transform_fct,'String');
4704param.menu_coord_val=get(handles.transform_fct,'Value');
4705
4706series(param); %run the series interface
4707
4708%------------------------------------------------------------------------
4709% -- open the GUI civ.fig for civx (PIV)
4710function MenuPIV_Callback(hObject, eventdata, handles)
4711%------------------------------------------------------------------------
4712 
4713[FileName,RootPath,filebase,FileIndices,ext,SubDir]=read_file_boxes(handles);
4714num1=stra2num(get(handles.i1,'String'));
4715num2=stra2num(get(handles.i2,'String'));
4716num_a=stra2num(get(handles.j1,'String'));
4717num_b=stra2num(get(handles.j2,'String'));
4718NomType=get(handles.FileIndex,'UserData');
4719ind_opening=1; % default (images): will advice civ1 option by default in the civ interface
4720if isequal(ext,'.nc') ||  isequal(ext,'.cdf')% netcdf files
4721    ind_opening=2;% propose 'fix' as the default option
4722% +read the current netcdf rootfile
4723    Data=nc2struct(FileName,'ListGlobalAttribute','fix','patch','civ2','fix2');
4724    if isfield(Data,'fix') && isequal(Data.fix,1)
4725        ind_opening=3;
4726    end
4727    if isfield(Data,'patch') && isequal(Data.patch,1)
4728        ind_opening=4;
4729    end
4730    if isfield(Data,'civ2') && isequal(Data.civ2,1)
4731        ind_opening=5;
4732    end
4733    if isfield(Data,'fix2') && isequal(Data.fix2,1)
4734        ind_opening=6;
4735    end
4736end     
4737param.RootName=filebase;
4738param.NomType=NomType;
4739param.num1=num1;
4740param.num2=num2;
4741param.num_a=num_a;
4742param.num_b=num_b;
4743param.SubDir=SubDir;
4744param.IndOpening=ind_opening;% A REVOIR +TRANSMETTRE IMADOC INFO
4745param.ImaExt=ext;
4746civ(param);% interface de civ(not in the uvmat file)
4747
4748%------------------------------------------------------------------------
4749function MenuTools_Callback(hObject, eventdata, handles)
4750%------------------------------------------------------------------------
4751
4752%------------------------------------------------------------------------
4753function MenuEditObject_Callback(hObject, eventdata, handles)
4754%------------------------------------------------------------------------
4755set(handles.edit_object,'Value',1)
4756edit_Callback(hObject, eventdata, handles)
4757
4758%------------------------------------------------------------------------
4759function enable_transform(handles,state)
4760%------------------------------------------------------------------------
4761set(handles.transform_fct,'Visible',state)
4762set(handles.TRANSFORM_txt,'Visible',state)   
4763set(handles.transform_fct,'Visible',state) 
4764set(handles.path_transform,'Visible',state)
4765set(handles.pxcmx_txt,'Visible',state)
4766set(handles.pxcmy_txt,'Visible',state)
4767set(handles.pxcm,'Visible',state)
4768set(handles.pycm,'Visible',state)
4769
4770%------------------------------------------------------------------------
4771function MenuEditVectors_Callback(hObject, eventdata, handles)
4772%------------------------------------------------------------------------
4773set(handles.edit_vect,'Visible','on')
4774set(handles.edit_vect,'Value',1)
4775edit_vect_Callback(hObject, eventdata, handles)
4776
4777% -----------------------------------------------------------------------
4778function Menupoints_Callback(hObject, eventdata, handles)
4779%------------------------------------------------------------------------
4780data.Style='points';
4781data.ProjMode='projection';%default
4782create_object(data,handles)
4783
4784% -----------------------------------------------------------------------
4785function Menuline_Callback(hObject, eventdata, handles)
4786%------------------------------------------------------------------------
4787data.Style='line';
4788data.ProjMode='projection';%default
4789create_object(data,handles)
4790
4791%------------------------------------------------------------------------
4792function Menupolyline_Callback(hObject, eventdata, handles)
4793%------------------------------------------------------------------------
4794data.Style='polyline';
4795data.ProjMode='projection';%default
4796create_object(data,handles)
4797
4798%------------------------------------------------------------------------
4799function Menupolygon_Callback(hObject, eventdata, handles)
4800%------------------------------------------------------------------------
4801data.Style='polygon';
4802data.ProjMode='inside';%default
4803create_object(data,handles)
4804
4805%------------------------------------------------------------------------
4806function Menurectangle_Callback(hObject, eventdata, handles)
4807%------------------------------------------------------------------------
4808data.Style='rectangle';
4809data.ProjMode='inside';%default
4810create_object(data,handles)
4811
4812%------------------------------------------------------------------------
4813function Menuellipse_Callback(hObject, eventdata, handles)
4814%------------------------------------------------------------------------
4815data.Style='ellipse';
4816data.ProjMode='inside';%default
4817create_object(data,handles)
4818
4819%------------------------------------------------------------------------
4820function MenuMaskObject_Callback(hObject, eventdata, handles)
4821%------------------------------------------------------------------------
4822data.Style='polygon';
4823data.StyleMenu={'polygon'};
4824data.ProjMode='mask_inside';%default
4825data.ProjMenu={'mask_inside';'mask_outside'};
4826create_object(data,handles)
4827
4828%------------------------------------------------------------------------
4829function Menuplane_Callback(hObject, eventdata, handles)
4830%------------------------------------------------------------------------
4831data.Style='plane';
4832data.ProjMode='projection';%default
4833
4834create_object(data,handles)
4835
4836%------------------------------------------------------------------------
4837function Menuvolume_Callback(hObject, eventdata, handles)
4838%------------------------------------------------------------------------
4839data.Style='volume';
4840data.ProjMode='interp';%default
4841% set(handles.create,'Visible','on')
4842% set(handles.create,'Value',1)
4843% VOLUME_Callback(hObject,eventdata,handles)
4844create_object(data,handles)
4845
4846%------------------------------------------------------------------------
4847function MenuBrowseObject_Callback(hObject, eventdata, handles)
4848%------------------------------------------------------------------------
4849%get the object file
4850[FileName, PathName, filterindex] = uigetfile( ...
4851       {'*.xml;*.mat', ' (*.xml,*.mat)';
4852       '*.xml',  '.xml files '; ...
4853        '*.mat',  '.mat matlab files '}, ...
4854        'Pick an xml Object file',get(handles.RootPath,'String'));
4855fileinput=[PathName FileName];%complete file name
4856% testblank=findstr(fileinput,' ');%look for blanks
4857% if ~isempty(testblank)
4858%     msgbox_uvmat('ERROR','forbidden input file name: contain blanks')
4859%     return
4860% end
4861sizf=size(fileinput);
4862if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
4863
4864%read the file
4865t=xmltree(fileinput);
4866data=convert(t);
4867data.enable_plot=1;
4868[pp,data.Name]=fileparts(FileName);
4869%PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
4870hset_object=findobj(allchild(0),'tag','set_object');
4871if ~isempty(hset_object)
4872    delete(hset_object)% delete existing version of set_object
4873end
4874% UvData=get(handles.uvmat,'UserData');
4875set_object(data);% call the set_object interface
4876% %position the set_object GUI with respect to uvmat
4877% pos_uvmat=get(handles.uvmat,'Position');
4878% if isfield(UvData,'SetObjectOrigin')
4879%     pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2);
4880%     pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4);
4881%     set(hset_object,'Position',pos_set_object)
4882% end
4883set(handles.edit_object,'Value',0); %suppress the object edit mode
4884set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4885set(handles.MenuObject,'checked','on')
4886%UvData.MouseAction='create_object';
4887% set(handles.uvmat,'UserData',UvData)
4888set(handles.delete_object,'Visible','on')
4889set(handles.uvmat_title,'Visible','on')
4890set(handles.view_field_title,'Visible','on')
4891
4892%------------------------------------------------------------------------
4893% --- generic function used for the creation of a projection object
4894function create_object(data,handles)
4895%------------------------------------------------------------------------
4896hset_object=findobj(allchild(0),'tag','set_object');
4897if ~isempty(hset_object)
4898    delete(hset_object)% delete existing version of set_object
4899end
4900hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4901if ishandle(hgeometry_calib)
4902    hhgeometry_calib=guidata(hgeometry_calib);
4903    set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4904    set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4905end
4906UvData=get(handles.uvmat,'UserData');
4907set(handles.edit_object,'Value',0); %suppress the object edit mode
4908set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4909data.enable_plot=1;
4910transform_list=get(handles.transform_fct,'String');
4911val=get(handles.transform_fct,'Value');
4912%data.CoordType=transform_list{val};
4913if isfield(UvData,'Field')
4914    Field=UvData.Field;
4915    if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
4916        data.RangeX=Field.Mesh;
4917        data.RangeY=Field.Mesh;
4918        data.DX=Field.Mesh;
4919        data.DY=Field.Mesh;
4920    elseif isfield(Field,'AX')&& isfield(Field,'AY')&& isfield(Field,'A')%only image
4921        np=size(Field.A);
4922        meshx=(Field.AX(end)-Field.AX(1))/np(2);
4923        meshy=abs(Field.AY(end)-Field.AY(1))/np(1);
4924        data.RangeY=max(meshx,meshy);
4925        data.RangeX=max(meshx,meshy);
4926        data.DX=max(meshx,meshy);
4927    end
4928    if isfield(Field,'NbDim')
4929        data.NbDim=Field.NbDim;
4930    end
4931    if isfield(Field,'CoordUnit')
4932        data.CoordUnit=Field.CoordUnit;
4933    end
4934end
4935data.Coord=[0 0 0]; %default
4936if isfield(data,'Style') && isequal(data.Style,'line')
4937    if isfield(data,'DX')
4938        data.Coord=[[0 0 0];[data.DX 0 0]]; %default
4939    else
4940        data.Coord=[[0 0 0];[1 0 0]]; %default
4941    end
4942end
4943if ishandle(handles.UVMAT_title)
4944    delete(handles.UVMAT_title)%delete the initial display of uvmat if no field has been entered
4945end
4946%PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
4947set_object(data,handles);% call the set_object interface
4948set(handles.MenuObject,'checked','on')
4949set(handles.uvmat,'UserData',UvData)
4950set(handles.zoom,'Value',0)
4951zoom_Callback(handles.uvmat, [], handles)
4952set(handles.delete_object,'Visible','on')
4953set(handles.uvmat_title,'Visible','on')
4954set(handles.view_field_title,'Visible','on')
4955
4956%------------------------------------------------------------------------
4957function MenuRuler_Callback(hObject, eventdata, handles)
4958%------------------------------------------------------------------------
4959set(handles.zoom,'Value',0)
4960zoom_Callback(handles.uvmat, [], handles)
4961set(handles.MenuRuler,'checked','on')
4962UvData=get(handles.uvmat,'UserData');
4963UvData.MouseAction='ruler';
4964set(handles.uvmat,'UserData',UvData);
4965
4966%------------------------------------------------------------------------
4967% --- executed when closing: set the parent interface button to value 0
4968function closefcn(gcbo,eventdata)
4969%------------------------------------------------------------------------
4970%delete all the associated figures if exist
4971hh=findobj(allchild(0),'tag','view_field');
4972if ~isempty(hh)
4973    delete(hh)
4974end
4975hh=findobj(allchild(0),'tag','geometry_calib');
4976if ~isempty(hh)
4977    delete(hh)
4978end
4979hh=findobj(allchild(0),'tag','set_object');
4980if ~isempty(hh)
4981    hhh=findobj(hh,'tag','PLOT');
4982    set(hhh,'enable','off')
4983end
4984
4985%------------------------------------------------------------------------
4986% --- Executes on button press in delete_object.
4987function delete_object_Callback(hObject, eventdata, handles)
4988%------------------------------------------------------------------------
4989IndexObj=get(handles.list_object_2,'Value');
4990if IndexObj>1
4991    delete_object(IndexObj)
4992end
4993
4994
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