source: trunk/src/series/civ_input.m @ 598

Last change on this file since 598 was 598, checked in by sommeria, 8 years ago

various bugs repaired . civ_series further developed

File size: 170.4 KB
Line 
1
2%'civ_input': function associated with the interface 'civ_input.fig' for PIV, spline interpolation and stereo PIV (patch)
3%------------------------------------------------------------------------
4%  provides an interface for the software menucivx
5% function varargout = civ_input(varargin)
6% provides an interface for the software menucivx
7%
8%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
9%  Copyright Joel Sommeria, 2011, LEGI / CNRS-UJF-INPG, sommeria@legi.grenoble-inp.fr
10%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11%     This file is part of the toolbox UVMAT.
12%
13%     UVMAT is free software; you can redistribute it and/or modify
14%     it under the terms of the GNU General Public License as published by
15%     the Free Software Foundation; either version 2 of the License, or
16%     (at your option) any later version.
17%
18%     UVMAT is distributed in the hope that it will be useful,
19%     but WITHOUT ANY WARRANTY; without even the implied warranty of
20%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
21%     GNU General Public License (file UVMAT/COPYING.txt) for more details.
22%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
23function varargout = civ_input(varargin)
24%TODO: search range
25
26
27% Last Modified by GUIDE v2.5 01-Apr-2013 10:00:57
28% Begin initialization code - DO NOT EDIT
29gui_Singleton = 1;
30gui_State = struct('gui_Name',       mfilename, ...
31    'gui_Singleton',  gui_Singleton, ...
32    'gui_OpeningFcn', @civ_input_OpeningFcn, ...
33    'gui_OutputFcn',  @civ_input_OutputFcn, ...
34    'gui_LayoutFcn',  [] , ...
35    'gui_Callback',   []);
36
37if nargin && ischar(varargin{1}) && ~isempty(regexp(varargin{1},'_Callback$','once'))
38        gui_State.gui_Callback = str2func(varargin{1});
39end
40
41if nargout
42    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
43else
44    gui_mainfcn(gui_State, varargin{:});
45end
46
47% End initialization code - DO NOT EDIT
48
49%------------------------------------------------------------------------
50% --- Executes just before civ_input is made visible.
51function civ_input_OpeningFcn(hObject, eventdata, handles, Param)
52%------------------------------------------------------------------------
53% This function has no output args, see OutputFcn.
54
55%% General settings
56handles.output = Param;
57guidata(hObject, handles); % Update handles structure
58set(hObject,'WindowButtonDownFcn',{'mouse_down'}) % allows mouse action with right button (zoom for uicontrol display)
59
60%% set visibility options
61        set(handles.num_MaxDiff,'Visible','on')
62        set(handles.num_MaxVel,'Visible','on')
63        set(handles.title_MaxVel,'Visible','on')
64        set(handles.title_MaxDiff,'Visible','on')
65        set(handles.num_Nx,'Visible','off')
66        set(handles.num_Ny,'Visible','off')
67        set(handles.title_Nx,'Visible','off')
68        set(handles.title_Ny,'Visible','off')
69        set(handles.num_CorrSmooth,'Style','popupmenu')
70        set(handles.num_CorrSmooth,'Value',1)
71        set(handles.num_CorrSmooth,'String',{'1';'2'})
72        set(handles.CheckThreshold,'Visible','on')
73        set(handles.CheckDeformation,'Value',0)% desactivate (work in progress)
74        set(handles.CheckDecimal,'Value',0)% desactivate (work in progress)
75       
76%% prepare the GUI with input parameters
77% from the GUI series
78
79%from the input file
80filecell=get_file_series(Param);
81set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
82errormsg=display_file_name(handles,filecell{1});
83if ~isempty(errormsg)
84    msgbox_uvmat('ERROR',errormsg)
85end
86set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
87if isfield(Param,'ActionInput')&&isfield(Param.ActionInput,'Program')&& strcmp(Param.ActionInput.Program,'civ_series')
88    fill_GUI(Param.ActionInput,handles.civ_input)
89end
90set(handles.civ_input,'WindowStyle','modal')% Make the GUI modal
91drawnow
92uiwait(handles.civ_input);
93
94%Program_Callback([],[], handles)
95
96%------------------------------------------------------------------------
97% --- Outputs from this function are returned to the command line.
98function varargout = civ_input_OutputFcn(hObject, eventdata, handles)
99%------------------------------------------------------------------------
100% Get default command line output from handles structure
101varargout{1} = handles.output;
102delete(handles.civ_input)
103
104% --- Executes when user attempts to close get_field.
105function civ_input_CloseRequestFcn(hObject, eventdata, handles)
106if isequal(get(handles.get_field, 'waitstatus'), 'waiting')
107    % The GUI is still in UIWAIT, us UIRESUME
108    uiresume(handles.civ_input);
109else
110    % The GUI is no longer waiting, just close it
111    delete(handles.civ_input);
112end
113%------------------------------------------------------------------------
114% --- Function activated by the Open/Browse... option in the upper menu bar.
115function MenuBrowse_Callback(hObject, eventdata, handles)
116%------------------------------------------------------------------------
117%% get the current input root file name to initiate the browser
118filebase=get(handles.RootPath,'String');
119oldfile=''; %default
120if isempty(filebase)|| isequal(filebase,'')%loads the previously stored root file name
121    dir_perso=prefdir;
122    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
123    if exist(profil_perso,'file')
124        h=load (profil_perso);
125        if isfield(h,'filebase')&& ischar(h.filebase)
126            oldfile=h.filebase;
127        end
128        if isfield(h,'RootPath') && ischar(h.RootPath)
129            oldfile=h.RootPath;
130        end
131    end
132else
133    oldfile=filebase;
134end
135
136%% get the new input file with the browser
137menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)';
138    '*.xml',  '.xml files '; ...
139    '*.civ',  '.civ files '; ...
140    '*.png','.png image files'; ...
141    '*.jpg',' jpeg image files'; ...
142    '*.tif','.tif image files'; ...
143    '*.avi;*.AVI','.avi movie files'; ...
144    '*.nc','.netcdf files'; ...
145    '*.*',  'All Files (*.*)'};
146[FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file',oldfile);
147fileinput=[PathName FileName];%complete file name
148sizf=size(fileinput);
149if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
150
151%% case of the xml file opened as input (TODO: check and see whether it is useful)
152[path,name,ext]=fileparts(fileinput);
153testeditxml=0;
154% if isequal(ext,'.xml')
155%     testeditxml=1;
156%     t_browse=xmltree(fileinput);
157%     head_element=get(t_browse,1);
158%     if isfield(head_element,'name')&& isequal(head_element.name,'ImaDoc')
159%         testeditxml=0;
160%     end
161% end
162% if testeditxml==1 || isequal(ext,'.xls')
163%     heditxml=editxml({fileinput});
164%     set(heditxml,'Tag','browser')
165%     waitfor(heditxml,'Tag','idle')
166%     if ~ishandle(heditxml)
167%         return
168%     end
169%     attr=findobj(get(heditxml,'children'),'Tag','CurrentAttributes');
170%     set(handles.browse,'UserData',fileinput)% store for future opening with browser
171%     fileinput=get(attr,'UserData');
172%     if ~exist(fileinput,'file')
173%         return
174%     end
175% end
176[tild,tild,tild,i1,i2,j1,j2,FileExt,NomType]=fileparts_uvmat(fileinput);
177
178%% prepare the GUI with parameters from the input file
179set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
180errormsg=display_file_name(handles,fileinput);
181if ~isempty(errormsg)
182    msgbox_uvmat('ERROR',erromsg)
183end
184set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
185
186%------------------------------------------------------------------------
187% --- Open again the file whose name has been recorded in MenuFile_1
188function MenuFile_1_Callback(hObject, eventdata, handles)
189%------------------------------------------------------------------------
190set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
191fileinput=get(handles.MenuFile_1,'Label');
192errormsg=display_file_name(handles,fileinput);
193if ~isempty(errormsg)
194    msgbox_uvmat('ERROR',errormsg)
195end
196set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
197
198% -----------------------------------------------------------------------
199% --- Open again the file whose name has been recorded in MenuFile_2
200function MenuFile_2_Callback(hObject, eventdata, handles)
201%------------------------------------------------------------------------
202set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
203fileinput=get(handles.MenuFile_2,'Label');
204errormsg=display_file_name(handles,fileinput);
205if ~isempty(errormsg)
206    msgbox_uvmat('ERROR',errormsg)
207end
208set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
209
210% -----------------------------------------------------------------------
211% --- Open again the file whose name has been recorded in MenuFile_3
212function MenuFile_3_Callback(hObject, eventdata, handles)
213%------------------------------------------------------------------------
214set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
215fileinput=get(handles.MenuFile_3,'Label');
216errormsg=display_file_name(handles,fileinput);
217if ~isempty(errormsg)
218    msgbox_uvmat('ERROR',errormsg)
219end
220set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
221
222% -----------------------------------------------------------------------
223% --- Open again the file whose name has been recorded in MenuFile_4
224function MenuFile_4_Callback(hObject, eventdata, handles)
225%------------------------------------------------------------------------
226set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
227fileinput=get(handles.MenuFile_4,'Label');
228errormsg=display_file_name(handles,fileinput);
229if ~isempty(errormsg)
230    msgbox_uvmat('ERROR',errormsg)
231end
232set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
233
234% -----------------------------------------------------------------------
235% --- Open again the file whose name has been recorded in MenuFile_5
236function MenuFile_5_Callback(hObject, eventdata, handles)
237%------------------------------------------------------------------------
238set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
239fileinput=get(handles.MenuFile_5,'Label');
240errormsg=display_file_name(handles,fileinput);
241if ~isempty(errormsg)
242    msgbox_uvmat('ERROR',errormsg)
243end
244set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
245
246% -----------------------------------------------------------------------
247% -----------------------------------------------------------------------
248% --- Open the help html file
249function MenuHelp_Callback(hObject, eventdata, handles)
250% -----------------------------------------------------------------------
251path_civ=fileparts(which ('civ'));
252helpfile=fullfile(path_civ,'uvmat_doc','uvmat_doc.html');
253if isempty(dir(helpfile))
254    msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
255else
256    addpath (fullfile(path_civ,'uvmat_doc'))
257    web([helpfile '#civ'])
258end
259
260%------------------------------------------------------------------------
261% --- Function activated when a new filebase (image series) is introduced
262function RootPath_Callback(hObject, eventdata, handles)
263%------------------------------------------------------------------------
264set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
265RootPath=get(handles.RootPath,'String');
266SubDirImages=get(handles.SubDirImages,'String');
267RootFile=get(handles.RootFile,'String');
268ref_i=str2num(get(handles.ref_i,'String'));
269ref_j=str2num(get(handles.ref_j,'String'));
270NomType=get(handles.NomType,'String');
271ImaExt=get(handles.ImaExt,'String');
272fileinput=fullfile_uvmat(RootPath,SubDirImages,RootFile,ImaExt,NomType,ref_i,[],ref_j);
273errormsg=display_file_name(handles,fileinput);
274if ~isempty(errormsg)
275    msgbox_uvmat('ERROR',errormsg)
276end
277set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
278
279%------------------------------------------------------------------------
280% --- general function activated for an input file series
281function errormsg=display_file_name(handles,fileinput)
282%------------------------------------------------------------------------
283set(handles.ListCompareMode,'Visible','on')
284errormsg='';%default empty error message
285drawnow
286
287%% enable OK, BATCH button and 'status' display
288% set(handles.OK, 'Enable','On')
289% set(handles.OK,'BackgroundColor',[1 0 0])%set RUN button to red color
290% if isfield(handles,'status')
291%     set(handles.status,'Value',0);       %suppress the 'status' display
292%     status_Callback([], [], handles)
293% end
294
295%% determine nomenclature types and extension of the input files
296[RootPath,SubDir,RootFile,i1,i2,j1,j2,ExtInput,NomTypeInput]=fileparts_uvmat(fileinput);
297NomTypeNc='';%default
298
299%% case of xml file as input, read the civ_input parameters
300ind_opening=0;%default
301if strcmp(ExtInput,'.xml')
302    %reinitialise menus
303        set(handles.ListPairMode,'Value',1)
304    set(handles.ListPairMode,'String',{''})
305    set(handles.ListPairCiv1,'Value',1)
306    set(handles.ListPairCiv1,'String',{''})
307        set(handles.ListPairCiv2,'Value',1)
308    set(handles.ListPairCiv2,'String',{''})
309    Param=xml2struct(fileinput);  %read parameters from the xml input file
310    fill_GUI(Param,handles);%fill the GUI with the parameters retrieved from the xml file
311    return
312end
313
314%% case of netcdf file as input, get the civ_input processing stage and look for a coresponding image
315imageinput=fileinput;%default
316if strcmp(ExtInput,'.nc')
317    NomTypeNc=NomTypeInput;
318    if isempty(regexp(NomTypeInput,'[ab|AB|-]', 'once'))
319        set(handles.ListCompareMode,'Value',2) %mode displacement advised if the nomencalture does not involve index pairs
320        set(handles.RootFile_1,'Visible','On');
321    else
322        set(handles.ListCompareMode,'Value',1)
323        set(handles.RootFile_1,'Visible','Off');
324    end
325    imageinput='';
326    Data=nc2struct(fileinput,'ListGlobalAttribute','Conventions','absolut_time_T0','CivStage','Civ2_ImageA','Civ1_ImageA','Civ2_ImageB','Civ1_ImageB','fix','patch','civ2','fix2');
327    if isfield(Data,'Txt')
328        errormsg=Data.Txt;
329        return
330    end
331    % settings for  new civ_input data,
332    if strcmp(Data.Conventions,'uvmat/civdata')% case of new civ data,
333        set(handles.Program,'Value',1) %select civ/Matlab by default
334        Program_Callback([],[], handles)
335        if ~isempty(Data.CivStage)%test for civ files
336            ind_opening=Data.CivStage;
337        end
338        if  ~isempty(Data.Civ2_ImageB)%get the corresponding input image in the netcdf file
339            imageinput=Data.Civ2_ImageB;
340            [tild,ImaName,ImaExt]=fileparts(Data.Civ2_ImageA);
341            set(handles.RootFile_1,'String',[ImaName ImaExt])
342        elseif ~isempty(Data.Civ1_ImageB)
343            imageinput=Data.Civ1_ImageB;
344            [tild,ImaName,ImaExt]=fileparts(Data.Civ1_ImageA);
345            set(handles.RootFile_1,'String',[ImaName ImaExt])
346        end
347        % settings for civx data,
348    elseif ~isempty(Data.absolut_time_T0')% case of  civx data,
349        set(handles.Program,'Value',3) %select Cix by default
350        Program_Callback([],[], handles)
351        if ~isempty(Data.fix2)
352            ind_opening=5;
353        elseif ~isempty(Data.civ2)
354            ind_opening=4;
355        elseif ~isempty(Data.patch)
356            ind_opening=3;
357        elseif ~isempty(Data.fix)
358            ind_opening=2;
359        end
360    else
361        errormsg='the input netcdf file is not civ data';
362        return
363    end
364    % look for the corresponding input images
365    check_letter=~isempty(regexp(NomTypeInput,'[ab|AB]$','once'));%detect pair label by letter
366    NomTypeIma=NomTypeInput;
367    if check_letter
368        NomTypeIma=NomTypeInput(1:end-1);
369    else
370        r=regexp(NomTypeIma,'.-(?<num2>\d+)$','names');
371        if ~isempty(r)
372            NomTypeIma=regexprep(NomTypeIma,['-' r.num2],'');
373        end
374        r=regexp(NomTypeIma,'.-(?<num2>\d+)','names');
375        if ~isempty(r)
376            NomTypeIma=regexprep(NomTypeIma,['-' r.num2],'');
377        end
378    end
379    if ~exist(imageinput,'file')
380    imageinput=fullfile_uvmat(RootPath,regexprep(SubDir,'.civ(_?)(\d*)$',''),RootFile,'.png',NomTypeIma,i1,[],j1);
381    end
382end
383
384%% no corresponding image found, select manually with the browser
385ImaExt=ExtInput;
386if ~isempty(NomTypeNc)
387    %no corresponding image found, select manually with the browser
388    if ~exist(imageinput,'file')
389        menu={'*.png;*.jpg;*.tif;*.avi;*.AVI', '(*.png,*.jpg ,*.tif, *.avi,*.AVI)';
390            '*.png','.png image files'; ...
391            '*.jpg',' jpeg image files'; ...
392            '*.tif','.tif image files'; ...
393            '*.avi;*.AVI','.avi movie files'; ...
394            '*.*',  'All Files (*.*)'};
395        [FileName, PathName] = uigetfile( menu, 'Pick an input image file',fileparts(fileparts(fileinput)));
396        imageinput=[PathName FileName];%complete file name
397        if ~exist(imageinput,'file')
398            return %abandon of the browser is cancelled
399        end
400    end   
401    %fileinput=imageinput;
402end
403
404%% scan the image file series
405[FilePath,FileName,ImaExt]=fileparts(imageinput);
406% detect the file type, get the movie object if relevant, and look for the corresponding file series:
407% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
408[RootPath,SubDirImages,RootFile,i1_series,tild,j1_series,tild,NomTypeIma,FileType,MovieObject]=find_file_series(FilePath,[FileName ImaExt]);
409switch FileType
410    case {'image','multimage','video','mmreader'}
411    otherwise
412        errormsg='invalid input file: enter an image, a movie or civ .nc file';
413        return
414end
415set(handles.RootPath,'String',RootPath)
416set(handles.SubDirImages,'String',SubDirImages)
417set(handles.RootFile,'String',RootFile)
418if strcmp(ExtInput,'.nc')
419    SubDirCiv=regexprep(SubDir,['^' SubDirImages],'');%suppress the root  SuddirImages;
420else
421    SubDirCiv= '.civ';
422end
423set(handles.SubdirCiv1,'String',SubDirCiv)
424set(handles.SubdirCiv2,'String',SubDirCiv)
425browse=get(handles.RootPath,'UserData');
426browse.incr_pair=[0 0];%default
427
428%% scan the images if a civ_input file has been opened
429MinIndex_i=min(i1_series(i1_series>0));
430MinIndex_j=min(j1_series(j1_series>0));
431MaxIndex_i=max(i1_series(i1_series>0));
432MaxIndex_j=max(j1_series(j1_series>0));
433
434%% look for an image documentation file
435XmlFileName=find_imadoc(RootPath,SubDir,RootFile,ImaExt);
436if isempty(XmlFileName)
437    if (strcmp(FileType,'video') || strcmp(FileType,'mmreader'))
438        ext_imadoc=ImaExt;% the timing from the video movie is used
439    else
440        ext_imadoc='';
441    end
442else
443    [tild,tild,ext_imadoc]=fileparts(XmlFileName);
444end
445set(handles.ImaDoc,'String',ext_imadoc)% display the extension name for the image documentation file used
446
447%%  read the time in the image documentation file 
448time=[];
449TimeUnit=''; %default
450CoordUnit='';%default
451pxcm_search=1;
452if ~isempty(XmlFileName)
453    set(handles.ImaDoc,'BackgroundColor',[1 1 0]) % set edit box to yellow cloro to indicate that the file reading is beginning
454    drawnow
455    [XmlData,warntext]=imadoc2struct(XmlFileName);
456    nom_type_read=[];
457    if isfield(XmlData,'Time') && ~isempty(XmlData.Time)
458        time=XmlData.Time;
459        %transform .Time to a column vector if it is a line vector thenomenclature uses a single index: correct possible bug in xml
460        if isequal(MaxIndex_i,1) && ~isequal(MaxIndex_j,1)% .Time is a line vector
461            if numel(nom_type_read)>=2 && isempty(regexp(nom_type_read(2:end),'\D','once'))
462                time=time';
463                MaxIndex_i=MaxIndex_j;
464                MaxIndex_j=1;
465            end
466        end
467    end
468    if isfield(XmlData,'Camera') && isfield(XmlData.Camera,'TimeUnit')
469        TimeUnit=XmlData.Camera.TimeUnit;
470    end
471    if isfield(XmlData,'GeometryCalib')
472        tsai=XmlData.GeometryCalib;
473        if isfield(tsai,'fx_fy')
474            pxcm_search=max(tsai.fx_fy(1),tsai.fx_fy(2));%pixels:cm estimated for the search range
475        end
476        if isfield(tsai,'CoordUnit')
477            CoordUnit=tsai.CoordUnit;
478        end
479    end
480end
481if isempty(time) && (strcmp(FileType,'video') || strcmp(FileType,'mmreader'))
482    set(handles.ListPairMode,'Value',1);
483    dt=1/get(MovieObject,'FrameRate');%time interval between successive frames
484    if strcmp(NomTypeIma,'*')
485        set(handles.ListPairMode,'String',{'series(Di)'})
486        MaxIndex_i=get(MovieObject,'NumberOfFrames');
487        time=(dt*(0:MaxIndex_i-1))';%list of image times
488    else
489        set(handles.ListPairMode,'String',[{'series(Dj)'};{'series(Di)'}])
490        MaxIndex_i=max(i1_series(i1_series>0));
491        MaxIndex_j=get(MovieObject,'NumberOfFrames');
492        time=ones(MaxIndex_i,1)*(dt*(0:MaxIndex_j-1));%list of image times
493        enable_j(handles,'on')
494    end
495    TimeUnit='s';
496    set(handles.ImaDoc,'BackgroundColor',[1 1 1])% set display box back to whiter
497end
498
499%% timing display
500%show the reference image edit box if relevant (not needed for movies or in the absence of time information
501if numel(time)>=2 % if there are at least two time values to define dt
502    if size(time,1)<MaxIndex_i;
503        msgbox_uvmat('WARNING','maximum i index restricted by the timing of the xml file');
504    elseif size(time,2)<MaxIndex_j
505        msgbox_uvmat('WARNING','maximum j index restricted by the timing of the xml file');
506    end
507    MaxIndex_i=min(size(time,1),MaxIndex_i);%possibly adjust the max index according to time data
508    MaxIndex_j=min(size(time,2),MaxIndex_j);
509    time=[zeros(size(time,1),1) time]; %insert a vertical line of zeros (to deal with zero file indices)
510    time=[zeros(1,size(time,2)); time]; %insert a horizontal line of zeros
511else
512    set(handles.ImaDoc,'String',''); %xml file not used for timing
513    time=(i1_series(:,1)+0:size(i1_series,3)-1);% time=index i
514    time=time'*ones(1,size(i1_series,2),1); %makes a time matrix with the same time for all j indices
515    TimeUnit='frame';
516end
517set(handles.ImaDoc,'UserData',time); %store the matrix of times
518set(handles.dt_unit,'String',['dt in m' TimeUnit]);%display dt in unit 10-3 of the time (e.g ms)
519set(handles.TimeUnit,'String',TimeUnit);
520set(handles.nb_field,'String',num2str(MaxIndex_i));
521set(handles.nb_field2,'String',num2str(MaxIndex_j));
522set(handles.CoordUnit,'String',CoordUnit)
523set(handles.SearchRange,'UserData', pxcm_search);
524set(handles.ImaExt,'String',ImaExt)
525set(handles.NomType,'String',NomTypeIma)
526
527%% set the reference indices from the input file indices
528num_ref_i=str2num(get(handles.ref_i,'String'));
529num_ref_j=str2num(get(handles.ref_j,'String'));
530% for movies don't modify except if the current ref is outside index bounds
531%if strcmp(ExtInput,'.nc')|| ~(strcmp(FileType,'mmreader')||strcmp(FileType,'VideoReader') && num_ref_i<=MaxIndex_i && num_ref_j<=MaxIndex_j)
532if ~isempty(i1)% if i1 has been selected by the input
533    num_ref_i=i1;%default ref index
534    if ~isempty(i2)
535        num_ref_i=floor((num_ref_i+i2)/2);
536    end
537    if ~isempty(j1)
538    num_ref_j=j1;
539    if ~isempty(j2)
540        num_ref_j=floor((num_ref_j+j2)/2);
541    end
542    end
543end
544if num_ref_i>MaxIndex_i||num_ref_i<MinIndex_i
545    num_ref_i=round((MinIndex_i+MaxIndex_i)/2);
546end
547if ~isempty(num_ref_j)&&~isempty(MaxIndex_j)&& ~isempty(MinIndex_j)
548    if (num_ref_j>MaxIndex_j||num_ref_j<MinIndex_j)
549        num_ref_j=round((MinIndex_j+MaxIndex_j)/2);
550    end
551end
552if isempty(num_ref_j)
553    num_ref_j=1;
554end
555
556%% update i and j index range if a nc file has been opened or pb withmin max image indices:
557% then set first and last to the inputfile index by default
558first_i=str2num(get(handles.first_i,'String'));
559last_i=str2num(get(handles.last_i,'String'));
560if isempty(first_i) || isempty(last_i)||isempty(MinIndex_i)||isempty(MaxIndex_i)||ind_opening~=0 || isempty(first_i) || isempty(last_i)|| first_i<MinIndex_i || last_i>MaxIndex_i
561   first_i=num_ref_i;
562   last_i=num_ref_i;
563    set(handles.first_i,'String',num2str(first_i));
564    set(handles.last_i,'String',num2str(last_i));%
565end
566
567%j index range
568first_j=str2num(get(handles.first_j,'String'));
569last_j=str2num(get(handles.last_j,'String'));
570if isempty(first_j) || isempty(last_j)||isempty(MinIndex_j)||isempty(MaxIndex_j)||ind_opening~=0 || first_j<MinIndex_j || last_j>MaxIndex_j
571       first_j=num_ref_j;
572   last_j=num_ref_j;
573    set(handles.first_j,'String',num2str(first_j));
574    set(handles.last_j,'String',num2str(last_j));%
575end
576if num_ref_i>last_i || num_ref_i<first_i
577    num_ref_i=round((first_i+last_i)/2);
578end
579if num_ref_j>last_j || num_ref_j<first_j
580    num_ref_j=round((first_j+last_j)/2);
581end
582set(handles.ref_i,'String',num2str(num_ref_i))
583set(handles.ref_j,'String',num2str(num_ref_j))
584
585%% set the civ_input options depending on the input file content when a nc file has been opened
586ListOptions={'CheckCiv1', 'CheckFix1' 'CheckPatch1', 'CheckCiv2', 'CheckFix2', 'CheckPatch2'};
587checkbox=zeros(size(ListOptions));%default
588if ind_opening==0%case of image opening, start with Civ1
589    for index=1:numel(ListOptions)
590        checkbox(index)=get(handles.(ListOptions{index}),'Value');
591    end
592    index_max=find(checkbox, 1, 'last' );
593    if isempty(index_max),index_max=1;end       
594    for index=1:index_max
595        set(handles.(ListOptions{index}),'Value',1)% select all operations starting from CIV1
596    end
597else
598    for index = 1:min(ind_opening,5)
599        set(handles.(ListOptions{index}),'value',0)
600    end
601    set(handles.(ListOptions{min(ind_opening+1,6)}),'value',1)
602    for index = ind_opening+2:6
603        set(handles.(ListOptions{index}),'value',0)
604    end
605end
606%list_operation={'CheckCiv1','CheckFix1','CheckPatch1','CheckCiv2','CheckFix2','CheckPatch2'};
607
608%set(handles.(ListOptions{min(ind_opening+1,6)}),'value',1)
609update_CivOptions(handles,ind_opening)
610
611%%  set the menus of image pairs and default selection for civ_input   %%%%%%%%%%%%%%%%%%%
612%check_letter=~isempty(regexp(NomTypeIma,'[ab|AB]$'));%detect pair label by letter
613if  isequal(NomTypeNc,'_1-2')||isempty(MaxIndex_j)|| (MaxIndex_j==1)
614    set(handles.ListPairMode,'Value',1)
615    set(handles.ListPairMode,'String',{'series(Di)'})   
616elseif  MaxIndex_i==1 && MaxIndex_j>1% simple series in j
617    set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)'})
618    if  MaxIndex_j <= 10
619        set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large
620    end
621elseif ~(strcmp(FileType,'video') || strcmp(FileType,'mmreader'))
622    set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)';'series(Di)'})%multiple choice
623    if strcmp(NomTypeNc,'_1-2_1')
624        set(handles.ListPairMode,'Value',3)% advise 'series(Di)'
625    elseif  MaxIndex_j <= 10
626        set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large
627    end
628end
629
630%% scan files to update the subdirectory list display
631listot=dir(RootPath);%directory of RootPath
632idir=0;
633listdir={''};%default
634% get the list of existing civ_input subdirectories in the path of theinput root  file
635for ilist=1:length(listot)
636    if listot(ilist).isdir
637        name=listot(ilist).name;
638        if ~isequal(name,'.') && ~isequal(name,'..')
639            idir=idir+1;
640            listdir{idir,1}=listot(ilist).name;
641        end
642    end
643end
644
645%% store info
646set(handles.RootPath,'UserData',browse)% store the nomenclature type
647
648%% list the possible index pairs, depending on the option set in ListPairMode
649ListPairMode_Callback([], [], handles)
650
651%% store the root input filename for future opening
652profil_perso=fullfile(prefdir,'uvmat_perso.mat');
653if exist(profil_perso,'file')
654    save (profil_perso,'RootPath','-append'); %store the root name for future opening of uvmat
655else
656    txt=ver('MATLAB');
657    Release=txt.Release;
658    relnumb=str2double(Release(3:4));
659    if relnumb >= 14
660        save (profil_perso,'RootPath','-V6'); %store the root name for future opening of uvmat
661    else
662        save (profil_perso,'RootPath'); %store the root name for future opening of uvmat
663    end
664end
665set(handles.RootPath,'BackgroundColor',[1 1 1])
666
667%------------------------------------------------------------------------
668% --- Executes on carriage return on the subdir checkciv1 edit window
669function SubdirCiv1_Callback(hObject, eventdata, handles)
670%------------------------------------------------------------------------
671SubDir=get(handles.SubdirCiv1,'String');
672menu_str=get(handles.ListSubdirCiv1,'String');% read the list of subdirectories for update
673ichoice=find(strcmp(SubDir,menu_str),1);
674if isempty(ichoice)
675    ilist=numel(menu_str); %select 'new...' in the menu
676else
677    ilist=ichoice;
678end
679set(handles.ListSubdirCiv1,'Value',ilist)% select the selected subdir in the menu
680if get(handles.CheckCiv1,'Value')% if Civ1 is performed
681    set(handles.SubdirCiv2,'String',SubDir);% set by default civ2 directory the same as civ1
682%     set(handles.ListSubdirCiv2,'Value',ilist)
683else % if Civ1 data already exist
684    errormsg=find_netcpair_civ(handles,1); %update the list of available pairs from netcdf files in the new directory
685    if ~isempty(errormsg)
686    msgbox_uvmat('ERROR',errormsg)
687    end
688end
689
690%------------------------------------------------------------------------
691% --- Executes on carriage return on the SubDir checkciv1 edit window
692function SubdirCiv2_Callback(hObject, eventdata, handles)
693%------------------------------------------------------------------------
694SubDir=get(handles.SubdirCiv1,'String');
695menu_str=get(handles.ListSubdirCiv2,'String');% read the list of subdirectories for update
696ichoice=find(strcmp(SubDir,menu_str),1);
697if isempty(ichoice)
698    ilist=numel(menu_str); %select 'new...' in the menu
699else
700    ilist=ichoice;
701end
702set(handles.ListSubdirCiv2,'Value',ilist)% select the selected subdir in the menu
703%update the list of available pairs from netcdf files in the new directory
704if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
705    errormsg=find_netcpair_civ(handles,2);
706        if ~isempty(errormsg)
707    msgbox_uvmat('ERROR',errormsg)
708    end
709end
710
711%------------------------------------------------------------------------
712% --- Executes on button press in CheckCiv1.
713function CheckCiv1_Callback(hObject, eventdata, handles)
714%------------------------------------------------------------------------
715update_CivOptions(handles,0)
716
717%------------------------------------------------------------------------
718% --- Executes on button press in CheckFix1.
719function CheckFix1_Callback(hObject, eventdata, handles)
720%------------------------------------------------------------------------
721update_CivOptions(handles,0)
722
723%------------------------------------------------------------------------
724% --- Executes on button press in CheckPatch1.
725function CheckPatch1_Callback(hObject, eventdata, handles)
726%------------------------------------------------------------------------
727update_CivOptions(handles,0)
728
729%------------------------------------------------------------------------
730% --- Executes on button press in CheckCiv2.
731function CheckCiv2_Callback(hObject, eventdata, handles)
732%------------------------------------------------------------------------
733update_CivOptions(handles,0)
734
735%------------------------------------------------------------------------
736% --- Executes on button press in CheckFix2.
737function CheckFix2_Callback(hObject, eventdata, handles)
738%------------------------------------------------------------------------
739update_CivOptions(handles,0)
740
741%------------------------------------------------------------------------
742% --- Executes on button press in CheckPatch2.
743function CheckPatch2_Callback(hObject, eventdata, handles)
744%------------------------------------------------------------------------
745update_CivOptions(handles,0)
746
747%------------------------------------------------------------------------
748% --- activated by any checkbox controling the selection of Civ1,Fix1,Patch1,Civ2,Fix2,Patch2
749function update_CivOptions(handles,opening)
750%------------------------------------------------------------------------
751checkbox=zeros(1,6);
752checkbox(1)=get(handles.CheckCiv1,'Value');
753checkbox(2)=get(handles.CheckFix1,'Value');
754checkbox(3)=get(handles.CheckPatch1,'Value');
755checkbox(4)=get(handles.CheckCiv2,'Value');
756checkbox(5)=get(handles.CheckFix2,'Value');
757checkbox(6)=get(handles.CheckPatch2,'Value');
758ind_selected=find(checkbox,1);
759if ~isempty(ind_selected)
760    RootPath=get(handles.RootPath,'String');
761    if isempty(RootPath)
762        msgbox_uvmat('ERROR','Please open an image or PIV .nc file with the upper bar menu Open/Browse...')
763        return
764    end
765end
766set(handles.PairIndices,'Visible','on')
767set(handles.SubdirCiv1,'Visible','on')
768set(handles.TitleSubdirCiv1,'Visible','on')
769if opening==0
770    errormsg=find_netcpair_civ(handles,1); % select the available netcdf files
771    if ~isempty(errormsg)
772        msgbox_uvmat('ERROR',errormsg)
773    end
774end
775if max(checkbox(4:6))% case of civ2 pair choice needed
776    set(handles.TitlePairCiv2,'Visible','on')
777    set(handles.TitleSubdirCiv2,'Visible','on')
778    set(handles.SubdirCiv2,'Visible','on')
779    %set(handles.ListSubdirCiv2,'Visible','on')
780    set(handles.ListPairCiv2,'Visible','on')
781    if ~opening
782        errormsg=find_netcpair_civ(handles,2); % select the available netcdf files
783        if ~isempty(errormsg)
784            msgbox_uvmat('ERROR',errormsg)
785        end
786    end
787else
788    set(handles.TitleSubdirCiv2,'Visible','off')
789    set(handles.SubdirCiv2,'Visible','off')
790    set(handles.ListPairCiv2,'Visible','off')
791end
792options={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'};
793for ilist=1:length(options)
794    if checkbox(ilist)
795        set(handles.(options{ilist}),'Visible','on')
796    else
797        set(handles.(options{ilist}),'Visible','off')
798    end
799end
800
801%------------------------------------------------------------------------
802% --- Executes on button press in OK: processing on local computer
803function OK_Callback(hObject, eventdata, handles)
804%------------------------------------------------------------------------
805
806handles.output.ActionInput=read_GUI(handles.civ_input);
807guidata(hObject, handles);% Update handles structure
808uiresume(handles.civ_input);
809drawnow
810
811return
812
813
814set(handles.OK, 'Enable','Off')
815set(handles.OK,'BackgroundColor',[0.831 0.816 0.784])
816set(handles.OK,'UserData',now)% record the time of launch
817
818errormsg=launch_jobs(hObject, eventdata, handles);
819set(handles.OK, 'Enable','On')
820set(handles.OK,'BackgroundColor',[1 0 0])
821
822% display errors or start status callback to visualise results
823if ~isempty(errormsg)
824    display(errormsg)
825    msgbox_uvmat('ERROR',errormsg)
826elseif  isfield(handles,'status') %&& ~isequal(get(handles.ListPairMode,'Value'),3)
827    set(handles.status,'Value',1);%suppress status display
828    status_Callback(hObject, eventdata, handles)
829end
830
831% %-------------------------------------------------------------------
832% % --- Executes on button press in status.
833% function status_Callback(hObject, eventdata, handles)
834% %-------------------------------------------------------------------
835% val=get(handles.status,'Value');
836% if val==0
837%     set(handles.status,'BackgroundColor',[0 1 0])
838%     hfig=findobj(allchild(0),'name','civ_status');
839%     if ~isempty(hfig)
840%         delete(hfig)
841%     end
842%     return
843% end
844% set(handles.status,'BackgroundColor',[1 1 0])
845% drawnow
846% listtype={'civ1','fix1','patch1','civ2','fix2','patch2'};
847% Param.CheckCiv1=get(handles.CheckCiv1,'Value');
848% Param.CheckFix1=get(handles.CheckFix1,'Value');
849% Param.CheckPatch1=get(handles.CheckPatch1,'Value');
850% Param.CheckCiv2=get(handles.CheckCiv2,'Value');
851% Param.CheckFix2=get(handles.CheckFix2,'Value');
852% Param.CheckPatch2=get(handles.CheckPatch2,'Value');
853% box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2];
854%
855% option_civ=find(box_test,1,'last');%last selected option (non-zero index of box_test)
856% filecell=get(handles.civ_input,'UserData');%retrieve the list of output files expected for PIV
857% test_new=0;
858% if ~isfield(filecell,'nc')
859%     test_new=1;
860%     [ref_i,ref_j,errormsg]=find_ref_indices(handles);
861%     if ~isempty(errormsg)
862%         msgbox_uvmat('ERROR',errormsg)
863%         return
864%     end
865%     filecell=set_civ_filenames(handles,ref_i,ref_j,box_test);%determine the output file expected from the GUI status
866% end
867% if ~isequal(box_test(4:6),[0 0 0])
868%     civ_files=filecell.nc.civ2;%case of civ2 operations
869% else
870%     civ_files=filecell.nc.civ1;
871% end
872% [root,filename,ext]=fileparts(civ_files{1});
873% [rootroot,SubDir,extdir]=fileparts(root);
874% hfig=findobj(allchild(0),'name','civ_status');
875% if isempty(hfig)
876%     hfig=figure('DeleteFcn',@stop_status);
877%     set(hfig,'MenuBar','none')% suppress the menu bar
878%     set(hfig,'NumberTitle','off')%suppress the fig number in the title
879%     set(hfig,'name','civ_status')
880%     set(hfig,'tag','civ_status')
881%     set(hfig,'UserData',civ_files)
882%     hlist= uicontrol('Style','listbox','Units','normalized', 'Position',[0.05 0.09 0.9 0.71], 'Callback', {'open_uvmat'},'tag','list');
883%     uicontrol('Style','edit','Units','normalized', 'Position', [0.05 0.87 0.9 0.1],'tag','msgbox','Max',2,'String','checking files...');
884%     uicontrol('Style','frame','Units','normalized', 'Position', [0.05 0.81 0.9 0.05]);
885%     %uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.7 0.01 0.2 0.07],'String','Close','FontWeight','bold','FontUnits','normalized','FontSize',0.9,'Callback',@close_GUI);
886%     uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.7 0.01 0.2 0.07],'String','Close','FontWeight','bold','FontUnits','normalized','FontSize',0.9,'Callback',@stop_status);
887%     hrefresh=uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.1 0.01 0.2 0.07],'String','Refresh','FontWeight','bold','FontUnits','normalized','FontSize',0.9,'Callback',@refresh_GUI);
888%     BarPosition=[0.05 0.81 0.01 0.05];
889%     uicontrol('Style','frame','Units','normalized', 'Position',BarPosition ,'BackgroundColor',[1 0 0],'tag','waitbar');
890%     drawnow
891% end
892% StatusData.time_ref=get(handles.OK,'UserData');% get the time of launch
893% StatusData.option_civ=option_civ;
894% set(hrefresh,'UserData',StatusData)
895% filepath=fileparts(civ_files{1});
896% set(hlist,'UserData',fileparts(filepath))
897% refresh_GUI(hrefresh,[])
898
899% %------------------------------------------------------------------------   
900% % launched by refreshing the status figure
901% function refresh_GUI(hObject, eventdata)
902% %------------------------------------------------------------------------
903% Tabchar={};
904% BarPosition=[0.05 0.81 0.01 0.05];
905% hfig=get(hObject,'parent');
906% StatusData=get(hObject,'UserData');
907% civ_files=get(hfig,'UserData');
908% [filepath,filename,ext]=fileparts(civ_files{1});
909% [tild,SubDir,extdir]=fileparts(filepath);
910% SubDir=[SubDir extdir];
911% option_civ=StatusData.option_civ;
912% nbfiles=numel(civ_files);
913% testrecent=0;
914% count=0;
915% datnum=zeros(1,nbfiles);
916% filefound=cell(1,nbfiles);
917% for ifile=1:nbfiles
918%     detect=exist(civ_files{ifile},'file'); % check the existence of the file
919%     option=0;
920%     if detect==0
921%         option_str='not created';
922%     else
923%         datfile=dir(civ_files{ifile});
924%         if isfield(datfile,'datenum')
925%             datnum(ifile)=datfile.datenum;%only available in recent matlab versions
926%             testrecent=1;
927%         end
928%         filefound(ifile)={datfile.name};
929%         
930%         % check the content  netcdf file
931%         Data=nc2struct(civ_files{ifile},'ListGlobalAttribute','CivStage','patch2','fix2','civ2','patch','fix');
932%         option_list={'civ1','fix1','patch1','civ2','fix2','patch2'};
933%         if ~isempty(Data.CivStage)
934%             option=Data.CivStage;%case of Matlab civ
935%         else
936%             if ~isempty(Data.patch2) && isequal(Data.patch2,1)
937%                 option=6;
938%             elseif ~isempty(Data.fix2) && isequal(Data.fix2,1)
939%                 option=5;
940%             elseif ~isempty(Data.civ2) && isequal(Data.civ2,1);
941%                 option=4;
942%             elseif ~isempty(Data.patch) && isequal(Data.patch,1);
943%                 option=3;
944%             elseif ~isempty(Data.fix) && isequal(Data.fix,1);
945%                 option=2;
946%             else
947%                 option=1;
948%             end
949%         end
950%         option_str=option_list{option};
951%         if datnum(ifile)<StatusData.time_ref
952%             option_str=[option_str '  --OLD--'];
953%         end
954%     end
955%     if option >= option_civ
956%         count=count+1;
957%     end
958%     [filepath,filename,ext]=fileparts(civ_files{ifile});
959%     Tabchar{ifile,1}=[fullfile(SubDir,filename) ext  '...' option_str];
960% end
961% datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
962% if isempty(datnum)
963%     if testrecent
964%         message='no civ result created yet';
965%     else
966%         message='';
967%     end
968% else
969%     datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
970%     [first,ind]=min(datnum);
971%     [last,indlast]=max(datnum);
972%     message={[num2str(count) ' file(s) done over ' num2str(nbfiles)] ;['oldest modification:  ' cell2mat(filefound(ind)) ' : ' datestr(first)];...
973%         ['latest modification:  ' cell2mat(filefound(indlast)) ' : ' datestr(last)]};
974% end
975% hlist=findobj(hfig,'tag','list');
976% hmsgbox=findobj(hfig,'tag','msgbox');
977% hwaitbar=findobj(hfig,'tag','waitbar');
978% set(hlist,'String',Tabchar)
979% set(hmsgbox,'String', message)
980% if count>0 %&& ~test_new
981%     BarPosition(3)=0.9*count/nbfiles;
982%     set(hwaitbar,'Position',BarPosition)
983% end
984%
985%
986% %------------------------------------------------------------------------   
987% % launched by deleting the status figure
988% function stop_status(hObject, eventdata)
989% %------------------------------------------------------------------------
990% hciv=findobj(allchild(0),'tag','civ');
991% hhciv=guidata(hciv);
992% set(hhciv.status,'value',0) %reset the status uicontrol in the GUI civ
993% set(hhciv.status,'BackgroundColor',[0 1 0])
994%
995% % %------------------------------------------------------------------------   
996% % % launched by pressing OK on the status figure
997% % function close_GUI(hObject, eventdata)
998% % %------------------------------------------------------------------------
999% %     delete(gcbf)
1000%
1001
1002% %------------------------------------------------------------------------
1003% % --- Main lauch command, called by OK and BATCH
1004% function errormsg=launch_jobs(hObject, eventdata, handles)
1005% %------------------------------------------------------------------------
1006% errormsg='';%default
1007%
1008% %% read the input parameters from the  GUI civ_input
1009% Param=read_GUI(handles.civ_input);
1010%
1011% %% check the selected list of operations:
1012% operations={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'};
1013% box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2];
1014% index_first=find(box_test==1,1);
1015% if isempty(index_first)
1016%     errormsg='no selected operation';
1017%     return
1018% end
1019% index_last=find(box_test==1,1,'last');
1020% box_used=box_test(index_first : index_last);
1021% [box_missing,ind_missing]=min(box_used);
1022% if isequal(box_missing,0); %there is a missing step in the sequence of operations
1023%     errormsg=['missing' cell2mat(operations(ind_missing))];
1024%     return
1025% end
1026%
1027% %% check mask if selecetd
1028% %could be included in get_mask callback ?
1029% if isequal(get(handles.CheckMask,'Value'),1)
1030%     maskname=get(handles.Mask,'String');
1031%     if ~exist(maskname,'file')
1032%         get_mask_civ1_Callback(hObject, eventdata, handles);
1033%     end
1034% end
1035% if isequal(get(handles.CheckMask,'Value'),1)
1036%     maskname=get(handles.Mask,'String');
1037%     if ~exist(maskname,'file')
1038%         get_mask_fix1_Callback(hObject, eventdata, handles);
1039%     end
1040% end
1041% if isequal(get(handles.CheckMask,'Value'),1)
1042%     maskname=get(handles.Mask,'String');
1043%     if ~exist(maskname,'file')
1044%         get_mask_civ2_Callback(hObject, eventdata, handles);
1045%     end
1046% end
1047% if isequal(get(handles.CheckMask,'Value'),1)
1048%     maskname=get(handles.Mask,'String');
1049%     if ~exist(maskname,'file')
1050%         get_mask_fix2_Callback(hObject, eventdata, handles);
1051%     end
1052% end
1053%
1054% %% reinitialise status callback
1055% if isfield(handles,'status')
1056%     set(handles.status,'Value',0);%suppress status display
1057%     status_Callback([], [], handles)
1058% end
1059%
1060% %% read the PARAM.xml file to get the binaries (and batch_mode if batch)
1061% % path_civ=fileparts(which('civ')); %path to the source directory of uvmat
1062% % xmlfile=fullfile(path_civ,'PARAM.xml');
1063% % s=[];
1064% % if exist(xmlfile,'file')% search parameter xml file in the whole matlab path
1065% %     t=xmltree(xmlfile);
1066% %     s=convert(t);
1067% % end% default configuration
1068% % if ~isfield(s,'RunParam')
1069% %     Param.xml.Civ1Bin=fullfile('bin','civ1');
1070% %     Param.xml.Civ2Bin=fullfile('bin','civ2');
1071% %     Param.xml.FixBin=fullfile('bin','fix_flag');
1072% %     Param.xml.PatchBin=fullfile('bin','patch_up');
1073% % end
1074% % if strcmp(Param.RunMode,'cluster') %computation dispatched on a cluster
1075% %     if isfield(s,'BatchParam')
1076% %         Param.xml=s.BatchParam;
1077% %         if isfield(Param.xml,'BatchMode')
1078% %             batch_mode=Param.xml.BatchMode;
1079% %             if ~ismember(batch_mode,{'sge','oar'})
1080% %                 errormsg=['batch mode ' batch_mode ' not supported by UVMAT'];
1081% %                 return
1082% %             end
1083% %         end
1084% %     else
1085% %         %default configuration
1086% %         Param.xml.Civ1Bin=fullfile('bin','civ1');
1087% %         Param.xml.Civ2Bin=fullfile('bin','civ2');
1088% %         Param.xml.FixBin=fullfile('bin','fix_flag');
1089% %         Param.xml.PatchBin=fullfile('bin','patch_up');
1090% %    %     Param.xml.CivmBin=fullfile('bin','civ_matlab');
1091% %         Param.xml.BatchMode='oar';% TODO : allow choice for sge
1092% %     end
1093% % else % run
1094% %     if isfield(s,'RunParam')
1095% %         Param.xml=s.RunParam;
1096% %     else %default configuration
1097% %         Param.xml.Civ1Bin=fullfile('bin','civ1');
1098% %         Param.xml.Civ2Bin=fullfile('bin','civ2');
1099% %         Param.xml.FixBin=fullfile('bin','fix_flag');
1100% %         Param.xml.PatchBin=fullfile('bin','patch_up');
1101% %     end
1102% % end
1103% % %Param.xml.CivmBin=fullfile('bin','civ_matlab');
1104% %
1105% % %% check if the binaries exist : to move in civ_opening
1106% % binary_list={};
1107% % switch Param.Program
1108% %     case 'CivX'
1109% %         binary_list={'Civ1Bin','Civ2Bin','PatchBin','FixBin'};
1110% %     case 'CivAll'% desactivated option
1111% %         binary_list={'Civ'};
1112% % %     case 'civ_matlab.sh'% compiled version of civ_matlab
1113% % %         binary_list={'CivmBin'};         
1114% % end
1115% % for bin_name=binary_list %loop on the list of binaries
1116% %     if isfield(Param.xml,bin_name{1})% bin_name{1} =current name in the list
1117% %         if ~isunix
1118% %         Param.xml.(bin_name{1})=[regexprep(Param.xml.(bin_name{1}),'/','\') '.exe'];
1119% %         end
1120% %         if exist(Param.xml.(bin_name{1}),'file')
1121% %             [path,name,ext]=fileparts(Param.xml.(bin_name{1}));
1122% %             currentdir=pwd;
1123% %             if isempty(path)
1124% %                 path=fileparts(which('civ.m'));
1125% %             end
1126% %             if exist(path,'dir')
1127% %                 cd(path);
1128% %                 binpath=pwd;%path of the binary
1129% %                 Param.xml.(bin_name{1})=fullfile(binpath,[name ext]);
1130% %                 cd(currentdir);
1131% %             else
1132% %                 errormsg=['path ' path ' for binaries specified in PARAM.xml does not exist'];
1133% %                 return
1134% %             end         
1135% %         else  %look for the full path if the file name has been defined with a relative path in PARAM.xm
1136% %             fullname=fullfile(path_civ,Param.xml.(bin_name{1}));
1137% %             if exist(fullname,'file')
1138% %                 Param.xml.(bin_name{1})=fullname;
1139% %             else
1140% %                 errormsg=['Binary ' Param.xml.(bin_name{1}) ' specified in PARAM.xml does not exist'];
1141% %                 return
1142% %             end
1143% %         end
1144% %     end
1145% % end
1146% % if strcmp(Param.Program,'civ_matlab.sh')
1147% %     if ~exist(fullfile(path_civ,'civ_matlab.sh'),'file')
1148% %         errormsg=[{'no file civ_matlab.sh found'}; {'run compile_functions.m to create it by compiling civ_matlab.m'}];
1149% %             return
1150% %     end
1151% % end
1152% %
1153% % %% set the list of files and check them
1154% % display('checking the files...')
1155% % [ref_i,ref_j,errormsg]=find_ref_indices(handles);
1156% % if ~isempty(errormsg)
1157% %     return
1158% % end
1159% % [filecell,i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,tild,tild,compare,errormsg]=...
1160% %     set_civ_filenames(handles,ref_i,ref_j,box_test);
1161% % if ~isempty(errormsg)
1162% %     return
1163% % end
1164% % set(handles.civ_input,'UserData',filecell);%store for futur use of status callback
1165% % display('files OK, processing...')
1166% %
1167% % %% create subfolders for log, cmx, nml, xml, bat
1168% % RootBat=fileparts(filecell.nc.civ1{1,1});
1169% % switch(Param.Program)
1170% %     case {'CivX','CivAll'}
1171% % dir_list={'0_BAT','0_CMX','0_LOG'};
1172% %     case {'civ_matlab','civ_matlab.sh'}
1173% %         dir_list={'0_BAT','0_XML'};
1174% % end
1175% % for k=1:length(dir_list)
1176% %     if ~exist(fullfile(RootBat,dir_list{k}),'dir')
1177% %         mkdir(fullfile(RootBat,dir_list{k}));
1178% %     end
1179% % end
1180%
1181% %% get information on input images or movies
1182% nbfield=numel(i1_civ1);
1183% nbslice=numel(j1_civ1);
1184% % if strcmp(Param.Program,'civ_matlab')
1185%     if Param.CheckCiv1
1186%         [Param.Civ1.FileTypeA,ImageInfoA_civ1,Param.Civ1.ImageA]=get_file_type(filecell.ima1.civ1{1});
1187%         [Param.Civ1.FileTypeB,ImageInfoB_civ1,Param.Civ1.ImageB]=get_file_type(filecell.ima2.civ1{1});
1188%     end
1189%     if Param.CheckCiv2
1190%         [Param.Civ2.FileTypeA,ImageInfoA_civ2,Param.Civ2.ImageA]=get_file_type(filecell.ima1.civ2{1});
1191%         [Param.Civ2.FileTypeB,ImageInfoB_civ2,Param.Civ2.ImageB]=get_file_type(filecell.ima2.civ2{1});
1192%     end
1193% % end
1194%
1195% %% MAIN LOOP
1196% time=get(handles.ImaDoc,'UserData'); %get the set of times
1197% TimeUnit=get(handles.TimeUnit,'String');
1198% checkframe=strcmp(TimeUnit,'frame');
1199% batch_file_list=[];%should be renamed file_list, can be used for xml or bash files
1200% NomTypeIma=get(handles.NomType,'String');
1201% for ifile=1:nbfield
1202%     for j=1:nbslice
1203%             
1204%         % define output file name
1205%         if Param.CheckCiv2==1 || Param.CheckFix2==1 || Param.CheckPatch2==1
1206%             Param.OutputFile=filecell.nc.civ2{ifile,j};
1207%         else
1208%             Param.OutputFile=filecell.nc.civ1{ifile,j};
1209%         end
1210%         Param.OutputFile=regexprep(Param.OutputFile,'.nc','');
1211%
1212%         if Param.CheckCiv1
1213%             % read image-dependent parameters         
1214%             if ~checkframe% && size(time,1)>=i2_civ1(ifile) && size(time,2)>=j2_civ1(j)
1215%                 Param.Civ1.Dt=(time(i2_civ1(ifile)+1,j2_civ1(j)+1)-time(i1_civ1(ifile)+1,j1_civ1(j)+1));
1216%             else
1217%                 Param.Civ1.Dt=1;
1218%             end
1219%             Param.Civ1.Time=((time(i2_civ1(ifile)+1,j2_civ1(j)+1)+time(i1_civ1(ifile)+1,j1_civ1(j)+1))/2);
1220%             if strcmp(Param.Program,'CivX')
1221%                 Param.Civ1.term_a=num2stra(j1_civ1(j),nom_type_nc);%UTILITE?
1222%                 Param.Civ1.term_b=num2stra(j2_civ1(j),nom_type_nc);%
1223%             end
1224%             Param.Civ1.ImageA=filecell.ima1.civ1{ifile,j};
1225%             Param.Civ1.ImageB=filecell.ima2.civ1{ifile,j};
1226%             Param.Civ1.ImageBitDepth=ImageInfoA_civ1.BitDepth;
1227%             Param.Civ1.ImageWidth=ImageInfoA_civ1.Width;
1228%             Param.Civ1.ImageHeight=ImageInfoA_civ1.Height;
1229%             if strcmp(NomTypeIma,'*')
1230%                 Param.Civ1.FrameIndexA=i1_civ1(ifile);
1231%                 Param.Civ1.FrameIndexB=i2_civ1(ifile);
1232%             else% case of movies indexed with i, the frame index is then in j
1233%                 Param.Civ1.FrameIndexA=j1_civ1(j);
1234%                 Param.Civ1.FrameIndexB=j2_civ1(j);
1235%             end
1236%             % read mask )parameters
1237%             if Param.Civ1.CheckMask % the lines below should be changed with the new gui
1238%                 if ~exist(Param.Civ1.Mask,'file')
1239%                     maskbase=[filecell.filebase '_' Param.Civ1.Mask]; %
1240%                     nbslice_mask=str2double(Param.Civ1.Mask(1:end-4)); %
1241%                     i1_mask=mod(i1_civ1(ifile)-1,nbslice_mask)+1;
1242%                     [RootPathMask,RootFileMask]=fileparts(maskbase);
1243%                     Param.Civ1.Mask=fullfile_uvmat(RootPathMask,[],RootFileMask,'.png','_1',i1_mask);
1244%                 end
1245%             end
1246%             % read grid parameters
1247%             if Param.Civ1.CheckGrid
1248%                 if numel(Param.Civ1.Grid)>=4 && isequal(Param.Civ1.Grid(end-3:end),'grid')
1249%                     nbslice_grid=str2double(Param.Civ1.Grid(1:end-4)); %
1250%                     if ~isnan(nbslice_grid)
1251%                         i1_grid=mod(i1_civ1(ifile)-1,nbslice_grid)+1;
1252%                         Param.Civ1.Grid=[filecell.filebase '_' fullfile_uvmat('','',Param.Civ1.Grid,'.grid','_1',i1_grid)];
1253%                         if ~exist(Param.Civ1.GridName,'file')
1254%                             errormsg='grid file absent for civ1';
1255%                             return
1256%                         end
1257%                     elseif ~exist(Param.Civ1.Grid,'file')
1258%                         errormsg='grid file absent for civ1';
1259%                         return
1260%                     end
1261%                 end
1262%             end
1263%             
1264%         end
1265%         
1266%         if Param.CheckCiv2==1
1267%             Param.Civ2.ImageA=filecell.ima1.civ2{ifile,j};
1268%             Param.Civ2.ImageB=filecell.ima2.civ2{ifile,j};         
1269%             if ~checkframe %&& size(time,1)>=i2_civ2(ifile) && size(time,2)>=j2_civ2(j)
1270%                 Param.Civ2.Dt=time(i2_civ2(ifile)+1,j2_civ2(j)+1)-time(i1_civ2(ifile)+1,j1_civ2(j)+1);
1271%             else
1272%                 Param.Civ2.Dt=1;
1273%             end
1274%             Param.Civ2.Time=(time(i2_civ2(ifile)+1,j2_civ2(j)+1)+time(i1_civ2(ifile)+1,j1_civ2(j)+1))/2;
1275%             if strcmp(Param.Program,'CivX')
1276%                 Param.Civ2.term_a=num2stra(j1_civ2(j),nom_type_nc);
1277%                 Param.Civ2.term_b=num2stra(j2_civ2(j),nom_type_nc);
1278%             end
1279%             Param.Civ2.filename_nc1=filecell.nc.civ1{ifile,j};
1280%             Param.Civ2.filename_nc1(end-2:end)=[]; % remove '.nc'
1281%             
1282%             % mask
1283%             if Param.Civ2.CheckMask
1284%                 if ~exist(Param.Civ2.Mask,'file')
1285%                     maskbase=[filecell.filebase '_' Param.Civ2.Mask]; %
1286%                     nbslice_mask=str2double(Param.Civ2.Mask(1:end-4)); %
1287%                     i1_mask=mod(i1_civ2(ifile)-1,nbslice_mask)+1;
1288%                     [RootPathMask,RootFileMask]=fileparts(maskbase);
1289%                     Param.Civ2.Mask=fullfile_uvmat(RootPathMask,[],RootFileMask,'.png','_1',i1_mask);
1290%                     %                     Param.Civ2.Mask=name_generator(maskbase,i1_mask,1,'.png','_i');
1291%                 end
1292%             end
1293%             %grid
1294%             if Param.Civ2.CheckGrid
1295%                 if numel(Param.Civ2.Grid)>=4 && isequal(Param.Civ2.Grid(end-3:end),'grid')
1296%                     nbslice_grid=str2double(Param.Civ2.Grid(1:end-4)); %
1297%                     if ~isnan(nbslice_grid)
1298%                         i1_grid=mod(i1_civ2(ifile)-1,nbslice_grid)+1;
1299%                         Param.Civ2.Grid=[filecell.filebase '_' fullfile_uvmat('','',gridname,'.grid','_1',i1_grid)];
1300%                         %                         Param.Civ2.Grid=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')];
1301%                     end
1302%                 end
1303%             end
1304%
1305%             Param.Civ2.ImageBitDepth=ImageInfoA_civ2.BitDepth;
1306%             Param.Civ2.ImageWidth=ImageInfoA_civ2.Width;
1307%             Param.Civ2.ImageHeight=ImageInfoA_civ2.Height;
1308%             if strcmp(NomTypeIma,'*')
1309%                 Param.Civ2.FrameIndexA=i1_civ2(ifile);
1310%                 Param.Civ2.FrameIndexB=i2_civ2(ifile);
1311%             else% case of movies indexed with i, the frame index is then in j
1312%                 Param.Civ2.FrameIndexA=j1_civ2(j);
1313%                 Param.Civ2.FrameIndexB=j2_civ2(j);
1314%             end
1315%         end
1316%       
1317%         % write the command and eventually the cmx, xml or nml files
1318%         cmd=write_cmd(Param);
1319%         write_param(Param);
1320%               
1321%         % create the command file name .m, .bat or .sh depending on the ok option
1322%         switch Param.Program
1323%             case {'civ_matlab'}
1324%                 filename_bat=regexprep(Param.OutputFile,'(.+)([/\\])(.+$)','$1$20_BAT$2$3.m');           
1325%                 [BatRoot,BatFile]=fileparts(filename_bat);
1326%                  BatFile=regexprep(BatFile,'-','__');%transform name to suppress'-' (not valid for .m files)
1327%                  filename_bat=[fullfile(BatRoot,BatFile) '.m'];
1328%             case {'CivX','CivAll','civ_matlab.sh'}
1329%                 switch computer
1330%                     case {'PCWIN','PCWIN64'}
1331%                         filename_bat=regexprep(Param.OutputFile,'(.+)([/\\])(.+$)','$1$20_BAT$2$3.bat');
1332%                     case {'GLNX86','GLNXA64','MACI64'}
1333%                         filename_bat=regexprep(Param.OutputFile,'(.+)([/\\])(.+$)','$1$20_BAT$2$3.sh');
1334%                 end
1335%         end
1336%         
1337%         % print the command in the bat file
1338%         [fid,message]=fopen(filename_bat,'w');
1339%         if isequal(fid,-1)
1340%             errormsg=['creation of .bat file: ' message];
1341%             return
1342%         end
1343%         fprintf(fid,cmd);
1344%         fclose(fid);
1345%         
1346%         % special case for civ_matlab on cluster
1347%         if strcmp(Param.Program,'civ_matlab') && strcmp(Param.RunMode,'cluster')
1348%             filename_bat2=regexprep(Param.OutputFile,'(.+)([/\\])(.+$)','$1$20_BAT$2$3.sh');
1349%             [fid,message]=fopen(filename_bat2,'w');
1350%             if isequal(fid,-1)
1351%                 errormsg=['creation of .bat file: ' message];
1352%                 return
1353%             end
1354%             fprintf(fid,['#!/bin/bash \n' ...
1355%                 '/etc/sysprofile \n'...
1356%                 'matlab -nodisplay -nosplash -nojvm <<END_MATLAB \n'...
1357%                 'addpath(''' path_civ ''');\n']);
1358% %             for p=1:length(batch_file_list)
1359%                 fprintf(fid,['run ' filename_bat '\n']);
1360% %             end
1361%             fprintf(fid, 'exit\nEND_MATLAB\n');
1362%             fclose(fid);
1363%             filename_bat=filename_bat2;
1364%         end
1365%         
1366%         switch computer
1367%             case {'GLNX86','GLNXA64','MACI64'}
1368%                 system(['chmod +x ' filename_bat]);
1369%         end
1370%         batch_file_list{length(batch_file_list)+1}=filename_bat;
1371%     end
1372% end
1373%
1374% %% start calculation
1375% %computation on cluster
1376% %if batch ==3
1377% switch Param.RunMode,
1378%     case 'cluster'
1379%         switch batch_mode
1380%             case 'sge' %at the moment only psmn ENS Lyon uses it
1381%                 for p=1:length(batch_file_list)
1382%                     %cmd=['!qsub -p ' pvalue ' -q civ_input.q -e ' flname '.errors -o ' flname '.log' ' ' batch_file_list{p}];
1383%                     cmd=['!qsub -q piv1,piv2,piv3 '...
1384%                         '-e ' regexprep(batch_file_list{p},'.bat','.errors') ' -o ' regexprep(batch_file_list{p},'.bat','.log ')...
1385%                         ' -v ' 'LD_LIBRARY_PATH=/home/sjoubaud/matlab_sylvain/civx/lib ' batch_file_list{p}];
1386%                     display(cmd);eval(cmd);
1387%                 end
1388%             case 'oar_old' % to remove
1389%                 for p=1:length(batch_file_list)
1390%                     oar_command=['!oarsub -n CIVX -q nicejob '...
1391%                         '-E ' regexprep(batch_file_list{p},'.bat','.errors') ' -O ' regexprep(batch_file_list{p},'.bat','.log ')...
1392%                         '-l "/core=1+{type = ''smalljob''}/licence=1,walltime=00:60:00"   ' batch_file_list{p}];
1393%                     display(oar_command);eval(oar_command);
1394%                 end
1395%             case 'oar'
1396%                 max_walltime=3600*12; % 12h max
1397%                 oar_modes={'oar-parexec','oar-dispatch','mpilauncher'};
1398%                 text={'Batch processing on servcalcul3 LEGI';...
1399%                     'Please choose one of the followint modes';...
1400%                     '* oar-parexec : default and best choice';...
1401%                     '* oar-dispatch : jobs in a container of several cores';...
1402%                     '* mpilauncher : one single parallel mpi job using several cores';...
1403%                     '**********************************'...
1404%                     };
1405%                 [S,v]=listdlg('PromptString',text,'ListString',oar_modes,...
1406%                     'SelectionMode','single','ListSize',[400 100],'Name','LEGI job mode');
1407%                 switch oar_modes{S}
1408%                     case 'oar-parexec' %oar-dispatch.pl
1409%                         if strcmp(Param.Program,'civ_matlab')
1410%                             ncores=1;
1411%                             msgbox_uvmat('WARNING','Number of cores =1: select the compiled version civ_matlab.sh for multi-core processing');
1412%                         else
1413%                         answer=inputdlg({'Number of cores (max 36)','extra oar options'},'oarsub parameter',1,{'12',''});
1414%                         ncores=str2double(answer{1});
1415%                         end
1416%
1417%                         extra_oar=answer{2};
1418%                         walltime_onejob=600;%seconds
1419%                         filename_joblist=fullfile(RootBat,'job_list.txt');
1420%                         fid=fopen(filename_joblist,'w');
1421%                         for p=1:length(batch_file_list)
1422%                             fprintf(fid,[batch_file_list{p} '\n']);
1423%                         end
1424%                         fclose(fid);
1425%                         oar_command=['oarsub -n CIVX '...
1426%                             '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
1427%                             '-l /core=' num2str(ncores) ','...
1428%                             'walltime=' datestr(min(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,max_walltime/86400),13) ' '...
1429%                             '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '...
1430%                             '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '...
1431%                             extra_oar ' '...
1432%                             '"oar-parexec -s -f ' filename_joblist ' '...
1433%                             '-l ' filename_joblist '.log"\n'];
1434%                         filename_oarcommand=fullfile(RootBat,'oar_command');
1435%                         fid=fopen(filename_oarcommand,'w');
1436%                         fprintf(fid,oar_command);
1437%                         fclose(fid);
1438%                         fprintf(oar_command);% display in command line
1439%                         system(oar_command);
1440% %                         eval(['! . ' filename
1441% %                             _oarcommand])
1442%                     case 'oar-dispatch' %oar-dispatch.pl
1443%                         ncores=str2double(...
1444%                             inputdlg('Number of cores (max 36)','oarsub parameter',1,{'6'})...
1445%                             );
1446%                         walltime_onejob=600;%seconds
1447%                         filename_joblist=fullfile(RootBat,'job_list.txt');
1448%                         fid=fopen(filename_joblist,'w');
1449%                         for p=1:length(batch_file_list)
1450%                             oar_command=['oarsub -n CIVX '...
1451%                                 '-E ' regexprep(batch_file_list{p},'\.bat\>','.stderr') ' -O ' regexprep(batch_file_list{p},'\.bat\>','.stdout ')...
1452%                                 '-l "/core=1,walltime=' datestr(walltime_onejob/86400,13) '"   ' batch_file_list{p}];
1453%                             fprintf(fid,[oar_command '\n']);
1454%                         end
1455%                         fclose(fid);
1456%                         oar_command=['oarsub -t container -n civx-container '...
1457%                             '-l /core=' num2str(ncores)...
1458%                             ',walltime=' datestr(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,13) ' '...
1459%                             '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '...
1460%                             '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '...
1461%                             '"oar-dispatch -f ' filename_joblist '"'];
1462%                         filename_oarcommand=fullfile(RootBat,'oar_command');
1463%                         fid=fopen(filename_oarcommand,'w');
1464%                         fprintf(fid,[oar_command '\n']);
1465%                         fclose(fid);
1466%                         display(oar_command);
1467%                         eval(['! . ' filename_oarcommand])
1468%                     case 'mpilauncher'
1469%                         filename_joblist=fullfile(RootBat,'job_list.txt');
1470%                         fid=fopen(filename_joblist,'w');
1471%                         
1472%                         for p=1:length(batch_file_list)
1473%                             fprintf(fid,[batch_file_list{p} '\n']);
1474%                         end
1475%                         fclose(fid)
1476%                         text_oarscript=[...
1477%                             '#!/bin/bash \n'...
1478%                             '#OAR -n Mylauncher \n'...
1479%                             '#OAR -l node=4/core=5,walltime=0:15:00 \n'...
1480%                             '#OAR -E ' fullfile(RootBat,'stderrfile.log') ' \n'...
1481%                             '#OAR -O ' fullfile(RootBat,'stdoutfile.log') ' \n'...
1482%                             '# ========================================================= \n'...
1483%                             '# This simple program launch a multinode parallel OpenMPI mpilauncher \n'...
1484%                             '# application for coriolis PIV post-processing. \n'...
1485%                             '# OAR uses oarshmost wrapper to propagate the user environement. \n'...
1486%                             '# This wrapper assert that the user has the same environment on all the \n'...
1487%                             '# allocated nodes (basic behavior needed by most MPI applications).  \n'...
1488%                             '# \n'...
1489%                             '# REQUIREMENT: \n'...
1490%                             '# the oarshmost wrapper should be installed in $HOME/bin directory. \n'...
1491%                             '# If a different location is used, change the line following the comment "Bidouille" \n'...
1492%                             '# ========================================================= \n'...
1493%                             '#   USER should only modify these 2 lines  \n'...
1494%                             'WORKDIR=' pwd ' \n'...
1495%                             'COMMANDE="mpilauncher  -f ' filename_joblist '" \n'...
1496%                             '# ========================================================= \n'...
1497%                             '# DO NOT MODIFY the FOLOWING LINES. (or be carefull) \n'...
1498%                             'echo "job starting on: "`hostname` \n'...
1499%                             'MPINODES="-host `tr [\\\\\\n] [,] <$OAR_NODEFILE |sed -e "s/,$/ /"`" \n'...
1500%                             'NCPUS=`cat $OAR_NODEFILE |wc -l` \n'...
1501%                             '#========== Bidouille ============== \n'...
1502%                             'export OMPI_MCA_plm_rsh_agent=oar-envsh \n'...%                     'cd $WORKDIR \n'...
1503%                             'CMD="mpirun -np $NCPUS -wdir $WORKDIR $MPINODES $COMMANDE" \n'...
1504%                             'echo "I run: $CMD"  \n'...
1505%                             '$CMD \n'...
1506%                             'echo "job ending" \n'...
1507%                             ];
1508%                         %                 oarsub -S ./oar.sub
1509%                         filename_oarscript=fullfile(RootBat,'oar_command');
1510%                         fid=fopen(filename_oarscript,'w');
1511%                         fprintf(fid,[text_oarscript]);
1512%                         fclose(fid);
1513%                         eval(['!chmod +x  ' filename_oarscript]);
1514%                         eval(['!oarsub -S ' filename_oarscript]);
1515%                 end
1516%         end
1517%     case {'background','local'}
1518%         switch Param.Program
1519%             case {'civ_matlab'}
1520%                 switch Param.RunMode
1521%                     case 'background'
1522%                         switch computer
1523%                             case {'PCWIN','PCWIN64'}
1524%                                 filename_superbat=fullfile(RootBat,'job_list.bat');
1525%                                 fid=fopen(filename_superbat,'w');
1526%                                 if fid==-1
1527%                                     msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat])
1528%                                     return
1529%                                 end
1530%                                  fprintf(fid,['matlab -automation '...
1531%                                      '-r "addpath(''' regexprep(path_civ,'\\','\\\\') ''');']);
1532%                                 for p=1:length(batch_file_list)
1533%                                     fprintf(fid,['run ' regexprep(batch_file_list{p},'\\','\\\\') ';']);
1534%                                 end
1535%                                  fprintf(fid, 'exit"');
1536%                                 fclose(fid);
1537%                                 dos([filename_superbat ' &']);
1538%                             case {'GLNX86','GLNXA64','MACI64'}
1539%                                 filename_superbat=fullfile(RootBat,'job_list.sh');
1540%                                 fid=fopen(filename_superbat,'w');
1541%                                 if fid==-1
1542%                                     msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat])
1543%                                     return
1544%                                 end
1545%                                 fprintf(fid,['#!/bin/bash \n' ...
1546%                                     '/etc/sysprofile \n'...
1547%                                     'matlab -nodisplay -nosplash -nojvm -logfile  <<END_MATLAB \n'...
1548%                                     'addpath(''' path_civ ''');\n']);
1549%                                 for p=1:length(batch_file_list)
1550%                                     fprintf(fid,['run ' batch_file_list{p} '\n']);
1551%                                 end
1552%                                 fprintf(fid, 'exit\nEND_MATLAB\n');
1553%                                 fclose(fid);
1554%                                 system(['chmod +x ' filename_superbat]);
1555%                                 system([filename_superbat ' &']);
1556%                         end
1557%                     case 'local'
1558%                         for p=1:length(batch_file_list)
1559%                             fid=fopen(batch_file_list{p});
1560%                             eval(fscanf(fid,'%s'));
1561%                             fclose(fid);
1562%                         end
1563%                 end
1564%             case {'CivX','CivAll','civ_matlab.sh'}
1565%                     switch computer
1566%                         case {'PCWIN','PCWIN64'}
1567%                             filename_superbat=fullfile(RootBat,'job_list.bat');
1568%                             fid=fopen(filename_superbat,'w');
1569%                             if fid==-1
1570%                                 msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat])
1571%                                 return
1572%                             end
1573%                             for p=1:length(batch_file_list)
1574%                                 fprintf(fid,['@call "' regexprep(batch_file_list{p},'\\','\\\\') '"' '\n']);
1575%                             end
1576%                             fclose(fid);
1577%                             system(['chmod +x ' filename_superbat]);
1578%                         case {'GLNX86','GLNXA64','MACI64'}
1579%                             filename_superbat=fullfile(RootBat,'job_list.bat');
1580%                             fid=fopen(filename_superbat,'w');
1581%                             if fid==-1
1582%                                 msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat])
1583%                                 return
1584%                             end
1585%                             for p=1:length(batch_file_list)
1586%                                 fprintf(fid,['sh ' batch_file_list{p} '\n']);
1587%                             end
1588%                             fclose(fid);
1589%                             system(['chmod +x ' filename_superbat]);
1590%                     end
1591%                 switch Param.RunMode
1592%                     case 'background'
1593%                         system([filename_superbat ' &']);% execute main commmand see what it does in dos ?
1594%                     case 'local'
1595%                         system(filename_superbat);
1596%                 end
1597%         end
1598% end
1599%
1600%
1601% %% save interface state
1602% if isfield(filecell,'nc')
1603%     if isfield(filecell.nc,'civ2')
1604%         fileresu=filecell.nc.civ2{1,1};
1605%     else
1606%         fileresu=filecell.nc.civ1{1,1};
1607%     end
1608% end
1609% [RootPath,SubDir,RootFile]=fileparts_uvmat(fileresu);
1610% namedoc=fullfile(RootPath,SubDir,RootFile);
1611% detect=1;
1612% while detect==1
1613%     namefigfull=[namedoc '.fig'];
1614%     hh=dir(namefigfull);
1615%     if ~isempty(hh)
1616%         detect=1;
1617%         namedoc=[namedoc '.0'];
1618%     else
1619%         detect=0;
1620%     end
1621% end
1622% Param=rmfield(Param,'status');
1623% Param=rmfield(Param,'xml');
1624% t=struct2xml(Param);
1625% t=set(t,1,'name','Civ');% set the head label
1626% save(t,[namedoc '.civ.xml']); %save GUI  parameters as xml file
1627% % saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER  .xml)
1628%
1629% %Save info in personal profile (initiate browser next time) TODO
1630% MenuFile={};
1631% dir_perso=prefdir;
1632% profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1633% if exist(profil_perso,'file')
1634%     hh=load (profil_perso);
1635%       if isfield(hh,'MenuFile')
1636%           MenuFile=hh.MenuFile;
1637%       end
1638%       if isfield(filecell.nc,'civ2')
1639%           MenuFile=[filecell.nc.civ2{1,1}; MenuFile];
1640%       else
1641%            MenuFile=[filecell.nc.civ1{1,1}; MenuFile];
1642%       end
1643%       save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
1644% else
1645%     MenuFile=filecell.ima1.civ1(1,1);
1646%     save (profil_perso,'MenuFile')
1647% end
1648
1649% %------------------------------------------------------------------------
1650% % --- determine the list of reference indices of processing file
1651% function [ref_i,ref_j,errormsg]=find_ref_indices(handles)
1652% %------------------------------------------------------------------------
1653% errormsg=''; %default error message
1654% first_i=str2double(get(handles.first_i,'String'));%first index i
1655% last_i=str2double(get(handles.last_i,'String'));%last index i
1656% incr_i=str2double(get(handles.incr_i,'String'));% increment
1657% if isequal(get(handles.first_j,'Visible'),'on')
1658%     first_j=str2double(get(handles.first_j,'String'));%first index j
1659%     last_j=str2double(get(handles.last_j,'String'));%last index j
1660%     incr_j=str2double(get(handles.incr_j,'String'));% increment
1661% else
1662%     first_j=1;
1663%     last_j=1;
1664%     incr_j=1;
1665% end
1666% ref_i=first_i:incr_i:last_i;% list of i indices (reference values for each pair)
1667% ref_j=first_j:incr_j:last_j;% list of j indices (reference values for each pair)
1668% if isnan(first_i)||isnan(first_j)
1669%     errormsg='first field number not defined';
1670% elseif isnan(last_i)||isnan(last_j)
1671%     errormsg='last field number not defined';
1672% elseif isnan(incr_i)||isnan(incr_j)
1673%     errormsg='increment in field number not defined';
1674% elseif last_i < first_i || last_j < first_j
1675%     errormsg='last field number must be larger than the first one';
1676% end
1677
1678%------------------------------------------------------------------------
1679% --- determine the list of filenames and indices needed for launch_job
1680%------------------------------------------------------------------------
1681% OUTPUT:
1682% filecell: structure of cell arrays {ref_i,ref_j} containing all the filenames involved in the civ_input process
1683%    the indices ref_i and ref_j correspond to the list of reference indices
1684%       .filebase=fullfile(RootPath,RootFile) used to construct mask names, grid names, CivDoc xml file
1685%       .ima1.civ1,.ima1.civ2: first image for civ1 and civ2 respectively (possibly different)
1686%       .ima2.civ1,.ima2.civ2: second image for civ1 and civ2 respectively (possibly different)
1687%       .nc.civ1,.nc.civ2: netcdf files containing civ1 and civ2 data respectively (possibly different)
1688% i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2: arrays of files indices, needed for timing records
1689function [filecell,i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2,NomType_nc,file_ref_fix1,file_ref_fix2,compare,errormsg]=...
1690    set_civ_filenames(handles,ref_i,ref_j,checkbox)
1691%------------------------------------------------------------------------
1692filecell=[];%default
1693errormsg='';
1694ListProgram=get(handles.Program,'String');
1695CivMode=ListProgram{get(handles.Program,'Value')};%Program to use , CivX or Matlab
1696
1697%% get the root name and check dir
1698RootPath=get(handles.RootPath,'String');
1699SubDirImages=get(handles.SubDirImages,'String');
1700RootFile=get(handles.RootFile,'String');
1701filecell.filebase=fullfile(RootPath,SubDirImages,RootFile);
1702if isempty(filecell.filebase)
1703    errormsg='please open an image with the upper menu option Open/Browse...';
1704    return
1705end
1706if ~exist(RootPath,'dir')
1707    errormsg=['path to images ' RootPath ' not found'];
1708    return
1709end
1710[tild,message]=fileattrib(RootPath);
1711if ~isempty(message) && ~isequal(message.UserWrite,1)
1712    errormsg=['No writting access to ' RootPath];
1713    return
1714end
1715%check result directory
1716subdir_civ1=regexprep(get(handles.SubdirCiv1,'String'),'^.','');%subdirectory subdir_civ1 for the netcdf output data
1717subdir_civ2=regexprep(get(handles.SubdirCiv2,'String'),'^.','');
1718if isequal(subdir_civ1,''),subdir_civ1='civ'; end% put default subdir
1719% subdir_civ1=[ '.' subdir_civ1];
1720% subdir_civ2=[ '.' subdir_civ2];
1721if isequal(subdir_civ2,''),subdir_civ2=subdir_civ1; end% put default subdir
1722subdir_civ1=[SubDirImages '.' subdir_civ1];
1723subdir_civ2=[SubDirImages '.' subdir_civ2];
1724
1725%% choose root names depending on ListCompareMode =displacement, shift, PIV or stereo PIV
1726ListCompareMode=get(handles.ListCompareMode,'String');
1727compare=ListCompareMode{get(handles.ListCompareMode,'Value')};
1728
1729% set the nomenclature type of the nc files depending on the pair mode
1730if strcmp(compare,'displacement')||strcmp(compare,'shift')
1731    mode='displacement';
1732else
1733    mode_list=get(handles.ListPairMode,'String');
1734    mode_value=get(handles.ListPairMode,'Value');
1735    mode=mode_list{mode_value};
1736end
1737NomType_ima2=get(handles.NomType,'String');
1738NomType_nc=nomtype2pair(NomType_ima2,mode);
1739
1740% set the rootfile and image indexing
1741RootFile_ima2=get(handles.RootFile,'String');%root file for the second image series
1742ext_ima=get(handles.ImaExt,'String'); % image extension (the same for all images)
1743switch compare
1744    case {'PIV','PIV volume'}
1745       RootFile_ima1=RootFile_ima2;% root name of the two image series is the same
1746       NomType_ima1=NomType_ima2;% the index of the first image follows the index of the second one
1747       RootFile_nc=RootFile_ima2;
1748    case 'displacement'
1749       RootFile_ima1=get(handles.RootFile_1,'String');% root name of the first image series set by handles.RootFile_1
1750       NomType_ima1='';% no indexing of the first image, a fixed reference for the whole series
1751       RootFile_nc=RootFile_ima2;
1752    case 'shift'
1753       RootFile_ima1=get(handles.RootFile_1,'String');% root name of the first image series set by handles.RootFile_1
1754       NomType_ima1=NomType_ima2;% the index of the first image follows the index of the second one
1755       RootFile_nc=[RootFile_ima1 '-' RootFile_ima2];
1756end
1757
1758%determine the list of file indices involved
1759[i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2]=...
1760    find_pair_indices(handles,ref_i,ref_j,mode);
1761
1762%determine the new filebase for 'displacement' ListPairMode (comparison of two series)
1763%filebase_B=filebase;% root name of the second field series for stereo
1764% filebase_A=filebase;%default
1765% if strcmp(compare,'PIV')
1766%     filebase_AB=filebase;
1767% else
1768%     [Path2,Name2]=fileparts(filebase_B);
1769%     Name1=RootFile_ima1;
1770%     filebase_AB=fullfile(Path2,[Name2 '-' Name1]);   
1771% end
1772% [RootPath_AB,RootFile_AB]=fileparts(filebase_AB);
1773% % [RootPath_ima1,RootFile_ima1]=fileparts(filebase_B);
1774% [RootPath_ima2,RootFile_ima2]=fileparts(filebase_B);
1775% [RootPath_nc,RootFile_nc]=fileparts(filebase_B);%default
1776% if strcmp(compare,'displacement')
1777% %     [RootPath_ima1,RootFile_ima1]=fileparts(filebase_B);
1778% %     [RootPath_ima2,RootFile_ima2]=fileparts(filebase_B);
1779%     [RootPath_nc,RootFile_nc]=fileparts(filebase_B);
1780% elseif strcmp(compare,'shift')
1781%     RootPath_nc=RootPath_AB;
1782%     RootFile_nc=RootFile_AB;
1783% end
1784% else
1785%     filebase_ima1=filebase_B;
1786%     filebase_ima2=filebase_B;
1787%     filebase_nc=filebase_B;
1788% [RootPath_ima1,RootFile_ima1]=fileparts(filebase_ima1);
1789% [RootPath_ima2,RootFile_ima2]=fileparts(filebase_ima2);
1790% [RootPath_nc,RootFile_nc]=fileparts(filebase_nc);
1791% [RootPath_A,RootFile_A]=fileparts(filebase_A);
1792
1793   
1794%% determine reference files for fix:
1795file_ref_fix1={};%default
1796file_ref_fix2={};
1797nbfield=length(i1_civ1);
1798nbslice=length(j1_civ1);
1799if checkbox(2)==1% fix1 performed
1800    ref=get(handles.ref_fix1,'UserData');%read data on the ref file stored by get_ref_fix1_Callback
1801    if ~isempty(ref)
1802        first_i=str2double(get(handles.first_i,'String'));
1803        last_i=str2double(get(handles.last_i,'String'));
1804        incr_i=str2double(get(handles.incr_i,'String'));
1805        first_j=str2double(get(handles.first_j,'String'));
1806        last_j=str2double(get(handles.last_j,'String'));
1807        incr_j=str2double(get(handles.incr_j,'String'));
1808        num_i_ref=first_i:incr_i:last_i;
1809        num_j_ref=first_j:incr_j:last_j;
1810        if isequal(mode,'displacement')
1811            num_i1=num_i_ref;
1812            num_i2=num_i_ref;
1813            num_j1=num_j_ref;
1814            num_j2=num_j_ref;
1815        elseif isequal(mode,'pair j1-j2')% isequal(mode,'st_pair j1-j2')
1816            num_i1=num_i_ref;
1817            num_i2=num_i1;
1818            num_j1=ref.num_a*ones(size(num_i_ref));
1819            num_j2=ref.num_b*ones(size(num_i_ref));
1820        elseif isequal(mode,'series(Di)') % isequal(mode,'st_series(Di)')
1821            delta1=floor((ref.num2-ref.num1)/2);
1822            delta2=ceil((ref.num2-ref.num1)/2);
1823            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
1824            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
1825            if isempty(ref.num_a)
1826                ref.num_a=1;
1827            end
1828            num_j1=ref.num_a*ones(size(num_i1));
1829            num_j2=num_j1;
1830        elseif isequal(mode,'series(Dj)')%| isequal(mode,'st_series(Dj)')
1831            delta1=floor((ref.num_b-ref.num_a)/2);
1832            delta2=ceil((ref.num_b-ref.num_a)/2);
1833            num_i1=ref.num1*ones(size(num_i_ref));
1834            num_i2=num_i1;
1835            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
1836            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
1837        end
1838        for ifile=1:nbfield
1839            for j=1:nbslice
1840                [RootPathRef,RootFile]=fileparts(ref.filebase);
1841                file_ref=fullfile_uvmat(RootPathRef,ref.subdir,RootFile,'.nc',ref.NomType,num_i1(ifile),num_i2(ifile),num_j1(j),num_j2(j));
1842                file_ref_fix1(ifile,j)={file_ref};
1843                if ~exist(file_ref,'file')
1844                    errormsg=['reference file ' file_ref ' not found for fix1'];
1845                    return
1846                end
1847            end
1848        end
1849    end
1850end
1851
1852%% determine reference files for fix2:
1853if checkbox(5)==1% fix2 performed
1854    ref=get(handles.ref_fix2,'UserData');
1855    if ~isempty(ref)
1856        first_i=str2double(get(handles.first_i,'String'));
1857        last_i=str2double(get(handles.last_i,'String'));
1858        incr_i=str2double(get(handles.incr_i,'String'));
1859        first_j=str2double(get(handles.first_j,'String'));
1860        last_j=str2double(get(handles.last_j,'String'));
1861        incr_j=str2double(get(handles.incr_j,'String'));
1862        num_i_ref=first_i:incr_i:last_i;
1863        num_j_ref=first_j:incr_j:last_j;
1864        if isequal(mode,'displacement')
1865            num_i1=num_i_ref;
1866            num_i2=num_i_ref;
1867            num_j1=num_j_ref;
1868            num_j2=num_j_ref;
1869        elseif isequal(mode,'pair j1-j2')
1870            num_i1=num_i_ref;
1871            num_i2=num_i1;
1872            num_j1=ref.num_a;
1873            num_j2=ref.num_b;
1874        elseif isequal(mode,'series(Di)')
1875            delta1=floor((ref.num2-ref.num1)/2);
1876            delta2=ceil((ref.num2-ref.num1)/2);
1877            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
1878            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
1879            num_j1=ref.num_a*ones(size(num_i1));
1880            num_j2=num_j1;
1881        elseif isequal(mode,'series(Dj)')
1882            delta1=floor((ref.num_b-ref.num_a)/2);
1883            delta2=ceil((ref.num_b-ref.num_a)/2);
1884            num_i1=ref.num1*ones(size(num_i_ref));
1885            num_i2=num_i1;
1886            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
1887            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
1888        end
1889        for ifile=1:nbfield
1890            for j=1:nbslice
1891                [RootPathRef,RootFile]=fileparts(ref.filebase);
1892                file_ref=fullfile_uvmat(RootPathRef,ref.subdir,RootFile,'.nc',ref.NomType,num_i1(ifile),num_i2(ifile),num_j1(j),num_j2(j));
1893                file_ref_fix2(ifile,j)={file_ref};
1894                if ~exist(file_ref,'file')
1895                    errormsg=['reference file ' file_ref ' not found for fix2'];
1896                    return
1897                end
1898            end
1899        end
1900    end
1901end
1902
1903%% check the existence of the netcdf and image files involved
1904% %%%%%%%%%%%%  case CheckCiv1 activated   %%%%%%%%%%%%%
1905if checkbox(1)==1;
1906    detect=1;
1907    vers=0;
1908    subdir_civ1_new=subdir_civ1;
1909    answer='No';
1910    while detect==1 %create a new subdir if the netcdf files already exist
1911        for ifile=1:nbfield
1912            for j=1:nbslice
1913                filename=fullfile_uvmat(RootPath,subdir_civ1_new,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
1914                detect=exist(filename,'file')==2;
1915                if detect% if a netcdf file already exists
1916                    if strcmp(answer,'No')
1917                        answer=msgbox_uvmat('INPUT_Y-N',['overwrite existing civ files in ' subdir_civ1_new]);
1918                    end
1919                    if strcmp(answer,'Yes')
1920                        detect=0;
1921                        filecell.nc.civ1(ifile,j)={filename};
1922                    else
1923                        r=regexp(subdir_civ1_new,'(?<root>.*\D)(?<num1>\d+)$','names');%detect whether name ends by a number
1924                        if isempty(r)
1925                            r(1).root=[subdir_civ1_new '_'];
1926                            r(1).num1='0';
1927                        end
1928                        subdir_civ1_new=[r(1).root num2str(str2num(r(1).num1)+1)];%increment the index by 1 or put 1
1929                        subdir_civ2=subdir_civ1_new;
1930                    end
1931                    break
1932                end
1933                filecell.nc.civ1(ifile,j)={filename};
1934            end
1935            if detect% if a netcdf file already exists
1936                break
1937            end
1938        end
1939 
1940        %create the new SubdirCiv1
1941        if ~exist(fullfile(RootPath,subdir_civ1_new),'dir')     
1942            [xx,msg1]=mkdir(fullfile(RootPath,subdir_civ1_new));
1943            if ~strcmp(msg1,'')
1944                errormsg=['cannot create ' subdir_civ1_new ': ' msg1];%error message for directory creation
1945                return
1946            elseif isunix         
1947                [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g)
1948                if ~strcmp(msg2,'')
1949                    errormsg=['pb of permission for  ' fullfile(RootPath,subdir_civ1_new) ': ' msg2];%error message for directory creation
1950                    return
1951                end
1952            end
1953        end
1954        if strcmp(compare,'stereo PIV')&&(strcmp(mode,'pair j1-j2')||strcmp(mode,'series(Dj)')||strcmp(mode,'series(Di)'))%check second nc series
1955            for ifile=1:nbfield
1956                for j=1:nbslice
1957                     filename=fullfile_uvmat(RootPath,subdir_civ1_new,RootFile_A,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
1958                    detect=exist(filename,'file')==2;
1959                    if detect% if a netcdf file already exists
1960                       indstr=regexp(subdir_civ1_new,'\D');
1961                       if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number
1962                           vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1;
1963                           subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)];
1964                       else
1965                           vers=vers+1;
1966                           subdir_civ1_new=[subdir_civ1_new '_' num2str(vers)];
1967                       end
1968                       subdir_civ2=subdir_civ1;
1969                       break
1970                    end
1971                    filecell.ncA.civ1(ifile,j)={filename};
1972                end
1973                if detect% if a netcdf file already exists
1974                    break
1975                end
1976            end
1977            %create the new SubdirCiv1
1978            if ~exist(fullfile(RootPath,subdir_civ1_new),'dir')       
1979                [xx,msg1]=mkdir(fullfile(RootPath,subdir_civ1_new));
1980                if ~strcmp(msg1,'')
1981                    errormsg=['cannot create ' subdir_civ1_new ': ' msg1];
1982                    return
1983                else
1984                    [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g)
1985                    if ~strcmp(msg2,'')
1986                        errormsg=['pb of permission for ' subdir_civ1_new ': ' msg2];%error message for directory creation
1987                        return
1988                    end
1989                end
1990            end
1991        end
1992    end
1993    subdir_civ1=subdir_civ1_new;
1994    % get image names
1995    for ifile=1:nbfield
1996        for j=1:nbslice
1997             filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima1,ext_ima,NomType_ima1,i1_civ1(ifile),[],j1_civ1(j));
1998            idetect(j)=exist(filename,'file')==2;
1999            filecell.ima1.civ1(ifile,j)={filename}; %first image
2000            filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima2,ext_ima,NomType_ima2,i2_civ1(ifile),[],j2_civ1(j));
2001            idetect_1(j)=exist(filename,'file')==2;
2002            filecell.ima2.civ1(ifile,j)={filename};%second image
2003        end
2004        [idetectmin,indexj]=min(idetect);
2005        if idetectmin==0,
2006            errormsg=[filecell.ima1.civ1{ifile,indexj} ' not found'];
2007            return
2008        end
2009        [idetectmin,indexj]=min(idetect_1);
2010        if idetectmin==0,
2011            errormsg=[filecell.ima2.civ1{ifile,indexj} ' not found'];
2012            return
2013        end
2014    end
2015    if strcmp(compare,'stereo PIV') && (strcmp(mode,'pair j1-j2') || strcmp(mode,'series(Dj)') || strcmp(mode,'series(Di)'))
2016        for ifile=1:nbfield
2017            for j=1:nbslice
2018                filename=fullfile_uvmat(RootPath,'',RootFile_A,ext_ima,NomType_ima1,i1_civ1(ifile),[],j1_civ1(j));
2019                idetect(j)=exist(filename,'file')==2;
2020                filecell.imaA1.civ1(ifile,j)={filename} ;%first image
2021                filename=fullfile_uvmat(RootPath,'',RootFile_A,ext_ima,NomType_ima2,i2_civ1(ifile),[],j2_civ1(j));
2022                idetect_1(j)=exist(filename,'file')==2;
2023                filecell.imaA2.civ1(ifile,j)={filename};%second image
2024            end
2025            [idetectmin,indexj]=min(idetect);
2026            if idetectmin==0,
2027                errormsg=[filecell.imaA1.civ1{ifile,indexj} ' not found'];
2028                return
2029            end
2030            [idetectmin,indexj]=min(idetect_1);
2031            if idetectmin==0,
2032                errormsg=[filecell.imaA2.civ1{ifile,indexj} ' not found'];
2033                return
2034            end
2035        end
2036    end
2037   
2038    %%%%%%%%%%%%%  checkfix1 or checkpatch1 activated but no checkciv1   %%%%%%%%%%%%%
2039elseif (checkbox(2)==1 || checkbox(3)==1);
2040    for ifile=1:nbfield
2041        for j=1:nbslice
2042            filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
2043            detect=exist(filename,'file')==2;
2044            if detect==0
2045                errormsg=[filename ' not found'];
2046                return
2047            end
2048            filecell.nc.civ1(ifile,j)={filename};
2049        end
2050    end
2051    if strcmp(compare,'stereo PIV')
2052        for ifile=1:nbfield
2053            for j=1:nbslice
2054                filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_A,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
2055                filecell.ncA.civ1(ifile,j)={filename};
2056                if ~exist(filename,'file')
2057                    errormsg=['input file ' filename ' not found'];
2058                    return
2059                end
2060            end
2061        end
2062    end
2063end
2064
2065%%%%%%%%%%%%%  if checkciv2 performed with pairs different than checkciv1  %%%%%%%%%%%%%
2066testdiff=0;
2067if (checkbox(4)==1)&&...
2068        ((get(handles.ListPairCiv1,'Value')~=get(handles.ListPairCiv2,'Value'))||~strcmp(subdir_civ2,subdir_civ1))
2069    testdiff=1;
2070    detect=1;
2071    vers=0;
2072    subdir_civ2_new=subdir_civ2;
2073    while detect==1 %create a new subdir if the netcdf files already exist
2074        for ifile=1:nbfield
2075            for j=1:nbslice
2076                filename=fullfile_uvmat(RootPath,subdir_civ2_new,RootFile_nc,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2077                detect=exist(filename,'file')==2;
2078                if detect% if a netcdf file already exists
2079                    indstr=regexp(subdir_civ2,'\D');
2080                    if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2081                        vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2082                        subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2083                    else
2084                        vers=vers+1;
2085                        subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2086                    end
2087                    break
2088                end
2089                filecell.nc.civ2(ifile,j)={filename};
2090            end
2091            if detect% if a netcdf file already exists
2092                break
2093            end
2094        end
2095        %create the new subdir_civ2_new
2096        if ~exist(fullfile(RootPath,subdir_civ2_new),'dir')
2097            [xx,m2]=mkdir(fullfile(RootPath,subdir_civ2_new));
2098            [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g)
2099            if ~isequal(m2,'')
2100                errormsg=['cannot create ' fullfile(RootPath,subdir_civ2_new) ': ' m2];
2101                return
2102            end
2103        end
2104        if strcmp(compare,'stereo PIV')%check second nc series
2105            for ifile=1:nbfield
2106                for j=1:nbslice
2107                    filename=fullfile_uvmat(RootPath,subdir_civ2_new,RootFile_A,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2108                    detect=exist(filename,'file')==2;
2109                    if detect% if a netcdf file already exists
2110                        indstr=regexp(subdir_civ2,'\D');
2111                        if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2112                           vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2113                           subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2114                        else
2115                           vers=vers+1;
2116                           subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2117                        end
2118                        break
2119                    end
2120                    filecell.ncA.civ2(ifile,j)={filename};
2121                end
2122                if detect% if a netcdf file already exists
2123                    break
2124                end
2125            end
2126            subdir_civ2=subdir_civ2_new;
2127            %create the new SubdirCiv1
2128            if ~exist(fullfile(RootPath,subdir_civ2_new),'dir')
2129                [xx,m2]=mkdir(subdir_civ2_new);
2130                 [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g)
2131                if ~isequal(m2,'')
2132                    errormsg= ['cannot create ' fullfile(RootPath,subdir_civ2_new) ': ' m2];%error message for directory creation
2133                    return
2134                end
2135            end
2136        end
2137    end
2138    subdir_civ2=subdir_civ2_new;
2139end
2140
2141%%%%%%%%%%%%%  if checkciv2 results are obtained or used  %%%%%%%%%%%%%
2142if checkbox(4)==1 || checkbox(5)==1 || checkbox(6)==1 %civ2
2143    %check source netcdf file of checkciv1 estimates
2144    if checkbox(1)==0; %no civ1 performed
2145        for ifile=1:nbfield
2146            for j=1:nbslice
2147                filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));%
2148                filecell.nc.civ1(ifile,j)={filename};% name of the civ1 file
2149                if ~exist(filename,'file')
2150                    errormsg=['input file ' filename ' not found'];
2151                    return
2152                end
2153                if ~testdiff % civ2 or patch2 are written in the same file as civ1
2154                    if checkbox(4)==0 ; %check the existence of civ2 if it is not calculated
2155                        Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2');
2156                        if isfield(Data,'Txt')
2157                            errormsg=Data.Txt;
2158                            return
2159                        elseif ~isempty(Data.CivStage)% case of new civ files
2160                            if Data.CivStage<4 %test for civ files
2161                            errormsg=['no civ2 data in ' filename];
2162                            return
2163                            end
2164                        elseif isempty(Data.civ2)||isequal(Data.civ2,0)
2165                            errormsg=['no civ2 data in ' filename];
2166                            return
2167                        end
2168                    elseif checkbox(3)==0; %check the existence of patch if it is not calculated
2169                        Data=nc2struct(filename,'ListGlobalAttribute','CivStage','patch');
2170                        if isfield(Data,'Txt')
2171                            errormsg=Data.Txt;
2172                            return
2173                        elseif ~isempty(Data.CivStage)
2174                            if Data.CivStage<3 %test for civ files
2175                                errormsg=['no patch data in ' filename];
2176                                return
2177                            end
2178                        elseif isempty(Data.patch)||isequal(Data.patch,0)
2179                            errormsg=['no patch data in ' filename];
2180                            return
2181                        end
2182                    end
2183                end
2184            end
2185        end
2186        if strcmp(compare,'stereo PIV')
2187            for ifile=1:nbfield
2188                for j=1:nbslice
2189                    filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_A,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2190                    filecell.ncA.civ2(ifile,j)={filename};
2191                    if ~exist(filename,'file')
2192                        errormsg=['input file ' filename ' not found'];
2193                        return
2194                    end
2195                end
2196            end
2197        end
2198    end
2199   
2200    detect=1;
2201    %     while detect==1%creates a new subdir if the netcdf files already contain checkciv2 data
2202    for ifile=1:nbfield
2203        for j=1:nbslice
2204            filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_nc,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2205            detect=exist(filename,'file')==2;
2206            filecell.nc.civ2(ifile,j)={filename};
2207        end
2208    end
2209    %get first image names for checkciv2
2210    if checkbox(1)==1 && isequal(i1_civ1,i1_civ2) && isequal(j1_civ1,j1_civ2)
2211        filecell.ima1.civ2=filecell.ima1.civ1;
2212    elseif checkbox(4)==1
2213        for ifile=1:nbfield
2214            for j=1:nbslice
2215                filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima1,ext_ima,NomType_ima1,i1_civ2(ifile),[],j1_civ2(j));
2216                idetect_2(j)=exist(filename,'file')==2;
2217                filecell.ima1.civ2(ifile,j)={filename};%first image
2218            end
2219            [idetectmin,indexj]=min(idetect_2);
2220            if idetectmin==0,
2221               errormsg=['input image ' filecell.ima1.civ2{ifile,indexj} ' not found'];
2222                return
2223            end
2224        end
2225    end
2226   
2227    %get second image names for checkciv2
2228    if checkbox(1)==1 && isequal(i2_civ1,i2_civ2) && isequal(j2_civ1,j2_civ2)
2229        filecell.ima2.civ2=filecell.ima2.civ1;
2230    elseif checkbox(4)==1
2231        for ifile=1:nbfield
2232            for j=1:nbslice
2233                filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima2,ext_ima,NomType_ima2,i2_civ2(ifile),[],j2_civ2(j));
2234                idetect_3(j)=exist(filename,'file')==2;
2235                filecell.ima2.civ2(ifile,j)={filename};%first image
2236            end
2237            [idetectmin,indexj]=min(idetect_3);
2238            if idetectmin==0,
2239                errormsg=['input image ' filecell.ima2.civ2{ifile,indexj} ' not found'];
2240                return
2241            end
2242        end
2243    end
2244end
2245if (checkbox(5) || checkbox(6)) && ~checkbox(4)  % need to read an existing netcdf civ2 file
2246    if ~testdiff
2247        filecell.nc.civ2=filecell.nc.civ1;% file already checked
2248    else     % check the civ2 files
2249        for ifile=1:nbfield
2250            for j=1:nbslice
2251                 filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_nc,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2252                filecell.nc.civ2(ifile,j)={filename};
2253                if ~exist(filename,'file')
2254                    errormsg=['input file ' filename ' not found'];
2255                    return
2256                else
2257                    Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2');
2258                    if ~isempty(Data.CivStage) && Data.CivStage<4 %test for civ files
2259                            errormsg=['no civ2 data in ' filename];
2260                            return
2261                    elseif isempty(Data.civ2)||isequal(Data.civ2,0)
2262                        errormsg=['no civ2 data in ' filename];
2263                        return
2264                    end
2265                end
2266            end
2267        end
2268    end
2269end
2270
2271%%%%%%%%%%%%%  if stereo fields are calculated by PATCH %%%%%%%%%%%%%
2272if strcmp(compare,'stereo PIV')
2273    if  checkbox(3) && isequal(get(handles.test_stereo1,'Value'),1)
2274        for ifile=1:nbfield
2275            for j=1:nbslice
2276                 filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_AB,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
2277                filecell.st(ifile,j)={filename};
2278            end
2279        end
2280    end
2281    if  checkbox(6) && isequal(get(handles.CheckStereo,'Value'),1)
2282        for ifile=1:nbfield
2283            for j=1:nbslice
2284                 filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_AB,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2285                filecell.st(ifile,j)={filename};
2286            end
2287        end
2288    end
2289end
2290set(handles.SubdirCiv1,'String',regexprep(subdir_civ1,['^' SubDirImages],''));%suppress the root  SuddirImages;);%update the edit box
2291set(handles.SubdirCiv2,'String',regexprep(subdir_civ2,['^' SubDirImages],''));%update the edit box
2292
2293% For CivX COPY IMAGES TO THE FORMAT .png IF NEEDED
2294if strcmp(CivMode,'CivX')
2295    NomType_imanew1=NomType_ima1;
2296    NomType_imanew2=NomType_ima2;
2297    if ~isequal(ext_ima,'.png')
2298        if checkbox(1) %if civ1 is performed
2299             [FileType,FileInfo,MovieObject]=get_file_type(filecell.ima1.civ1{1});
2300            check_j=0;
2301            if strcmp(FileType,'mmreader')||strcmp(FileType,'VideoReader')||strcmp(FileType,'multimage')
2302                if max(j1_civ1)>1
2303                    check_j=1;
2304                    NomType_imanew1='_1_1';
2305                else
2306                    NomType_imanew1='_1';
2307                end
2308            end
2309            h = waitbar(0,'copy images to the .png format for civ1');% display a wait bar
2310            for ifile=1:nbfield
2311                waitbar(ifile/nbfield);
2312                for j=1:nbslice
2313                    filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima1,'.png',NomType_imanew1,i1_civ1(ifile),[],j1_civ1(j));
2314                    if ~exist(filename,'file')
2315                        if check_j
2316                        A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,j1_civ1(j));
2317                        else
2318                            A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,i1_civ1(ifile));
2319                        end
2320                        imwrite(uint16(sum(A,3)),filename,'BitDepth',16);
2321                    end
2322                    filecell.ima1.civ1(ifile,j)={filename};
2323                    filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima2,'.png',NomType_imanew1,i2_civ1(ifile),[],j2_civ1(j));
2324                    if ~exist(filename,'file')
2325                         if check_j
2326                            A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,j2_civ1(j));
2327                        else
2328                            A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,i2_civ1(ifile));
2329                         end
2330                        imwrite(uint16(sum(A,3)),filename,'BitDepth',16);
2331                    end
2332                    filecell.ima2.civ1(ifile,j)={filename};
2333                end
2334            end
2335            close(h)
2336        end
2337        if checkbox(4) %if civ2 is performed
2338             [FileType,FileInfo,MovieObject]=get_file_type(filecell.ima1.civ2{1});
2339            check_j=0;
2340            if strcmp(FileType,'mmreader')||strcmp(FileType,'VideoReader')||strcmp(FileType,'multimage')
2341                if max(j1_civ2)>1
2342                    check_j=1;
2343                    NomType_imanew1='_1_1';
2344                else
2345                    NomType_imanew1='_1';
2346                end
2347            end
2348            h = waitbar(0,'copy images to the .png format for civ2');% display a wait bar
2349            for ifile=1:nbfield
2350                waitbar(ifile/nbfield);
2351                for j=1:nbslice
2352                    filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima1,'.png',NomType_imanew1,i1_civ2(ifile),[],j1_civ2(j));
2353                    if ~exist(filename,'file')
2354                        if check_j
2355                        A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,j1_civ2(j));
2356                        else
2357                            A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,i1_civ2(ifile));
2358                        end
2359                        imwrite(uint16(sum(A,3)),filename,'BitDepth',16);
2360                    end
2361                    filecell.ima1.civ2(ifile,j)={filename};
2362                    filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima2,'.png',NomType_imanew2,i2_civ2(ifile),[],j2_civ2(j));
2363                    if ~exist(filename,'file')
2364                        if check_j
2365                        A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,j1_civ2(j));
2366                        else
2367                            A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,i1_civ2(ifile));
2368                        end
2369                        imwrite(uint16(sum(A,3)),filename,'BitDepth',16);
2370                    end
2371                    filecell.ima2.civ2(ifile,j)={filename};
2372                end
2373            end
2374            close(h);
2375        end
2376    end
2377end
2378
2379%------------------------------------------------------------------------
2380% --- determine the list of index pairs of processing file
2381function [i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2]=...
2382    find_pair_indices(handles,ref_i,ref_j,mode)
2383%------------------------------------------------------------------------
2384
2385list_civ1=get(handles.ListPairCiv1,'String');
2386index_civ1=get(handles.ListPairCiv1,'Value');
2387str_civ1=list_civ1{index_civ1};%string defining the image pairs for civ1
2388if isempty(str_civ1)||isequal(str_civ1,'')
2389    msgbox_uvmat('ERROR','no image pair selected for civ1')
2390    return
2391end
2392list_civ2=get(handles.ListPairCiv2,'String');
2393index_civ2=get(handles.ListPairCiv2,'Value');
2394if index_civ2>length(list_civ2)
2395    list_civ2=list_civ1;
2396    index_civ2=index_civ1;
2397end
2398str_civ2=list_civ2{index_civ2};%string defining the image pairs for civ2
2399
2400if isequal (mode,'series(Di)')
2401    lastfield=str2double(get(handles.nb_field,'String'));
2402    i1_civ1=ref_i-floor(index_civ1/2)*ones(size(ref_i));% set of first image numbers
2403    i2_civ1=ref_i+ceil(index_civ1/2)*ones(size(ref_i));
2404    j1_civ1=ref_j;
2405    j2_civ1=ref_j;
2406    i1_civ2=ref_i-floor(index_civ2/2)*ones(size(ref_i));
2407    i2_civ2=ref_i+ceil(index_civ2/2)*ones(size(ref_i));
2408    j1_civ2=ref_j;
2409    j2_civ2=ref_j;   
2410   
2411    % adjust the first and last field number
2412    lastfield=str2double(get(handles.nb_field,'String'));
2413    if isnan(lastfield)
2414        indsel=find((i1_civ1 >= 1)&(i1_civ2 >= 1));
2415    else
2416        indsel=find((i2_civ1 <= lastfield)&(i2_civ2 <= lastfield)&(i1_civ1 >= 1)&(i1_civ2 >= 1));
2417    end
2418    if length(indsel)>=1
2419        firstind=indsel(1);
2420        lastind=indsel(end);
2421        set(handles.first_i,'String',num2str(ref_i(firstind)))%update the display of first and last fields
2422        set(handles.last_i,'String',num2str(ref_i(lastind)))
2423        ref_i=ref_i(indsel);
2424        i1_civ1=i1_civ1(indsel);
2425        i1_civ2=i1_civ2(indsel);
2426        i2_civ1=i2_civ1(indsel);
2427        i2_civ2=i2_civ2(indsel);
2428    end
2429elseif isequal (mode,'series(Dj)')
2430    lastfield_j=str2double(get(handles.nb_field2,'String'));
2431    i1_civ1=ref_i;% set of first image numbers
2432    i2_civ1=ref_i;
2433    j1_civ1=ref_j-floor(index_civ1/2)*ones(size(ref_j));
2434    j2_civ1=ref_j+ceil(index_civ1/2)*ones(size(ref_j));
2435    i1_civ2=ref_i;
2436    i2_civ2=ref_i;
2437    j1_civ2=ref_j-floor(index_civ2/2)*ones(size(ref_j));
2438    j2_civ2=ref_j+ceil(index_civ2/2)*ones(size(ref_j));
2439    % adjust the first and last field number
2440    if isnan(lastfield_j)
2441        indsel=find((j1_civ1 >= 1)&(j1_civ2 >= 1));
2442    else
2443        indsel=find((j2_civ1 <= lastfield_j)&(j2_civ2 <= lastfield_j)&(j1_civ1 >= 1)&(j1_civ2 >= 1));
2444    end
2445    if length(indsel)>=1
2446        firstind=indsel(1);
2447        lastind=indsel(end);
2448        set(handles.first_j,'String',num2str(ref_j(firstind)))%update the display of first and last fields
2449        set(handles.last_j,'String',num2str(ref_j(lastind)))
2450        ref_j=ref_j(indsel);
2451        j1_civ1=j1_civ1(indsel);
2452        j2_civ1=j2_civ1(indsel);
2453        j1_civ2=j1_civ2(indsel);
2454        j2_civ2=j2_civ2(indsel);
2455    end
2456elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)
2457    displ_num=get(handles.ListPairCiv1,'UserData');
2458    i1_civ1=ref_i;
2459    i2_civ1=ref_i;
2460    j1_civ1=displ_num(1,index_civ1);
2461    j2_civ1=displ_num(2,index_civ1);
2462    i1_civ2=ref_i;
2463    i2_civ2=ref_i;
2464    j1_civ2=displ_num(1,index_civ2);
2465    j2_civ2=displ_num(2,index_civ2);
2466elseif isequal(mode,'displacement')
2467    i1_civ1=ref_i;
2468    i2_civ1=ref_i;
2469    j1_civ1=ref_j;
2470    j2_civ1=ref_j;
2471    i1_civ2=ref_i;
2472    i2_civ2=ref_i;
2473    j1_civ2=ref_j;
2474    j2_civ2=ref_j;
2475end
2476
2477%------------------------------------------------------------------------
2478% --- Executes on button press in ListCompareMode.
2479function ListCompareMode_Callback(hObject, eventdata, handles)
2480%------------------------------------------------------------------------
2481ListCompareMode=get(handles.ListCompareMode,'String');
2482option=ListCompareMode{get(handles.ListCompareMode,'Value')};
2483switch option
2484    case 'PIV'
2485        set(handles.RootFile_1,'Visible','Off');
2486        set(handles.sub_txt,'Visible','off')
2487        set(handles.RootFile_1,'String',[]);
2488        mode_store=get(handles.ListCompareMode,'UserData');
2489        set(handles.ListPairMode,'Visible','on')
2490        set(handles.ListPairMode,'Value',1)
2491        set(handles.ListPairMode,'String',mode_store)
2492        set(handles.CheckStereo,'Value',0)     
2493    case 'PIV volume'     
2494        set(handles.RootFile_1,'Visible','Off');
2495        set(handles.sub_txt,'Visible','off')
2496        set(handles.RootFile_1,'String',[]);
2497        mode_store=get(handles.ListCompareMode,'UserData');
2498        set(handles.ListPairMode,'Visible','on')
2499        set(handles.ListPairMode,'Value',1)
2500        set(handles.ListPairMode,'String',{'series(Di)'})
2501        set(handles.CheckStereo,'Value',0)
2502        set(handles.last_j,'String',get(handles.nb_field2,'String'))% select the whole volume scan by default
2503        set(handles.incr_i,'String',num2str(2))%
2504    otherwise
2505        filebase=get(handles.RootPath,'String');
2506        set(handles.sub_txt,'Visible','on')
2507        set(handles.RootFile_1,'Visible','On');%mkes the second file input window visible
2508        mode_store=get(handles.ListPairMode,'String');%get the present 'mode'
2509        set(handles.ListCompareMode,'UserData',mode_store);%store the mode display
2510        set(handles.ListPairMode,'Visible','off')
2511       
2512        %% open an image file with the browser
2513        ind_opening=1;%default
2514        browse.incr_pair=[0 0]; %default
2515        oldfile=get(handles.RootPath,'String');
2516        menu={'*.png;*.jpg;*.tif;*.avi;*.AVI;', ' (*.png,*.jpg ,.tif, *.avi,*.AVI)';
2517            '*.png','.png image files'; ...
2518            '*.jpg',' jpeg image files'; ...
2519            '*.tif','.tif image files'; ...
2520            '*.avi;*.AVI','.avi movie files'; ...
2521            '*.*',  'All Files (*.*)'};
2522        if strcmp(option,'displacement')
2523            comment='Pick the reference file for displacements';
2524        else
2525            comment='Pick a file of the second series';
2526        end
2527        [FileName, PathName] = uigetfile( menu, comment,oldfile);
2528        fileinput=[PathName FileName];%complete file name
2529        sizf=size(fileinput);
2530        if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
2531        [path,name,ext]=fileparts(fileinput);
2532        [path1]=fileparts(filebase);
2533        if isunix
2534            [status,path]=system(['readlink ' path]);
2535            [status,path1]=system(['readlink ' path1]);% look for the true path in case of symbolic paths
2536        end
2537        if ~strcmp(path1,path)
2538            msgbox_uvmat('ERROR','The second image or series must be in the same directory as the first one')
2539            return
2540        end
2541        if strcmp(option,'displacement')
2542            [tild,RootFile_1]=fileparts(name);
2543        else
2544            [FilePath,FileName,Ext]=fileparts(fileinput);
2545            % detect the file type, get the movie object if relevant, and look for the corresponding file series:
2546            % the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
2547            [RootPath,SubDir,RootFile_1,i1_series,i2_series,j1_series,j2_series,nom_type_1,FileType,Object,i1,i2,j1,j2]=find_file_series(FilePath,[FileName Ext]);
2548           
2549            %check image nom type
2550            if ~strcmp(nom_type_1,get(handles.NomType,'String'))
2551                msgbox_uvmat('ERROR','The second image series must have the same indexing type as the first one, or use the option displacement for a fixed image')
2552                return
2553            end
2554        end
2555        %check image  extension
2556        if ~strcmp(ext,get(handles.ImaExt,'String'))
2557            msgbox_uvmat('ERROR','The second image series must have the same extension name as the first one')
2558            return
2559        end
2560        set(handles.RootFile_1,'String',RootFile_1);
2561       
2562end
2563ListPairMode_Callback(hObject, eventdata, handles)
2564
2565
2566%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2567% Callbacks in the uipanel Pair Indices
2568%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2569%------------------------------------------------------------------------
2570% --- Executes on button press in ListPairMode.
2571function ListPairMode_Callback(hObject, eventdata, handles)
2572%------------------------------------------------------------------------
2573compare_list=get(handles.ListCompareMode,'String');
2574val=get(handles.ListCompareMode,'Value');
2575compare=compare_list{val};
2576if strcmp(compare,'displacement')||strcmp(compare,'shift')
2577    mode='displacement';
2578else
2579    mode_list=get(handles.ListPairMode,'String');
2580    if ischar(mode_list)
2581        mode_list={mode_list};
2582    end
2583    mode_value=get(handles.ListPairMode,'Value');
2584    mode=mode_list{mode_value};
2585end
2586displ_num=[];%default
2587ref_i=str2double(get(handles.ref_i,'String'));
2588% last_i=str2num(get(handles.last_i,'String'));
2589time=get(handles.ImaDoc,'UserData'); %get the set of times
2590TimeUnit=get(handles.TimeUnit,'String');
2591checkframe=strcmp(TimeUnit,'frame');
2592siztime=size(time);
2593nbfield=siztime(1)-1;
2594nbfield2=siztime(2)-1;
2595indchosen=1;  %%first pair selected by default
2596%displ_num used to define the indices of the civ_input pairs
2597% in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices
2598% are relative to the reference indices ref_i and ref_j respectively.
2599if isequal(mode,'pair j1-j2')%| isequal(mode,'st_pair j1-j2')
2600    dt=1;
2601    displ='';
2602    index=0;
2603    numlist_a=[];
2604    numlist_B=[];
2605    %get all the time intervals in bursts
2606    displ_dt=1;%default
2607    nbfield2=min(nbfield2,10);%limitate the number of pairs to 10x10
2608    for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'pair j1-j2' mode
2609        for numod_b=(numod_a+1):nbfield2
2610            index=index+1;
2611            numlist_a(index)=numod_a;
2612            numlist_b(index)=numod_b;
2613            if size(time,2)>1 && ~checkframe
2614                dt(numod_a,numod_b)=time(ref_i+1,numod_b+1)-time(ref_i+1,numod_a+1);%first time interval dt
2615                displ_dt(index)=dt(numod_a,numod_b);
2616            else
2617                displ_dt(index)=1;
2618            end
2619        end
2620    end
2621    [dtsort,indsort]=sort(displ_dt);
2622    if ~isempty(numlist_a)
2623        displ_num(1,:)=numlist_a(indsort);
2624        displ_num(2,:)=numlist_b(indsort);
2625    end
2626    displ_num(3,:)=0;
2627    displ_num(4,:)=0;
2628    enable_j(handles, 'off')
2629elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)')
2630    index=1:200;
2631    displ_num(1,index)=-floor(index/2);
2632    displ_num(2,index)=ceil(index/2);
2633    displ_num(3:4,index)=zeros(2,200);
2634    enable_j(handles, 'on')
2635elseif isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)')
2636    index=1:200;
2637    displ_num(1:2,index)=zeros(2,200);
2638    displ_num(3,index)=-floor(index/2);
2639    displ_num(4,index)=ceil(index/2);
2640    enable_i(handles, 'on')
2641    if nbfield2 > 1
2642        enable_j(handles, 'on')
2643    else
2644        enable_j(handles, 'off')
2645    end
2646elseif isequal(mode,'displacement')%the pairs have the same indices
2647    displ_num(1,1)=0;
2648    displ_num(2,1)=0;
2649    displ_num(3,1)=0;
2650    displ_num(4,1)=0;
2651    if nbfield > 1 || nbfield==0
2652        enable_i(handles, 'on')
2653    else
2654        enable_j(handles, 'off')
2655    end
2656    if nbfield2 > 1
2657        enable_j(handles, 'on')
2658    else
2659        enable_j(handles, 'off')
2660    end
2661end
2662set(handles.ListPairCiv1,'UserData',displ_num);
2663errormsg=find_netcpair_civ( handles,1);
2664    if ~isempty(errormsg)
2665    msgbox_uvmat('ERROR',errormsg)
2666    end
2667% find_netcpair_civ2(handles)
2668
2669function enable_i(handles, state)
2670set(handles.itext,'Visible',state)
2671set(handles.first_i,'Visible',state)
2672set(handles.last_i,'Visible',state)
2673set(handles.incr_i,'Visible',state)
2674set(handles.nb_field,'Visible',state)
2675set(handles.ref_i,'Visible',state)
2676
2677function enable_j(handles, state)
2678set(handles.jtext,'Visible',state)
2679set(handles.first_j,'Visible',state)
2680set(handles.last_j,'Visible',state)
2681set(handles.incr_j,'Visible',state)
2682set(handles.nb_field2,'Visible',state)
2683set(handles.ref_j,'Visible',state)
2684
2685
2686%------------------------------------------------------------------------
2687% --- Executes on selection change in ListPairCiv1.
2688function ListPairCiv1_Callback(hObject, eventdata, handles)
2689%------------------------------------------------------------------------
2690%reproduce by default the chosen pair in the checkciv2 menu
2691list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
2692index_pair=get(handles.ListPairCiv1,'Value');
2693displ_num=get(handles.ListPairCiv1,'UserData');
2694list_pair2=get(handles.ListPairCiv2,'String');%get the menu of image pairs
2695if index_pair<=length(list_pair2)
2696    set(handles.ListPairCiv2,'Value',index_pair);
2697end
2698
2699%update first_i and last_i according to the chosen image pairs
2700mode_list=get(handles.ListPairMode,'String');
2701mode_value=get(handles.ListPairMode,'Value');
2702mode=mode_list{mode_value};
2703if isequal(mode,'series(Di)')
2704    first_i=str2double(get(handles.first_i,'String'));
2705    last_i=str2double(get(handles.last_i,'String'));
2706    incr_i=str2double(get(handles.incr_i,'String'));
2707    num_i=first_i:incr_i:last_i;
2708    lastfield=str2double(get(handles.nb_field,'String'));
2709    if ~isnan(lastfield)
2710        test_find=(num_i-floor(index_pair/2)*ones(size(num_i))>0)& ...
2711            (num_i+ceil(index_pair/2)*ones(size(num_i))<=lastfield);
2712        num_i=num_i(test_find);
2713    end
2714    set(handles.first_i,'String',num2str(num_i(1)));
2715    set(handles.last_i,'String',num2str(num_i(end)));
2716elseif isequal(mode,'series(Dj)')
2717    first_j=str2double(get(handles.first_j,'String'));
2718    last_j=str2double(get(handles.last_j,'String'));
2719    incr_j=str2double(get(handles.incr_j,'String'));
2720    num_j=first_j:incr_j:last_j;
2721    lastfield2=str2double(get(handles.nb_field2,'String'));
2722    if ~isnan(lastfield2)
2723        test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
2724            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2);
2725        num_j=num_j(test_find);
2726    end
2727    set(handles.first_j,'String',num2str(num_j(1)));
2728    set(handles.last_j,'String',num2str(num_j(end)));
2729end
2730
2731%------------------------------------------------------------------------
2732% --- Executes on selection change in ListPairCiv2.
2733function ListPairCiv2_Callback(hObject, eventdata, handles)
2734%------------------------------------------------------------------------
2735index_pair=get(handles.ListPairCiv2,'Value');%get the selected position index in the menu
2736
2737%update first_i and last_i according to the chosen image pairs
2738mode_list=get(handles.ListPairMode,'String');
2739mode_value=get(handles.ListPairMode,'Value');
2740mode=mode_list{mode_value};
2741if isequal(mode,'series(Di)')
2742    first_i=str2double(get(handles.first_i,'String'));
2743    last_i=str2double(get(handles.last_i,'String'));
2744    incr_i=str2double(get(handles.incr_i,'String'));
2745    num_i=first_i:incr_i:last_i;
2746    lastfield=str2double(get(handles.nb_field,'String'));
2747    if ~isnan(lastfield)
2748        test_find=(num_i-floor(index_pair/2)*ones(size(num_i))>0)& ...
2749            (num_i+ceil(index_pair/2)*ones(size(num_i))<=lastfield);
2750        num_i=num_i(test_find);
2751    end
2752    set(handles.first_i,'String',num2str(num_i(1)));
2753    set(handles.last_i,'String',num2str(num_i(end)));
2754elseif isequal(mode,'series(Dj)')
2755    first_j=str2double(get(handles.first_j,'String'));
2756    last_j=str2double(get(handles.last_j,'String'));
2757    incr_j=str2double(get(handles.incr_j,'String'));
2758    num_j=first_j:incr_j:last_j;
2759    lastfield2=str2double(get(handles.nb_field2,'String'));
2760    if ~isnan(lastfield2)
2761        test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
2762            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2);
2763        num_j=num_j(test_find);
2764    end
2765    set(handles.first_j,'String',num2str(num_j(1)));
2766    set(handles.last_j,'String',num2str(num_j(end)));
2767end
2768
2769%------------------------------------------------------------------------
2770function ref_i_Callback(hObject, eventdata, handles)
2771%------------------------------------------------------------------------
2772mode_list=get(handles.ListPairMode,'String');
2773mode_value=get(handles.ListPairMode,'Value');
2774mode=mode_list{mode_value};
2775errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files
2776if isequal(mode,'series(Di)') || ...% we do patch2 only
2777        (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
2778    errormsg=find_netcpair_civ( handles,2);
2779end
2780    if ~isempty(errormsg)
2781    msgbox_uvmat('ERROR',errormsg)
2782    end
2783
2784%------------------------------------------------------------------------
2785function ref_j_Callback(hObject, eventdata, handles)
2786%------------------------------------------------------------------------
2787mode_list=get(handles.ListPairMode,'String');
2788mode_value=get(handles.ListPairMode,'Value');
2789mode=mode_list{mode_value};
2790if isequal(get(handles.CheckCiv1,'Value'),0)|| isequal(mode,'series(Dj)')
2791    errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files
2792end
2793if isequal(mode,'series(Dj)') || ...
2794        (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
2795    errormsg=find_netcpair_civ(handles,2);
2796end
2797    if ~isempty(errormsg)
2798    msgbox_uvmat('ERROR',errormsg)
2799    end
2800
2801%------------------------------------------------------------------------
2802% determine the menu for checkciv1 pairs depending on existing netcdf file at the middle of
2803% the field series set by first_i, incr, last_i
2804% index=1: look for pairs for civ1
2805% index=2: look for pairs for civ2
2806function errormsg=find_netcpair_civ(handles,index)
2807%------------------------------------------------------------------------
2808set(gcf,'Pointer','watch')% set the mouse pointer to 'watch' (clock)
2809
2810%% initialisation
2811errormsg='';
2812browse=get(handles.RootPath,'UserData');
2813compare_list=get(handles.ListCompareMode,'String');
2814val=get(handles.ListCompareMode,'Value');
2815compare=compare_list{val};
2816if strcmp(compare,'displacement')||strcmp(compare,'shift')
2817    mode='displacement';
2818else
2819    mode_list=get(handles.ListPairMode,'String');
2820    mode_value=get(handles.ListPairMode,'Value');
2821    if isempty(mode_list)
2822        return
2823    end
2824    mode=mode_list{mode_value};
2825end
2826nom_type_ima=get(handles.NomType,'String');
2827
2828%% determine nom_type_nc, nomenclature type of the .nc files:
2829[nom_type_nc]=nomtype2pair(nom_type_ima,mode);
2830
2831%% reads .nc subdirectoy and image numbers from the interface
2832SubDirImages=get(handles.SubDirImages,'String');
2833subdir_civ1=[SubDirImages get(handles.SubdirCiv1,'String')];%subdirectory subdir_civ1 for the netcdf data
2834subdir_civ2=[SubDirImages get(handles.SubdirCiv2,'String')];%subdirectory subdir_civ2 for the netcdf data
2835ref_i=str2double(get(handles.ref_i,'String'));
2836ref_j=[];
2837if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
2838    ref_j=0;
2839elseif strcmp(get(handles.ref_j,'Visible'),'on')
2840    ref_j=str2double(get(handles.ref_j,'String'));
2841end
2842if isempty(ref_j)
2843    ref_j=1;
2844end
2845time=get(handles.ImaDoc,'UserData');%get the set of times
2846TimeUnit=get(handles.TimeUnit,'String');
2847checkframe=strcmp(TimeUnit,'frame');
2848displ_num=get(handles.ListPairCiv1,'UserData');
2849
2850%% eliminate the first pairs inconsistent with the position
2851if isempty(displ_num)
2852    nbpair=0;
2853else
2854    nbpair=length(displ_num(1,:));%nbre of displayed pairs
2855    if  isequal(mode,'series(Di)')  %| isequal(mode,'st_series(Di)')
2856        nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index
2857    elseif  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
2858        nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index
2859    end
2860end
2861nbpair=min(200,nbpair);%limit the number of displayed pairs to 200
2862
2863%% case with no Civ1 operation, netcdf files need to exist for reading
2864displ_pair={''};
2865select=ones(size(1:nbpair));%flag for displayed pairs =1 for display
2866testpair=0;
2867RootPath=get(handles.RootPath,'String');
2868RootFile=get(handles.RootFile,'String');
2869if index==1 % case civ1
2870    if ~get(handles.CheckCiv1,'Value') %
2871        if ~exist(fullfile(RootPath,subdir_civ1),'dir')
2872            errormsg=['no civ1 file available: subdirectory ' subdir_civ1 ' does not exist'];
2873            set(handles.ListPairCiv1,'String',{});
2874            return
2875        end
2876        for ipair=1:nbpair
2877            filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,...
2878                ref_i+displ_num(3,ipair),ref_i+displ_num(4,ipair),ref_j+displ_num(1,ipair),ref_j+displ_num(2,ipair));
2879            select(ipair)=exist(filename,'file')==2;% put flag to 0 if the file does not exist
2880        end
2881        % case of no displayed pair
2882        if isequal(select,zeros(size(1:nbpair)))
2883            if isfield(browse,'incr_pair') && ~isequal(browse.incr_pair,[0 0])
2884                num_i1=ref_i-floor(browse.incr_pair(1)/2);
2885                num_i2=ref_i+ceil(browse.incr_pair(1)/2);
2886                num_j1=ref_j-floor(browse.incr_pair(2)/2);
2887                num_j2=ref_j+ceil(browse.incr_pair(2)/2);
2888                filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,num_i1,num_i2,num_j1,num_j2);
2889                select(1)=exist(filename,'file')==2;
2890                testpair=1;
2891            else
2892%                 if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
2893%                     errormsg=['no civ1 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ1];
2894%                 else
2895                    errormsg=['no civ1 file available for the selected reference indices (i,j)= ' num2str(ref_i) ', ' num2str(ref_j) ' and subdirectory ' subdir_civ1];
2896%                 end
2897                set(handles.ListPairCiv1,'String',{''});
2898                %COMPLETER CAS STEREO
2899                return
2900            end
2901        end
2902    end
2903else %case civ2 alone
2904    if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
2905        if ~exist(fullfile(RootPath,subdir_civ2),'dir')
2906            msgbox_uvmat('ERROR',['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist'])
2907            set(handles.ListPairCiv2,'Value',1);
2908            set(handles.ListPairCiv2,'String',{''});
2909            return
2910        end
2911        for ipair=1:nbpair
2912            filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,...
2913                ref_i+displ_num(3,ipair),ref_i+displ_num(4,ipair),ref_j+displ_num(1,ipair),ref_j+displ_num(2,ipair));
2914            select(ipair)=exist(filename,'file')==2;
2915        end
2916        if  isequal(select,zeros(size(1:nbpair)))
2917            if isfield(browse,'incr_pair')
2918                num_i1=ref_i-floor(browse.incr_pair(1)/2);
2919                num_i2=ref_i+floor((browse.incr_pair(1)+1)/2);
2920                num_j1=ref_j-floor(browse.incr_pair(2)/2);
2921                num_j2=ref_j+floor((browse.incr_pair(2)+1)/2);
2922                filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile,'.nc',nom_type_nc,num_i1,num_i2,num_j1,num_j2);
2923                select(1)=exist(filename,'file')==2;
2924            else
2925                if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
2926                    errormsg=['no civ2 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ2];
2927                else
2928                    errormsg=['no civ2 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ2];
2929                end
2930                set(handles.ListPairCiv2,'Value',1);
2931                set(handles.ListPairCiv2,'String',{''});
2932                return
2933            end
2934        end
2935    end
2936end
2937
2938%% determine the menu display in .ListPairCiv1
2939% the menu depends on the mode defined in ListPairMode_callback through the array displ_num:
2940% displ_num(1,:)=indices j1
2941% displ_num(2,:)=indices j2
2942% displ_num(3,:)=indices i1
2943% displ_num(4,:)=indices i2
2944% in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices
2945% are relative to the reference indices ref_i and ref_j respectively.
2946if isequal(mode,'series(Di)')
2947    if testpair
2948        displ_pair{1}=['Di= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
2949    else
2950        for ipair=1:nbpair
2951            if select(ipair)
2952                displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
2953                %if ~checkframe && size(time,1)>=ref_i+1+displ_num(4,ipair) && size(time,2)>=ref_j+1+displ_num(2,ipair)&&displ_num(2,ipair)>=1 &&displ_num(1,ipair)>=1
2954                 %   dt=time(ref_i+1+displ_num(4,ipair),ref_j+1+displ_num(2,ipair))-time(ref_i+1+displ_num(3,ipair),ref_j+1+displ_num(1,ipair));%time interval dt
2955               if ~checkframe && size(time,1)>=ref_i+1+ceil(ipair/2) && size(time,2)>=ref_j+1&& ref_i-floor(ipair/2)>=0 && ref_j>=0
2956                 dt=time(ref_i+1+ceil(ipair/2),ref_j+1)-time(ref_i+1-floor(ipair/2),ref_j+1);%time interval dtref_j+1
2957                else
2958                    dt=1;
2959                end
2960                 displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
2961            else
2962                displ_pair{ipair}='...'; %pair not displayed in the menu
2963            end
2964        end
2965    end
2966elseif isequal(mode,'series(Dj)')
2967    if testpair
2968        displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
2969    else
2970        for ipair=1:nbpair
2971            if select(ipair)
2972                displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
2973                if ~checkframe && size(time,1)>=ref_i+1+displ_num(4,ipair) && size(time,2)>=ref_j+1+displ_num(2,ipair)
2974                    dt=time(ref_i+1+displ_num(4,ipair),ref_j+1+displ_num(2,ipair))-time(ref_i+1+displ_num(3,ipair),ref_j+1+displ_num(1,ipair));%time interval dt
2975                    displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
2976                end
2977            else
2978                displ_pair{ipair}='...'; %pair not displayed in the menu
2979            end
2980        end
2981    end
2982elseif isequal(mode,'pair j1-j2')%case of pairs
2983    for ipair=1:nbpair
2984        if select(ipair)
2985            if ~checkframe && size(time,2)>1
2986            dt=time(ref_i+1+displ_num(4,ipair),displ_num(2,ipair)+1)-time(ref_i+1+displ_num(3,ipair),displ_num(1,ipair)+1);%time interval dt
2987            else % time set by default to i index
2988                dt=1;
2989            end
2990            displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ...
2991                ' :dt= ' num2str(dt*1000)];
2992        else
2993            displ_pair{ipair}='...'; %pair not displayed in the menu
2994        end
2995    end
2996elseif isequal(mode,'displacement')
2997    displ_pair={'Di=Dj=0'};
2998end
2999if index==1
3000set(handles.ListPairCiv1,'String',displ_pair');
3001end
3002
3003%% determine the default selection in the pair menu
3004ichoice=find(select,1);% index of selected pair
3005if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
3006initial=get(handles.ListPairCiv1,'Value');%initial choice of pair
3007if initial>nbpair || (numel(select)>=initial && ~isequal(select(initial),1))
3008    set(handles.ListPairCiv1,'Value',ichoice);% first valid pair proposed by default in the menu
3009end
3010initial=get(handles.ListPairCiv2,'Value');
3011if initial>length(displ_pair')%|~isequal(select(initial),1)
3012    if ichoice <= length(displ_pair')
3013        set(handles.ListPairCiv2,'Value',ichoice);% same pair proposed by default for civ2
3014    else
3015        set(handles.ListPairCiv2,'Value',1);% same pair proposed by default for civ2
3016    end
3017end
3018set(handles.ListPairCiv2,'String',displ_pair');
3019set(gcf,'Pointer','arrow')
3020
3021
3022   
3023% %------------------------------------------------------------------------   
3024% % call 'view_field.fig' to display the  field selected in the list of 'status'
3025% function open_view_field(hObject, eventdata)
3026% %------------------------------------------------------------------------
3027% list=get(hObject,'String');
3028% index=get(hObject,'Value');
3029% rootroot=get(hObject,'UserData');
3030% filename=list{index};
3031% ind_dot=strfind(filename,'...');
3032% filename=filename(1:ind_dot-1);
3033% filename=fullfile(rootroot,filename);
3034% delete(get(hObject,'parent'))%delete the display figure to stop the check process
3035% if exist(filename,'file')%visualise the vel field if it exists
3036%     uvmat(filename)
3037%     set(gcbo,'Value',1)
3038% end
3039
3040
3041%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3042% Callbacks in the uipanel Reference Indices
3043%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3044%------------------------------------------------------------------------
3045function first_i_Callback(hObject, eventdata, handles)
3046%------------------------------------------------------------------------
3047first_i=str2double(get(handles.first_i,'String'));
3048set(handles.ref_i,'String', num2str(first_i))% reference index for pair dt = first index
3049ref_i_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
3050
3051%------------------------------------------------------------------------
3052function first_j_Callback(hObject, eventdata, handles)
3053%------------------------------------------------------------------------
3054first_j=str2num(get(handles.first_j,'String'));
3055set(handles.ref_j,'String', num2str(first_j))% reference index for pair dt = first index
3056ref_j_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
3057
3058%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3059% Callbacks in the uipanel Civ1
3060%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3061%------------------------------------------------------------------------
3062% --- Executes on button press in SearchRange: determine the search range num_SearchBoxSize_1,num_SearchBoxSize_2
3063function SearchRange_Callback(hObject, eventdata, handles)
3064%------------------------------------------------------------------------
3065%determine pair numbers
3066if strcmp(get(handles.num_UMin,'Visible'),'off')
3067    set(handles.u_title,'Visible','on')
3068    set(handles.v_title,'Visible','on')
3069    set(handles.num_UMin,'Visible','on')
3070    set(handles.num_UMax,'Visible','on')
3071    set(handles.num_VMin,'Visible','on')
3072    set(handles.num_VMax,'Visible','on')
3073    set(handles.CoordUnit,'Visible','on')
3074    set(handles.TimeUnit,'Visible','on')
3075    set(handles.slash_title,'Visible','on')
3076    set(handles.min_title,'Visible','on')
3077    set(handles.max_title,'Visible','on')
3078    set(handles.unit_title,'Visible','on')
3079else
3080    get_search_range(hObject, eventdata, handles)
3081end
3082
3083%------------------------------------------------------------------------
3084% ---  determine the search range num_SearchBoxSize_1,num_SearchBoxSize_2 and shift
3085function get_search_range(hObject, eventdata, handles)
3086%------------------------------------------------------------------------
3087param_civ1=read_GUI(handles.Civ1);
3088umin=param_civ1.UMin;
3089umax=param_civ1.UMax;
3090vmin=param_civ1.VMin;
3091vmax=param_civ1.VMax;
3092%switch min_title and max_title in case of error
3093if umax<=umin
3094    umin_old=umin;
3095    umin=umax;
3096    umax=umin_old;
3097    set(handles.num_UMin,'String', num2str(umin))
3098    set(handles.num_UMax,'String', num2str(umax))
3099end
3100if vmax<=vmin
3101    vmin_old=vmin;
3102    vmin=vmax;
3103    vmax=vmin_old;
3104    set(handles.num_VMin,'String', num2str(vmin))
3105    set(handles.num_VMax,'String', num2str(vmax))
3106end   
3107if ~(isempty(umin)||isempty(umax)||isempty(vmin)||isempty(vmax))
3108    list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
3109    index=get(handles.ListPairCiv1,'Value');
3110    pair_string=list_pair{index};
3111    time=get(handles.ImaDoc,'UserData'); %get the set of times
3112    pxcm=get(handles.SearchRange,'UserData');
3113    mode_list=get(handles.ListPairMode,'String');
3114    mode_value=get(handles.ListPairMode,'Value');
3115    mode=mode_list{mode_value};     
3116    if isequal (mode, 'series(Di)' )
3117        ref_i=str2double(get(handles.ref_i,'String'));
3118        num1=ref_i-floor(index/2);%  first image numbers
3119        num2=ref_i+ceil(index/2);
3120        num_a=1;
3121        num_b=1;
3122    elseif isequal (mode, 'series(Dj)')
3123        num1=1;
3124        num2=1;
3125        ref_j=str2double(get(handles.ref_j,'String'));
3126        num_a=ref_j-floor(index/2);%  first image numbers
3127        num_b=ref_j+ceil(index/2);
3128    elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)     
3129        ref_i=str2double(get(handles.ref_i,'String'));
3130        num1=ref_i;
3131        num2=ref_i;
3132                r=regexp(pair_string,'(?<mode>(Di=)|(Dj=)) -*(?<num1>\d+)\|(?<num2>\d+)','names');
3133        if isempty(r)
3134            r=regexp(pair_string,'(?<num1>\d+)(?<mode>-)(?<num2>\d+)','names');
3135        end 
3136        num_a=str2num(r.num1);
3137        num_b=str2num(r.num2);
3138    end
3139    dt=time(num2+1,num_b+1)-time(num1+1,num_a+1);
3140    ibx=str2double(get(handles.num_CorrBoxSize_1,'String'));
3141    iby=str2double(get(handles.num_CorrBoxSize_2,'String'));
3142    umin=dt*pxcm*umin;
3143    umax=dt*pxcm*umax;
3144    vmin=dt*pxcm*vmin;
3145    vmax=dt*pxcm*vmax;
3146    shiftx=round((umin+umax)/2);
3147    shifty=round((vmin+vmax)/2);
3148    isx=(umax+2-shiftx)*2+param_civ1.Bx;
3149    isx=2*ceil(isx/2)+1;
3150    isy=(vmax+2-shifty)*2+param_civ1.Bx;
3151    isy=2*ceil(isy/2)+1;
3152    set(handles.num_SearchBoxShift_1,'String',num2str(shiftx));
3153    set(handles.num_SearchBoxShift_2,'String',num2str(shifty));
3154    set(handles.num_SearchBoxSize_1,'String',num2str(isx));
3155    set(handles.num_SearchBoxSize_2,'String',num2str(isy));
3156end
3157
3158%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3159% Callbacks in the uipanel Fix1
3160%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3161%------------------------------------------------------------------------
3162% --- Executes on button press in CheckMask.
3163function get_mask_fix1_Callback(hObject, eventdata, handles)
3164%------------------------------------------------------------------------
3165maskval=get(handles.CheckMask,'Value');
3166if isequal(maskval,0)
3167    set(handles.Mask,'String','')
3168else
3169    mask_displ='no mask'; %default
3170    filebase=get(handles.RootPath,'String');
3171    [nbslice, flag_mask]=get_mask(filebase,handles);
3172    if isequal(flag_mask,1)
3173        mask_displ=[num2str(nbslice) 'mask'];
3174    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3175        filebase_a=get(handles.RootFile_1,'String');
3176        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3177        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3178            mask_displ='no mask';
3179        end
3180    end
3181    if isequal(mask_displ,'no mask')
3182        [FileName, PathName, filterindex] = uigetfile( ...
3183            {'*.png', ' (*.png)';
3184            '*.png',  '.png files '; ...
3185            '*.*', 'All Files (*.*)'}, ...
3186            'Pick a mask file *.png',filebase);
3187        mask_displ=fullfile(PathName,FileName);
3188        if ~exist(mask_displ,'file')
3189            mask_displ='no mask';
3190        end
3191    end
3192    if isequal(mask_displ,'no mask')
3193        set(handles.CheckMask,'Value',0)
3194        set(handles.CheckMask,'Value',0)
3195        set(handles.CheckMask,'Value',0)
3196    else
3197        %set(handles.CheckMask,'Value',1)
3198        set(handles.CheckMask,'Value',1)
3199    end
3200    set(handles.Mask,'String',mask_displ)
3201    set(handles.Mask,'String',mask_displ)
3202    set(handles.Mask,'String',mask_displ)
3203end
3204
3205%------------------------------------------------------------------------
3206% --- Executes on button press in CheckMask: select box for mask option
3207function get_mask_civ2_Callback(hObject, eventdata, handles)
3208%------------------------------------------------------------------------
3209maskval=get(handles.CheckMask,'Value');
3210if isequal(maskval,0)
3211    set(handles.Mask,'String','')
3212else
3213    mask_displ='no mask'; %default
3214    filebase=get(handles.RootPath,'String');
3215    [nbslice, flag_mask]=get_mask(filebase,handles);
3216    if isequal(flag_mask,1)
3217        mask_displ=[num2str(nbslice) 'mask'];
3218    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3219        filebase_a=get(handles.RootFile_1,'String');
3220        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3221        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3222            mask_displ='no mask';
3223        end
3224    end
3225    if isequal(mask_displ,'no mask')
3226        [FileName, PathName, filterindex] = uigetfile( ...
3227            {'*.png', ' (*.png)';
3228            '*.png',  '.png files '; ...
3229            '*.*', 'All Files (*.*)'}, ...
3230            'Pick a mask file *.png',filebase);
3231        mask_displ=fullfile(PathName,FileName);
3232        if ~exist(mask_displ,'file')
3233            mask_displ='no mask';
3234        end
3235    end
3236    if isequal(mask_displ,'no mask')
3237        set(handles.CheckMask,'Value',0)
3238        set(handles.CheckMask,'Value',0)
3239    else
3240        set(handles.CheckMask,'Value',1)
3241    end
3242    set(handles.Mask,'String',mask_displ)
3243    set(handles.Mask,'String',mask_displ)
3244end
3245
3246%------------------------------------------------------------------------
3247% --- Executes on button press in CheckMask.
3248function get_mask_fix2_Callback(hObject, eventdata, handles)
3249%------------------------------------------------------------------------
3250maskval=get(handles.CheckMask,'Value');
3251if isequal(maskval,0)
3252    set(handles.Mask,'String','')
3253else
3254    mask_displ='no mask'; %default
3255    filebase=get(handles.RootPath,'String');
3256    [nbslice, flag_mask]=get_mask(filebase,handles);
3257    if isequal(flag_mask,1)
3258        mask_displ=[num2str(nbslice) 'mask'];
3259    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3260        filebase_a=get(handles.RootFile_1,'String');
3261        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3262        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3263            mask_displ='no mask';
3264        end
3265    end
3266    if isequal(mask_displ,'no mask')
3267        [FileName, PathName, filterindex] = uigetfile( ...
3268            {'*.png', ' (*.png)';
3269            '*.png',  '.png files '; ...
3270            '*.*', 'All Files (*.*)'}, ...
3271            'Pick a mask file *.png',filebase);
3272        mask_displ=fullfile(PathName,FileName);
3273        if ~exist(mask_displ,'file')
3274            mask_displ='no mask';
3275        end
3276    end
3277    if isequal(mask_displ,'no mask')
3278        set(handles.CheckMask,'Value',0)
3279    end
3280    set(handles.Mask,'String',mask_displ)
3281end
3282
3283%------------------------------------------------------------------------
3284% --- function called to look for mask files
3285function [nbslice, flag_mask]=get_mask(filebase,handles)
3286%------------------------------------------------------------------------
3287%detect mask files, images with appropriate file base
3288%[filebase '_' xx 'mask'], xx=nbslice
3289%flag_mask=1 indicates detection
3290
3291flag_mask=0;%default
3292nbslice=1;
3293
3294% subdir=get(handles.SubdirCiv1,'String');
3295[Path,Name]=fileparts(filebase);
3296if ~isdir(Path)
3297    msgbox_uvmat('ERROR','no path for input files')
3298    return
3299end
3300% currentdir=pwd;
3301% cd(Path);%move in the dir of the root name filebase
3302maskfiles=dir(fullfile(Path,[Name '_*mask_*.png']));%look for mask files
3303% cd(currentdir);%come back to the current working directory
3304if ~isempty(maskfiles)
3305    %     msgbox_uvmat('ERROR','no mask available, to create it use Tools/Make mask in the upper menu bar of uvmat')
3306    % else
3307    flag_mask=1;
3308    maskname=maskfiles(1).name;% take the first mask file in the list
3309    [Path2,Name,ext]=fileparts(maskname);
3310    Namedouble=double(Name);
3311    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3312    ind_mask=findstr('mask',Name);
3313    i=ind_mask-1;
3314    while val(i)==0 && i>0
3315        i=i-1;
3316    end
3317    nbslice=str2double(Name(i+1:ind_mask-1));
3318    if ~isnan(nbslice) && Name(i)=='_'
3319        flag_mask=1;
3320    else
3321        msgbox_uvmat('ERROR',['bad mask file ' Name ext ' found in ' Path2])
3322        return
3323        nbslice=1;
3324    end
3325end
3326
3327%------------------------------------------------------------------------
3328% --- function called to look for grid files
3329function [nbslice, flag_grid]=get_grid(filebase,handles)
3330%------------------------------------------------------------------------
3331flag_grid=0;%default
3332nbslice=1;
3333[Path,Name]=fileparts(filebase);
3334currentdir=pwd;
3335cd(Path);%move in the dir of the root name filebase
3336gridfiles=dir([Name '_*grid_*.grid']);%look for grid files
3337cd(currentdir);%come back to the current working directory
3338if ~isempty(gridfiles)
3339    flag_grid=1;
3340    gridname=gridfiles(1).name;% take the first grid file in the list
3341    [Path2,Name,ext]=fileparts(gridname);
3342    Namedouble=double(Name);
3343    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3344    ind_grid=findstr('grid',Name);
3345    i=ind_grid-1;
3346    while val(i)==0 && i>0
3347        i=i-1;
3348    end
3349    nbslice=str2double(Name(i+1:ind_grid-1));
3350    if ~isnan(nbslice) && Name(i)=='_'
3351        flag_grid=1;
3352    else
3353        msgbox_uvmat('ERROR',['bad grid file ' Name ext ' found in ' Path2])
3354        return
3355        nbslice=1;
3356    end
3357end
3358
3359%------------------------------------------------------------------------
3360% --- transform numbers to letters
3361function str=num2stra(num,nom_type)
3362%------------------------------------------------------------------------
3363if isempty(nom_type)
3364    str='';
3365elseif strcmp(nom_type(end),'a')
3366    str=char(96+num);
3367elseif strcmp(nom_type(end),'A')
3368    str=char(96+num);
3369elseif isempty(nom_type(2:end))%a single index
3370    str='';
3371else
3372    str=num2str(num);
3373end
3374
3375% %------------------------------------------------------------------------
3376% % --- Executes on button press in ListSubdirCiv1.
3377% function ListSubdirCiv1_Callback(hObject, eventdata, handles)
3378% %------------------------------------------------------------------------
3379% list_subdir_civ1=get(handles.ListSubdirCiv1,'String');
3380% val=get(handles.ListSubdirCiv1,'Value');
3381% SubDir=list_subdir_civ1{val};
3382% if strcmp(SubDir,'new...')
3383%     if get(handles.CheckCiv1,'Value')
3384%         SubDir='CIV_INPUT'; %default subdirectory
3385%     else
3386%         msgbox_uvmat('ERROR','select CheckCiv1 to perform a new civ_input operation')
3387%         return
3388%     end   
3389% end
3390% set(handles.SubdirCiv1,'String',SubDir);
3391% errormsg=find_netcpair_civ(handles,1);
3392% if ~isempty(errormsg)
3393%     msgbox_uvmat('ERROR',errormsg)
3394% end
3395%     
3396%------------------------------------------------------------------------
3397% % --- Executes on button press in ListSubdirCiv2.
3398% function ListSubdirCiv2_Callback(hObject, eventdata, handles)
3399% %------------------------------------------------------------------------
3400% list_subdir_civ2=get(handles.ListSubdirCiv2,'String');
3401% val=get(handles.ListSubdirCiv2,'Value');
3402% SubDir=list_subdir_civ2{val};
3403% if strcmp(SubDir,'new...')
3404%     if get(handles.CheckCiv2,'Value')
3405%         SubDir='CIV_INPUT'; %default subdirectory
3406%     else
3407%         msgbox_uvmat('ERROR','select CheckCiv2 to perform a new civ_input operation')
3408%         return
3409%     end
3410% end
3411% set(handles.SubdirCiv2,'String',SubDir);
3412
3413%------------------------------------------------------------------------
3414% --- Executes on button press in CheckGrid.
3415function CheckGrid_Callback(hObject, eventdata, handles)
3416%------------------------------------------------------------------------
3417value=get(hObject,'Value');
3418hparent=get(hObject,'parent');%handles of the parent panel
3419hchildren=get(hparent,'children');
3420handle_txtbox=findobj(hchildren,'tag','Grid');% look for the grid name box in the same panel
3421handle_dx=findobj(hchildren,'tag','num_Dx');
3422handle_dy=findobj(hchildren,'tag','num_Dy');
3423handle_title_dx=findobj(hchildren,'tag','title_Dx');
3424handle_title_dy=findobj(hchildren,'tag','title_Dy');
3425testgrid=0;
3426filegrid='';
3427if value
3428    filebase=get(handles.RootPath,'String');
3429    [nbslice, flag_grid]=get_grid(filebase,handles);% look for a grid with appropriate name
3430    if isequal(flag_grid,1)
3431        filegrid=[num2str(nbslice) 'grid'];
3432        testgrid=1;
3433    else % browse for a grid
3434        filegrid=get(hObject,'UserData');%look for previous grid name stored as UserData
3435        if exist(filegrid,'file')
3436            filebase=filegrid;
3437        end
3438        [FileName, PathName] = uigetfile( ...
3439            {'*.grid', ' (*.grid)';
3440            '*.grid',  '.grid files '; ...
3441            '*.*', 'All Files (*.*)'}, ...
3442            'Pick a file',filebase);
3443        filegrid=fullfile(PathName,FileName);
3444        set(hObject,'UserData',filegrid);%store for future use
3445        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filegrid,'file'))
3446            testgrid=1;
3447        end
3448    end
3449end
3450if testgrid
3451    set(handle_dx,'Visible','off');
3452    set(handle_dy,'Visible','off');
3453    set(handle_title_dy,'Visible','off');
3454    set(handle_title_dx,'Visible','off');
3455    set(handle_txtbox,'Visible','on')
3456    set(handle_txtbox,'String',filegrid)
3457else
3458    set(hObject,'Value',0);
3459    set(handle_dx,'Visible','on');
3460    set(handle_dy,'Visible','on');
3461    set(handle_title_dy,'Visible','on');
3462    set(handle_title_dx,'Visible','on');
3463    set(handle_txtbox,'Visible','off')
3464end
3465
3466%% if hObject is on the checkciv1 frame, duplicate action for checkciv2 frame
3467PanelName=get(hparent,'tag');
3468if strcmp(PanelName,'Civ1')
3469    hchildren=get(handles.Civ2,'children');
3470    handle_checkbox=findobj(hchildren,'tag','CheckGrid');
3471    handle_txtbox=findobj(hchildren,'tag','Grid');
3472    handle_dx=findobj(hchildren,'tag','num_Dx');
3473    handle_dy=findobj(hchildren,'tag','num_Dy');
3474    handle_title_dx=findobj(hchildren,'tag','title_Dx');
3475    handle_title_dy=findobj(hchildren,'tag','title_Dy');
3476    set(handle_checkbox,'UserData',filegrid);%store for future use
3477    if testgrid
3478        set(handle_checkbox,'Value',1);
3479        set(handle_dx,'Visible','off');
3480        set(handle_dy,'Visible','off');
3481        set(handle_title_dx,'Visible','off');
3482        set(handle_title_dy,'Visible','off');
3483        set(handle_txtbox,'Visible','on')
3484        set(handle_txtbox,'String',filegrid)
3485    end
3486end
3487
3488%------------------------------------------------------------------------
3489% --- Executes on button press in CheckMask: common to all panels (civ1, Civ2..)
3490function CheckMask_Callback(hObject, eventdata, handles)
3491%------------------------------------------------------------------------
3492value=get(hObject,'Value');
3493hparent=get(hObject,'parent');
3494parent_tag=get(hparent,'Tag');
3495hchildren=get(hparent,'children');
3496handle_txtbox=findobj(hchildren,'tag','Mask');% look for the mask name box in the same panel
3497testmask=0;
3498if value
3499    filebase=get(handles.RootPath,'String');
3500    [nbslice, flag_mask]=get_mask(filebase,handles);% look for a mask with appropriate name
3501    if isequal(flag_mask,1)
3502        filemask=[num2str(nbslice) 'mask'];
3503        testmask=1;
3504    else % browse for a mask
3505        filemask=get(hObject,'UserData');%look for previous mask name stored as UserData
3506        if exist(filemask,'file')
3507            filebase=filemask;
3508        end
3509        [FileName, PathName] = uigetfile( ...
3510            {'*.png', ' (*.png)';
3511            '*.png',  '.png files '; ...
3512            '*.*', 'All Files (*.*)'}, ...
3513            'Pick a mask file *.png',filebase);
3514        filemask=fullfile(PathName,FileName);
3515        set(hObject,'UserData',filemask);%store for future use
3516        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filemask,'file'))
3517            testmask=1;
3518        end
3519    end
3520end
3521if testmask
3522    if strcmp(parent_tag,'Civ1')
3523        set(handles.Mask,'Visible','on')
3524        set(handles.Mask,'String',filemask)
3525    set(handles.CheckMask,'Value',1)
3526    end
3527else
3528    set(hObject,'Value',0);
3529    set(handle_txtbox,'Visible','off')
3530end
3531
3532%------------------------------------------------------------------------
3533% --- Executes on button press in get_gridpatch1.
3534function get_gridpatch1_Callback(hObject, eventdata, handles)
3535%------------------------------------------------------------------------
3536filebase=get(handles.RootPath,'String');
3537[FileName, PathName, filterindex] = uigetfile( ...
3538    {'*.grid', ' (*.grid)';
3539    '*.grid',  '.grid files '; ...
3540    '*.*', 'All Files (*.*)'}, ...
3541    'Pick a file',filebase);
3542filegrid=fullfile(PathName,FileName);
3543set(handles.grid_patch1,'string',filegrid);
3544
3545
3546%------------------------------------------------------------------------
3547% --- Executes on button press in get_gridpatch2.
3548function get_gridpatch2_Callback(hObject, eventdata, handles)
3549%------------------------------------------------------------------------
3550
3551
3552%------------------------------------------------------------------------
3553% --- STEREO Interp
3554function cmd=RUN_STINTERP(stinterpBin,filename_A_nc,filename_B_nc,filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,xmlA,xmlB)
3555%------------------------------------------------------------------------
3556namelog=[filename_nc(1:end-3) '_stinterp.log'];
3557cmd=[stinterpBin ' -f1 ' filename_A_nc  ' -f2 ' filename_B_nc ' -f  ' filename_nc ...
3558    ' -m ' nx_patch  ' -n ' ny_patch ' -ro ' rho_patch ' -nopt ' subdomain_patch ' -c1 ' xmlA ' -c2 ' xmlB '  -xy  x -Nfy 1024 > ' namelog ' 2>&1']; % redirect standard output to the log file
3559
3560% %------------------------------------------------------------------------
3561% %--read images and convert them to the uint16 format used for PIV
3562% function A=read_image(filename,type_ima,num,movieobject)
3563% %------------------------------------------------------------------------
3564% %num is the view number needed for an avi movie
3565% switch type_ima
3566%     case 'movie'
3567%         A=read(movieobject,num);
3568%     case 'avi'
3569%         mov=aviread(filename,num);
3570%         A=frame2im(mov(1));
3571%     case 'multimage'
3572%         A=imread(filename,num);
3573%     case 'image'
3574%         A=imread(filename);
3575% end
3576% siz=size(A);
3577% if length(siz)==3;%color images
3578%     A=sum(double(A),3);
3579%     A=uint16(A);
3580% end
3581
3582
3583%------------------------------------------------------------------------
3584% --- Executes on button press in get_ref_fix1.
3585function get_ref_fix1_Callback(hObject, eventdata, handles)
3586%------------------------------------------------------------------------
3587filebase=get(handles.RootPath,'String');
3588[FileName, PathName, filterindex] = uigetfile( ...
3589    {'*.nc', ' (*.nc)';
3590    '*.nc',  'netcdf files '; ...
3591    '*.*', 'All Files (*.*)'}, ...
3592    'Pick a file',filebase);
3593
3594fileinput=[PathName FileName];
3595sizf=size(fileinput);
3596if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
3597%[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
3598[Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput);
3599ref.filebase=fullfile(Path,File);
3600% ref.num_a=stra2num(str_a);
3601% ref.num_b=stra2num(str_b);
3602% ref.num1=str2double(field_count);
3603% ref.num2=str2double(str2);
3604browse=[];%initialisation
3605if ~isequal(ref.ext,'.nc')
3606    msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
3607    return
3608end
3609set(handles.ref_fix1,'String',[fullfile(ref.subdir,File) '....nc']);
3610set(handles.ref_fix1,'UserData',ref)
3611menu_field{1}='civ1';
3612Data=nc2struct(fileinput,[]);
3613if isfield(Data,'patch') && isequal(Data.patch,1)
3614    menu_field{2}='filter1';
3615end
3616if isfield(Data,'civ2') && isequal(Data.civ2,1)
3617    menu_field{3}='civ2';
3618end
3619if isfield(Data,'patch2') && isequal(Data.patch2,1)
3620    menu_field{4}='filter2';
3621end
3622set(handles.field_ref1,'String',menu_field);
3623set(handles.field_ref1,'Value',length(menu_field));
3624set(handles.num_MinVel,'Value',2);
3625set(handles.num_MinVel,'String','1');%default threshold
3626set(handles.ref_fix1,'Enable','on')
3627
3628%------------------------------------------------------------------------
3629% --- Executes on button press in get_ref_fix2.
3630function get_ref_fix2_Callback(hObject, eventdata, handles)
3631%------------------------------------------------------------------------
3632if isequal(get(handles.get_ref_fix2,'Value'),1)
3633    filebase=get(handles.RootPath,'String');
3634    [FileName, PathName, filterindex] = uigetfile( ...
3635        {'*.nc', ' (*.nc)';
3636        '*.nc',  'netcdf files '; ...
3637        '*.*', 'All Files (*.*)'}, ...
3638        'Pick a file',filebase);
3639    fileinput=[PathName FileName];
3640    sizf=size(fileinput);
3641    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
3642    %[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
3643    [Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput);
3644    ref.filebase=fullfile(Path,File);
3645%     ref.num_a=stra2num(str_a);
3646%     ref.num_b=stra2num(str_b);
3647%     ref.num1=str2num(field_count);
3648%     ref.num2=str2num(str2);
3649    browse=[];%initialisation
3650    if ~isequal(ref.ext,'.nc')
3651        msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
3652        return
3653    end
3654    set(handles.ref_fix2,'String',[fullfile(ref.subdir,File) '....nc']);
3655    set(handles.ref_fix2,'UserData',ref)
3656    menu_field{1}='civ1';
3657    Data=nc2struct(fileinput,[]);
3658    if isfield(Data,'patch') && isequal(Data.patch,1)
3659        menu_field{2}='filter1';
3660    end
3661    if isfield(Data,'civ2') && isequal(Data.civ2,1)
3662        menu_field{3}='civ2';
3663    end
3664    if isfield(Data,'patch2') && isequal(Data.patch2,1)
3665        menu_field{4}='filter2';
3666    end
3667    set(handles.field_ref2,'String',menu_field);
3668    set(handles.field_ref2,'Value',length(menu_field));
3669    set(handles.num_MinVel,'Value',2);
3670    set(handles.num_MinVel,'String','1');%default threshold
3671    set(handles.ref_fix2,'Enable','on')
3672    set(handles.ref_fix2,'Visible','on')
3673    set(handles.field_ref2,'Visible','on')
3674else
3675    set(handles.ref_fix2,'Visible','off')
3676    set(handles.field_ref2,'Visible','off')
3677end
3678
3679%------------------------------------------------------------------------
3680function ref_fix1_Callback(hObject, eventdata, handles)
3681%------------------------------------------------------------------------
3682set(handles.num_MinVel,'Value',1);
3683set(handles.field_ref1,'Value',1)
3684set(handles.field_ref1,'String',{' '})
3685set(handles.ref_fix1,'UserData',[]);
3686set(handles.ref_fix1,'String','');
3687set(handles.thresh_vel1,'String','0');
3688
3689%------------------------------------------------------------------------
3690function ref_fix2_Callback(hObject, eventdata, handles)
3691%------------------------------------------------------------------------
3692set(handles.num_MinVel,'Value',1);
3693set(handles.field_ref2,'Value',1)
3694set(handles.field_ref2,'String',{' '})
3695set(handles.ref_fix2,'UserData',[]);
3696set(handles.ref_fix2,'String','');
3697set(handles.num_MinVel,'String','0');
3698
3699%------------------------------------------------------------------------
3700% --- TO ABANDON Executes on button press in test_stereo1.
3701function CheckStereo_Callback(hObject, eventdata, handles)
3702%------------------------------------------------------------------------
3703hparent=get(hObject,'parent');
3704parent_tag=get(hparent,'Tag');
3705hchildren=get(hparent,'children');
3706handle_txtbox=findobj(hchildren,'tag','txt_Mask');
3707if isequal(get(hObject,'Value'),0)
3708    set(handles.num_SubDomainSize,'Visible','on')
3709    set(handles.num_FieldSmooth,'Visible','on')
3710else
3711    set(handles.num_SubDomainSize,'Visible','off')
3712    set(handles.num_FieldSmooth,'Visible','off')
3713end
3714
3715% %------------------------------------------------------------------------
3716% % --- Executes on button press in CheckStereo.
3717% function StereoCheck_Callback(hObject, eventdata, handles)
3718% %------------------------------------------------------------------------
3719% if isequal(get(handles.CheckStereo,'Value'),0)
3720%     set(handles.num_subdomainsize,'Visible','on')
3721%     set(handles.num_FieldSmooth,'Visible','on')
3722% else
3723%     set(handles.num_subdomainsize,'Visible','off')
3724%     set(handles.num_FieldSmooth,'Visible','off')
3725% end
3726
3727%------------------------------------------------------------------------
3728% --- Executes on button press in TestCiv1: prepare the image correlation function
3729% activated by mouse motion
3730function TestCiv1_Callback(hObject, eventdata, handles)
3731%------------------------------------------------------------------------
3732drawnow
3733if get(handles.TestCiv1,'Value')
3734    set(handles.TestCiv1,'BackgroundColor',[0.7 0.7 0.7])% paint TestCiv1 button to grey to confirm civ launch
3735    ref_i=str2double(get(handles.ref_i,'String'));% read reference i index
3736    if strcmp(get(handles.ref_j,'Visible'),'on')
3737        ref_j=str2double(get(handles.ref_j,'String'));% read reference j index if relevant
3738    else
3739        ref_j=1;%default j index
3740    end
3741    [filecell,i1,i2]=set_civ_filenames(handles,ref_i,ref_j,[1 0 0 0 0 0]);% get the corresponding file name and indices
3742    Data.ListVarName={'ny','nx','A'};
3743    Data.VarDimName= {'ny','nx',{'ny','nx'}};
3744
3745    Data.A=imread(filecell.ima1.civ1{1}); % read the first image
3746    if ndims(Data.A)==3 %case of color image
3747        Data.VarDimName= {'ny','nx',{'ny','nx','rgb'}};
3748    end
3749    Data.ny=[size(Data.A,1) 1];
3750    Data.nx=[1 size(Data.A,2)];
3751    Data.CoordUnit='pixel';% used to set equal scaling for x and y in image dispaly
3752    par_civ1=read_GUI(handles.Civ1);
3753    par_civ1.FileTypeA=get_file_type(filecell.ima1.civ1{1});
3754    par_civ1.ImageWidth=size(Data.A,2);
3755    par_civ1.ImageHeight=size(Data.A,1);
3756    par_civ1.Mask='all';% will provide only the grid set for PIV, no image correlation
3757    par_civ1.FrameIndexA=num2str(i1);
3758    par_civ1.FrameIndexB=num2str(i2);
3759    Param.Civ1=par_civ1;
3760    Grid=civ_matlab(Param);% get the grid of x, y positions set for PIV
3761    hview_field=view_field(Data); %view the image in the GUI view_field
3762    set(0,'CurrentFigure',hview_field)
3763    hhview_field=guihandles(hview_field);
3764    set(hview_field,'CurrentAxes',hhview_field.PlotAxes)
3765    ViewData=get(hview_field,'UserData');
3766    ViewData.CivHandle=handles.civ_input;% indicate the handle of the civ GUI in view_field
3767    ViewData.PlotAxes.B=imread(filecell.ima2.civ1{1});%store the second image in the UserData of the GUI view_field
3768    ViewData.PlotAxes.X=Grid.Civ1_X; %keep the set of points in memeory
3769    ViewData.PlotAxes.Y=Grid.Civ1_Y;
3770    set(hview_field,'UserData',ViewData)
3771    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
3772    if isempty(corrfig)
3773        corrfig=figure;
3774        set(corrfig,'tag','corrfig')
3775        set(corrfig,'name','image correlation')
3776        set(corrfig,'DeleteFcn',{@closeview_field})%
3777    end
3778    set(handles.TestCiv1,'BackgroundColor',[1 0 0])
3779else
3780    set(handles.TestCiv1,'BackgroundColor',[1 0 0])% paint button to red
3781    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
3782    if ~isempty(corrfig)
3783        delete(corrfig)
3784    end
3785    hview_field=findobj(allchild(0),'tag','view_field');% look for view_field   
3786    if ~isempty(hview_field)
3787        delete(hview_field)
3788    end
3789end
3790
3791%------------------------------------------------------------------------
3792%----function introduced for the correlation window figure, activated by deleting this window
3793function closeview_field(gcbo,eventdata)
3794%------------------------------------------------------------------------
3795hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
3796if ~isempty(hview_field)
3797    delete(hview_field)
3798end
3799
3800%------------------------------------------------------------------------
3801% --- Executes on button press in CheckThreshold.
3802function CheckThreshold_Callback(hObject, eventdata, handles)
3803%------------------------------------------------------------------------
3804huipanel=get(hObject,'parent');
3805obj(1)=findobj(huipanel,'Tag','num_MinIma');
3806obj(2)=findobj(huipanel,'Tag','num_MaxIma');
3807obj(3)=findobj(huipanel,'Tag','title_Threshold');
3808if get(hObject,'Value')
3809    set(obj,'Visible','on')
3810else
3811    set(obj,'Visible','off')
3812end
3813
3814
3815
3816
3817%'nomtype2pair': creates nomencalture for index pairs knowing the image nomenclature
3818%---------------------------------------------------------------------
3819function NomTypeNc=nomtype2pair(NomTypeIma,mode)
3820%---------------------------------------------------------------------           
3821% OUTPUT:
3822% NomTypeNc
3823%---------------------------------------------------------------------
3824% INPUT:
3825% 'NomTypeIma': string defining the kind of nomenclature used for images
3826
3827NomTypeNc=NomTypeIma;%default
3828switch mode
3829    case 'pair j1-j2'     
3830    if ~isempty(regexp(NomTypeIma,'a$'))
3831        NomTypeNc=[NomTypeIma 'b'];
3832    elseif ~isempty(regexp(NomTypeIma,'A$'))
3833        NomTypeNc=[NomTypeIma 'B'];
3834    else
3835        r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
3836        if ~isempty(r)
3837            NomTypeNc='_1_1-2';
3838        end
3839    end
3840    case 'series(Dj)' 
3841%         r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
3842%         if ~isempty(r)
3843            NomTypeNc='_1_1-2';
3844%         end
3845   case 'series(Di)'
3846        r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
3847        if ~isempty(r)
3848            NomTypeNc='_1-2_1';
3849        else
3850            NomTypeNc='_1-2';
3851        end
3852end
3853
3854function NomType_Callback(hObject, eventdata, handles)
3855set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
3856RootPath=get(handles.RootPath,'String');
3857RootFile=get(handles.RootFile,'String');
3858SubDirImages=get(handles.SubDirImages,'String');
3859ref_i=str2num(get(handles.ref_i,'String'));
3860ref_j=str2num(get(handles.ref_j,'String'));
3861NomType=get(handles.NomType,'String');
3862ImaExt=get(handles.ImaExt,'String');
3863fileinput=fullfile_uvmat(RootPath,SubDirImages,RootFile,ImaExt,NomType,ref_i,[],ref_j);
3864errormsg=display_file_name(handles,fileinput);
3865if ~isempty(errormsg)
3866    msgbox_uvmat('ERROR',errormsg)
3867end
3868set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
3869
3870% --- Executes on selection change in Program.
3871function Program_Callback(hObject, eventdata, handles)
3872ListProgram=get(handles.Program,'String');
3873Program=ListProgram{get(handles.Program,'value')};
3874switch Program
3875    case 'CivX'
3876        set(handles.num_MaxDiff,'Visible','off')
3877        set(handles.num_MaxVel,'Visible','off')
3878        set(handles.title_MaxVel,'Visible','off')
3879        set(handles.num_Nx,'Visible','on')
3880        set(handles.num_Ny,'Visible','on')
3881        set(handles.title_Nx,'Visible','on')
3882        set(handles.title_Ny,'Visible','on')
3883        set(handles.title_MaxDiff,'Visible','off')
3884        set(handles.num_CorrSmooth,'Style','edit')
3885        set(handles.num_CorrSmooth,'String','1')
3886        set(handles.BATCH,'Enable','on')
3887        set(handles.CheckThreshold,'Visible','off')
3888        set(handles.CheckDeformation,'Value',1)
3889        set(handles.CheckDecimal,'Value',1)
3890    case {'civ_matlab','civ_matlab.sh'}
3891        set(handles.num_MaxDiff,'Visible','on')
3892        set(handles.num_MaxVel,'Visible','on')
3893        set(handles.title_MaxVel,'Visible','on')
3894        set(handles.title_MaxDiff,'Visible','on')
3895        set(handles.num_Nx,'Visible','off')
3896        set(handles.num_Ny,'Visible','off')
3897        set(handles.title_Nx,'Visible','off')
3898        set(handles.title_Ny,'Visible','off')
3899        set(handles.num_CorrSmooth,'Style','popupmenu')
3900        set(handles.num_CorrSmooth,'Value',1)
3901        set(handles.num_CorrSmooth,'String',{'1';'2'})
3902        set(handles.CheckThreshold,'Visible','on')
3903        set(handles.CheckDeformation,'Value',0)% desactivate (work in progress)
3904        set(handles.CheckDecimal,'Value',0)% desactivate (work in progress)
3905end
3906
3907% --- Executes on button press in TestPatch1.
3908function TestPatch1_Callback(hObject, eventdata, handles)
3909set(handles.TestPatch1,'BackgroundColor',[1 1 0])
3910drawnow
3911if get(handles.TestPatch1,'Value')
3912    ref_i=str2double(get(handles.ref_i,'String'));
3913    if strcmp(get(handles.ref_j,'Visible'),'on')
3914        ref_j=str2double(get(handles.ref_j,'String'));
3915    else
3916        ref_j=1;%default
3917    end
3918    filecell=set_civ_filenames(handles,ref_i,ref_j,[0 0 1 0 0 0]);   
3919    Data.ListVarName={'ny','nx','A'};
3920    Data.VarDimName= {'ny','nx',{'ny','nx'}};   
3921    param_patch1=read_GUI(handles.Patch1);
3922    param_patch1.CivFile=filecell.nc.civ1{1};
3923    Param.Patch1=param_patch1;
3924    for irho=1:7
3925        [Data,errormsg]=civ_matlab(Param);% get the grid of x, y positions set for PIV
3926        if ~isempty(errormsg)
3927            msgbox_uvmat('ERROR',errormsg)
3928            return
3929        end
3930        SmoothingParam(irho)=Param.Patch1.FieldSmooth;
3931        Data.Civ1_U_Diff=Data.Civ1_U_Diff(Data.Civ1_FF==0);
3932        Data.Civ1_V_Diff=Data.Civ1_V_Diff(Data.Civ1_FF==0);
3933        DiffVel(irho)=sqrt(mean(Data.Civ1_U_Diff.*Data.Civ1_U_Diff+Data.Civ1_V_Diff.*Data.Civ1_V_Diff))
3934        NbSites(irho,:)=Data.Civ1_NbSites*numel(Data.Civ1_NbSites)/numel(Data.Civ1_U_Diff);
3935        Param.Patch1.SmoothingParam=2*Param.Patch1.FieldSmooth;
3936    end
3937    figure
3938    plot(SmoothingParam,DiffVel,'b',SmoothingParam,NbSites,'r')
3939    set(handles.TestPatch1,'BackgroundColor',[1 0 0])
3940else
3941    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
3942    if ~isempty(corrfig)
3943        delete(corrfig)
3944    end
3945    hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
3946    if ~isempty(hview_field)
3947        delete(hview_field)
3948    end
3949end
3950
3951
3952% --- Executes on button press in TestCiv2.
3953function TestCiv2_Callback(hObject, eventdata, handles)
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