source: trunk/src/civ.m @ 353

Last change on this file since 353 was 353, checked in by sommeria, 9 years ago

functions adapted to Matlab version 2009 (~ replaced by 'tild' in function output)
svn test put under 'try' (error observed)
fullfile_uvmat introduced, aimed at replacing name_generator

File size: 188.8 KB
Line 
1%'civ': function associated with the interface 'civ.fig' for PIV, spline interpolation and stereo PIV (patch)
2%------------------------------------------------------------------------
3%  provides an interface for the software menucivx
4% function varargout = civ(varargin)
5% provides an interface for the software menucivx
6%
7%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
8%  Copyright Joel Sommeria, 2011, LEGI / CNRS-UJF-INPG, sommeria@legi.grenoble-inp.fr
9%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
10%     This file is part of the toolbox UVMAT.
11%
12%     UVMAT is free software; you can redistribute it and/or modify
13%     it under the terms of the GNU General Public License as published by
14%     the Free Software Foundation; either version 2 of the License, or
15%     (at your option) any later version.
16%
17%     UVMAT is distributed in the hope that it will be useful,
18%     but WITHOUT ANY WARRANTY; without even the implied warranty of
19%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
20%     GNU General Public License (file UVMAT/COPYING.txt) for more details.
21%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
22function varargout = civ(varargin)
23%TODO: search range
24
25% Last Modified by GUIDE v2.5 21-Dec-2011 00:34:49
26% Begin initialization code - DO NOT EDIT
27gui_Singleton = 1;
28gui_State = struct('gui_Name',       mfilename, ...
29    'gui_Singleton',  gui_Singleton, ...
30    'gui_OpeningFcn', @civ_OpeningFcn, ...
31    'gui_OutputFcn',  @civ_OutputFcn, ...
32    'gui_LayoutFcn',  [] , ...
33    'gui_Callback',   []);
34if nargin && ischar(varargin{1})
35    gui_State.gui_Callback = str2func(varargin{1});
36end
37
38if nargout
39    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
40else
41    gui_mainfcn(gui_State, varargin{:});
42end
43% End initialization code - DO NOT EDIT
44
45%------------------------------------------------------------------------
46% --- Executes just before civ is made visible.
47function civ_OpeningFcn(hObject, eventdata, handles, fileinput)
48%------------------------------------------------------------------------
49% This function has no output args, see OutputFcn.
50
51%% General settings
52handles.output = hObject;
53guidata(hObject, handles); % Update handles structure
54set(hObject,'WindowButtonDownFcn',{'mouse_down'}) % allows mouse action with right button (zoom for uicontrol display)
55
56%% Adjust the GUI according to the binaries available in PARAM.xml
57path_civ=fileparts(which('civ')); %path to civ
58addpath (path_civ) ; %add the path to civ, (useful in case of change of working directory after civ has been s opened in the working directory)
59errormsg=[];%default error message
60xmlfile='PARAM.xml';
61if exist(xmlfile,'file')
62    try
63        t=xmltree(xmlfile);
64        sparam=convert(t);
65    catch
66        errormsg={' Unable to read the file PARAM.xml defining the civx binaries:'; lasterr};
67    end
68else
69    errormsg=[xmlfile ' not found: path to civx binaries undefined'];
70end
71if ~isempty(errormsg)
72    msgbox_uvmat('WARNING',errormsg);
73end
74test_batch=0;%default: ,no batch mode available
75if isfield(sparam,'BatchParam') && isfield(sparam.BatchParam,'BatchMode')
76    test_batch=strcmp(sparam.BatchParam.BatchMode,'sge'); %sge is currently the only implemented batch mod
77end
78if test_batch==0
79    set(handles.BATCH,'Enable','off')% put the BATCH button in grey (unactivated)
80    set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])% put the BATCH button in grey (unactivated)
81end
82if isfield(sparam.RunParam,'CivBin')
83    if ~exist(sparam.RunParam.CivBin,'file')
84        sparam.RunParam.CivBin=fullfile(path_civ,sparam.RunParam.CivBin);
85    end
86else
87    sparam.RunParam.CivBin='';
88end
89
90%% load the list of previously browsed files in the upper bar menu Open/
91dir_perso=prefdir; % path to the directory .matlab for personal data
92profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmauvmat_perso.mat' in .matlab
93if exist(profil_perso,'file')
94    h=load (profil_perso);
95    if isfield(h,'MenuFile')
96        for ifile=1:min(length(h.MenuFile),5)
97            eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',h.MenuFile{ifile});'])
98        end
99    end
100end
101
102%% prepare the GUI with parameters from the input file if opened from uvmat
103if exist('fileinput','var')% && isfield(param,'RootName') && ~isempty(param.RootName)
104    errormsg=display_file_name(handles,fileinput);
105    if ~isempty(errormsg)
106        msgbox_uvmat('ERROR',errormsg)
107    end
108end
109
110%------------------------------------------------------------------------
111% --- Outputs from this function are returned to the command line.
112function varargout = civ_OutputFcn(hObject, eventdata, handles)
113%------------------------------------------------------------------------
114% Get default command line output from handles structure
115varargout{1} = handles.output;
116
117%------------------------------------------------------------------------
118% --- Function activated by the Open/Browse... option in the upper menu bar.
119function MenuBrowse_Callback(hObject, eventdata, handles)
120%------------------------------------------------------------------------
121%% get the current input root file name to initiate the browser
122filebase=get(handles.RootName,'String');
123oldfile=''; %default
124if isempty(filebase)|| isequal(filebase,'')%loads the previously stored root file name
125    dir_perso=prefdir;
126    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
127    if exist(profil_perso,'file')
128        h=load (profil_perso);
129        if isfield(h,'filebase')&& ischar(h.filebase)
130            oldfile=h.filebase;
131        end
132        if isfield(h,'RootPath') && ischar(h.RootPath)
133            oldfile=h.RootPath;
134        end
135    end
136else
137    oldfile=filebase;
138end
139% ind_opening=1;%default
140% browse.incr_pair=[0 0]; %default
141%% get the new input fiel with the browser
142menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)';
143    '*.xml',  '.xml files '; ...
144    '*.civ',  '.civ files '; ...
145    '*.png','.png image files'; ...
146    '*.jpg',' jpeg image files'; ...
147    '*.tif','.tif image files'; ...
148    '*.avi;*.AVI','.avi movie files'; ...
149    '*.nc','.netcdf files'; ...
150    '*.*',  'All Files (*.*)'};
151[FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file',oldfile);
152fileinput=[PathName FileName];%complete file name
153sizf=size(fileinput);
154if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
155
156%% case of the xml file opened as input (TODO: check and see whether it is useful)
157[path,name,ext]=fileparts(fileinput);
158testeditxml=0;
159if isequal(ext,'.xml')
160    testeditxml=1;
161    t_browse=xmltree(fileinput);
162    head_element=get(t_browse,1);
163    if isfield(head_element,'name')&& isequal(head_element.name,'ImaDoc')
164        testeditxml=0;
165    end
166end
167if testeditxml==1 || isequal(ext,'.xls')
168    heditxml=editxml({fileinput});
169    set(heditxml,'Tag','browser')
170    waitfor(heditxml,'Tag','idle')
171    if ~ishandle(heditxml)
172        return
173    end
174    attr=findobj(get(heditxml,'children'),'Tag','CurrentAttributes');
175    set(handles.browse,'UserData',fileinput)% store for future opening with browser
176    fileinput=get(attr,'UserData');
177    if ~exist(fileinput,'file')
178        return
179    end
180end
181%[RootPath,RootFile,str1,str2,str_a,str_b,FileExt,NomType,subdir]=name2display(fileinput);
182[tild,tild,tild,i1,i2,j1,j2,FileExt,NomType]=fileparts_uvmat(fileinput);
183% filebase=fullfile(RootPath,RootFile);
184
185%% record the information obtained from the input file
186% if isempty(i1),i1=1;end
187% if isempty(i2),i2=i1;end
188% if isempty(j1),j1=1;end
189% if isempty(j2),j2=j1;end
190% if isequal(get(handles.ListCompareMode,'Value'),1)
191%     browse=[];%initialisation
192% else
193%     browse=get(handles.RootName,'UserData');
194% end
195% browse.num_i1=i1;
196% browse.num_i2=i2;
197% browse.num_j1=j1;
198% browse.num_j2=j2;
199% if length(FileExt)>1 && (~isempty(imformats(FileExt(2:end)))||strcmpi(FileExt,'.avi'));%if an image file has been opened by uvmat
200%     browse.nom_type_ima=NomType;
201%     browse.ext_ima=FileExt;
202%     set(handles.ImaExt,'String',FileExt)
203% end
204% set(handles.RootName,'UserData',browse);% store information from browser
205
206%% prepare the GUI with parameters from the input file
207errormsg=display_file_name(handles,fileinput);
208if ~isempty(errormsg)
209    msgbox_uvmat('ERROR',erromsg)
210end
211
212
213%------------------------------------------------------------------------
214% --- Open again the file whose name has been recorded in MenuFile_1
215function MenuFile_1_Callback(hObject, eventdata, handles)
216%------------------------------------------------------------------------
217fileinput=get(handles.MenuFile_1,'Label');
218errormsg=display_file_name(handles,fileinput);
219if ~isempty(errormsg)
220    msgbox_uvmat('ERROR',erromsg)
221end
222
223% -----------------------------------------------------------------------
224% --- Open again the file whose name has been recorded in MenuFile_2
225function MenuFile_2_Callback(hObject, eventdata, handles)
226%------------------------------------------------------------------------
227fileinput=get(handles.MenuFile_2,'Label');
228errormsg=display_file_name(handles,fileinput);
229if ~isempty(errormsg)
230    msgbox_uvmat('ERROR',erromsg)
231end
232
233% -----------------------------------------------------------------------
234% --- Open again the file whose name has been recorded in MenuFile_3
235function MenuFile_3_Callback(hObject, eventdata, handles)
236%------------------------------------------------------------------------
237fileinput=get(handles.MenuFile_3,'Label');
238errormsg=display_file_name(handles,fileinput);
239if ~isempty(errormsg)
240    msgbox_uvmat('ERROR',erromsg)
241end
242
243% -----------------------------------------------------------------------
244% --- Open again the file whose name has been recorded in MenuFile_4
245function MenuFile_4_Callback(hObject, eventdata, handles)
246%------------------------------------------------------------------------
247fileinput=get(handles.MenuFile_4,'Label');
248errormsg=display_file_name(handles,fileinput);
249if ~isempty(errormsg)
250    msgbox_uvmat('ERROR',erromsg)
251end
252
253% -----------------------------------------------------------------------
254% --- Open again the file whose name has been recorded in MenuFile_5
255function MenuFile_5_Callback(hObject, eventdata, handles)
256%------------------------------------------------------------------------
257fileinput=get(handles.MenuFile_5,'Label');
258errormsg=display_file_name(handles,fileinput);
259if ~isempty(errormsg)
260    msgbox_uvmat('ERROR',erromsg)
261end
262
263% -----------------------------------------------------------------------
264% --- Prepare the GUI for the compiled CivX program
265function MenuCivX_Callback(hObject, eventdata, handles)
266set(handles.MenuMatlab,'checked','off')
267set(handles.MenuCivX,'checked','on')
268%set(handles.thresh_patch1,'Visible','off')
269% set(handles.thresh_text1,'Visible','off')
270set(handles.num_MaxDiff,'Visible','off')
271set(handles.title_MaxDiff,'Visible','off')
272set(handles.num_Rho,'Style','edit')
273set(handles.num_Rho,'String','1')
274set(handles.BATCH,'Enable','on')
275% -----------------------------------------------------------------------
276
277% -----------------------------------------------------------------------
278% --- Prepare the GUI for the Matlab PIV program
279function MenuMatlab_Callback(hObject, eventdata, handles)
280% -----------------------------------------------------------------------
281set(handles.MenuMatlab,'checked','on')
282set(handles.MenuCivX,'checked','off')
283% if get(handles.CheckPatch1,'Value')
284set(handles.num_MaxDiff,'Visible','on')
285set(handles.title_MaxDiff,'Visible','on')
286
287% end
288set(handles.num_Rho,'Style','popupmenu')
289set(handles.num_Rho,'Value',1)
290set(handles.num_Rho,'String',{'1';'2'})
291% set(handles.BATCH,'Enable','off')
292
293% -----------------------------------------------------------------------
294% --- Open the help html file
295function MenuHelp_Callback(hObject, eventdata, handles)
296% -----------------------------------------------------------------------
297path_civ=fileparts(which ('civ'));
298helpfile=fullfile(path_civ,'uvmat_doc','uvmat_doc.html');
299if isempty(dir(helpfile))
300    msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
301else
302    addpath (fullfile(path_civ,'uvmat_doc'))
303    web([helpfile '#civ'])
304end
305
306%------------------------------------------------------------------------
307% --- Function activated when a new filebase (image series) is introduced
308function RootName_Callback(hObject, eventdata, handles)
309%------------------------------------------------------------------------
310filebase=get(handles.RootName,'String');
311errormsg=display_file_name(handles,filebase);
312if ~isempty(errormsg)
313    msgbox_uvmat('ERROR',erromsg)
314end
315
316%------------------------------------------------------------------------
317% --- general function activated for an input file series
318function errormsg=display_file_name(handles,fileinput)
319%------------------------------------------------------------------------
320set(handles.ListCompareMode,'Visible','on')
321errormsg='';%default empty error message
322
323%% enable RUN, BATCH button and 'status' display
324set(handles.RUN, 'Enable','On')
325set(handles.RUN,'BackgroundColor',[1 0 0])%set RUN button to red color
326set(handles.BATCH,'Enable','On')
327set(handles.BATCH,'BackgroundColor',[1 0 0])%set BATCH button to red color
328if isfield(handles,'status')
329    set(handles.status,'Value',0);       %suppress the 'status' display
330    status_Callback([], [], handles)
331end
332
333%% determine nomenclature types and extension of the input files
334ext_ima='';%default
335nom_type_ima='';%default
336nom_type_nc='';
337%[RootPath,RootFile,i1_str,i2_str,j1_str,j2_str,ext_input,nom_type_input,SubDir]=name2display(fileinput);
338[RootPath,SubDir,RootFile,i1,i2,j1,j2,ext_input,nom_type_input]=fileparts_uvmat(fileinput);
339RootName=fullfile(RootPath,RootFile);
340set(handles.RootName,'String',RootName)
341set(handles.RootName,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
342drawnow
343% i1=str2double(i1_str);
344% i2=str2double(i2_str);
345% j1=str2double(j1_str);
346% j2=str2double(j2_str);
347num_ref_i=i1;%efaulmt ref index
348num_ref_j=j1;
349browse=get(handles.RootName,'UserData');
350browse.incr_pair=[0 0];%default
351
352% form=imformats(ext_input(2:end));
353check_letter=0;
354check_separator=0;
355if ~isempty(ext_input)&&(~isempty(imformats(ext_input(2:end)))||strcmpi(ext_input,'.avi'))% if the extension corresponds to an image or movie format recognized by Matlab
356    ext_ima=ext_input;
357    nom_type_ima=nom_type_input;
358    imagename=fileinput;
359    check_letter=~isempty(regexp(nom_type_ima,'[a|A]$'));%detect pair label by letter
360else %case of netcdf input file, look for corresponding images
361    nom_type_nc=nom_type_input;
362    imagename=fullfile_uvmat(RootPath,[],RootFile,ext_ima,nom_type_ima,1,[],1);
363    %imagename=name_generator(fullfile(RootPath,RootFile),1,1,ext_ima,nom_type_ima);
364    i1_str='';
365    j1_str='';
366    if ~isnan(i2)
367        num_ref_i=floor((num_ref_i+i2)/2);% reference image number corresponding to the file
368        browse.incr_pair(1)=i2-i1;
369        browse.incr_pair(2)=0;
370    end
371    %TODO: read the image name in the netcdf file (if documented)
372    %look for double image series '_i_j'
373    check_letter=~isempty(regexp(nom_type_nc,'[ab|AB]$'));%detect pair label by letter
374    if check_letter
375        j1_str=nom_type_nc(end-1);
376        r=regexp(nom_type_nc,'_(?<num1>\d+)','names');
377        if ~isempty(r)
378            i1_str=r.num1;
379        end
380    else
381        NomTypeIma=regexprep(nom_type_nc,'-\d','');%
382        r_end=regexp(NomTypeIma,'.\D(?<num2>\d+$','names');
383        if ~isempty(r_end)
384            j1_str=r.num2;
385        end
386    end
387    r=regexp(NomTypeIma,'_(?<num1>\d+)','names');
388    if ~isempty(r)
389        i1_str=r.num1;
390    end 
391    dirima=dir([RootName '_' i1_str '_' j1_str '.*']);
392    if isempty(dirima)
393        % look for images series  with sub marker '_'
394        dirima=dir([RootName '_*' i1_str  '.*']);
395        if isempty(dirima)
396            % look for other images series
397            dirima=dir([RootName '*' i1_str '.*']);
398            if isempty(dirima)
399                % look for other images series witth letter appendix
400                appendix=char(96+j1_str);
401                dirima=dir([RootName '*' i1_str appendix '.*']);
402            end
403        end
404    end
405    for ilist=1:numel(dirima)
406        %[pp,ff,i1_str,i2_str,j1_str,j2_str,ext_list,nom_type_list]=name2display(dirima(ilist).name);
407        [tild,tild,tild,i1,i2,j1,j2,ext_list,nom_type_list]=fileparts_uvmat(dirima(ilist).name);
408        form=imformats(ext_list(2:end));
409        if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
410            ext_ima=ext_list;
411            nom_type_ima=nom_type_list;
412%             i1=str2double(i1_str);
413%             j1=str2double(j1_str);
414%             i2=str2double(i2_str);
415%             j2=str2double(j2_str);         
416            % set the range of fields (1:1 by default) and selected pair
417            if isempty(i2)
418                num_ref_i=i1;
419            else
420                num_ref_i=floor((i1+i2)/2);
421                browse.incr_pair(1)=i2-i1;
422                browse.incr_pair(2)=0;
423            end
424            if isempty(j2)
425                if isempty(j1)
426                    num_ref_j=1;
427                else
428                    num_ref_j=j1;
429                end
430            else
431                num_ref_j=floor((j1+j2)/2);
432                browse.incr_pair(2)=j2-j1;
433            end
434            break
435        end
436    end
437end
438[RootPath,RootFile,i1_series,tild,j1_series,tild,NomType,FileType,Object]=find_file_series(imagename);
439MaxIndex_i=max(i1_series(i1_series>0));
440MaxIndex_j=max(j1_series(j1_series>0));
441
442%% look for an image documentation file
443ext_imadoc='';%default
444if exist([RootName '.xml'],'file')
445    ext_imadoc='.xml';
446elseif exist([RootName '.civxml'],'file')
447    ext_imadoc='.civxml';
448elseif exist([RootName '.civ'],'file')
449    ext_imadoc='.civ';
450elseif exist([RootName '.avi'],'file')
451    ext_imadoc='.avi';
452elseif exist([RootName '.AVI'],'file')
453    ext_imadoc='.AVI';
454end
455set(handles.ImaDoc,'String',ext_imadoc)% display the extension name for the image documentation file used
456
457
458%%  read the time in the image documentation file 
459mode=''; %default
460time=[];
461TimeUnit=''; %default
462CoordUnit='';%default
463pxcmx_search=[];%default
464pxcmy_search=[];%default
465if ~isempty(ext_imadoc)
466    set(handles.ImaDoc,'BackgroundColor',[1 1 0]) % set edit box to yellow cloro to indicate that the file reading is beginning
467    drawnow
468    switch ext_imadoc
469        case '.civxml'%OBSOLETE
470            [tild,tild,time]=read_civxml([RootName '.civxml']);
471            mode='pair j1-j2';
472            if isempty(nom_type_ima)% dtermine types by default if not already selected by browser or uvmat
473                nom_type_ima='_i_j';
474            end
475        case '.xml'
476            [XmlData,warntext]=imadoc2struct([RootName '.xml']);
477            ext_ima_read=[];
478            nom_type_read=[];
479            if isfield(XmlData,'Heading')&&isfield(XmlData.Heading','ImageName')&&ischar(XmlData.Heading.ImageName)% get image nom type and extension from the xml file
480                %[PP,FF,fc,str2,str_a,str_b,ext_ima_read,nom_type_read]=name2display(XmlData.Heading.ImageName);
481                [tild,tild,tild,tild,tild,tild,tild,tild,nom_type_read]=fileparts_uvmat(XmlData.Heading.ImageName);
482                fullname=fullfile(fileparts(RootName),XmlData.Heading.ImageName); %full name (including path) of the first image defined by the xmle file,
483                if ~exist(fullname,'file')
484                    msgbox_uvmat('WARNING',['FirstImage ' fullname ' defined in the xml file does not exist'])
485                end
486            end
487            if isfield(XmlData,'Time')
488                time=XmlData.Time;
489                %transform .Time to a column vector if it is a line vector thenomenclature uses a single index: correct possible bug in xml
490                if isequal(MaxIndex_i,1) && ~isequal(MaxIndex_j,1)% .Time is a line vector
491                    if numel(nom_type_read)>=2 && isempty(regexp(nom_type_read(2:end),'\D','once'))
492                        time=time';
493                        MaxIndex_i=MaxIndex_j;
494                        MaxIndex_j=1;
495                    end
496                end
497            end
498            if isfield(XmlData,'TimeUnit')
499                TimeUnit=XmlData.TimeUnit;
500            end
501            pxcmx_search=1;
502            pxcmy_search=1;
503            if isfield(XmlData,'GeometryCalib')
504                tsai=XmlData.GeometryCalib;
505                if isfield(tsai,'f') && isfield(tsai,'Tz') && isfield(tsai,'dpx') && isfield(tsai,'dpy')&& isfield(tsai,'R')
506                    rot2D=tsai.R(1:2,[1,2]);
507                    pxcmx_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpx);
508                    pxcmy_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpy);
509                end
510                if isfield(tsai,'CoordUnit')
511                    CoordUnit=tsai.CoordUnit;
512                end
513            end
514        case '.civ'% OBSOLETE: case of .civ image documentation file
515            [error,time,TimeUnit,mode,npx,npy]=read_imatext([RootName '.civ']);
516            if error==2, msgbox_uvmat('WARNING',['no file ' RootName '.civ']);
517            elseif error==1, msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file');
518            end
519            nom_type_ima='001a';
520        case {'.avi','.AVI'}
521            nom_type_ima='*';
522            ext_ima=ext_imadoc;
523            set(handles.ListPairMode,'Value',1);
524            set(handles.ListPairMode,'String',{'series(Di)'})
525            dt=0.04;%default
526            if exist([RootName ext_imadoc],'file')==2
527                info=aviinfo([RootName ext_imadoc]);%read infos on the avi movie
528                dt=1/info.FramesPerSecond;%time interval between successive frames
529                MaxIndex_i=info.NumFrames;%number of frames
530            end
531            time=(dt*(0:MaxIndex_i-1))';%list of image times
532            TimeUnit='s';
533    end
534    set(handles.ImaDoc,'BackgroundColor',[1 1 1])% set display box back to whiter
535end
536
537%% timing display
538%show the reference image edit box if relevant (not needed for movies or in the absence of time information
539if numel(time)>=2 % if there are at least two time values to define dt
540    MaxIndex_i=min(size(time,1),MaxIndex_i);
541    MaxIndex_j=min(size(time,2),MaxIndex_j);
542    time=[zeros(size(time,1),1) time]; %insert a vertical line of zeros (to deal with zero file indices)
543    time=[zeros(1,size(time,2)); time]; %insert a horizontal line of zeros
544    set(handles.ImaDoc,'UserData',time); %store the matrix of times
545    set(handles.dt_unit,'String',['dt in m' TimeUnit]);
546    set(handles.TimeUnit,'String',TimeUnit);
547else
548    set(handles.ImaDoc,'String',''); %xml file not used for timing
549    time=(i1_series(:,1)+0:size(i1_series,1)-1);% time=index i
550    time=time'*ones(1,size(i1_series,2),1); %makes a time matrix with the same time for all j indices
551    TimeUnit='frame';
552end
553set(handles.ImaDoc,'UserData',time); %store the matrix of times
554set(handles.dt_unit,'String',['dt in m' TimeUnit]);%display dt in unit 10-3 of the time (e.g ms)
555set(handles.TimeUnit,'String',TimeUnit);
556set(handles.nb_field,'String',num2str(MaxIndex_i));
557set(handles.nb_field2,'String',num2str(MaxIndex_j));
558set(handles.CoordUnit,'String',CoordUnit)
559set(handles.SearchRange,'UserData',[pxcmx_search pxcmy_search]);
560set(handles.ImaExt,'String',ext_ima)
561set(handles.ref_i,'String',num2str(num_ref_i))
562set(handles.first_i,'String',num2str(num_ref_i));
563set(handles.last_i,'String',num2str(num_ref_i));%
564set(handles.ref_j,'String',num2str(num_ref_j))
565set(handles.first_j,'String',num2str(num_ref_j));
566set(handles.last_j,'String',num2str(num_ref_j));%
567
568%% set the civ options depending on the input file content
569ind_opening=0;%default
570if isequal(ext_input,'.nc')
571    browse.nom_type_nc=nom_type_input;
572    ind_opening=2;% propose 'fix' as the default option
573    Data=nc2struct(fileinput,'ListGlobalAttribute','CivStage','absolut_time_T0','fix','patch','civ2','fix2');
574    if isfield(Data,'Txt')
575        msgbox_uvmat('ERROR',Data.Txt)
576        return
577    end
578    if ~isempty(Data.CivStage)%test for civ files
579        ind_opening=Data.CivStage;
580        set(handles.ListPairMode,'Value',3)
581    end
582end
583ListOptions={'CheckCiv1', 'CheckFix1' 'CheckPatch1', 'CheckCiv2', 'CheckFix2', 'CheckPatch2'};
584for index = 1:ind_opening
585    set(handles.(ListOptions{index}),'value',0)
586end
587for index = ind_opening+1
588    set(handles.(ListOptions{index}),'value',1)
589end
590update_CivOptions(handles,1)
591
592
593%%  set the menus of image pairs and default selection for civ   %%%%%%%%%%%%%%%%%%%
594% test_ima_i=numel(nom_type_ima)>1 && isempty(regexp(nom_type_ima(2:end),'\D','once'))%=1 for images with single indexing
595% TODO: determine MaxIndex_i and MaxIndex_j using find_file_series (in the absence of xml file)
596% try
597if ~check_letter|| isequal(nom_type_nc,'_1-2')|| (MaxIndex_j==1)
598    set(handles.ListPairMode,'Value',1)
599    set(handles.ListPairMode,'String',{'series(Di)'})   
600elseif  MaxIndex_i==1 && MaxIndex_j>1% simple series in j
601    set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)'})
602    if  MaxIndex_j <= 10
603        set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large
604    end
605else
606    set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)';'series(Di)'})%multiple choice
607    if  MaxIndex_j <= 10
608        set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large
609    end
610end
611% end
612
613%% update the subdirectory display
614listot=dir(RootPath);%directory of RootPath
615idir=0;
616listdir={''};%default
617% get the list of existing civ subdirectories in the path of theinput root  file
618for ilist=1:length(listot)
619    if listot(ilist).isdir
620        name=listot(ilist).name;
621        if ~isequal(name,'.') && ~isequal(name,'..')
622            idir=idir+1;
623            listdir{idir,1}=listot(ilist).name;
624        end
625    end
626end
627Value=find(strcmp(SubDir,listdir));%search the index of subdir in the cell listdir
628if isempty(Value)% if the input subdir is not found
629    ValueCiv1=get(handles.ListSubdirCiv1,'Value');%read the currrently selected dir name
630    if ValueCiv1>numel(listdir)
631        ValueCiv1=1;
632    end
633    set(handles.txt_SubdirCiv1,'String',listdir{ValueCiv1})
634    ValueCiv2=get(handles.ListSubdirCiv2,'Value');
635    if ValueCiv2>numel(listdir)
636        ValueCiv2=1;
637    end
638    set(handles.txt_SubdirCiv2,'String',listdir{ValueCiv2})
639else
640    ValueCiv1=Value;
641    ValueCiv2=Value;
642     set(handles.txt_SubdirCiv1,'String',listdir{Value})
643     set(handles.txt_SubdirCiv2,'String',listdir{Value})
644end
645set(handles.ListSubdirCiv1,'Value',ValueCiv1)
646set(handles.ListSubdirCiv2,'Value',ValueCiv2)
647set(handles.ListSubdirCiv1,'String',[listdir;'new...'])
648set(handles.ListSubdirCiv2,'String',[listdir;'new...'])
649if isempty(listdir)
650    set(handles.txt_SubdirCiv1,'String','CIV')
651    set(handles.txt_SubdirCiv2,'String','CIV')
652end
653
654%% store info
655browse.nom_type_ima=nom_type_ima;
656set(handles.RootName,'UserData',browse)% store the nomenclature type
657
658%% list the possible index pairs, depending on the option set in ListPairMode
659ListPairMode_Callback([], [], handles)
660browse=get(handles.RootName,'UserData');
661
662%% store the root input filename for future opening
663profil_perso=fullfile(prefdir,'uvmat_perso.mat');
664% RootPath=fileparts(RootName);
665if exist(profil_perso,'file')
666    save (profil_perso,'RootPath','-append'); %store the root name for future opening of uvmat
667else
668    txt=ver('MATLAB');
669    Release=txt.Release;
670    relnumb=str2double(Release(3:4));
671    if relnumb >= 14
672        save (profil_perso,'RootPath','-V6'); %store the root name for future opening of uvmat
673    else
674        save (profil_perso,'RootPath'); %store the root name for future opening of uvmat
675    end
676end
677set(handles.RootName,'BackgroundColor',[1 1 1])
678
679%------------------------------------------------------------------------
680% --- Executes on carriage return on the subdir checkciv1 edit window
681function txt_SubdirCiv1_Callback(hObject, eventdata, handles)
682%------------------------------------------------------------------------
683SubDir=get(handles.txt_SubdirCiv1,'String');
684menu_str=get(handles.ListSubdirCiv1,'String');% read the list of subdirectories for update
685ichoice=find(strcmp(SubDir,menu_str),1);
686if isempty(ichoice)
687    ilist=numel(menu_str); %select 'new...' in the menu
688else
689    ilist=ichoice;
690end
691set(handles.ListSubdirCiv1,'Value',ilist)% select the selected subdir in the menu
692if get(handles.CheckCiv1,'Value')% if Civ1 is performed
693    set(handles.txt_SubdirCiv2,'String',SubDir);% set by default civ2 directory the same as civ1
694    set(handles.ListSubdirCiv2,'Value',ilist)
695else % if Civ1 data already exist
696    find_netcpair_civ1(handles); %update the list of available pairs from netcdf files in the new directory
697end
698
699%------------------------------------------------------------------------
700% --- Executes on carriage return on the SubDir checkciv1 edit window
701function txt_SubdirCiv2_Callback(hObject, eventdata, handles)
702%------------------------------------------------------------------------
703SubDir=get(handles.txt_SubdirCiv1,'String');
704menu_str=get(handles.ListSubdirCiv2,'String');% read the list of subdirectories for update
705ichoice=find(strcmp(SubDir,menu_str),1);
706if isempty(ichoice)
707    ilist=numel(menu_str); %select 'new...' in the menu
708else
709    ilist=ichoice;
710end
711set(handles.ListSubdirCiv2,'Value',ilist)% select the selected subdir in the menu
712%update the list of available pairs from netcdf files in the new directory
713if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
714    find_netcpair_civ2(handles);
715end
716
717%------------------------------------------------------------------------
718% --- Executes on button press in CheckCiv1.
719function CheckCiv1_Callback(hObject, eventdata, handles)
720%------------------------------------------------------------------------
721update_CivOptions(handles,0)
722
723%------------------------------------------------------------------------
724% --- Executes on button press in CheckFix1.
725function CheckFix1_Callback(hObject, eventdata, handles)
726%------------------------------------------------------------------------
727update_CivOptions(handles,0)
728
729%------------------------------------------------------------------------
730% --- Executes on button press in CheckPatch1.
731function CheckPatch1_Callback(hObject, eventdata, handles)
732%------------------------------------------------------------------------
733update_CivOptions(handles,0)
734
735%------------------------------------------------------------------------
736% --- Executes on button press in CheckCiv2.
737function CheckCiv2_Callback(hObject, eventdata, handles)
738%------------------------------------------------------------------------
739update_CivOptions(handles,0)
740
741%------------------------------------------------------------------------
742% --- Executes on button press in CheckFix2.
743function CheckFix2_Callback(hObject, eventdata, handles)
744%------------------------------------------------------------------------
745update_CivOptions(handles,0)
746
747%------------------------------------------------------------------------
748% --- Executes on button press in CheckPatch2.
749function CheckPatch2_Callback(hObject, eventdata, handles)
750%------------------------------------------------------------------------
751update_CivOptions(handles,0)
752
753%------------------------------------------------------------------------
754% --- activated by any checkbox controling the selection of Civ1,Fix1,Patch1,Civ2,Fix2,Patch2
755function update_CivOptions(handles,opening)
756%------------------------------------------------------------------------
757checkbox=zeros(1,6);
758checkbox(1)=get(handles.CheckCiv1,'Value');
759checkbox(2)=get(handles.CheckFix1,'Value');
760checkbox(3)=get(handles.CheckPatch1,'Value');
761checkbox(4)=get(handles.CheckCiv2,'Value');
762checkbox(5)=get(handles.CheckFix2,'Value');
763checkbox(6)=get(handles.CheckPatch2,'Value');
764ind_selected=find(checkbox,1);
765if ~isempty(ind_selected)
766  RootName=get(handles.RootName,'String');
767    if isempty(RootName)
768         msgbox_uvmat('ERROR','Please open an image or PIV .nc file with the upper bar menu Open/Browse...')
769        returnopening
770    end
771end
772set(handles.PairIndices,'Visible','on')
773set(handles.txt_SubdirCiv1,'Visible','on')
774set(handles.ListSubdirCiv1,'Visible','on')
775if ~opening
776find_netcpair_civ1(handles) % select the available netcdf files
777end
778if max(checkbox(4:6))% case of civ2 pair choice needed
779    set(handles.TitlePairCiv2,'Visible','on')
780    set(handles.TitleSubdirCiv2,'Visible','on')
781    set(handles.txt_SubdirCiv2,'Visible','on')
782    set(handles.ListSubdirCiv2,'Visible','on')
783    set(handles.ListPairCiv2,'Visible','on')
784    if ~opening
785    find_netcpair_civ2(handles) % select the available netcdf files
786    end
787else
788    set(handles.TitleSubdirCiv2,'Visible','off')
789    set(handles.txt_SubdirCiv2,'Visible','off')
790    set(handles.ListSubdirCiv2,'Visible','off')
791    set(handles.ListPairCiv2,'Visible','off')
792end
793options={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'};
794for ilist=1:length(options)
795    if checkbox(ilist)
796        set(handles.(options{ilist}),'Visible','on')
797    else
798        set(handles.(options{ilist}),'Visible','off')
799    end
800end
801
802%------------------------------------------------------------------------
803% --- Executes on button press in RUN: processing on local computer
804function RUN_Callback(hObject, eventdata, handles)
805%------------------------------------------------------------------------
806set(handles.RUN, 'Enable','Off')
807set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
808batch=0;
809errormsg=launch_jobs(hObject, eventdata, handles,batch);
810set(handles.RUN, 'Enable','On')
811set(handles.RUN,'BackgroundColor',[1 0 0])
812
813% start status callback to visualise results
814if ~isempty(errormsg)
815    display(errormsg)
816    msgbox_uvmat('ERROR',errormsg)
817elseif  isfield(handles,'status') %&& ~isequal(get(handles.ListPairMode,'Value'),3)
818    set(handles.status,'Value',1);%suppress status display
819    status_Callback(hObject, eventdata, handles)
820end
821
822%------------------------------------------------------------------------
823% --- Executes on button press in BATCH: remote processing
824function BATCH_Callback(hObject, eventdata, handles)
825% -----------------------------------------------------------------------
826set(handles.BATCH, 'Enable','Off')
827set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])
828batch=1;
829errormsg=launch_jobs(hObject, eventdata, handles, batch);
830set(handles.BATCH, 'Enable','On')
831set(handles.BATCH,'BackgroundColor',[1 0 0])
832
833% start status callback to visualise results
834if ~isempty(errormsg)
835    display(errormsg)
836    msgbox_uvmat('ERROR',errormsg)
837elseif isfield(handles,'status')
838    set(handles.status,'Value',1);%suppress status display
839    status_Callback(hObject, eventdata, handles)
840end
841
842%-------------------------------------------------------------------
843% --- Executes on button press in status.
844function status_Callback(hObject, eventdata, handles)
845%-------------------------------------------------------------------
846val=get(handles.status,'Value');
847if val==0
848    set(handles.status,'BackgroundColor',[0 1 0])
849    hfig=findobj(allchild(0),'name','civ_status');
850    if ~isempty(hfig)
851        delete(hfig)
852    end
853    return
854end
855set(handles.status,'BackgroundColor',[1 1 0])
856drawnow
857listtype={'civ1','fix1','patch1','civ2','fix2','patch2'};
858Param.CheckCiv1=get(handles.CheckCiv1,'Value');
859Param.CheckFix1=get(handles.CheckFix1,'Value');
860Param.CheckPatch1=get(handles.CheckPatch1,'Value');
861Param.CheckCiv2=get(handles.CheckCiv2,'Value');
862Param.CheckFix2=get(handles.CheckFix2,'Value');
863Param.CheckPatch2=get(handles.CheckPatch2,'Value');
864box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2];
865
866option_civ=find(box_test,1,'last');%last selected option (non-zero index of box_test)
867filecell=get(handles.civ,'UserData');%retrieve the list of output files expected for PIV
868test_new=0;
869if ~isfield(filecell,'nc')
870    test_new=1;
871    [ref_i,ref_j,errormsg]=find_ref_indices(handles);
872    if ~isempty(errormsg)
873        msgbox_uvmat('ERROR',errormsg)
874        return
875    end
876    filecell=set_civ_filenames(handles,ref_i,ref_j,box_test);%determine the output file expected from the GUI status
877end
878if ~isequal(box_test(4:6),[0 0 0])
879    civ_files=filecell.nc.civ2;%case of civ2 operations
880else
881    civ_files=filecell.nc.civ1;
882end
883[root,filename,ext]=fileparts(civ_files{1});
884[rootroot,SubDir,extdir]=fileparts(root);
885hfig=findobj(allchild(0),'name','civ_status');
886if isempty(hfig)
887    hfig=figure('DeleteFcn',@stop_status);
888    set(hfig,'name','civ_status')
889    %hlist=uicontrol('Style','listbox','Units','normalized', 'Position',[0.05 0.09 0.9 0.71], 'Callback', @open_view_field,'tag','list');
890     uicontrol('Style','listbox','Units','normalized', 'Position',[0.05 0.09 0.9 0.71], 'Callback', {'open_uvmat'},'tag','list');
891    uicontrol('Style','edit','Units','normalized', 'Position', [0.05 0.87 0.9 0.1],'tag','msgbox','Max',2,'String','checking files...');
892    uicontrol('Style','frame','Units','normalized', 'Position', [0.05 0.81 0.9 0.05]);
893    uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.7 0.01 0.2 0.07],'String','OK','FontWeight','bold','FontUnits','normalized','FontSize',0.9,'Callback',@close_GUI);
894    BarPosition=[0.05 0.81 0.01 0.05];
895    hwaitbar=uicontrol('Style','frame','Units','normalized', 'Position',BarPosition ,'BackgroundColor',[1 0 0],'tag','waitbar');
896    drawnow
897end
898% datnum=[];
899Tabchar={};
900nbfiles=numel(civ_files);
901count=0;
902testrecent=0;
903while count<nbfiles
904    count=0;
905    datnum=zeros(1,nbfiles);
906    for ifile=1:nbfiles
907        detect=exist(civ_files{ifile},'file'); % check the existence of the file
908        option=0;
909        if detect==0
910            option_str='not created';
911        else
912            datfile=dir(civ_files{ifile});
913            if isfield(datfile,'datenum')
914                datnum(ifile)=datfile.datenum;%only available in recent matlab versions
915                testrecent=1;
916            end
917            filefound(ifile)={datfile.name};
918            lastfield='';
919            % check the content  netcdf file
920            Data=nc2struct(civ_files{ifile},'ListGlobalAttribute','CivStage','patch2','fix2','civ2','patch','fix');
921            option_list={'civ1','fix1','patch1','civ2','fix2','patch2'};
922            if ~isempty(Data.CivStage)
923                option=Data.CivStage;
924            else
925                if ~isempty(Data.patch2) && isequal(Data.patch2,1)
926                    option=6;
927                    %                 option_str='patch2';
928                elseif ~isempty(Data.fix2) && isequal(Data.fix2,1)
929                    option=5;
930                    %                 option_str='fix2';
931                elseif ~isempty(Data.civ2) && isequal(Data.civ2,1);
932                    option=4;
933                    %                 option_str='civ2';
934                elseif ~isempty(Data.patch) && isequal(Data.patch,1);
935                    option=3;
936                    %                 option_str='patch1';
937                elseif ~isempty(Data.fix) && isequal(Data.fix,1);
938                    option=2;
939                    %                 option_str='fix1';
940                else
941                    option=1;
942                    %                 option_str='civ1';
943                end
944            end
945            option_str=option_list{option};
946        end
947        if option >= option_civ
948            count=count+1;
949        end
950        [rr,filename,ext]=fileparts(civ_files{ifile});
951        Tabchar{ifile,1}=[fullfile([SubDir extdir],filename) ext  '...' option_str];
952    end
953    datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
954    if isempty(datnum)
955        if testrecent
956            message='no civ result created yet';
957        else
958            message='';
959        end
960    else
961        datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
962        [first,ind]=min(datnum);
963        [last,indlast]=max(datnum);
964        if test_new
965            message='existing file status, no processing launched yet';
966        else
967        message={[num2str(count) ' file(s) done over ' num2str(nbfiles)] ;['oldest modification:  ' cell2mat(filefound(ind)) ' : ' datestr(first)];...
968            ['latest modification:  ' cell2mat(filefound(indlast)) ' : ' datestr(last)]};
969        end
970    end
971    hfig=findobj(allchild(0),'name','civ_status');
972    if isempty(hfig)% the status list has been deleted
973        return
974    else
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    end
985    set(hlist,'UserData',rootroot)
986    if count<10||(nbfiles-count)<10
987    pause(.5)% wait 0.5 seconds for next check
988    else
989        pause(10)% wait 10 seconds for next check
990    end
991end
992
993%------------------------------------------------------------------------
994% --- Main lauch command, called by RUN and BATCH
995function errormsg=launch_jobs(hObject, eventdata, handles, batch)
996%-----------------------------------------------------------------------
997errormsg='';%default
998
999%% read the input parameters from the  GUI civ
1000Param=read_GUI(handles.civ);
1001
1002%% check the selected list of operations:
1003operations={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'};
1004box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2];
1005index_first=find(box_test==1,1);
1006if isempty(index_first)
1007    errormsg='no selected operation';
1008    return
1009end
1010index_last=find(box_test==1,1,'last');
1011box_used=box_test(index_first : index_last);
1012[box_missing,ind_missing]=min(box_used);
1013if isequal(box_missing,0); %there is a missing step in the sequence of operations
1014    errormsg=['missing' cell2mat(operations(ind_missing))];
1015    return
1016end
1017
1018%% check mask if selecetd
1019%could be included in get_mask callback ?
1020if isequal(get(handles.CheckMask,'Value'),1)
1021    maskname=get(handles.txt_Mask,'String');
1022    if ~exist(maskname,'file')
1023        get_mask_civ1_Callback(hObject, eventdata, handles);
1024    end
1025end
1026if isequal(get(handles.CheckMask,'Value'),1)
1027    maskname=get(handles.txt_Mask,'String');
1028    if ~exist(maskname,'file')
1029        get_mask_fix1_Callback(hObject, eventdata, handles);
1030    end
1031end
1032if isequal(get(handles.CheckMask,'Value'),1)
1033    maskname=get(handles.txt_Mask,'String');
1034    if ~exist(maskname,'file')
1035        get_mask_civ2_Callback(hObject, eventdata, handles);
1036    end
1037end
1038if isequal(get(handles.CheckMask,'Value'),1)
1039    maskname=get(handles.txt_Mask,'String');
1040    if ~exist(maskname,'file')
1041        get_mask_fix2_Callback(hObject, eventdata, handles);
1042    end
1043end
1044
1045%% reinitialise status callback
1046if isfield(handles,'status')
1047    set(handles.status,'Value',0);%suppress status display
1048    status_Callback(hObject, eventdata, handles)
1049end
1050
1051%% read the PARAM.xml file to get the binaries (and batch_mode if batch)
1052path_civ=fileparts(which('civ')); %path to the source directory of uvmat
1053xmlfile='PARAM.xml';
1054if exist(xmlfile,'file')% search parameter xml file in the whole matlab path
1055    t=xmltree(xmlfile);
1056    s=convert(t);
1057else
1058    errormsg=['no file ' xmlfile];
1059    return
1060end
1061test_interp=0; %eviter les variables test_ (LG)
1062if batch
1063    if isfield(s,'BatchParam')
1064        Param.xml=s.BatchParam;
1065        if isfield(Param.xml,'BatchMode')
1066            batch_mode=Param.xml.BatchMode;
1067            if ~ismember(batch_mode,{'sge','oar'})
1068                errormsg=['batch mode ' batch_mode ' not supported by UVMAT'];
1069                return
1070            end
1071        end
1072    else
1073        errormsg='no batch civ binaries defined in PARAM.xml';
1074        return
1075    end
1076else % run
1077    if isfield(s,'RunParam')
1078        Param.xml=s.RunParam;
1079    else
1080        msgbox_uvmat('ERROR','no run civ binaries defined in PARAM.xml')
1081        return
1082    end
1083end
1084
1085%% check batch mode supported
1086if batch
1087    switch batch_mode
1088        case 'sge'
1089            test_command='qstat';
1090        case 'oar'
1091            test_command='oarstat';
1092    end   
1093    [s,w]=system(test_command);
1094    if ~isequal(s,0)
1095        msgbox_uvmat('ERROR',[batch_mode ' batch system not available'])
1096        return
1097    end
1098end
1099
1100%% check if the binaries exist
1101if isequal(get(handles.MenuMatlab,'checked'),'on')
1102    CivMode='Matlab';
1103else
1104    CivMode='CivX';
1105end
1106binary_list={};
1107switch CivMode
1108    case 'CivX'
1109        binary_list={'Civ1Bin','Civ2Bin','PatchBin','FixBin'};
1110    case 'CivAll'
1111        binary_list={'Civ'};
1112    case 'Matlab'
1113        if batch
1114            % vérifier MenuMatlab installé sur le cluster
1115            % difficile a faire a priori
1116        end         
1117end
1118for bin_name=binary_list %loop on the list of binaries
1119    if isfield(Param.xml,bin_name{1})% bin_name{1} =current name in the list
1120        if ~exist(Param.xml.(bin_name{1}),'file')%look for the full path if the file name has been defined with a relative path in PARAM.xml
1121            fullname=fullfile(path_civ,Param.xml.(bin_name{1}));
1122            if exist(fullname,'file')
1123                Param.xml.(bin_name{1})=fullname;
1124            else
1125                msgbox_uvmat('ERROR',['Binary ' Param.xml.(bin_name{1}) ' defined in PARAM.xml does not exist'])
1126                return
1127            end
1128        else
1129            [path,name,ext]=fileparts(Param.xml.(bin_name{1}));
1130            currentdir=pwd;
1131            cd(path);
1132            binpath=pwd;%path of the binary
1133            Param.xml.(bin_name{1})=fullfile(binpath,[name ext]);
1134            cd(currentdir);
1135        end
1136       
1137    end
1138end
1139display('files OK, processing...')
1140
1141%% set the list of files and check them
1142display('checking the files...')
1143[ref_i,ref_j,errormsg]=find_ref_indices(handles);
1144if ~isempty(errormsg)
1145    return
1146end
1147[filecell,i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,xx,yy,compare]=...
1148    set_civ_filenames(handles,ref_i,ref_j,box_test);
1149Rootbat=fileparts(filecell.nc.civ1{1,1});%output netcdf file (without extention)
1150set(handles.civ,'UserData',filecell);%store for futur use of status callback
1151if isempty(filecell)% (error message displayed in fct set_civ_filenames)
1152    return
1153end
1154nbfield=numel(i1_civ1);
1155nbslice=numel(j1_civ1);
1156
1157%% MAIN LOOP
1158time=get(handles.ImaDoc,'UserData'); %get the set of times
1159TimeUnit=get(handles.TimeUnit,'String');
1160checkframe=strcmp(TimeUnit,'frame');
1161batch_file_list=[];%should be renamed file_list, can be used for xml or bash files
1162 
1163for ifile=1:nbfield
1164    for j=1:nbslice
1165        % initiate system command
1166        switch CivMode
1167            case 'CivX'
1168                if isunix % check: necessaire aussi en RUN?
1169                    cmd=['#!/bin/bash \n '...
1170                        '#$ -cwd \n '...
1171                        'hostname && date \n '...
1172                        'umask 002 \n'];%allow writting access to created files for user group
1173                else
1174                    cmd=[];
1175                end
1176            case 'CivAll'
1177                CivAllxml=xmltree;% xml contents,  all parameters
1178                CivAllCmd='';
1179                CivAllxml=set(CivAllxml,1,'name','CivDoc');
1180        end
1181           
1182        % define output file name
1183        if Param.CheckCiv2==1 || Param.CheckFix2==1 || Param.CheckPatch2==1
1184            OutputFile=filecell.nc.civ2{ifile,j};
1185        else
1186            OutputFile=filecell.nc.civ1{ifile,j};
1187        end
1188        OutputFile=regexprep(OutputFile,'.nc','');
1189       
1190        if Param.CheckCiv1
1191            % read image-dependent parameters
1192            Param.Civ1.ImageA=filecell.ima1.civ1{ifile,j};
1193            Param.Civ1.ImageB=filecell.ima2.civ1{ifile,j};
1194            if ~checkframe% && size(time,1)>=i2_civ1(ifile) && size(time,2)>=j2_civ1(j)
1195                Param.Civ1.Dt=(time(i2_civ1(ifile)+1,j2_civ1(j)+1)-time(i1_civ1(ifile)+1,j1_civ1(j)+1));
1196            else
1197                Param.Civ1.Dt=1;
1198            end
1199            Param.Civ1.Time=((time(i2_civ1(ifile)+1,j2_civ1(j)+1)+time(i1_civ1(ifile)+1,j1_civ1(j)+1))/2);
1200            Param.Civ1.term_a=num2stra(j1_civ1(j),nom_type_nc);%UTILITE?
1201            Param.Civ1.term_b=num2stra(j2_civ1(j),nom_type_nc);%   
1202            ImageInfo=imfinfo(filecell.ima1.civ1{1,1});%read the first image to get the size
1203            Param.Civ1.ImageWidth=ImageInfo.Width;
1204            Param.Civ1.ImageHeight=ImageInfo.Height;
1205            Param.Civ1.ImageBitDepth=ImageInfo.BitDepth;
1206            % read mask parameters
1207            if Param.Civ1.CheckMask % the lines below should be changed with the new gui
1208                if ~exist(Param.Civ1.Mask,'file')
1209                    maskbase=[filecell.filebase '_' Param.Civ1.Mask]; %
1210                    nbslice_mask=str2double(Param.Civ1.Mask(1:end-4)); %
1211                    i1_mask=mod(i1_civ1(ifile)-1,nbslice_mask)+1;
1212                    Param.Civ1.Mask=name_generator(maskbase,i1_mask,1,'.png','_i');
1213                end
1214            end
1215            % read grid parameters
1216            if Param.Civ1.CheckGrid
1217                if numel(Param.Civ1.Grid)>=4 && isequal(Param.Civ1.Grid(end-3:end),'grid')
1218                    nbslice_grid=str2double(Param.Civ1.Grid(1:end-4)); %
1219                    if ~isnan(nbslice_grid)
1220                        i1_grid=mod(i1_civ1(ifile)-1,nbslice_grid)+1;
1221                        Param.Civ1.Grid=[filecell.filebase '_' name_generator(Param.Civ1.Grid,i1_grid,1,'.grid','_i')];
1222                        if ~exist(Param.Civ1.GridName,'file')
1223                            msgbox_uvmat('ERROR','grid file absent for civ1')
1224                        end
1225                    elseif ~exist(Param.Civ1.Grid,'file')
1226                        msgbox_uvmat('ERROR','grid file absent for civ1')
1227                    end
1228                end
1229            end
1230           
1231            % send command
1232            switch CivMode
1233                case 'CivX'
1234                    cmd=[cmd...
1235                        cmd_civ1(filecell.nc.civ1{ifile,j},Param) '\n'];
1236                    if ~isempty(errormsg)
1237                        msgbox_uvmat('ERROR',errormsg)
1238                        return
1239                    end
1240                case 'CivAll'
1241                    CivAllCmd=[CivAllCmd ' civ1 '];
1242                    str=CIV1_CMD_Unified(filecell.nc.civ1{ifile,j},'',Param.Civ1);
1243                    fieldnames=fields(str);
1244                    [CivAllxml,uid_civ1]=add(CivAllxml,1,'element','civ1');
1245                    for ilist=1:length(fieldnames)
1246                        val=eval(['str.' fieldnames{ilist}]);
1247                        if ischar(val)
1248                            [CivAllxml,uid_t]=add(CivAllxml,uid_civ1,'element',fieldnames{ilist});
1249                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1250                        end
1251                    end
1252            end
1253        end
1254       
1255        if Param.CheckFix1
1256            switch CivMode
1257                case 'CivX'
1258                    cmd=[cmd...
1259                        cmd_fix(filecell.nc.civ1{ifile,j},Param,'Fix1') '\n'];
1260                case 'CivAll'%to abandon
1261                    fix1.inputFileName=filecell.nc.civ1{ifile,j} ;
1262                    fix1.fi1=num2str(param.fix1.flagindex1(1));
1263                    fix1.fi2=num2str(param.fix1.flagindex1(2));
1264                    fix1.fi3=num2str(param.fix1.flagindex1(3));
1265                    fix1.threshC=num2str(param.fix1.thresh_vecC1);
1266                    fix1.threshV=num2str(param.fix1.thresh_vel1);
1267                    fieldnames=fields(fix1);
1268                    [CivAllxml,uid_fix1]=add(CivAllxml,1,'element','fix1');
1269                    for ilist=1:length(fieldnames)
1270                        val=eval(['fix1.' fieldnames{ilist}]);
1271                        if ischar(val)
1272                            [CivAllxml,uid_t]=add(CivAllxml,uid_fix1,'element',fieldnames{ilist});
1273                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1274                        end
1275                    end
1276                    CivAllCmd=[CivAllCmd ' fix1 '];
1277            end
1278        end
1279       
1280        %CheckPatch1
1281        if Param.CheckPatch1==1
1282            switch CivMode
1283                case 'CivX'
1284                    cmd=[cmd...
1285                        cmd_patch(filecell.nc.civ1{ifile,j},Param,'Patch1') '\n'];
1286                case 'CivAll'
1287                    patch1.inputFileName=filecell.nc.civ1{ifile,j} ;
1288                    patch1.nopt=subdomain_patch1;
1289                    patch1.maxdiff=thresh_patch1;
1290                    patch1.ro=rho_patch1;
1291                    test_grid=get(handles.get_gridpatch1,'Value');
1292                    if test_grid
1293                        patch1.gridflag='y';
1294                        gridname=get(handles.grid_patch1,'String');
1295                        if isequal(gridname(end-3:end),'grid')
1296                            nbslice_grid=str2double(gridname(1:end-4)); %
1297                            if ~isnan(nbslice_grid)
1298                                i1_grid=mod(i1_civ1(ifile)-1,nbslice_grid)+1;
1299                                patch1.gridPatch=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')];
1300                                if ~exist(patch1.gridPatch,'file')
1301                                    msgbox_uvmat('ERROR','grid file absent for patch1')
1302                                end
1303                            elseif exist(gridname,'file')
1304                                patch1.gridPatch=gridname;
1305                            else
1306                                msgbox_uvmat('ERROR','grid file absent for patch1')
1307                            end
1308                        end
1309                    else
1310                        patch1.gridPatch='none';
1311                        patch1.gridflag='n';
1312                        patch1.m=nx_patch1;
1313                        patch1.n=ny_patch1;
1314                    end
1315                    patch1.convectFlow='n';
1316                    fieldnames=fields(patch1);
1317                    [CivAllxml,uid_patch1]=add(CivAllxml,1,'element','patch1');
1318                    for ilist=1:length(fieldnames)
1319                        val=eval(['patch1.' fieldnames{ilist}]);
1320                        if ischar(val)
1321                            [CivAllxml,uid_t]=add(CivAllxml,uid_patch1,'element',fieldnames{ilist});
1322                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1323                        end
1324                    end
1325                    CivAllCmd=[CivAllCmd ' patch1 '];
1326            end
1327        end
1328        if Param.CheckCiv2==1
1329            Param.Civ2.ImageA=filecell.ima1.civ2{ifile,j};
1330            Param.Civ2.ImageB=filecell.ima2.civ2{ifile,j};
1331            if ~checkframe %&& size(time,1)>=i2_civ2(ifile) && size(time,2)>=j2_civ2(j)
1332                Param.Civ2.Dt=num2str(time(i2_civ2(ifile)+1,j2_civ2(j)+1)-time(i1_civ2(ifile)+1,j1_civ2(j)+1));
1333            else
1334                Param.Civ2.Dt=1;
1335            end
1336            Param.Civ2.Time=num2str((time(i2_civ2(ifile)+1,j2_civ2(j)+1)+time(i1_civ2(ifile)+1,j1_civ2(j)+1))/2);
1337            Param.Civ2.term_a=num2stra(j1_civ2(j),nom_type_nc);
1338            Param.Civ2.term_b=num2stra(j2_civ2(j),nom_type_nc);
1339            Param.Civ2.filename_nc1=filecell.nc.civ1{ifile,j};
1340            Param.Civ2.filename_nc1(end-2:end)=[]; % remove '.nc'
1341           
1342            % mask
1343            if Param.Civ2.CheckMask
1344                if ~exist(Param.Civ2.Mask,'file')
1345                    maskbase=[filecell.filebase '_' Param.Civ2.Mask]; %
1346                    nbslice_mask=str2double(Param.Civ2.Mask(1:end-4)); %
1347                    i1_mask=mod(i1_civ2(ifile)-1,nbslice_mask)+1;
1348                    Param.Civ2.Mask=name_generator(maskbase,i1_mask,1,'.png','_i');
1349                end
1350            end
1351            %grid
1352            if Param.Civ2.CheckGrid
1353                if numel(Param.Civ2.Grid)>=4 && isequal(Param.Civ2.Grid(end-3:end),'grid')
1354                    nbslice_grid=str2double(Param.Civ2.Grid(1:end-4)); %
1355                    if ~isnan(nbslice_grid)
1356                        i1_grid=mod(i1_civ2(ifile)-1,nbslice_grid)+1;
1357                        Param.Civ2.Grid=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')];
1358                    end
1359                end
1360            end
1361            ImageInfo=imfinfo(filecell.ima1.civ2{1,1});%read the first image to get the size
1362            Param.Civ2.ImageWidth=ImageInfo.Width;
1363            Param.Civ2.ImageHeight=ImageInfo.Height;
1364            Param.Civ2.ImageBitDepth=ImageInfo.BitDepth;
1365            % TODO: case of movie   
1366            switch CivMode
1367                case 'CivX'
1368                    cmd=[cmd...
1369                        cmd_civ2(filecell.nc.civ2{ifile,j},Param) '\n'];
1370                case 'CivAll'
1371                    CivAllCmd=[CivAllCmd ' civ2 '];
1372                    str=CIV2_CMD_Unified(filecell.nc.civ2{ifile,j},'',Param.Civ2);
1373                    fieldnames=fields(str);
1374                    [CivAllxml,uid_civ2]=add(CivAllxml,1,'element','civ2');
1375                    for ilist=1:length(fieldnames)
1376                        val=eval(['str.' fieldnames{ilist}]);
1377                        if ischar(val)
1378                            [CivAllxml,uid_t]=add(CivAllxml,uid_civ2,'element',fieldnames{ilist});
1379                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1380                        end
1381                    end
1382            end
1383        end
1384       
1385        % CheckFix2
1386        if Param.CheckFix2==1
1387            switch CivMode
1388                case 'CivX'
1389                    cmd=[cmd...
1390                        cmd_fix(filecell.nc.civ2{ifile,j},Param,'Fix2') '\n'];
1391                case 'CivAll'
1392                    fix2.inputFileName=filecell.nc.civ2{ifile,j} ;
1393                    fix2.fi1=num2str(flagindex2(1));
1394                    fix2.fi2=num2str(flagindex2(2));
1395                    fix2.fi3=num2str(flagindex2(3));
1396                    fix2.threshC=num2str(thresh_vec2C);
1397                    fix2.threshV=num2str(thresh_vel2);
1398                    fieldnames=fields(fix2);
1399                    [CivAllxml,uid_fix2]=add(CivAllxml,1,'element','fix2');
1400                    for ilist=1:length(fieldnames)
1401                        val=eval(['fix2.' fieldnames{ilist}]);
1402                        if ischar(val)
1403                            [CivAllxml,uid_t]=add(CivAllxml,uid_fix2,'element',fieldnames{ilist});
1404                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1405                        end
1406                    end
1407                    CivAllCmd=[CivAllCmd ' fix2 '];
1408            end
1409        end
1410       
1411        %CheckPatch2
1412        if Param.CheckPatch2==1
1413           
1414            switch CivMode
1415               
1416                case 'CivX'
1417                    cmd=[cmd...
1418                        cmd_patch(filecell.nc.civ1{ifile,j},Param,'Patch2') '\n'];
1419                   
1420                case 'CivAll'
1421                    patch2.inputFileName=filecell.nc.civ1{ifile,j} ;
1422                    patch2.nopt=subdomain_patch2;
1423                    patch2.maxdiff=thresh_patch2;
1424                    patch2.ro=rho_patch2;
1425                    test_grid=get(handles.get_gridpatch2,'Value');
1426                    if test_grid
1427                        patch2.gridflag='y';
1428                        gridname=get(handles.grid_patch2,'String');
1429                        if isequal(gridname(end-3:end),'grid')
1430                            nbslice_grid=str2double(gridname(1:end-4)); %
1431                            if ~isnan(nbslice_grid)
1432                                i1_grid=mod(i1_civ2(ifile)-1,nbslice_grid)+1;
1433                                patch2.gridPatch=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')];
1434                                if ~exist(patch2.gridPatch,'file')
1435                                    msgbox_uvmat('ERROR','grid file absent for patch2')
1436                                end
1437                            elseif exist(gridname,'file')
1438                                patch2.gridPatch=gridname;
1439                            else
1440                                msgbox_uvmat('ERROR','grid file absent for patch2')
1441                            end
1442                        end
1443                    else
1444                        patch2.gridPatch='none';
1445                        patch2.gridflag='n';
1446                        patch2.m=nx_patch2;
1447                        patch2.n=ny_patch2;
1448                    end
1449                    patch2.convectFlow='n';
1450                    fieldnames=fields(patch2);
1451                    [CivAllxml,uid_patch2]=add(CivAllxml,1,'element','patch2');
1452                    for ilist=1:length(fieldnames)
1453                        val=eval(['patch2.' fieldnames{ilist}]);
1454                        if ischar(val)
1455                            [CivAllxml,uid_t]=add(CivAllxml,uid_patch2,'element',fieldnames{ilist});
1456                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1457                        end
1458                    end
1459                    CivAllCmd=[CivAllCmd ' patch2 '];
1460            end
1461        end
1462       
1463        switch CivMode
1464           
1465            case {'CivX','CivAll'}
1466                if isequal(CivMode,'CivAll')
1467                    save(CivAllxml,[OutputFile '.xml']);
1468                    cmd=[cmd sparam.CivBin ' -f ' OutputFile '.xml '  CivAllCmd ' >' OutputFile '.log' '\n'];
1469                end             
1470                % create the .bat file used in run or batch
1471                filename_bat=[OutputFile '.bat'];
1472                [fid,message]=fopen(filename_bat,'w');
1473                if isequal(fid,-1)
1474                    msgbox_uvmat('ERROR', ['creation of .bat file: ' message])
1475                    return
1476                end
1477                fprintf(fid,cmd);
1478                fclose(fid);           
1479                if isunix
1480                    system(['chmod +x ' filename_bat]);
1481                end             
1482                batch_file_list{length(batch_file_list)+1}=filename_bat;
1483               
1484            case 'Matlab'
1485                drawnow
1486                if ~strcmp(compare,'stereo PIV')
1487                    filename_xml=[OutputFile '.civ.xml'];
1488                    t=struct2xml(Param);
1489                    save(t,filename_xml)
1490                    if batch   
1491                        path_civ=fileparts(which('civ'));
1492                        filename_bat=[OutputFile '.bat'];
1493                        [fid,message]=fopen(filename_bat,'w');
1494                        if isequal(fid,-1)
1495                            msgbox_uvmat('ERROR', ['creation of .bat file: ' message])
1496                            return
1497                        end
1498                        fprintf(fid,['/opt/matlab/R2011a/bin/matlab -nodisplay -nosplash -r "cd(''' path_civ ''');'...
1499                            'civ_matlab(''' filename_xml ''',''' OutputFile '.nc'');exit"']);
1500                        fclose(fid);
1501                        if isunix
1502                            system(['chmod +x ' filename_bat]);
1503                        end
1504                        batch_file_list{length(batch_file_list)+1}=filename_bat;
1505                    else
1506                        [Data,erromsg]=civ_matlab(Param,filecell.nc.civ1{ifile,j});
1507                        if isempty(errormsg)
1508                            display([filecell.nc.civ1{ifile,j} ' written'])
1509                        else
1510                            msgbox_uvmat('ERROR',errormsg)
1511                        end
1512                    end
1513                end
1514        end
1515    end
1516end
1517
1518if batch 
1519    switch batch_mode   
1520       
1521        case 'sge'
1522            for p=1:length(batch_file_list)
1523                cmd=['!qsub -p ' pvalue ' -q civ.q -e ' flname '.errors -o ' flname '.log' ' ' batch_file_list{p}];
1524                display(cmd);eval(cmd);
1525            end           
1526        case 'oar_old'
1527                for p=1:length(batch_file_list)
1528                    oar_command=['!oarsub -n CIVX -q nicejob '...
1529                   '-E ' regexprep(batch_file_list{p},'.bat','.errors') ' -O ' regexprep(batch_file_list{p},'.bat','.log ')...
1530                    '-l "/core=1+{type = ''smalljob''}/licence=1,walltime=00:60:00"   ' batch_file_list{p}];
1531                display(oar_command);eval(oar_command);
1532                end               
1533        case 'oar'
1534           
1535            oar_modes={'oar-dispatch','mpilauncher','oar-parexec'};
1536            text={'Batch processing on servcalcul3 LEGI';...
1537                'Please choose one of the followint modes';...
1538                '* oar-dispatch : jobs in a container of several cores';...
1539                '* mpilauncher : one single parallel mpi job using several cores';...
1540                '* oar-parexec (under development) ';...
1541                '**********************************'...
1542                };
1543            [S,v]=listdlg('PromptString',text,'ListString',oar_modes,...
1544                'SelectionMode','single','ListSize',[400 100],'Name','LEGI job mode');
1545            switch oar_modes{S}
1546                case 'oar-parexec' %oar-dispatch.pl
1547                    ncores=str2double(...
1548                        inputdlg('Number of cores (max 36)','oarsub parameter',1,{'12'})...
1549                        );
1550                    walltime_onejob=600;%seconds
1551                    filename_joblist=fullfile(Rootbat,'job_list.txt');
1552                    fid=fopen(filename_joblist,'w');
1553                    for p=1:length(batch_file_list)
1554                        fprintf(fid,[batch_file_list{p} '\n']);
1555                    end
1556                    fclose(fid)
1557                    oar_command=['oarsub -n test '...
1558                         '-l /core=' num2str(ncores) ','...
1559                        'walltime=' datestr(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,13) ' '...
1560                        '-E ' regexprep(filename_joblist,'\.txt\>','.errors') ' '...
1561                        '-O ' regexprep(filename_joblist,'\.txt\>','.log') ' '...
1562                        '"oar-parexec -f ' filename_joblist ' -l ' filename_joblist '.log"'];
1563                    filename_oarcommand=fullfile(Rootbat,'oar_command');
1564                    fid=fopen(filename_oarcommand,'w');
1565                    fprintf(fid,[oar_command '\n']);
1566                    fclose(fid);
1567                    display(oar_command);
1568                    eval(['! . ' filename_oarcommand])
1569                case 'oar-dispatch' %oar-dispatch.pl
1570                    ncores=str2double(...
1571                        inputdlg('Number of cores (max 36)','oarsub parameter',1,{'12'})...
1572                        );
1573                    walltime_onejob=600;%seconds
1574                    filename_joblist=fullfile(Rootbat,'job_list.txt');
1575                    fid=fopen(filename_joblist,'w');
1576                    for p=1:length(batch_file_list)
1577                        oar_command=['oarsub -n CIVX '...
1578                            '-E ' regexprep(batch_file_list{p},'\.bat\>','.errors') ' -O ' regexprep(batch_file_list{p},'\.bat\>','.log ')...
1579                            '-l "/core=1,walltime=' datestr(walltime_onejob/86400,13) '"   ' batch_file_list{p}];
1580                        fprintf(fid,[oar_command '\n']);
1581                    end
1582                    fclose(fid);
1583                    oar_command=['oarsub -t container -n civx-container '...
1584                        '-l /core=' num2str(ncores)...
1585                        ',walltime=' datestr(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,13) ' '...
1586                        '-E ' regexprep(filename_joblist,'\.txt\>','.errors') ' '...
1587                        '-O ' regexprep(filename_joblist,'\.txt\>','.log') ' '...
1588                        '"oar-dispatch -f ' filename_joblist '"'];
1589                    filename_oarcommand=fullfile(Rootbat,'oar_command');
1590                    fid=fopen(filename_oarcommand,'w');
1591                    fprintf(fid,[oar_command '\n']);
1592                    fclose(fid);
1593                    display(oar_command);
1594                    eval(['! . ' filename_oarcommand])
1595                case 'mpilauncher'
1596                    filename_joblist=fullfile(Rootbat,'job_list.txt');
1597                    fid=fopen(filename_joblist,'w');
1598                   
1599                    for p=1:length(batch_file_list)
1600                        fprintf(fid,[batch_file_list{p} '\n']);
1601                    end
1602                    fclose(fid)
1603                    text_oarscript=[...
1604                        '#!/bin/bash \n'...
1605                        '#OAR -n Mylauncher \n'...
1606                        '#OAR -l node=4/core=5,walltime=0:15:00 \n'...
1607                        '#OAR -E ' fullfile(Rootbat,'stderrfile.log') ' \n'...
1608                        '#OAR -O ' fullfile(Rootbat,'stdoutfile.log') ' \n'...
1609                        '# ========================================================= \n'...
1610                        '# This simple program launch a multinode parallel OpenMPI mpilauncher \n'...
1611                        '# application for coriolis PIV post-processing. \n'...
1612                        '# OAR uses oarshmost wrapper to propagate the user environement. \n'...
1613                        '# This wrapper assert that the user has the same environment on all the \n'...
1614                        '# allocated nodes (basic behavior needed by most MPI applications).  \n'...
1615                        '# \n'...
1616                        '# REQUIREMENT: \n'...
1617                        '# the oarshmost wrapper should be installed in $HOME/bin directory. \n'...
1618                        '# If a different location is used, change the line following the comment "Bidouille" \n'...
1619                        '# ========================================================= \n'...
1620                        '#   USER should only modify these 2 lines  \n'...
1621                        'WORKDIR=' pwd ' \n'...
1622                        'COMMANDE="mpilauncher  -f ' filename_joblist '" \n'...
1623                        '# ========================================================= \n'...
1624                        '# DO NOT MODIFY the FOLOWING LINES. (or be carefull) \n'...
1625                        'echo "job starting on: "`hostname` \n'...
1626                        'MPINODES="-host `tr [\\\\\\n] [,] <$OAR_NODEFILE |sed -e "s/,$/ /"`" \n'...
1627                        'NCPUS=`cat $OAR_NODEFILE |wc -l` \n'...
1628                        '#========== Bidouille ============== \n'...
1629                        'export OMPI_MCA_plm_rsh_agent=oar-envsh \n'...%                     'cd $WORKDIR \n'...
1630                        'CMD="mpirun -np $NCPUS -wdir $WORKDIR $MPINODES $COMMANDE" \n'...
1631                        'echo "I run: $CMD"  \n'...
1632                        '$CMD \n'...
1633                        'echo "job ending" \n'...
1634                        ];
1635                    %                 oarsub -S ./oar.sub
1636                    filename_oarscript=fullfile(Rootbat,'oar_command');
1637                    fid=fopen(filename_oarscript,'w');
1638                    fprintf(fid,[text_oarscript]);
1639                    fclose(fid);
1640                    eval(['!chmod +x  ' filename_oarscript]);
1641                    eval(['!oarsub -S ' filename_oarscript]);
1642            end
1643    end
1644else
1645    if ~isequal(CivMode,'Matlab')
1646        filename_superbat=fullfile(Rootbat,'job_list.bat');
1647        fid=fopen(filename_superbat,'w');
1648        if fid==-1
1649            msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat])
1650            return
1651        end
1652        for p=1:length(batch_file_list)
1653            if isunix
1654                fprintf(fid,['sh ' batch_file_list{p} '\n']);
1655            else
1656                fprintf(fid,['@call "' regexprep(filename_bat,'\\','\\\\') '"' '\n']);
1657            end
1658        end
1659        fclose(fid);
1660        if(isunix)
1661            system(['chmod +x ' filename_superbat]);
1662        end
1663        system([filename_superbat ' &']);% execute main commmand
1664    end
1665end
1666
1667
1668%% save interface state
1669if isfield(filecell,'nc')
1670    if isfield(filecell.nc,'civ2')
1671        fileresu=filecell.nc.civ2{1,1};
1672    else
1673        fileresu=filecell.nc.civ1{1,1};
1674    end
1675end
1676%[RootPath,RootFile,field_count,str2,str_a,str_b,ext,nom_type,SubDir]=name2display(fileresu);
1677[RootPath,SubDir,RootFile]=fileparts_uvmat(fileresu);
1678namedoc=fullfile(RootPath,SubDir,RootFile);
1679detect=1;
1680while detect==1
1681    namefigfull=[namedoc '.fig'];
1682    hh=dir(namefigfull);
1683    if ~isempty(hh)
1684        detect=1;
1685        namedoc=[namedoc '.0'];
1686    else
1687        detect=0;
1688    end
1689end
1690saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER  .xml)
1691
1692%Save info in personal profile (initiate browser next time) TODO
1693MenuFile={};
1694dir_perso=prefdir;
1695profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1696if exist(profil_perso,'file')
1697    hh=load (profil_perso);
1698      if isfield(hh,'MenuFile')
1699          MenuFile=hh.MenuFile;
1700      end
1701      if isfield(filecell.nc,'civ2')
1702          MenuFile=[filecell.nc.civ2{1,1}; MenuFile];
1703      else
1704           MenuFile=[filecell.nc.civ1{1,1}; MenuFile];
1705      end
1706      save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
1707else
1708    MenuFile=filecell.ima1.civ1(1,1);
1709    save (profil_perso,'MenuFile')
1710end
1711
1712%------------------------------------------------------------------------
1713% --- determine the list of reference indices of processing file
1714function [ref_i,ref_j,errormsg]=find_ref_indices(handles)
1715%------------------------------------------------------------------------
1716errormsg=''; %default error message
1717first_i=str2double(get(handles.first_i,'String'));%first index i
1718last_i=str2double(get(handles.last_i,'String'));%last index i
1719incr_i=str2double(get(handles.incr_i,'String'));% increment
1720if isequal(get(handles.first_j,'Visible'),'on')
1721    first_j=str2double(get(handles.first_j,'String'));%first index j
1722    last_j=str2double(get(handles.last_j,'String'));%last index j
1723    incr_j=str2double(get(handles.incr_j,'String'));% increment
1724else
1725    first_j=1;
1726    last_j=1;
1727    incr_j=1;
1728end
1729ref_i=first_i:incr_i:last_i;% list of i indices (reference values for each pair)
1730ref_j=first_j:incr_j:last_j;% list of j indices (reference values for each pair)
1731if isnan(first_i)||isnan(first_j)
1732    errormsg='first field number not defined';
1733elseif isnan(last_i)||isnan(last_j)
1734    errormsg='last field number not defined';
1735elseif isnan(incr_i)||isnan(incr_j)
1736    errormsg='increment in field number not defined';
1737elseif last_i < first_i || last_j < first_j
1738    errormsg='last field number must be larger than the first one';
1739end
1740
1741%------------------------------------------------------------------------
1742% --- determine the list of filenames and indices needed for launch_job
1743function [filecell,num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2,nom_type_nc,file_ref_fix1,file_ref_fix2,compare]=...
1744    set_civ_filenames(handles,ref_i,ref_j,checkbox)
1745%------------------------------------------------------------------------
1746filecell=[];%default
1747
1748%% get the root names nomenclature and numbers
1749filebase=get(handles.RootName,'String');
1750
1751if isempty(filebase)||isequal(filebase,'')
1752    msgbox_uvmat('ERROR','please open an image with the upper menu option Open/Browse...')
1753    return
1754end
1755
1756%filebase=regexprep(filebase,'\.fsnet','fsnet');% temporary fix for cluster Coriolis
1757filecell.filebase=filebase;
1758
1759browse=get(handles.RootName,'UserData');
1760compare_list=get(handles.ListCompareMode,'String');
1761val=get(handles.ListCompareMode,'Value');
1762compare=compare_list{val};
1763if strcmp(compare,'displacement')
1764    mode='displacement';
1765else
1766    mode_list=get(handles.ListPairMode,'String');
1767    mode_value=get(handles.ListPairMode,'Value');
1768    mode=mode_list{mode_value};
1769end
1770%time=get(handles.RootName,'UserData'); %get the set of times
1771ext_ima=get(handles.ImaExt,'String');
1772nom_type_nc=browse.nom_type_nc;
1773if isfield(browse,'nom_type_ima')
1774    nom_type_ima2=browse.nom_type_ima;
1775end
1776if isempty(nom_type_ima2),nom_type_ima2='1';end; %default
1777if isempty(nom_type_nc),nom_type_nc='_1-2';end; %default
1778[num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=...
1779    find_pair_indices(handles,ref_i,ref_j,mode);
1780%determine the new filebase for 'displacement' ListPairMode (comparison of two series)
1781filebase_B=filebase;% root name of the second field series for stereo
1782if strcmp(compare,'displacement') || strcmp(compare,'stereo PIV')
1783%     test_disp=1;
1784    nom_type_ima1=browse.nom_type_ima_1; %nomenclature type of the second file series
1785    [Path2,Name2]=fileparts(filebase_B);
1786    Path1=Path2;
1787    Name1=get(handles.RootName_1,'String');% root name of the first field series for stereo
1788    filebase_A=fullfile(Path1,Name1);
1789    if length(Name1)>6
1790        Name1=Name1(end-5:end);
1791    end
1792    if length(Name2)>6
1793        Name2=Name2(end-5:end);
1794    end
1795    filebase_AB=fullfile(Path2,[Name2 '-' Name1]);
1796else
1797%     test_disp=0;
1798    filebase_A=filebase;
1799    nom_type_ima1=nom_type_ima2;
1800    filebase_AB=filebase;
1801end
1802if strcmp(compare,'displacement')
1803    filebase_ima1=filebase_A;
1804    filebase_ima2=filebase_B;
1805    filebase_nc=filebase_AB; %root name for the result of civ2
1806else
1807    filebase_ima1=filebase_B;
1808    filebase_ima2=filebase_B;
1809    filebase_nc=filebase_B;
1810end
1811    [RootPath_ima1,RootFile_ima1]=fileparts(filebase_ima1);
1812    [RootPath_ima2,RootFile_ima2]=fileparts(filebase_ima2);
1813    [RootPath_nc,RootFile_ima1]=fileparts(filebase_nc);
1814   
1815%determine reference files for fix:
1816file_ref_fix1={};%default
1817file_ref_fix2={};
1818nbfield=length(num1_civ1);
1819nbslice=length(num_a_civ1);
1820if checkbox(2)==1% fix1 performed
1821    ref=get(handles.ref_fix1,'UserData');%read data on the ref file stored by get_ref_fix1_Callback
1822    if ~isempty(ref)
1823        first_i=str2double(get(handles.first_i,'String'));
1824        last_i=str2double(get(handles.last_i,'String'));
1825        incr_i=str2double(get(handles.incr_i,'String'));
1826        first_j=str2double(get(handles.first_j,'String'));
1827        last_j=str2double(get(handles.last_j,'String'));
1828        incr_j=str2double(get(handles.incr_j,'String'));
1829        num_i_ref=first_i:incr_i:last_i;
1830        num_j_ref=first_j:incr_j:last_j;
1831        if isequal(mode,'displacement')
1832            num_i1=num_i_ref;
1833 name_genna           num_i2=num_i_ref;
1834            num_j1=num_j_ref;
1835            num_j2=num_j_ref;
1836        elseif isequal(mode,'pair j1-j2')% isequal(mode,'st_pair j1-j2')
1837            num_i1=num_i_ref;
1838            num_i2=num_i1;
1839            num_j1=ref.num_a*ones(size(num_i_ref));
1840            num_j2=ref.num_b*ones(size(num_i_ref));
1841        elseif isequal(mode,'series(Di)') % isequal(mode,'st_series(Di)')
1842            delta1=floor((ref.num2-ref.num1)/2);
1843            delta2=ceil((ref.num2-ref.num1)/2);
1844            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
1845            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
1846            if isempty(ref.num_a)
1847                ref.num_a=1;
1848            end
1849            num_j1=ref.num_a*ones(size(num_i1));
1850            num_j2=num_j1;
1851        elseif isequal(mode,'series(Dj)')%| isequal(mode,'st_series(Dj)')
1852            delta1=floor((ref.num_b-ref.num_a)/2);
1853            delta2=ceil((ref.num_b-ref.num_a)/2);
1854            num_i1=ref.num1*ones(size(num_i_ref));
1855            num_i2=num_i1;
1856            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
1857            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
1858        end
1859        for ifile=1:nbfield
1860            for j=1:nbslice
1861                [RootPath,RootFile]=fileparts(ref.filebase);
1862                file_ref=fullfile_uvmat(RootPath,ref.subdir,RootFile,'.nc',ref.nom_type,num_i1(ifile),num_i2(ifile),num_j1(j),num_j2(j));
1863%                 file_ref=name_generator(ref.filebase,num_i1(ifile),num_j1(j),'.nc',ref.nom_type,1,num_i2(ifile),num_j2(j),ref.subdir);%
1864                file_ref_fix1(ifile,j)={file_ref};
1865                if ~exist(file_ref,'file')
1866                    msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix1'])
1867                    filecell=[];
1868                    return
1869                end
1870            end
1871        end
1872    end
1873end
1874
1875%determine reference files for checkfix2:
1876if checkbox(5)==1% fix2 performed
1877    ref=get(handles.ref_fix2,'UserData');
1878    if ~isempty(ref)
1879        first_i=str2double(get(handles.first_i,'String'));
1880        last_i=str2double(get(handles.last_i,'String'));
1881        incr_i=str2double(get(handles.incr_i,'String'));
1882        first_j=str2double(get(handles.first_j,'String'));
1883        last_j=str2double(get(handles.last_j,'String'));
1884        incr_j=str2double(get(handles.incr_j,'String'));
1885        num_i_ref=first_i:incr_i:last_i;
1886        num_j_ref=first_j:incr_j:last_j;
1887        if isequal(mode,'displacement')
1888            num_i1=num_i_ref;
1889            num_i2=num_i_ref;
1890            num_j1=num_j_ref;
1891            num_j2=num_j_ref;
1892        elseif isequal(mode,'pair j1-j2')
1893            num_i1=num_i_ref;
1894            num_i2=num_i1;
1895            num_j1=ref.num_a;
1896            num_j2=ref.num_b;
1897        elseif isequal(mode,'series(Di)')
1898            delta1=floor((ref.num2-ref.num1)/2);
1899            delta2=ceil((ref.num2-ref.num1)/2);
1900            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
1901            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
1902            num_j1=ref.num_a*ones(size(num_i1));
1903            num_j2=num_j1;
1904        elseif isequal(mode,'series(Dj)')
1905            delta1=floor((ref.num_b-ref.num_a)/2);
1906            delta2=ceil((ref.num_b-ref.num_a)/2);
1907            num_i1=ref.num1*ones(size(num_i_ref));
1908            num_i2=num_i1;
1909            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
1910            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
1911        end
1912        for ifile=1:nbfield
1913            for j=1:nbslice
1914                [RootPath,RootFile]=fileparts(ref.filebase);
1915                file_ref=fullfile_uvmat(RootPath,ref.subdir,RootFile,'.nc',ref.nom_type,num_i1(ifile),num_i2(ifile),num_j1(j),num_j2(j));
1916                %file_ref=name_generator(ref.filebase,num_i1(ifile),num_j1(j),'.nc',ref.nom_type,1,num_i2(ifile),num_j2(j),ref.subdir);%
1917                file_ref_fix2(ifile,j)={file_ref};
1918                if ~exist(file_ref,'file')
1919                    msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix2'])
1920                    filecell={};
1921                    return
1922                end
1923            end
1924        end
1925    end
1926end
1927
1928%check dir
1929subdir_civ1=get(handles.txt_SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf output data
1930subdir_civ2=get(handles.txt_SubdirCiv2,'String');
1931if isequal(subdir_civ1,''),subdir_civ1='CIV'; end% put default subdir
1932if isequal(subdir_civ2,''),subdir_civ2=subdir_civ1; end% put default subdir
1933% currentdir=pwd;%store the current working directory
1934[Path_ima,Name]=fileparts(filebase);%Path of the image files (.civ)
1935if ~exist(Path_ima,'dir')
1936    msgbox_uvmat('ERROR',['path to images ' Path_ima ' not found'])
1937    filecell={};
1938    return
1939end
1940[xx,message]=fileattrib(Path_ima);
1941if ~isempty(message) && ~isequal(message.UserWrite,1)
1942    msgbox_uvmat('ERROR',['No writting access to ' Path_ima])
1943    filecell={};
1944%     cd(currentdir);
1945    return
1946end
1947
1948%check the existence of the netcdf and image files involved
1949% %%%%%%%%%%%%  case CheckCiv1 activated   %%%%%%%%%%%%%
1950if checkbox(1)==1;
1951    detect=1;
1952    vers=0;
1953    subdir_civ1_new=subdir_civ1;
1954    while detect==1 %create a new subdir if the netcdf files already exist
1955        for ifile=1:nbfield
1956            for j=1:nbslice
1957                [RootPath,RootFile]=fileparts(ref.filebase_nc);
1958                filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1_new);
1959                detect=exist(filename,'file')==2;
1960                if detect% if a netcdf file already exists
1961                    indstr=regexp(subdir_civ1_new,'\D');
1962                    if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number
1963                        vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1;
1964                        subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)];
1965                    else
1966                        vers=vers+1;
1967                        subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) '_' num2str(vers)];       
1968                    end
1969                    subdir_civ2=subdir_civ1_new;
1970                    break
1971                end
1972                filecell.nc.civ1(ifile,j)={filename};
1973            end
1974            if detect% if a netcdf file already exists
1975                break
1976            end
1977        end
1978 
1979        %create the new txt_SubdirCiv1
1980        if ~exist(fullfile(Path_ima,subdir_civ1_new),'dir')
1981%             cd(Path_ima);         
1982            [xx,msg1]=mkdir(fullfile(Path_ima,subdir_civ1_new));
1983
1984            if ~strcmp(msg1,'')
1985                msgbox_uvmat('ERROR',['cannot create ' subdir_civ1_new ': ' msg1])%error message for directory creation
1986                filecell={};
1987                return
1988            elseif isunix         
1989                [xx,msg2] = fileattrib(fullfile(Path_ima,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g)
1990                if ~strcmp(msg2,'')
1991                    msgbox_uvmat('ERROR',['pb of permission for  ' fullfile(Path_ima,subdir_civ1_new) ': ' msg2])%error message for directory creation
1992                    filecell={};
1993                    return
1994                end
1995            end
1996%             cd(currentdir);
1997        end
1998        if strcmp(compare,'stereo PIV')&&(strcmp(mode,'pair j1-j2')||strcmp(mode,'series(Dj)')||strcmp(mode,'series(Di)'))%check second nc series
1999            for ifile=1:nbfield
2000                for j=1:nbslice
2001                    filename=name_generator(filebase_A,num1_civ1(ifile),num_a_civ1(j),'.nc',nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1_new);%
2002                    detect=exist(filename,'file')==2;
2003                    if detect% if a netcdf file already exists
2004                       indstr=regexp(subdir_civ1_new,'\D');
2005                       if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number
2006                           vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1;
2007                           subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)];
2008                       else
2009                           vers=vers+1;
2010                           subdir_civ1_new=[subdir_civ1_new '_' num2str(vers)];
2011                       end
2012                       subdir_civ2=subdir_civ1;
2013                       break
2014                    end
2015                    filecell.ncA.civ1(ifile,j)={filename};
2016                end
2017                if detect% if a netcdf file already exists
2018                    break
2019                end
2020            end
2021            %create the new txt_SubdirCiv1
2022            if ~exist(fullfile(Path_ima,subdir_civ1_new),'dir')
2023%                    cd(Path_ima);         
2024                [xx,msg1]=mkdir(fullfile(Path_ima,subdir_civ1_new));
2025%                             cd(currentdir);
2026                if ~strcmp(msg1,'')
2027                    msgbox_uvmat('ERROR',['cannot create ' subdir_civ1_new ': ' msg1])
2028%                     cd(currentdir)
2029                    filecell={};
2030                    return
2031                else
2032                    [xx,msg2] = fileattrib(fullfile(Path_ima,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g)
2033                    if ~strcmp(msg2,'')
2034                        msgbox_uvmat('ERROR',['pb of permission for ' subdir_civ1_new ': ' msg2])%error message for directory creation
2035%                         cd(currentdir)
2036                        filecell={};
2037                        return
2038                    end
2039                end
2040            end
2041        end
2042    end
2043    subdir_civ1=subdir_civ1_new;
2044    % get image names
2045    for ifile=1:nbfield
2046        for j=1:nbslice
2047            filename=name_generator(filebase_ima1, num1_civ1(ifile),num_a_civ1(j),ext_ima,nom_type_ima1);
2048            idetect(j)=exist(filename,'file')==2;
2049            filecell.ima1.civ1(ifile,j)={filename}; %first image
2050            filename=name_generator(filebase_ima2, num2_civ1(ifile),num_b_civ1(j),ext_ima,nom_type_ima2);
2051            idetect_1(j)=exist(filename,'file')==2;
2052            filecell.ima2.civ1(ifile,j)={filename};%second image
2053        end
2054        [idetectmin,indexj]=min(idetect);
2055        if idetectmin==0,
2056            msgbox_uvmat('ERROR',[filecell.ima1.civ1{ifile,indexj} ' not found'])
2057            filecell={};
2058           % cd(currentdir)
2059            return
2060        end
2061        [idetectmin,indexj]=min(idetect_1);
2062        if idetectmin==0,
2063            msgbox_uvmat('ERROR',[filecell.ima2.civ1{ifile,indexj} ' not found'])
2064            filecell={};
2065            %cd(currentdir)
2066            return
2067        end
2068    end
2069    if strcmp(compare,'stereo PIV') && (strcmp(mode,'pair j1-j2') || strcmp(mode,'series(Dj)') || strcmp(mode,'series(Di)'))
2070        for ifile=1:nbfield
2071            for j=1:nbslice
2072                filename=name_generator(filebase_A, num1_civ1(ifile),num_a_civ1(j),ext_ima,nom_type_ima1);
2073                idetect(j)=exist(filename,'file')==2;
2074                filecell.imaA1.civ1(ifile,j)={filename} ;%first image
2075                filename=name_generator(filebase_A, num2_civ1(ifile),num_b_civ1(j),ext_ima,nom_type_ima2);
2076                idetect_1(j)=exist(filename,'file')==2;
2077                filecell.imaA2.civ1(ifile,j)={filename};%second image
2078            end
2079            [idetectmin,indexj]=min(idetect);
2080            if idetectmin==0,
2081                msgbox_uvmat('ERROR',[filecell.imaA1.civ1{ifile,indexj} ' not found'])
2082                filecell={};
2083               % cd(currentdir)
2084                return
2085            end
2086            [idetectmin,indexj]=min(idetect_1);
2087            if idetectmin==0,
2088                msgbox_uvmat('ERROR',[filecell.imaA2.civ1{ifile,indexj} ' not found'])
2089                filecell={};
2090               % cd(currentdir)
2091                return
2092            end
2093        end
2094    end
2095   
2096    %%%%%%%%%%%%%  checkfix1 or checkpatch1 activated but no checkciv1   %%%%%%%%%%%%%
2097elseif (checkbox(2)==1 || checkbox(3)==1);
2098    for ifile=1:nbfield
2099        for j=1:nbslice
2100            filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',...
2101                nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
2102            detect=exist(filename,'file')==2;
2103            if detect==0
2104                msgbox_uvmat('ERROR',[filename ' not found'])
2105                filecell={};
2106               % cd(currentdir)
2107                return
2108            end
2109            filecell.nc.civ1(ifile,j)={filename};
2110        end
2111    end
2112    if strcmp(compare,'stereo PIV')
2113        for ifile=1:nbfield
2114            for j=1:nbslice
2115                filename=name_generator(filebase_A,num1_civ1(ifile),num_a_civ1(j),'.nc',nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
2116                filecell.ncA.civ1(ifile,j)={filename};
2117                if ~exist(filename,'file')
2118                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2119                    set(handles.RUN, 'Enable','On')
2120                    set(handles.RUN,'BackgroundColor',[1 0 0])
2121                    filecell={};
2122                    %cd(currentdir)
2123                    return
2124                end
2125            end
2126        end
2127    end
2128end
2129
2130%%%%%%%%%%%%%  if checkciv2 performed with pairs different than checkciv1  %%%%%%%%%%%%%
2131testdiff=0;
2132if (checkbox(4)==1)&&...
2133        ((get(handles.ListPairCiv1,'Value')~=get(handles.ListPairCiv2,'Value'))||~strcmp(subdir_civ2,subdir_civ1))
2134    testdiff=1;
2135    detect=1;
2136    vers=0;
2137    subdir_civ2_new=subdir_civ2;
2138    while detect==1 %create a new subdir if the netcdf files already exist
2139        for ifile=1:nbfield
2140            for j=1:nbslice
2141                filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2_new);%
2142                detect=exist(filename,'file')==2;
2143                if detect% if a netcdf file already exists
2144                    indstr=regexp(subdir_civ2,'\D');
2145                    if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2146                        vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2147                        subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2148                    else
2149                        vers=vers+1;
2150                        subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2151                    end
2152                    break
2153                end
2154                filecell.nc.civ2(ifile,j)={filename};
2155            end
2156            if detect% if a netcdf file already exists
2157                break
2158            end
2159        end
2160        %create the new subdir_civ2_new
2161        if ~exist(fullfile(Path_ima,subdir_civ2_new),'dir')
2162            [xx,m2]=mkdir(fullfile(Path_ima,subdir_civ2_new));
2163            [xx,msg2] = fileattrib(fullfile(Path_ima,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g)
2164            if ~isequal(m2,'')
2165                msgbox_uvmat('ERROR',['cannot create ' fullfile(Path_ima,subdir_civ2_new) ': ' m2])
2166                filecell={};
2167               % cd(currentdir)
2168                return
2169            end
2170        end
2171        if strcmp(compare,'stereo PIV')%check second nc series
2172            for ifile=1:nbfield
2173                for j=1:nbslice
2174                    filename=name_generator(filebase_A,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2175                        nom_type_nc,1,num2_civ2(ifile),num_b_civ1(j),subdir_civ2_new);%
2176                    detect=exist(filename,'file')==2;
2177                    if detect% if a netcdf file already exists
2178                        indstr=regexp(subdir_civ2,'\D');
2179                        if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2180                           vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2181                           subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2182                        else
2183                           vers=vers+1;
2184                           subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2185                        end
2186                        break
2187                    end
2188                    filecell.ncA.civ2(ifile,j)={filename};
2189                end
2190                if detect% if a netcdf file already exists
2191                    break
2192                end
2193            end
2194            subdir_civ2=subdir_civ2_new;
2195            %create the new txt_SubdirCiv1
2196            if ~exist(fullfile(Path_ima,subdir_civ2_new),'dir')
2197                [xx,m2]=mkdir(subdir_civ2_new);
2198                 [xx,msg2] = fileattrib(fullfile(Path_ima,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g)
2199                if ~isequal(m2,'')
2200                    msgbox_uvmat('ERROR', ['cannot create ' fullfile(Path_ima,subdir_civ2_new) ': ' m2])%error message for directory creation
2201                  %  cd(currentdir)
2202                    filecell={};
2203                    return
2204                end
2205            end
2206        end
2207    end
2208    subdir_civ2=subdir_civ2_new;
2209end
2210%cd(currentdir);%come back to the current working directory
2211
2212%%%%%%%%%%%%%  if checkciv2 results are obtained or used  %%%%%%%%%%%%%
2213if checkbox(4)==1 || checkbox(5)==1 || checkbox(6)==1 %civ2
2214    %check source netcdf file of checkciv1 estimates
2215    if checkbox(1)==0; %no civ1 performed
2216        for ifile=1:nbfield
2217            for j=1:nbslice
2218                filename=fullfile_uvmat(RootPath_nc,subdir_civ1,RootFile_nc,'.nc',nom_type_nc,num1_civ1(ifile),num2_civ1(ifile),num_a_civ1(j),num_b_civ1(j));
2219                %filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',...
2220%                     nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
2221                filecell.nc.civ1(ifile,j)={filename};% name of the civ1 file
2222                if ~exist(filename,'file')
2223                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2224                    filecell={};
2225                    return
2226                end
2227                if ~testdiff % civ2 or patch2 are written in the same file as civ1
2228                    if checkbox(4)==0 ; %check the existence of civ2 if it is not calculated
2229                        Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2');
2230                        if ~isempty(Data.CivStage) && Data.CivStage<4 %test for civ files
2231                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2232                            filecell=[];
2233                            return
2234                        elseif isempty(Data.civ2)||isequal(Data.civ2,0)
2235                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2236                            filecell=[];
2237                            return
2238                        end
2239                    elseif checkbox(3)==0; %check the existence of patch if it is not calculated
2240                        Data=nc2struct(filename,'ListGlobalAttribute','CivStage','patch');
2241                        if ~isempty(Data.CivStage)
2242                            if Data.CivStage<3 %test for civ files
2243                                msgbox_uvmat('ERROR',['no patch data in ' filename])
2244                                filecell=[];
2245                                return
2246                            end
2247                        elseif isempty(Data.patch)||isequal(Data.patch,0)
2248                            msgbox_uvmat('ERROR',['no patch data in ' filename])
2249                            filecell=[];
2250                            return
2251                        end
2252                    end
2253                end
2254            end
2255        end
2256        if strcmp(compare,'stereo PIV')
2257            for ifile=1:nbfield
2258                for j=1:nbslice
2259                    filename=fullfile_uvmat(RootPath_A,subdir_civ2,RootFile_A,'.nc',nom_type_nc,num1_civ2(ifile),num2_civ2(ifile),num_a_civ2(j),num_b_civ2(j));
2260%                     filename=name_generator(filebase_A,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2261%                         nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
2262                    filecell.ncA.civ2(ifile,j)={filename};
2263                    if ~exist(filename,'file')
2264                        msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2265                        set(handles.RUN, 'Enable','On')
2266                        set(handles.RUN,'BackgroundColor',[1 0 0])
2267                        return
2268                    end
2269                end
2270            end
2271        end
2272    end
2273   
2274    detect=1;
2275    %     while detect==1%creates a new subdir if the netcdf files already contain checkciv2 data
2276    for ifile=1:nbfield
2277        for j=1:nbslice
2278            filename=fullfile_uvmat(RootPath_nc,subdir_civ2,RootFile_nc,'.nc',nom_type_nc,num1_civ2(ifile),num2_civ2(ifile),num_a_civ2(j),num_b_civ2(j));
2279%             filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2280%                 nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);
2281            detect=exist(filename,'file')==2;
2282            filecell.nc.civ2(ifile,j)={filename};
2283        end
2284    end
2285    %get first image names for checkciv2
2286    if checkbox(1)==1 && isequal(num1_civ1,num1_civ2) && isequal(num_a_civ1,num_a_civ2)
2287        filecell.ima1.civ2=filecell.ima1.civ1;
2288    elseif checkbox(4)==1
2289        for ifile=1:nbfield
2290            for j=1:nbslice
2291                filename=fullfile_uvmat(RootPath_ima1,[],RootFile_ima1,ext_ima,nom_type_ima1,num1_civ2(ifile),num2_civ2(ifile),num_a_civ2(j),num_b_civ2(j));
2292                %filename=name_generator(filebase_ima1, num1_civ2(ifile),num_a_civ2(j),ext_ima,nom_type_ima1);
2293                idetect_2(j)=exist(filename,'file')==2;
2294                filecell.ima1.civ2(ifile,j)={filename};%first image
2295            end
2296            [idetectmin,indexj]=min(idetect_2);
2297            if idetectmin==0,
2298                msgbox_uvmat('ERROR',['input image ' filecell.ima1.civ2{ifile,indexj} ' not found'])
2299                filecell=[];
2300                return
2301            end
2302        end
2303    end
2304   
2305    %get second image names for checkciv2
2306    if checkbox(1)==1 && isequal(num2_civ1,num2_civ2) && isequal(num_b_civ1,num_b_civ2)
2307        filecell.ima2.civ2=filecell.ima2.civ1;
2308    elseif checkbox(4)==1
2309        for ifile=1:nbfield
2310            for j=1:nbslice
2311                filename=fullfile_uvmat(RootPath_ima2,[],RootFile_ima2,ext_ima,nom_type_ima2,num1_civ2(ifile),num2_civ2(ifile),num_a_civ2(j),num_b_civ2(j));
2312               % filename=name_generator(filebase_ima2, num2_civ2(ifile),num_b_civ2(j),ext_ima,nom_type_ima2);
2313                idetect_3(j)=exist(filename,'file')==2;
2314                filecell.ima2.civ2(ifile,j)={filename};%first image
2315            end
2316            [idetectmin,indexj]=min(idetect_3);
2317            if idetectmin==0,
2318                msgbox_uvmat('ERROR',['input image ' filecell.ima2.civ2{ifile,indexj} ' not found'])
2319                filecell=[];
2320                return
2321            end
2322        end
2323    end
2324end
2325if (checkbox(5) || checkbox(6)) && ~checkbox(4)  % need to read an existing netcdf civ2 file
2326    if ~testdiff
2327        filecell.nc.civ2=filecell.nc.civ1;% file already checked
2328    else     % check the civ2 files
2329        for ifile=1:nbfield
2330            for j=1:nbslice
2331                 filename=fullfile_uvmat(RootPath_nc,subdir_civ2,RootFile_nc,'.nc',nom_type_nc,num1_civ2(ifile),num2_civ2(ifile),num_a_civ2(j),num_b_civ2(j));
2332%                 filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2333%                     nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
2334                filecell.nc.civ2(ifile,j)={filename};
2335                if ~exist(filename,'file')
2336                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2337                    filecell=[];
2338                    return
2339                else
2340                    Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2');
2341                    if ~isempty(Data.CivStage) && Data.CivStage<4 %test for civ files
2342                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2343                            filecell=[];
2344                            return
2345                    elseif isempty(Data.civ2)||isequal(Data.civ2,0)
2346                        msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2347                        filecell=[];
2348                        return
2349                    end
2350                end
2351            end
2352        end
2353    end
2354end
2355
2356%%%%%%%%%%%%%  if stereo fields are calculated by PATCH %%%%%%%%%%%%%
2357if strcmp(compare,'stereo PIV')
2358    if  checkbox(3) && isequal(get(handles.test_stereo1,'Value'),1)
2359        for ifile=1:nbfield
2360            for j=1:nbslice
2361                 filename=fullfile_uvmat(RootPath_AB,subdir_civ1,RootFile_AB,'.nc',nom_type_nc,num1_civ1(ifile),num2_civ1(ifile),num_a_civ1(j),num_b_civ1(j));
2362%                 filename=name_generator(filebase_AB,num1_civ1(ifile),num_a_civ1(j),'.nc',...
2363%                     nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
2364                filecell.st(ifile,j)={filename};
2365            end
2366        end
2367    end
2368    if  checkbox(6) && isequal(get(handles.CheckStereo,'Value'),1)
2369        for ifile=1:nbfield
2370            for j=1:nbslice
2371                 filename=fullfile_uvmat(RootPath_AB,subdir_civ2,RootFile_AB,'.nc',nom_type_nc,num1_civ2(ifile),num2_civ2(ifile),num_a_civ2(j),num_b_civ2(j));
2372%                 filename=name_generator(filebase_AB,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2373%                     nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
2374                filecell.st(ifile,j)={filename};
2375            end
2376        end
2377    end
2378end
2379set(handles.txt_SubdirCiv1,'String',subdir_civ1);%update the edit box
2380set(handles.txt_SubdirCiv2,'String',subdir_civ2);%update the edit box
2381browse.nom_type_nc=nom_type_nc;
2382set(handles.RootName,'UserData',browse); %update the nomenclature type for uvmat
2383
2384
2385%COPY IMAGES TO THE FORMAT .png IF NEEDED
2386if isequal(nom_type_ima1,'*')%case of movie files
2387    nom_type_imanew1='_i';
2388else
2389    nom_type_imanew1=nom_type_ima1;
2390end
2391if isequal(nom_type_ima2,'*')%case of movie files
2392    nom_type_imanew2='_i';
2393else
2394    nom_type_imanew2=nom_type_ima2;
2395end
2396if ~isequal(ext_ima,'.png')
2397    %%type of image file
2398    type_ima1='none';%default
2399    movieobject1=[];%default
2400    if strcmpi(ext_ima,'.avi')
2401        hhh=which('mmreader');
2402        if ~isequal(hhh,'')&& mmreader.isPlatformSupported()% if the mmreader function is found (recent version of matlab)
2403            type_ima1='movie';
2404            movieobject1=mmreader([filebase_ima2 ext_ima]);
2405        else
2406            type_ima1='avi';
2407        end
2408    elseif ischar(ext_ima) && ~isempty(ext_ima(2:end))
2409        form=imformats(ext_ima(2:end));
2410        if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2411            if isequal(nom_type_ima1,'*');
2412                type_ima1='multimage';%image series in a single image file
2413            else
2414                type_ima1='image';
2415            end
2416        end
2417    end
2418    type_ima2='none';%default
2419    movieobject2=[];
2420    if strcmpi(ext_ima,'.avi')
2421        hhh=which('mmreader');
2422        if ~isequal(hhh,'')&& mmreader.isPlatformSupported()% if the mmreader function is found (recent version of matlab)
2423            type_ima2='movie';
2424            movieobject2=mmreader([filebase_ima2 ext_ima]);
2425        else
2426            type_ima2='avi';
2427        end
2428    elseif ischar(ext_ima) && ~isempty(ext_ima(2:end))
2429        form=imformats(ext_ima(2:end));
2430        if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2431            if isequal(nom_type_ima1,'*');
2432                type_ima2='multimage';%image series in a single image file
2433            else
2434                type_ima2='image';
2435            end
2436        end
2437    end
2438    %npxy=get(handles.ImaExt,'UserData');
2439    % %     if numel(npxy)<2
2440    %
2441    %         filename=name_generator(filebase_ima1,num1_civ1(1),num_a_civ1(1),ImaExt,nom_type_ima1);
2442    %         A=imread(filename);
2443    %         npxy=size(A);
2444    % %     end
2445    %     npy=npxy(1);
2446    %     npx=npxy(2);
2447    if checkbox(1) %if civ1 is performed
2448        h = waitbar(0,'copy images to the .png format for civ1');% display a wait bar
2449        for ifile=1:nbfield
2450            waitbar(ifile/nbfield);
2451            for j=1:nbslice
2452                 filename=fullfile_uvmat(RootPath_ima1,[],RootFile_ima1,'.png',nom_type_imanew1,num1_civ1(ifile),num2_civ1(ifile),num_a_civ1(j),num_b_civ1(j));
2453%                 filename=name_generator(filebase_ima1,num1_civ1(ifile),num_a_civ1(j),'.png',nom_type_imanew1);
2454                if ~exist(filename,'file')
2455                    A=read_image(filecell.ima1.civ1{ifile,j},type_ima1,num1_civ1(ifile),movieobject1);
2456                    imwrite(A,filename,'BitDepth',16);
2457                end
2458                filecell.ima1.civ1(ifile,j)={filename};
2459                filename=fullfile_uvmat(RootPath_ima2,[],RootFile_ima2,'.png',nom_type_imanew2,num2_civ1(ifile),num2_civ1(ifile),num_b_civ1(j),num_b_civ1(j));
2460                %filename=name_generator(filebase_ima2, num2_civ1(ifile),num_b_civ1(j),'.png',nom_type_imanew2);
2461                if ~exist(filename,'file')
2462                    A=read_image(filecell.ima2.civ1{ifile,j},type_ima2,num2_civ1(ifile),movieobject2);
2463                    imwrite(A,filename,'BitDepth',16);
2464                end
2465                filecell.ima2.civ1(ifile,j)={filename};
2466            end
2467        end
2468        close(h)
2469    end
2470    if checkbox(4) %if civ2 is performed
2471        h = waitbar(0,'copy images to the .png format for civ2');% display a wait bar
2472        for ifile=1:nbfield
2473            waitbar(ifile/nbfield);
2474            for j=1:nbslice
2475                filename=fullfile_uvmat(RootPath_ima1,[],RootFile_ima1,'.png',nom_type_imanew1,num1_civ2(ifile),[],num_a_civ1(j));
2476                %filename=name_generator(filebase_ima1,num1_civ2(ifile),num_a_civ2(j),'.png',nom_type_imanew1);
2477                if ~exist(filename,'file')
2478                    A=read_image(cell2mat(filecell.ima1.civ2(ifile,j)),type_ima2,num1_civ2(ifile));
2479                    imwrite(A,filename,'BitDepth',16);
2480                end
2481                filecell.ima1.civ2(ifile,j)={filename};
2482                filename=name_generator(filebase_ima2, num2_civ2(ifile),num_b_civ2(j),'.png',nom_type_imanew2);
2483                if ~exist(filename,'file')
2484                    A=read_image(cell2mat(filecell.ima2.civ2(ifile,j)),type_ima2,num2_civ2(ifile));
2485                    imwrite(A,filename,'BitDepth',16);
2486                end
2487                filecell.ima2.civ2(ifile,j)={filename};
2488            end
2489        end
2490        close(h);
2491    end
2492end
2493
2494%------------------------------------------------------------------------
2495% --- determine the list of index pairs of processing file
2496function [num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=...
2497    find_pair_indices(handles,ref_i,ref_j,mode)
2498%------------------------------------------------------------------------
2499
2500list_civ1=get(handles.ListPairCiv1,'String');
2501index_civ1=get(handles.ListPairCiv1,'Value');
2502str_civ1=list_civ1{index_civ1};%string defining the image pairs for civ1
2503if isempty(str_civ1)||isequal(str_civ1,'')
2504    msgbox_uvmat('ERROR','no image pair selected for civ1')
2505    return
2506end
2507list_civ2=get(handles.ListPairCiv2,'String');
2508index_civ2=get(handles.ListPairCiv2,'Value');
2509if index_civ2>length(list_civ2)
2510    list_civ2=list_civ1;
2511    index_civ2=index_civ1;
2512end
2513str_civ2=list_civ2{index_civ2};%string defining the image pairs for civ2
2514
2515if isequal (mode,'series(Di)')
2516    lastfield=str2double(get(handles.nb_field,'String'));
2517    num1_civ1=ref_i-floor(index_civ1/2)*ones(size(ref_i));% set of first image numbers
2518    num2_civ1=ref_i+ceil(index_civ1/2)*ones(size(ref_i));
2519    num_a_civ1=ref_j;
2520    num_b_civ1=ref_j;
2521    num1_civ2=ref_i-floor(index_civ2/2)*ones(size(ref_i));
2522    num2_civ2=ref_i+ceil(index_civ2/2)*ones(size(ref_i));
2523    num_a_civ2=ref_j;
2524    num_b_civ2=ref_j;   
2525   
2526    % adjust the first and last field number
2527    lastfield=str2double(get(handles.nb_field,'String'));
2528    if isnan(lastfield)
2529        indsel=find((num1_civ1 >= 1)&(num1_civ2 >= 1));
2530    else
2531        indsel=find((num2_civ1 <= lastfield)&(num2_civ2 <= lastfield)&(num1_civ1 >= 1)&(num1_civ2 >= 1));
2532    end
2533    if length(indsel)>=1
2534        firstind=indsel(1);
2535        lastind=indsel(end);
2536        set(handles.first_i,'String',num2str(ref_i(firstind)))%update the display of first and last fields
2537        set(handles.last_i,'String',num2str(ref_i(lastind)))
2538        ref_i=ref_i(indsel);
2539        num1_civ1=num1_civ1(indsel);
2540        num1_civ2=num1_civ2(indsel);
2541        num2_civ1=num2_civ1(indsel);
2542        num2_civ2=num2_civ2(indsel);
2543    end
2544elseif isequal (mode,'series(Dj)')
2545    lastfield_j=str2double(get(handles.nb_field2,'String'));
2546    num1_civ1=ref_i;% set of first image numbers
2547    num2_civ1=ref_i;
2548    num_a_civ1=ref_j-floor(index_civ1/2)*ones(size(ref_j));
2549    num_b_civ1=ref_j+ceil(index_civ1/2)*ones(size(ref_j));
2550    num1_civ2=ref_i;
2551    num2_civ2=ref_i;
2552    num_a_civ2=ref_j-floor(index_civ2/2)*ones(size(ref_j));
2553    num_b_civ2=ref_j+ceil(index_civ2/2)*ones(size(ref_j));
2554    % adjust the first and last field number
2555    if isnan(lastfield_j)
2556        indsel=find((num_a_civ1 >= 1)&(num_a_civ2 >= 1));
2557    else
2558        indsel=find((num_b_civ1 <= lastfield_j)&(num_b_civ2 <= lastfield_j)&(num_a_civ1 >= 1)&(num_a_civ2 >= 1));
2559    end
2560    if length(indsel)>=1
2561        firstind=indsel(1);
2562        lastind=indsel(end);
2563        set(handles.first_j,'String',num2str(ref_j(firstind)))%update the display of first and last fields
2564        set(handles.last_j,'String',num2str(ref_j(lastind)))
2565        ref_j=ref_j(indsel);
2566        num_a_civ1=num_a_civ1(indsel);
2567        num_b_civ1=num_b_civ1(indsel);
2568        num_a_civ2=num_a_civ2(indsel);
2569        num_b_civ2=num_b_civ2(indsel);
2570    end
2571elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)
2572    displ_num=get(handles.ListPairCiv1,'UserData');
2573    num1_civ1=ref_i;
2574    num2_civ1=ref_i;
2575    num_a_civ1=displ_num(1,index_civ1);
2576    num_b_civ1=displ_num(2,index_civ1);
2577    num1_civ2=ref_i;
2578    num2_civ2=ref_i;
2579    num_a_civ2=displ_num(1,index_civ2);
2580    num_b_civ2=displ_num(2,index_civ2);
2581elseif isequal(mode,'displacement')
2582    num1_civ1=ref_i;
2583    num2_civ1=ref_i;
2584    num_a_civ1=ref_j;
2585    num_b_civ1=ref_j;
2586    num1_civ2=ref_i;
2587    num2_civ2=ref_i;
2588    num_a_civ2=ref_j;
2589    num_b_civ2=ref_j;
2590end
2591
2592%------------------------------------------------------------------------
2593% --- Executes on button press in ListCompareMode.
2594function ListCompareMode_Callback(hObject, eventdata, handles)
2595%------------------------------------------------------------------------
2596test=get(handles.ListCompareMode,'Value');
2597if test==2 || test==3 % case 'displacement' or 'stereo PIV'
2598    filebase=get(handles.RootName,'String');
2599    browse=get(handles.RootName,'Userdata');
2600    browse.nom_type_ima1=browse.nom_type_ima;
2601    set(handles.RootName,'UserData',browse);
2602    set(handles.sub_txt,'Visible','on')
2603    set(handles.RootName_1,'Visible','On');%mkes the second file input window visible
2604    mode_store=get(handles.ListPairMode,'String');%get the present 'mode'
2605    set(handles.ListCompareMode,'UserData',mode_store);%store the mode display
2606    set(handles.ListPairMode,'Visible','off')
2607    if test==2
2608        set(handles.ListPairMode,'Visible','off')
2609        set(handles.ListPairMode,'Value',1) % mode 'civX' selected by default
2610    else
2611        set(handles.ListPairMode,'Visible','on')
2612        set(handles.ListPairMode,'Value',3) % mode 'Matlab' selected for stereo
2613    end
2614   
2615    %% menuopen an image file with the browser
2616    ind_opening=1;%default
2617    browse.incr_pair=[0 0]; %default
2618    oldfile=get(handles.RootName,'String');
2619     menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)';
2620       '*.xml',  '.xml files '; ...
2621        '*.civ',  '.civ files '; ...
2622        '*.png','.png image files'; ...
2623        '*.jpg',' jpeg image files'; ...
2624        '*.tif','.tif image files'; ...
2625        '*.avi;*.AVI','.avi movie files'; ...
2626        '*.nc','.netcdf files'; ...
2627        '*.*',  'All Files (*.*)'};
2628    [FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file of the second series',oldfile);
2629    fileinput=[PathName FileName];%complete file name
2630    sizf=size(fileinput);
2631    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
2632    [path,name,ext]=fileparts(fileinput);
2633    [path1]=fileparts(filebase);
2634    if isunix
2635        [status,path]=system(['readlink ' path]);
2636        [status,path1]=system(['readlink ' path1]);% look for the true path in case of symbolic paths
2637    end
2638    if ~strcmp(path1,path)
2639        msgbox_uvmat('ERROR','The second image series must be in the same directory as the first one')
2640        return
2641     end
2642%     set(handles.RootName_1,'String',name);
2643    %[RootPath,RootFile,field_count,str2,str_a,str_b,xx,nom_type,SubDir]=name2display(name);
2644    [tild,tild,RootFile,tild,tild,tild,tild,tild,nom_type]=fileparts_uvmat(name);
2645    set(handles.RootName_1,'String',RootFile);
2646    browse=get(handles.RootName,'UserData');
2647    browse.nom_type_ima_1=nom_type;
2648    set(handles.RootName,'UserData',browse)
2649   
2650    %check image extension
2651    if ~strcmp(ext,get(handles.ImaExt,'String'))
2652        msgbox_uvmat('ERROR','The second image series must have the same extension name as the first one')
2653        return
2654    end
2655   
2656    %% check coincidence of image sizes
2657%     ref_i=get(handles.ref_i,'string');
2658%     ref_j=get(handles.ref_j,'string');
2659%     [filecell,num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2,nom_type_nc]=set_civ_filenames(handles,ref_i,ref_j,[1 0 0 0 0 0]);
2660%     A=imread(filecell.ima1.checkciv1{1});
2661%     A_1=imread(fileinput);
2662%     npxy=size(A);
2663%     npxy_1=size(A_1);
2664%     if ~isequal(size(A),size(A_1))
2665%         msgbox_uvmat('ERROR','The two input image series do not have the same size')
2666%         return
2667%     end
2668else
2669    set(handles.ListPairMode,'Visible','on')
2670    set(handles.RootName_1,'Visible','Off');
2671    set(handles.sub_txt,'Visible','off')
2672    set(handles.RootName_1,'String',[]);
2673    mode_store=get(handles.ListCompareMode,'UserData');
2674    set(handles.ListPairMode,'Value',1)
2675    set(handles.ListPairMode,'String',mode_store)
2676%     set(handles.test_stereo1,'Value',0)
2677    set(handles.CheckStereo,'Value',0)
2678    set(handles.ListPairMode,'Value',1) % mode 'civX' selected by default
2679end
2680if test==3 && get(handles.CheckPatch1,'Value')
2681    set(handles.CheckStereo,'Visible','on')
2682else
2683    set(handles.CheckStereo,'Visible','off')
2684end
2685if test==3 && get(handles.CheckPatch2,'Value')
2686    set(handles.CheckStereo,'Visible','on')
2687else
2688    set(handles.CheckStereo,'Visible','off')
2689end
2690ListPairMode_Callback(hObject, eventdata, handles)
2691
2692
2693%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2694% Callbacks in the uipanel Pair Indices
2695%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2696%------------------------------------------------------------------------
2697% --- Executes on button press in ListPairMode.
2698function ListPairMode_Callback(hObject, eventdata, handles)
2699%------------------------------------------------------------------------
2700compare_list=get(handles.ListCompareMode,'String');
2701val=get(handles.ListCompareMode,'Value');
2702compare=compare_list{val};
2703if strcmp(compare,'displacement')
2704    mode='displacement';
2705else
2706    mode_list=get(handles.ListPairMode,'String');
2707    if ischar(mode_list)
2708        mode_list={mode_list};
2709    end
2710    mode_value=get(handles.ListPairMode,'Value');
2711    mode=mode_list{mode_value};
2712end
2713displ_num=[];%default
2714ref_i=str2double(get(handles.ref_i,'String'));
2715% last_i=str2num(get(handles.last_i,'String'));
2716time=get(handles.ImaDoc,'UserData'); %get the set of times
2717TimeUnit=get(handles.TimeUnit,'String');
2718checkframe=strcmp(TimeUnit,'frame');
2719siztime=size(time);
2720nbfield=siztime(1)-1;
2721nbfield2=siztime(2)-1;
2722indchosen=1;  %%first pair selected by default
2723%displ_num used to define the indices of the civ pairs
2724% in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices
2725% are relative to the reference indices ref_i and ref_j respectively.
2726if isequal(mode,'pair j1-j2')%| isequal(mode,'st_pair j1-j2')
2727
2728    dt=1;
2729    displ='';
2730    index=0;
2731    numlist_a=[];
2732    numlist_B=[];
2733    %get all the time intervals in bursts
2734    displ_dt=1;%default
2735    nbfield2=min(nbfield2,10);%limitate the number of pairs to 10x10
2736    for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'pair j1-j2' mode
2737        for numod_b=(numod_a+1):nbfield2
2738            index=index+1;
2739            numlist_a(index)=numod_a;
2740            numlist_b(index)=numod_b;
2741            if size(time,2)>1 && ~checkframe
2742                dt(numod_a,numod_b)=time(ref_i+1,numod_b+1)-time(ref_i+1,numod_a+1);%first time interval dt
2743                displ_dt(index)=dt(numod_a,numod_b);
2744            else
2745                displ_dt(index)=1;
2746            end
2747        end
2748    end
2749    [dtsort,indsort]=sort(displ_dt);
2750    if ~isempty(numlist_a)
2751        displ_num(1,:)=numlist_a(indsort);
2752        displ_num(2,:)=numlist_b(indsort);
2753    end
2754    displ_num(3,:)=0;
2755    displ_num(4,:)=0;
2756    set(handles.jtext,'Visible','Off')
2757    set(handles.first_j,'Visible','Off')
2758    set(handles.last_j,'Visible','Off')
2759    set(handles.incr_j,'Visible','Off')
2760    set(handles.nb_field2,'Visible','Off')
2761    set(handles.ref_j,'Visible','Off')
2762elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)')
2763    index=1:200;
2764    displ_num(1,index)=-floor(index/2);
2765    displ_num(2,index)=ceil(index/2);
2766    displ_num(3:4,index)=zeros(2,200);
2767%     for index=1:min(nbfield2-1,200)
2768%         displ_num(1,index)=-floor(index/2);
2769%         displ_num(2,index)=ceil(index/2);
2770%         displ_num(3,index)=0;
2771%         displ_num(4,index)=0;
2772%     end
2773    set(handles.jtext,'Visible','On')
2774    set(handles.first_j,'Visible','On')
2775    set(handles.last_j,'Visible','On')
2776    set(handles.incr_j,'Visible','On')
2777    set(handles.nb_field2,'Visible','On')
2778    set(handles.ref_j,'Visible','On')
2779%     if nbfield > 1
2780%         set(handles.itext,'Visible','On')
2781%         set(handles.first_i,'Visible','On')
2782%         set(handles.last_i,'Visible','On')
2783%         set(handles.incr_i,'Visible','On')
2784%         set(handles.nb_field,'Visible','On')
2785%         set(handles.ref_i,'Visible','On')
2786%     else
2787%         set(handles.itext,'Visible','Off')
2788%         set(handles.first_i,'Visible','Off')
2789%         set(handles.last_i,'Visible','Off')
2790%         set(handles.incr_i,'Visible','Off')
2791%         set(handles.nb_field,'Visible','Off')
2792%         set(handles.ref_i,'Visible','Off')
2793%     end
2794elseif isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)')
2795    index=1:200;
2796    displ_num(1:2,index)=zeros(2,200);
2797    displ_num(3,index)=-floor(index/2);
2798    displ_num(4,index)=ceil(index/2);
2799%     for index=1:200%min(nbfield-1,200)
2800%         displ_num(1,index)=0;
2801%         displ_num(2,index)=0;
2802%         displ_num(3,index)=-floor(index/2);
2803%         displ_num(4,index)=ceil(index/2);
2804%     end
2805    set(handles.itext,'Visible','On')
2806    set(handles.first_i,'Visible','On')
2807    set(handles.last_i,'Visible','On')
2808    set(handles.incr_i,'Visible','On')
2809    set(handles.nb_field,'Visible','On')
2810    set(handles.ref_i,'Visible','On')
2811    if nbfield2 > 1
2812        set(handles.jtext,'Visible','On')
2813        set(handles.first_j,'Visible','On')
2814        set(handles.last_j,'Visible','On')
2815        set(handles.incr_j,'Visible','On')
2816        set(handles.nb_field2,'Visible','On')
2817        set(handles.ref_j,'Visible','On')
2818    else
2819        set(handles.jtext,'Visible','Off')
2820        set(handles.first_j,'Visible','Off')
2821        set(handles.last_j,'Visible','Off')
2822        set(handles.incr_j,'Visible','Off')
2823        set(handles.nb_field2,'Visible','Off')
2824        set(handles.ref_j,'Visible','Off')
2825    end
2826elseif isequal(mode,'displacement')%the pairs have the same indices
2827    displ_num(1,1)=0;
2828    displ_num(2,1)=0;
2829    displ_num(3,1)=0;
2830    displ_num(4,1)=0;
2831    if nbfield > 1 || nbfield==0
2832        set(handles.itext,'Visible','On')
2833        set(handles.first_i,'Visible','On')
2834        set(handles.last_i,'Visible','On')
2835        set(handles.incr_i,'Visible','On')
2836        set(handles.nb_field,'Visible','On')
2837        set(handles.ref_i,'Visible','On')
2838    else
2839        set(handles.itext,'Visible','Off')
2840        set(handles.first_i,'Visible','Off')
2841        set(handles.last_i,'Visible','Off')
2842        set(handles.incr_i,'Visible','Off')
2843        set(handles.nb_field,'Visible','Off')
2844        set(handles.ref_i,'Visible','Off')
2845    end
2846    if nbfield2 > 1
2847        set(handles.jtext,'Visible','On')
2848        set(handles.first_j,'Visible','On')
2849        set(handles.last_j,'Visible','On')
2850        set(handles.incr_j,'Visible','On')
2851        set(handles.nb_field2,'Visible','On')
2852        set(handles.ref_j,'Visible','On')
2853    else
2854        set(handles.jtext,'Visible','Off')
2855        set(handles.first_j,'Visible','Off')
2856        set(handles.last_j,'Visible','Off')
2857        set(handles.incr_j,'Visible','Off')
2858        set(handles.nb_field2,'Visible','Off')
2859        set(handles.ref_j,'Visible','Off')
2860    end
2861end
2862set(handles.ListPairCiv1,'UserData',displ_num);
2863find_netcpair_civ1( handles)
2864find_netcpair_civ2(handles)
2865browse=get(handles.RootName,'UserData');
2866
2867%------------------------------------------------------------------------
2868% --- Executes on selection change in ListPairCiv1.
2869function ListPairCiv1_Callback(hObject, eventdata, handles)
2870%------------------------------------------------------------------------
2871%reproduce by default the chosen pair in the checkciv2 menu
2872list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
2873index_pair=get(handles.ListPairCiv1,'Value');
2874displ_num=get(handles.ListPairCiv1,'UserData');
2875% num_a=displ_num(1,index_pair);
2876% num_b=displ_num(2,index_pair);
2877list_pair2=get(handles.ListPairCiv2,'String');%get the menu of image pairs
2878if index_pair<=length(list_pair2)
2879    set(handles.ListPairCiv2,'Value',index_pair);
2880end
2881
2882%update first_i and last_i according to the chosen image pairs
2883mode_list=get(handles.ListPairMode,'String');
2884mode_value=get(handles.ListPairMode,'Value');
2885mode=mode_list{mode_value};
2886if isequal(mode,'series(Di)')
2887    first_i=str2double(get(handles.first_i,'String'));
2888    last_i=str2double(get(handles.last_i,'String'));
2889    incr_i=str2double(get(handles.incr_i,'String'));
2890    num1=first_i:incr_i:last_i;
2891    lastfield=str2double(get(handles.nb_field,'String'));
2892    if ~isnan(lastfield)
2893        test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ...
2894            (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield);
2895        num1=num1(test_find);
2896    end
2897    set(handles.first_i,'String',num2str(num1(1)));
2898    set(handles.last_i,'String',num2str(num1(end)));
2899elseif isequal(mode,'series(Dj)')
2900    first_j=str2double(get(handles.first_j,'String'));
2901    last_j=str2double(get(handles.last_j,'String'));
2902    incr_j=str2double(get(handles.incr_j,'String'));
2903    num_j=first_j:incr_j:last_j;
2904    lastfield2=str2double(get(handles.nb_field2,'String'));
2905    if ~isnan(lastfield2)
2906        test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
2907            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2);
2908        num1=num_j(test_find);
2909    end
2910    set(handles.first_j,'String',num2str(num1(1)));
2911    set(handles.last_j,'String',num2str(num1(end)));
2912end
2913
2914%------------------------------------------------------------------------
2915% --- Executes on selection change in ListPairCiv2.
2916function ListPairCiv2_Callback(hObject, eventdata, handles)
2917%------------------------------------------------------------------------
2918index_pair=get(handles.ListPairCiv2,'Value');%get the selected position index in the menu
2919
2920%update first_i and last_i according to the chosen image pairs
2921mode_list=get(handles.ListPairMode,'String');
2922mode_value=get(handles.ListPairMode,'Value');
2923mode=mode_list{mode_value};
2924if isequal(mode,'series(Di)')
2925    first_i=str2double(get(handles.first_i,'String'));
2926    last_i=str2double(get(handles.last_i,'String'));
2927    incr_i=str2double(get(handles.incr_i,'String'));
2928    num1=first_i:incr_i:last_i;
2929    lastfield=str2double(get(handles.nb_field,'String'));
2930    if ~isnan(lastfield)
2931        test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ...
2932            (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield);
2933        num1=num1(test_find);
2934    end
2935    set(handles.first_i,'String',num2str(num1(1)));
2936    set(handles.last_i,'String',num2str(num1(end)));
2937elseif isequal(mode,'series(Dj)')
2938    first_j=str2double(get(handles.first_j,'String'));
2939    last_j=str2double(get(handles.last_j,'String'));
2940    incr_j=str2double(get(handles.incr_j,'String'));
2941    num_j=first_j:incr_j:last_j;
2942    lastfield2=str2double(get(handles.nb_field2,'String'));
2943    if ~isnan(lastfield2)
2944        test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
2945            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2);
2946        num1=num_j(test_find);
2947    end
2948    set(handles.first_j,'String',num2str(num1(1)));
2949    set(handles.last_j,'String',num2str(num1(end)));
2950end
2951
2952%------------------------------------------------------------------------
2953function ref_i_Callback(hObject, eventdata, handles)
2954%------------------------------------------------------------------------
2955mode_list=get(handles.ListPairMode,'String');
2956mode_value=get(handles.ListPairMode,'Value');
2957mode=mode_list{mode_value};
2958find_netcpair_civ1(handles);% update the menu of pairs depending on the available netcdf files
2959if isequal(mode,'series(Di)') || ...% we do patch2 only
2960        (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
2961    find_netcpair_civ2( handles);
2962end
2963
2964%------------------------------------------------------------------------
2965function ref_j_Callback(hObject, eventdata, handles)
2966%------------------------------------------------------------------------
2967mode_list=get(handles.ListPairMode,'String');
2968mode_value=get(handles.ListPairMode,'Value');
2969mode=mode_list{mode_value};
2970if isequal(get(handles.CheckCiv1,'Value'),0)|| isequal(mode,'series(Dj)')
2971    find_netcpair_civ1(handles);% update the menu of pairs depending on the available netcdf files
2972end
2973if isequal(mode,'series(Dj)') || ...
2974        (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
2975    find_netcpair_civ2(handles);
2976end
2977%
2978%------------------------------------------------------------------------
2979% determine the menu for checkciv1 pairs depending on existing netcdf file at the middle of
2980% the field series set by first_i, incr, last_i
2981function find_netcpair_civ1(handles)
2982%------------------------------------------------------------------------
2983set(gcf,'Pointer','watch')
2984%nomenclature types
2985filebase=get(handles.RootName,'String');
2986[filepath,Nme,ext_dir]=fileparts(filebase);
2987browse=get(handles.RootName,'UserData');
2988compare_list=get(handles.ListCompareMode,'String');
2989val=get(handles.ListCompareMode,'Value');
2990compare=compare_list{val};
2991if strcmp(compare,'displacement')
2992    mode='displacement';
2993else
2994    mode_list=get(handles.ListPairMode,'String');
2995    mode_value=get(handles.ListPairMode,'Value');
2996    if isempty(mode_list)
2997        return
2998    end
2999    mode=mode_list{mode_value};
3000end
3001
3002% nomenclature type of the .nc files
3003nom_type_ima=[];%default
3004if isfield(browse,'nom_type_ima')
3005    nom_type_ima=browse.nom_type_ima;
3006end
3007
3008%determine nom_type_nc:
3009nom_type_nc=[];%default
3010if isfield(browse,'nom_type_nc')
3011    nom_type_nc=browse.nom_type_nc;
3012end
3013if isempty(nom_type_nc)
3014    [nom_type_nc]=nomtype2pair(nom_type_ima,isequal(mode,'series(Di)'),isequal(mode,'series(Dj)'));
3015end
3016browse.nom_type_nc=nom_type_nc;
3017set(handles.RootName,'UserData',browse)
3018
3019%reads .nc subdirectoy and image numbers from the interface
3020subdir_civ1=get(handles.txt_SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf data
3021ref_i=str2double(get(handles.ref_i,'String'));
3022if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
3023    ref_j=0;
3024else
3025    ref_j=str2double(get(handles.ref_j,'String'));
3026end
3027time=get(handles.ImaDoc,'UserData');%get the set of times
3028% if isempty(time)
3029%     time=[0 1];
3030% end
3031TimeUnit=get(handles.TimeUnit,'String');
3032checkframe=strcmp(TimeUnit,'frame');
3033
3034displ_num=get(handles.ListPairCiv1,'UserData');
3035
3036%eliminate the first pairs inconsistent with the position
3037if isempty(displ_num)
3038    nbpair=0;
3039else
3040    nbpair=length(displ_num(1,:));%nbre of displayed pairs
3041    if  isequal(mode,'series(Di)')  %| isequal(mode,'st_series(Di)')
3042        nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index
3043    elseif  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
3044        nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index
3045    end
3046end
3047nbpair=min(200,nbpair);%limit the number of displayed pairs to 200
3048
3049%look for existing processed pairs involving the field at the middle of the series if checkciv1 will not
3050% be performed, while the result is needed for next steps.
3051displ_pair={''};
3052select=ones(size(1:nbpair));%flag for displayed pairs =1 for display
3053testpair=0;
3054
3055%% case with no Civ1 operation, netcdf files need to exist for reading
3056if ~get(handles.CheckCiv1,'Value') %
3057    if ~exist(fullfile(filepath,subdir_civ1,ext_dir),'dir')
3058        msgbox_uvmat('ERROR',['no civ1 file available: subdirectory ' subdir_civ1 ' does not exist']);
3059        set(handles.ListPairCiv1,'String',{});
3060        return
3061    end
3062    for ipair=1:nbpair
3063        filename=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,...
3064            ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1);
3065        select(ipair)=exist(filename,'file')==2;% put flag to 0 if the file does not exist
3066    end   
3067    % case of no displayed pair
3068    if isequal(select,zeros(size(1:nbpair)))
3069        if isfield(browse,'incr_pair') && ~isequal(browse.incr_pair,[0 0])
3070            num_i1=ref_i-floor(browse.incr_pair(1)/2);
3071            num_i2=ref_i+ceil(browse.incr_pair(1)/2);
3072            num_j1=ref_j-floor(browse.incr_pair(2)/2);
3073            num_j2=ref_j+ceil(browse.incr_pair(2)/2);
3074            filename=name_generator(filebase,num_i1,num_j1,'.nc',nom_type_nc,1,num_i2,num_j2,subdir_civ1);
3075            select(1)=exist(filename,'file')==2;
3076            testpair=1;
3077        else
3078            if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
3079                msgbox_uvmat('ERROR',['no civ1 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ1]);
3080            else
3081                msgbox_uvmat('ERROR',['no civ1 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ1]);
3082            end
3083            set(handles.ListPairCiv1,'String',{''});
3084            %COMPLETER CAS STEREO
3085            return
3086        end
3087    end
3088end
3089
3090%% determine the menu display in .ListPairCiv1
3091% the menu depends on the mode defined in ListPairMode_callback through the array displ_num:
3092% displ_num(1,:)=indices j1
3093% displ_num(2,:)=indices j2
3094% displ_num(3,:)=indices i1
3095% displ_num(4,:)=indices i2
3096% in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices
3097% are relative to the reference indices ref_i and ref_j respectively.
3098if isequal(mode,'series(Di)')
3099    if testpair
3100        displ_pair{1}=['Di= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
3101    else
3102        for ipair=1:nbpair
3103            if select(ipair)
3104                displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
3105                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
3106                    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
3107                else
3108                    dt=1;
3109                end
3110                 displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
3111            else
3112                displ_pair{ipair}='...'; %pair not displayed in the menu
3113            end
3114        end
3115    end
3116elseif isequal(mode,'series(Dj)')
3117    if testpair
3118        displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
3119    else
3120        for ipair=1:nbpair
3121            if select(ipair)
3122                displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
3123                if ~checkframe && size(time,1)>=ref_i+1+displ_num(4,ipair) && size(time,2)>=ref_j+1+displ_num(2,ipair)
3124                    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
3125                    displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
3126                end
3127            else
3128                displ_pair{ipair}='...'; %pair not displayed in the menu
3129            end
3130        end
3131    end
3132elseif isequal(mode,'pair j1-j2')%case of pairs
3133    for ipair=1:nbpair
3134        if select(ipair)
3135            if ~checkframe && size(time,2)>1
3136            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
3137            else % time set by default to i index
3138                dt=1;
3139            end
3140            displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ...
3141                ' :dt= ' num2str(dt*1000)];
3142        else
3143            displ_pair{ipair}='...'; %pair not displayed in the menu
3144        end
3145    end
3146elseif isequal(mode,'displacement')
3147    displ_pair={'Di=Dj=0'};
3148end
3149set(handles.ListPairCiv1,'String',displ_pair');
3150
3151%% determine the default selection in the pair menu
3152ichoice=find(select,1);% index of selected pair
3153if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
3154initial=get(handles.ListPairCiv1,'Value');%initial choice of pair
3155if initial>nbpair || (numel(select)>=initial && ~isequal(select(initial),1))
3156    set(handles.ListPairCiv1,'Value',ichoice);% first valid pair proposed by default in the menu
3157end
3158initial=get(handles.ListPairCiv2,'Value');
3159if initial>length(displ_pair')%|~isequal(select(initial),1)
3160    if ichoice <= length(displ_pair')
3161        set(handles.ListPairCiv2,'Value',ichoice);% same pair proposed by default for civ2
3162    else
3163        set(handles.ListPairCiv2,'Value',1);% same pair proposed by default for civ2
3164    end
3165end
3166set(handles.ListPairCiv2,'String',displ_pair');
3167set(gcf,'Pointer','arrow')
3168
3169%------------------------------------------------------------------------
3170% determine the menu for checkciv2 pairs depending on the existing netcdf file at the
3171%middle of the series set by first_i, incr, last_i
3172function find_netcpair_civ2(handles)
3173%------------------------------------------------------------------------
3174set(gcf,'Pointer','watch')
3175%nomenclature types
3176filebase=get(handles.RootName,'String');
3177[filepath,Nme,ext_dir]=fileparts(filebase);
3178browse=get(handles.RootName,'UserData');
3179compare_list=get(handles.ListCompareMode,'String');
3180val=get(handles.ListCompareMode,'Value');
3181compare=compare_list{val};
3182if strcmp(compare,'displacement')
3183    mode='displacement';
3184else
3185    mode_list=get(handles.ListPairMode,'String');
3186    if isempty(mode_list)
3187        msgbox_uvmat('ERROR','please enter an input image or netcdf file')
3188        return
3189    end
3190    mode_value=get(handles.ListPairMode,'Value');
3191    mode=mode_list{mode_value};
3192end
3193
3194% nomenclature type of the .nc files
3195nom_type_ima='ima_num';%default
3196if isfield(browse,'nom_type_ima')
3197    nom_type_ima=browse.nom_type_ima;
3198end
3199nom_type_nc='_1-2';%default
3200if isfield(browse,'nom_type_nc')
3201    nom_type_nc=browse.nom_type_nc;
3202end
3203if isequal(nom_type_ima,'png_old') || isequal(nom_type_ima,'netc_old')|| isequal(nom_type_ima,'raw_SMD')|| isequal(nom_type_nc,'netc_old')
3204    nom_type_nc='netc_old';%nom_type for the netcdf files
3205elseif isequal(nom_type_ima,'none')||isequal(nom_type_nc,'none')
3206    nom_type_nc='none';
3207elseif isequal(nom_type_ima,'avi')||isequal(nom_type_ima,'_i')||isequal(nom_type_ima,'ima_num')||isequal(nom_type_nc,'_1-2')
3208    nom_type_nc='_1-2';
3209else
3210    if  isequal(mode,'series(Di)')%|isequal(mode,'st_series(Di)')
3211        nom_type_nc='_1-2_1'; % PIV in volume
3212    else
3213        nom_type_nc='_1_1-2';
3214    end
3215end
3216browse.nom_type_nc=nom_type_nc;
3217set(handles.RootName,'UserData',browse)
3218
3219%reads .nc subdirectory and image numbers from the interface
3220subdir_civ1=get(handles.txt_SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf data
3221subdir_civ2=get(handles.txt_SubdirCiv2,'String');%subdirectory subdir_civ2 for the netcdf data
3222ref_i=str2double(get(handles.ref_i,'String'));
3223if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
3224    ref_j=0;
3225else
3226    ref_j=str2double(get(handles.ref_j,'String'));
3227end
3228time=get(handles.ImaDoc,'UserData'); %get the set of times
3229TimeUnit=get(handles.TimeUnit,'String');
3230checkframe=strcmp(TimeUnit,'frame');
3231% if isempty(time)
3232%     time=[0 1];%default
3233% end
3234displ_num=get(handles.ListPairCiv1,'UserData');
3235
3236%eliminate the first pairs inconsistent with the position
3237if isempty(displ_num)
3238    nbpair=0;
3239else
3240    nbpair=length(displ_num(1,:));%nbre of displayed pairs
3241    if  isequal(mode,'series(Di)')% | isequal(mode,'st_series(Di)')
3242        nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index
3243    elseif  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
3244        nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index
3245    end
3246end
3247nbpair=min(200,nbpair);%limit the number of displayed pairs to 200
3248
3249%% look for existing processed pairs at the reference indices if Civ1 will not
3250% be performed, while the result is needed for next steps.
3251displ_pair={''}; %default
3252select=ones(size(1:nbpair));%default =1 for numbers of displayed pairs
3253if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
3254    if ~exist(fullfile(filepath,subdir_civ2,ext_dir),'dir')
3255        errordlg(['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist'])
3256        set(handles.ListPairCiv2,'Value',1);
3257        set(handles.ListPairCiv2,'String',{''});
3258        return
3259    end
3260    for ipair=1:nbpair
3261        filename=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,...
3262            ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1);
3263        select(ipair)=exist(filename,'file')==2;
3264    end
3265    if  isequal(select,zeros(size(1:nbpair)))
3266        if isfield(browse,'incr_pair')
3267            num_i1=ref_i-floor(browse.incr_pair(1)/2);
3268            num_i2=ref_i+floor((browse.incr_pair(1)+1)/2);
3269            num_j1=ref_j-floor(browse.incr_pair(2)/2);
3270            num_j2=ref_j+floor((browse.incr_pair(2)+1)/2);
3271            filename=name_generator(filebase,num_i1,num_j1,'.nc',nom_type_nc,1,num_i2,num_j2,subdir_civ2);
3272            select(1)=exist(filename,'file')==2;
3273        else
3274            if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
3275                errordlg(['no civ2 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ2])
3276            else
3277                errordlg(['no civ2 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ2])
3278            end
3279            set(handles.ListPairCiv2,'Value',1);
3280            set(handles.ListPairCiv2,'String',{''});
3281            return
3282        end
3283    end
3284end
3285if isequal(mode,'series(Di)')
3286    for ipair=1:nbpair
3287        if select(ipair)
3288            displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
3289            if  ~checkframe && size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
3290                dt=time(ref_i+displ_num(4,ipair)+1,ref_j+displ_num(2,ipair)+1)-time(ref_i+displ_num(3,ipair)+1,ref_j+displ_num(1,ipair)+1);%time interval dt
3291                displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
3292            end
3293        else
3294            displ_pair{ipair}='...'; %pair not displayed in the menu
3295        end
3296    end
3297elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)') % series on the j index
3298    for ipair=1:nbpair
3299        if select(ipair)
3300            displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
3301            if ~checkframe && size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)&& displ_num(1,ipair)>=1 && displ_num(2,ipair)>=1
3302                dt=time(ref_i+displ_num(4,ipair)+1,ref_j+displ_num(2,ipair)+1)-time(ref_i+displ_num(3,ipair)+1,ref_j+displ_num(1,ipair)+1);%time interval dt
3303            else
3304                dt=1;
3305            end
3306                displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
3307        else
3308            displ_pair{ipair}='...'; %pair not displayed in the menu
3309        end
3310    end
3311elseif isequal(mode,'pair j1-j2')% | isequal(mode,'st_pair j1-j2') %case of pairs
3312    for ipair=1:nbpair
3313        if select(ipair)
3314            if  ~checkframe && size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair) && displ_num(1,ipair)>=1 && displ_num(2,ipair)>=1
3315            dt=time(ref_i+displ_num(4,ipair)+1,displ_num(2,ipair)+1)-time(ref_i+displ_num(3,ipair)+1,displ_num(1,ipair)+1);%time interval dt
3316            else
3317                dt=1;
3318            end
3319            displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair)+1,nom_type_ima) '-' num2stra(displ_num(2,ipair)+1,nom_type_ima) ...
3320                ' :dt= ' num2str(dt*1000)];
3321               
3322        else
3323            displ_pair{ipair}='...'; %pair not displayed in the menu
3324        end
3325    end
3326elseif isequal(mode,'displacement')
3327    displ_pair={'Di=Dj=0'};
3328end
3329val=get(handles.ListPairCiv2,'Value');
3330ichoice=find(select,1);
3331if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
3332if get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0
3333    val=ichoice;% first valid pair proposed by default in the menu
3334end
3335if val>length(displ_pair')
3336    set(handles.ListPairCiv2,'Value',1);% first valid pair proposed by default in the menu
3337else
3338    set(handles.ListPairCiv2,'Value',val);
3339end
3340set(handles.ListPairCiv2,'String',displ_pair');
3341set(gcf,'Pointer','arrow')
3342
3343%-------------------------------------------------------------------
3344% ---
3345function closeview_field(gcbo,eventdata)
3346hview_field=findobj(allchild(0),'tag','view_field');% look for view_field   
3347    if ~isempty(hview_field)
3348        delete(hview_field)
3349    end
3350   
3351   
3352%------------------------------------------------------------------------   
3353% call 'view_field.fig' to display the  field selected in the list of 'status'
3354function open_view_field(hObject, eventdata)
3355%------------------------------------------------------------------------
3356list=get(hObject,'String');
3357index=get(hObject,'Value');
3358rootroot=get(hObject,'UserData');
3359filename=list{index};
3360ind_dot=strfind(filename,'...');
3361filename=filename(1:ind_dot-1);
3362filename=fullfile(rootroot,filename);
3363delete(get(hObject,'parent'))%delete the display figure to stop the check process
3364if exist(filename,'file')%visualise the vel field if it exists
3365    uvmat(filename)
3366    set(gcbo,'Value',1)
3367end
3368
3369%------------------------------------------------------------------------   
3370% launched by pressing OK on the status figure
3371function close_GUI(hObject, eventdata)
3372%------------------------------------------------------------------------
3373    delete(gcbf)
3374   
3375%------------------------------------------------------------------------   
3376% launched by deleting the status figure
3377function stop_status(hObject, eventdata)
3378%------------------------------------------------------------------------
3379hciv=findobj(allchild(0),'tag','civ');
3380hhciv=guidata(hciv);
3381set(hhciv.status,'value',0) %reset the status uicontrol in the GUI civ
3382set(hhciv.status,'BackgroundColor',[0 1 0])
3383
3384
3385%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3386% Callbacks in the uipanel Reference Indices
3387%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3388%------------------------------------------------------------------------
3389function first_i_Callback(hObject, eventdata, handles)
3390%------------------------------------------------------------------------
3391first_i=str2double(get(handles.first_i,'String'));
3392set(handles.ref_i,'String', num2str(first_i))% reference index for pair dt = first index
3393ref_i_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
3394
3395%------------------------------------------------------------------------
3396function first_j_Callback(hObject, eventdata, handles)
3397%------------------------------------------------------------------------
3398first_j=str2num(get(handles.first_j,'String'));
3399set(handles.ref_j,'String', num2str(first_j))% reference index for pair dt = first index
3400ref_j_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
3401
3402%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3403% Callbacks in the uipanel Civ1
3404%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3405%------------------------------------------------------------------------
3406% --- Executes on button press in SearchRange: determine the search range num_Searchx,num_Searchy
3407function SearchRange_Callback(hObject, eventdata, handles)
3408%------------------------------------------------------------------------
3409%determine pair numbers
3410if strcmp(get(handles.umin,'Visible'),'off')
3411    set(handles.u_title,'Visible','on')
3412    set(handles.v_title,'Visible','on')
3413    set(handles.umin,'Visible','on')
3414    set(handles.umax,'Visible','on')
3415    set(handles.vmin,'Visible','on')
3416    set(handles.vmax,'Visible','on')
3417    set(handles.CoordUnit,'Visible','on')
3418    set(handles.TimeUnit,'Visible','on')
3419    set(handles.slash_title,'Visible','on')
3420    set(handles.min_title,'Visible','on')
3421    set(handles.max_title,'Visible','on')
3422    set(handles.unit_title,'Visible','on')
3423else
3424    get_search_range(hObject, eventdata, handles)
3425end
3426
3427%------------------------------------------------------------------------
3428% ---  determine the search range num_Searchx,num_Searchy and shift
3429function get_search_range(hObject, eventdata, handles)
3430umin=str2double(get(handles.umin,'String'));
3431umax=str2double(get(handles.umax,'String'));
3432vmin=str2double(get(handles.umin,'String'));
3433vmax=str2double(get(handles.vmax,'String'));
3434%switch min_title and max_title in case of error
3435if umax<=umin
3436    umin_old=umin;
3437    umin=umax;
3438    umax=umin_old;
3439    set(handles.umin,'String', num2str(umin))
3440    set(handles.umax,'String', num2str(umax))
3441end
3442if vmax<=vmin
3443    vmin_old=vmin;
3444    vmin=vmax;
3445    vmax=vmin_old;
3446    set(handles.vmin,'String', num2str(vmin))
3447    set(handles.vmax,'String', num2str(vmax))
3448end   
3449if ~(isnan(umin)||isnan(umax)||isnan(vmin)||isnan(vmax))
3450    list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
3451    index=get(handles.ListPairCiv1,'Value');
3452    displ_num=get(handles.ListPairCiv1,'UserData');
3453    time=get(handles.ImaDoc,'UserData'); %get the set of times
3454    pxcm_xy=get(handles.SearchRange,'UserData');
3455    pxcmx=pxcm_xy(1);
3456    pxcmy=pxcm_xy(2);
3457    mode_list=get(handles.ListPairMode,'String');
3458    mode_value=get(handles.ListPairMode,'Value');
3459    mode=mode_list{mode_value};
3460    if isequal (mode, 'series(Di)' )
3461        ref_i=str2double(get(handles.ref_i,'String'));
3462        num1=ref_i-floor(index/2);%  first image numbers
3463        num2=ref_i+ceil(index/2);
3464        num_a=1;
3465        num_b=1;
3466    elseif isequal (mode, 'series(Dj)')
3467        num1=1;
3468        num2=1;
3469        ref_j=str2double(get(handles.ref_j,'String'));
3470        num_a=ref_j-floor(index/2);%  first image numbers
3471        num_b=ref_j+ceil(index/2);
3472    elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)
3473        ref_i=str2double(get(handles.ref_i,'String'));
3474        num1=ref_i;
3475        num2=ref_i;
3476        num_a=displ_num(1,index);
3477        num_b=displ_num(2,index);
3478    end
3479    dt=time(num2,num_b)-time(num1,num_a);
3480    ibx=str2double(get(handles.num_Bx,'String'));
3481    iby=str2double(get(handles.num_By,'String'));
3482    umin=dt*pxcmx*umin;
3483    umax=dt*pxcmx*umax;
3484    vmin=dt*pxcmy*vmin;
3485    vmax=dt*pxcmy*vmax;
3486    shiftx=round((umin+umax)/2);
3487    shifty=round((vmin+vmax)/2);
3488    isx=(umax+2-shiftx)*2+ibx;
3489    isx=2*ceil(isx/2)+1;
3490    isy=(vmax+2-shifty)*2+iby;
3491    isy=2*ceil(isy/2)+1;
3492    set(handles.num_Shiftx,'String',num2str(shiftx));
3493    set(handles.num_Shifty,'String',num2str(shifty));
3494    set(handles.num_Searchx,'String',num2str(isx));
3495    set(handles.num_Searchy,'String',num2str(isy));
3496end
3497
3498%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3499% Callbacks in the uipanel Fix1
3500%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3501%------------------------------------------------------------------------
3502% --- Executes on button press in CheckMask.
3503function get_mask_fix1_Callback(hObject, eventdata, handles)
3504%------------------------------------------------------------------------
3505maskval=get(handles.CheckMask,'Value');
3506if isequal(maskval,0)
3507    set(handles.txt_Mask,'String','')
3508else
3509    mask_displ='no mask'; %default
3510    filebase=get(handles.RootName,'String');
3511    [nbslice, flag_mask]=get_mask(filebase,handles);
3512    if isequal(flag_mask,1)
3513        mask_displ=[num2str(nbslice) 'mask'];
3514    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3515        filebase_a=get(handles.RootName_1,'String');
3516        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3517        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3518            mask_displ='no mask';
3519        end
3520    end
3521    if isequal(mask_displ,'no mask')
3522        [FileName, PathName, filterindex] = uigetfile( ...
3523            {'*.png', ' (*.png)';
3524            '*.png',  '.png files '; ...
3525            '*.*', 'All Files (*.*)'}, ...
3526            'Pick a mask file *.png',filebase);
3527        mask_displ=fullfile(PathName,FileName);
3528        if ~exist(mask_displ,'file')
3529            mask_displ='no mask';
3530        end
3531    end
3532    if isequal(mask_displ,'no mask')
3533        set(handles.CheckMask,'Value',0)
3534        set(handles.CheckMask,'Value',0)
3535        set(handles.CheckMask,'Value',0)
3536    else
3537        %set(handles.CheckMask,'Value',1)
3538        set(handles.CheckMask,'Value',1)
3539    end
3540    set(handles.txt_Mask,'String',mask_displ)
3541    set(handles.txt_Mask,'String',mask_displ)
3542    set(handles.txt_Mask,'String',mask_displ)
3543end
3544
3545%------------------------------------------------------------------------
3546% --- Executes on button press in CheckMask: select box for mask option
3547function get_mask_civ2_Callback(hObject, eventdata, handles)
3548%------------------------------------------------------------------------
3549maskval=get(handles.CheckMask,'Value');
3550if isequal(maskval,0)
3551    set(handles.txt_Mask,'String','')
3552else
3553    mask_displ='no mask'; %default
3554    filebase=get(handles.RootName,'String');
3555    [nbslice, flag_mask]=get_mask(filebase,handles);
3556    if isequal(flag_mask,1)
3557        mask_displ=[num2str(nbslice) 'mask'];
3558    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3559        filebase_a=get(handles.RootName_1,'String');
3560        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3561        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3562            mask_displ='no mask';
3563        end
3564    end
3565    if isequal(mask_displ,'no mask')
3566        [FileName, PathName, filterindex] = uigetfile( ...
3567            {'*.png', ' (*.png)';
3568            '*.png',  '.png files '; ...
3569            '*.*', 'All Files (*.*)'}, ...
3570            'Pick a mask file *.png',filebase);
3571        mask_displ=fullfile(PathName,FileName);
3572        if ~exist(mask_displ,'file')
3573            mask_displ='no mask';
3574        end
3575    end
3576    if isequal(mask_displ,'no mask')
3577        set(handles.CheckMask,'Value',0)
3578        set(handles.CheckMask,'Value',0)
3579    else
3580        set(handles.CheckMask,'Value',1)
3581    end
3582    set(handles.txt_Mask,'String',mask_displ)
3583    set(handles.txt_Mask,'String',mask_displ)
3584end
3585
3586%------------------------------------------------------------------------
3587% --- Executes on button press in CheckMask.
3588function get_mask_fix2_Callback(hObject, eventdata, handles)
3589%------------------------------------------------------------------------
3590maskval=get(handles.CheckMask,'Value');
3591if isequal(maskval,0)
3592    set(handles.txt_Mask,'String','')
3593else
3594    mask_displ='no mask'; %default
3595    filebase=get(handles.RootName,'String');
3596    [nbslice, flag_mask]=get_mask(filebase,handles);
3597    if isequal(flag_mask,1)
3598        mask_displ=[num2str(nbslice) 'mask'];
3599    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3600        filebase_a=get(handles.RootName_1,'String');
3601        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3602        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3603            mask_displ='no mask';
3604        end
3605    end
3606    if isequal(mask_displ,'no mask')
3607        [FileName, PathName, filterindex] = uigetfile( ...
3608            {'*.png', ' (*.png)';
3609            '*.png',  '.png files '; ...
3610            '*.*', 'All Files (*.*)'}, ...
3611            'Pick a mask file *.png',filebase);
3612        mask_displ=fullfile(PathName,FileName);
3613        if ~exist(mask_displ,'file')
3614            mask_displ='no mask';
3615        end
3616    end
3617    if isequal(mask_displ,'no mask')
3618        set(handles.CheckMask,'Value',0)
3619    end
3620    set(handles.txt_Mask,'String',mask_displ)
3621end
3622
3623%------------------------------------------------------------------------
3624% --- function called to look for mask files
3625function [nbslice, flag_mask]=get_mask(filebase,handles)
3626%------------------------------------------------------------------------
3627%detect mask files, images with appropriate file base
3628%[filebase '_' xx 'mask'], xx=nbslice
3629%flag_mask=1 indicates detection
3630
3631flag_mask=0;%default
3632nbslice=1;
3633
3634% subdir=get(handles.txt_SubdirCiv1,'String');
3635[Path,Name]=fileparts(filebase);
3636if ~isdir(Path)
3637    msgbox_uvmat('ERROR','no path for input files')
3638    return
3639end
3640% currentdir=pwd;
3641% cd(Path);%move in the dir of the root name filebase
3642maskfiles=dir(fullfile(Path,[Name '_*mask_*.png']));%look for mask files
3643% cd(currentdir);%come back to the current working directory
3644if ~isempty(maskfiles)
3645    %     msgbox_uvmat('ERROR','no mask available, to create it use Tools/Make mask in the upper menu bar of uvmat')
3646    % else
3647    flag_mask=1;
3648    maskname=maskfiles(1).name;% take the first mask file in the list
3649    [Path2,Name,ext]=fileparts(maskname);
3650    Namedouble=double(Name);
3651    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3652    ind_mask=findstr('mask',Name);
3653    i=ind_mask-1;
3654    while val(i)==0 && i>0
3655        i=i-1;
3656    end
3657    nbslice=str2double(Name(i+1:ind_mask-1));
3658    if ~isnan(nbslice) && Name(i)=='_'
3659        flag_mask=1;
3660    else
3661        msgbox_uvmat('ERROR',['bad mask file ' Name ext ' found in ' Path2])
3662        return
3663        nbslice=1;
3664    end
3665end
3666
3667%------------------------------------------------------------------------
3668% --- function called to look for grid files
3669function [nbslice, flag_mask]=get_grid(filebase,handles)
3670%------------------------------------------------------------------------
3671flag_mask=0;%default
3672nbslice=1;
3673[Path,Name]=fileparts(filebase);
3674currentdir=pwd;
3675cd(Path);%move in the dir of the root name filebase
3676maskfiles=dir([Name '_*grid_*.grid']);%look for mask files
3677cd(currentdir);%come back to the current working directory
3678if ~isempty(maskfiles)
3679    flag_mask=1;
3680    maskname=maskfiles(1).name;% take the first mask file in the list
3681    [Path2,Name,ext]=fileparts(maskname);
3682    Namedouble=double(Name);
3683    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3684    ind_mask=findstr('grid',Name);
3685    i=ind_mask-1;
3686    while val(i)==0 && i>0
3687        i=i-1;
3688    end
3689    nbslice=str2double(Name(i+1:ind_mask-1));
3690    if ~isnan(nbslice) && Name(i)=='_'
3691        flag_mask=1;
3692    else
3693        msgbox_uvmat('ERROR',['bad grid file ' Name ext ' found in ' Path2])
3694        return
3695        nbslice=1;
3696    end
3697end
3698
3699%------------------------------------------------------------------------
3700% --- transform numbers to letters
3701function str=num2stra(num,nom_type)
3702%------------------------------------------------------------------------
3703if isempty(nom_type)
3704    str='';
3705elseif strcmp(nom_type(end),'a')
3706    str=char(96+num);
3707elseif strcmp(nom_type(end),'A')
3708    str=char(96+num);
3709elseif isempty(nom_type(2:end))%a single index
3710    str='';
3711else
3712    str=num2str(num);
3713end
3714
3715%------------------------------------------------------------------------
3716% --- Executes on button press in ListSubdirCiv1.
3717function ListSubdirCiv1_Callback(hObject, eventdata, handles)
3718%------------------------------------------------------------------------
3719list_subdir_civ1=get(handles.ListSubdirCiv1,'String');
3720val=get(handles.ListSubdirCiv1,'Value');
3721SubDir=list_subdir_civ1{val};
3722if strcmp(SubDir,'new...')
3723    if get(handles.CheckCiv1,'Value')
3724        SubDir='CIV'; %default subdirectory
3725    else
3726        msgbox_uvmat('ERROR','select CheckCiv1 to perform a new Civ operation')
3727        return
3728    end   
3729end
3730set(handles.txt_SubdirCiv1,'String',SubDir);
3731find_netcpair_civ1(handles)
3732
3733%------------------------------------------------------------------------
3734% --- Executes on button press in ListSubdirCiv2.
3735function ListSubdirCiv2_Callback(hObject, eventdata, handles)
3736%------------------------------------------------------------------------
3737list_subdir_civ2=get(handles.ListSubdirCiv2,'String');
3738val=get(handles.ListSubdirCiv2,'Value');
3739SubDir=list_subdir_civ2{val};
3740if strcmp(SubDir,'new...')
3741    if get(handles.CheckCiv2,'Value')
3742        SubDir='CIV'; %default subdirectory
3743    else
3744        msgbox_uvmat('ERROR','select CheckCiv2 to perform a new Civ operation')
3745        return
3746    end
3747end
3748set(handles.txt_SubdirCiv2,'String',SubDir);
3749
3750%------------------------------------------------------------------------
3751% --- Executes on button press in CheckGrid.
3752function CheckGrid_Callback(hObject, eventdata, handles)
3753%------------------------------------------------------------------------
3754value=get(hObject,'Value');
3755hparent=get(hObject,'parent');
3756hchildren=get(hparent,'children');
3757handle_txtbox=findobj(hchildren,'tag','txt_Grid');
3758handle_dx=findobj(hchildren,'tag','num_Dx');
3759handle_dy=findobj(hchildren,'tag','num_Dy');
3760handle_title_dx=findobj(hchildren,'tag','title_Dx');
3761handle_title_dy=findobj(hchildren,'tag','title_Dy');
3762testgrid=0;
3763filegrid='';
3764if value
3765    filebase=get(handles.RootName,'String');
3766    [nbslice, flag_grid]=get_grid(filebase,handles);% look for a grid with appropriate name
3767    if isequal(flag_grid,1)
3768        filegrid=[num2str(nbslice) 'grid'];
3769        testgrid=1;
3770    else % browse for a grid
3771        filegrid=get(hObject,'UserData');%look for previous grid name stored as UserData
3772        if exist(filegrid,'file')
3773            filebase=filegrid;
3774        end
3775        [FileName, PathName, filterindex] = uigetfile( ...
3776            {'*.grid', ' (*.grid)';
3777            '*.grid',  '.grid files '; ...
3778            '*.*', 'All Files (*.*)'}, ...
3779            'Pick a file',filebase);
3780        filegrid=fullfile(PathName,FileName);
3781        set(hObject,'UserData',filegrid);%store for future use
3782        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filegrid,'file'))
3783            testgrid=1;
3784        end
3785    end
3786end
3787if testgrid
3788    set(handle_dx,'Visible','off');
3789    set(handle_dy,'Visible','off');
3790    set(handle_title_dy,'Visible','off');
3791    set(handle_title_dx,'Visible','off');
3792    set(handle_txtbox,'Visible','on')
3793    set(handle_txtbox,'String',filegrid)
3794else
3795    set(hObject,'Value',0);
3796    set(handle_dx,'Visible','on');
3797    set(handle_dy,'Visible','on');
3798    set(handle_title_dy,'Visible','on');
3799    set(handle_title_dx,'Visible','on');
3800    set(handle_txtbox,'Visible','off')
3801end
3802
3803%% if hObject is on the checkciv1 frame, duplicate action for checkciv2 frame
3804PanelName=get(hparent,'tag');
3805if strcmp(PanelName,'Civ1')
3806    hchildren=get(handles.Civ2,'children');
3807    handle_checkbox=findobj(hchildren,'tag','CheckGrid');
3808    handle_txtbox=findobj(hchildren,'tag','txt_Grid');
3809    handle_dx=findobj(hchildren,'tag','num_Dx');
3810    handle_dy=findobj(hchildren,'tag','num_Dy');
3811    handle_title_dx=findobj(hchildren,'tag','title_Dx');
3812    handle_title_dy=findobj(hchildren,'tag','title_Dy');
3813    set(handle_checkbox,'UserData',filegrid);%store for future use
3814    if testgrid
3815        set(handle_checkbox,'Value',1);
3816        set(handle_dx,'Visible','off');
3817        set(handle_dy,'Visible','off');
3818        set(handle_title_dx,'Visible','off');
3819        set(handle_title_dy,'Visible','off');
3820        set(handle_txtbox,'Visible','on')
3821        set(handle_txtbox,'String',filegrid)
3822%     else
3823%         set(handle_checkbox,'Value',0);
3824%         set(handles.CheckGrid,'Value',0);
3825%         set(handle_dx,'Visible','on');
3826%         set(handle_dy,'Visible','on');
3827%          set(handle_title_dx,'Visible','on');
3828%         set(handle_title_dy,'Visible','on');
3829%         set(handle_txtbox,'Visible','off')
3830    end
3831end
3832%------------------------------------------------------------------------
3833% --- Executes on button press in CheckMask.
3834function CheckMask_Callback(hObject, eventdata, handles)
3835%------------------------------------------------------------------------
3836value=get(hObject,'Value');
3837hparent=get(hObject,'parent');
3838parent_tag=get(hparent,'Tag');
3839hchildren=get(hparent,'children');
3840handle_txtbox=findobj(hchildren,'tag','txt_Mask');
3841% handle_dx=findobj(hchildren,'tag','num_Dx');
3842% handle_dy=findobj(hchildren,'tag','num_Dy');
3843testmask=0;
3844if value
3845    filebase=get(handles.RootName,'String');
3846    [nbslice, flag_mask]=get_mask(filebase,handles);% look for a mask with appropriate name
3847    if isequal(flag_mask,1)
3848        filemask=[num2str(nbslice) 'mask'];
3849        testmask=1;
3850    else % browse for a mask
3851        filemask=get(hObject,'UserData');%look for previous mask name stored as UserData
3852        if exist(filemask,'file')
3853            filebase=filemask;
3854        end
3855        [FileName, PathName] = uigetfile( ...
3856            {'*.png', ' (*.png)';
3857            '*.png',  '.png files '; ...
3858            '*.*', 'All Files (*.*)'}, ...
3859            'Pick a mask file *.png',filebase);
3860        filemask=fullfile(PathName,FileName);
3861        set(hObject,'UserData',filemask);%store for future use
3862        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filemask,'file'))
3863            testmask=1;
3864        end
3865    end
3866end
3867if testmask
3868%     stage=4;%default
3869    if strcmp(parent_tag,'Civ1')
3870            set(handles.txt_Mask,'Visible','on')
3871        set(handles.txt_Mask,'String',filemask)
3872    set(handles.CheckMask,'Value',1)
3873    end
3874%     switch parent_tag
3875% %         case 'Fix1'
3876% %             stage=2;
3877%         case 'Civ2'
3878%              stage=3;
3879% %         case 'Fix2'
3880% %             stage=4;
3881%     end
3882%     set(handles.txt_Mask(stage:end),'Visible','on')
3883%     set(handles.txt_Mask(stage:end),'String',filemask)
3884%     set(handles.CheckMask(stage:end),'Value',1)
3885else
3886    set(hObject,'Value',0);
3887    set(handle_txtbox,'Visible','off')
3888end
3889
3890
3891% --- Executes on button press in get_gridpatch1.
3892function get_gridpatch1_Callback(hObject, eventdata, handles)
3893% hObject    handle to get_gridpatch1 (see GCBO)
3894% eventdata  reserved - to be defined in a future version of MENUMATLAB
3895% handles    structure with handles and user data (see GUIDATA)
3896
3897filebase=get(handles.RootName,'String');
3898[FileName, PathName, filterindex] = uigetfile( ...
3899    {'*.grid', ' (*.grid)';
3900    '*.grid',  '.grid files '; ...
3901    '*.*', 'All Files (*.*)'}, ...
3902    'Pick a file',filebase);
3903filegrid=fullfile(PathName,FileName);
3904set(handles.grid_patch1,'string',filegrid);
3905% set(handles.grid_patch2,'string',filegrid
3906
3907%------------------------------------------------------------------------
3908% --- Executes on button press in get_gridpatch2.
3909function get_gridpatch2_Callback(hObject, eventdata, handles)
3910%------------------------------------------------------------------------
3911
3912
3913%------------------------------------------------------------------------
3914% --- STEREO Interp
3915function cmd=RUN_STINTERP(stinterpBin,filename_A_nc,filename_B_nc,filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,xmlA,xmlB)
3916%------------------------------------------------------------------------
3917namelog=[filename_nc(1:end-3) '_stinterp.log'];
3918cmd=[stinterpBin ' -f1 ' filename_A_nc  ' -f2 ' filename_B_nc ' -f  ' filename_nc ...
3919    ' -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
3920
3921%------------------------------------------------------------------------
3922%--read images and convert them to the uint16 format used for PIV
3923function A=read_image(filename,type_ima,num,movieobject)
3924%------------------------------------------------------------------------
3925%num is the view number needed for an avi movie
3926switch type_ima
3927    case 'movie'
3928        A=read(movieobject,num);
3929    case 'avi'
3930        mov=aviread(filename,num);
3931        A=frame2im(mov(1));
3932    case 'multimage'
3933        A=imread(filename,num);
3934    case 'image'
3935        A=imread(filename);
3936end
3937siz=size(A);
3938if length(siz)==3;%color images
3939    A=sum(double(A),3);
3940    A=uint16(A);
3941end
3942
3943
3944%------------------------------------------------------------------------
3945% --- Executes on button press in get_ref_fix1.
3946function get_ref_fix1_Callback(hObject, eventdata, handles)
3947%------------------------------------------------------------------------
3948filebase=get(handles.RootName,'String');
3949[FileName, PathName, filterindex] = uigetfile( ...
3950    {'*.nc', ' (*.nc)';
3951    '*.nc',  'netcdf files '; ...
3952    '*.*', 'All Files (*.*)'}, ...
3953    'Pick a file',filebase);
3954
3955fileinput=[PathName FileName];
3956sizf=size(fileinput);
3957if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
3958%[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
3959[Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput);
3960ref.filebase=fullfile(Path,File);
3961% ref.num_a=stra2num(str_a);
3962% ref.num_b=stra2num(str_b);
3963% ref.num1=str2double(field_count);
3964% ref.num2=str2double(str2);
3965browse=[];%initialisation
3966if ~isequal(ref.ext,'.nc')
3967    msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
3968    return
3969end
3970set(handles.ref_fix1,'String',[fullfile(ref.subdir,File) '....nc']);
3971set(handles.ref_fix1,'UserData',ref)
3972menu_field{1}='civ1';
3973Data=nc2struct(fileinput,[]);
3974if isfield(Data,'patch') && isequal(Data.patch,1)
3975    menu_field{2}='filter1';
3976end
3977if isfield(Data,'civ2') && isequal(Data.civ2,1)
3978    menu_field{3}='civ2';
3979end
3980if isfield(Data,'patch2') && isequal(Data.patch2,1)
3981    menu_field{4}='filter2';
3982end
3983set(handles.field_ref1,'String',menu_field);
3984set(handles.field_ref1,'Value',length(menu_field));
3985set(handles.num_MinVel,'Value',2);
3986set(handles.num_MinVel,'String','1');%default threshold
3987set(handles.ref_fix1,'Enable','on')
3988
3989%------------------------------------------------------------------------
3990% --- Executes on button press in get_ref_fix2.
3991function get_ref_fix2_Callback(hObject, eventdata, handles)
3992%------------------------------------------------------------------------
3993if isequal(get(handles.get_ref_fix2,'Value'),1)
3994    filebase=get(handles.RootName,'String');
3995    [FileName, PathName, filterindex] = uigetfile( ...
3996        {'*.nc', ' (*.nc)';
3997        '*.nc',  'netcdf files '; ...
3998        '*.*', 'All Files (*.*)'}, ...
3999        'Pick a file',filebase);
4000    fileinput=[PathName FileName];
4001    sizf=size(fileinput);
4002    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
4003    %[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
4004    [Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput);
4005    ref.filebase=fullfile(Path,File);
4006%     ref.num_a=stra2num(str_a);
4007%     ref.num_b=stra2num(str_b);
4008%     ref.num1=str2num(field_count);
4009%     ref.num2=str2num(str2);
4010    browse=[];%initialisation
4011    if ~isequal(ref.ext,'.nc')
4012        msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
4013        return
4014    end
4015    set(handles.ref_fix2,'String',[fullfile(ref.subdir,File) '....nc']);
4016    set(handles.ref_fix2,'UserData',ref)
4017    menu_field{1}='civ1';
4018    Data=nc2struct(fileinput,[]);
4019    if isfield(Data,'patch') && isequal(Data.patch,1)
4020        menu_field{2}='filter1';
4021    end
4022    if isfield(Data,'civ2') && isequal(Data.civ2,1)
4023        menu_field{3}='civ2';
4024    end
4025    if isfield(Data,'patch2') && isequal(Data.patch2,1)
4026        menu_field{4}='filter2';
4027    end
4028    set(handles.field_ref2,'String',menu_field);
4029    set(handles.field_ref2,'Value',length(menu_field));
4030    set(handles.num_MinVel,'Value',2);
4031    set(handles.num_MinVel,'String','1');%default threshold
4032    set(handles.ref_fix2,'Enable','on')
4033    set(handles.ref_fix2,'Visible','on')
4034    set(handles.field_ref2,'Visible','on')
4035else
4036    set(handles.ref_fix2,'Visible','off')
4037    set(handles.field_ref2,'Visible','off')
4038end
4039
4040%------------------------------------------------------------------------
4041function ref_fix1_Callback(hObject, eventdata, handles)
4042%------------------------------------------------------------------------
4043set(handles.num_MinVel,'Value',1);
4044set(handles.field_ref1,'Value',1)
4045set(handles.field_ref1,'String',{' '})
4046set(handles.ref_fix1,'UserData',[]);
4047set(handles.ref_fix1,'String','');
4048set(handles.thresh_vel1,'String','0');
4049
4050%------------------------------------------------------------------------
4051function ref_fix2_Callback(hObject, eventdata, handles)
4052%------------------------------------------------------------------------
4053set(handles.num_MinVel,'Value',1);
4054set(handles.field_ref2,'Value',1)
4055set(handles.field_ref2,'String',{' '})
4056set(handles.ref_fix2,'UserData',[]);
4057set(handles.ref_fix2,'String','');
4058set(handles.num_MinVel,'String','0');
4059
4060%------------------------------------------------------------------------
4061% --- Executes on button press in test_stereo1.
4062function test_stereo1_Callback(hObject, eventdata, handles)
4063%------------------------------------------------------------------------
4064if isequal(get(handles.test_stereo1,'Value'),0)
4065    set(handles.subdomain_patch1,'Visible','on')
4066    set(handles.rho_patch1,'Visible','on')
4067else
4068    set(handles.subdomain_patch1,'Visible','off')
4069    set(handles.rho_patch1,'Visible','off')
4070end
4071
4072%------------------------------------------------------------------------
4073% --- Executes on button press in CheckStereo.
4074function StereoCheck_Callback(hObject, eventdata, handles)
4075%------------------------------------------------------------------------
4076if isequal(get(handles.CheckStereo,'Value'),0)
4077    set(handles.num_SubdomainSize,'Visible','on')
4078    set(handles.num_SmoothingParam,'Visible','on')
4079else
4080    set(handles.num_SubdomainSize,'Visible','off')
4081    set(handles.num_SmoothingParam,'Visible','off')
4082end
4083
4084%------------------------------------------------------------------------
4085% --- Executes on button press in TestCiv1: display image correlation function
4086function TestCiv1_Callback(hObject, eventdata, handles)
4087%------------------------------------------------------------------------
4088set(handles.TestCiv1,'BackgroundColor',[1 1 0])
4089drawnow
4090if get(handles.TestCiv1,'Value')
4091    ref_i=str2double(get(handles.ref_i,'String'));
4092    if strcmp(get(handles.ref_j,'Visible'),'on')
4093        ref_j=str2double(get(handles.ref_j,'String'));
4094    else
4095        ref_j=1;%default
4096    end
4097    [filecell,i1,i21,j1,j2,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,file_ref_fix1,file_ref_fix2]=...
4098        set_civ_filenames(handles,ref_i,ref_j,[1 0 0 0 0 0]);
4099    Data.ListVarName={'ny','nx','A'};
4100    Data.VarDimName= {'ny','nx',{'ny','nx'}};
4101    Data.A=imread(filecell.ima1.civ1{1});
4102    Data.ny=[size(Data.A,1) 1];
4103    Data.nx=[1 size(Data.A,2)];
4104    par_civ1=read_GUI(handles.Civ1);
4105    par_civ1.ImageWidth=size(Data.A,1);
4106    par_civ1.ImageHeight=size(Data.A,2);
4107    par_civ1.Mask='all';% will provide only the grid set for PIV, no image correlation
4108    Param.Civ1=par_civ1;
4109    Grid=civ_matlab(Param);% get the grid of x, y positions set for PIV
4110    hview_field=view_field(Data);
4111    set(0,'CurrentFigure',hview_field)
4112    hhview_field=guihandles(hview_field);
4113    set(hview_field,'CurrentAxes',hhview_field.axes3)
4114    ViewData=get(hview_field,'UserData');
4115    ViewData.CivHandle=handles.civ;% indicate the handle of the civ GUI in view_field
4116    ViewData.axes3.B=imread(filecell.ima2.civ1{1});%store the second image in the UserData of the GUI view_field
4117    ViewData.axes3.X=Grid.Civ1_X; %keep the set of points in memeory
4118    ViewData.axes3.Y=Grid.Civ1_Y;
4119    set(hview_field,'UserData',ViewData)
4120    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
4121    if isempty(corrfig)
4122        corrfig=figure;
4123        set(corrfig,'tag','corrfig')
4124        set(corrfig,'name','image correlation')
4125        set(corrfig,'DeleteFcn',{@closeview_field})%
4126    end
4127    set(handles.TestCiv1,'BackgroundColor',[1 0 0])
4128else
4129    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
4130    if ~isempty(corrfig)
4131        delete(corrfig)
4132    end
4133    hview_field=findobj(allchild(0),'tag','view_field');% look for view_field   
4134    if ~isempty(hview_field)
4135        delete(hview_field)
4136    end
4137end
4138
4139
4140%------------------------------------------------------------------------
4141% --- Executes on button press in CheckThreshold.
4142function CheckThreshold_Callback(hObject, eventdata, handles)
4143%------------------------------------------------------------------------
4144huipanel=get(hObject,'parent');
4145obj(1)=findobj(huipanel,'Tag','num_MinIma');
4146obj(2)=findobj(huipanel,'Tag','num_MaxIma');
4147obj(3)=findobj(huipanel,'Tag','title_Threshold');
4148if get(hObject,'Value')
4149    set(obj,'Visible','on')
4150else
4151    set(obj,'Visible','off')
4152end
4153
4154
4155%------------------------------------------------------------------------
4156% % --- Executes on button press in ListPairMode.
4157% function CivMode_Callback(hObject, eventdata, handles)
4158% %------------------------------------------------------------------------
4159% Listprog=get(handles.ListPairMode,'String');
4160% index=get(handles.ListPairMode,'Value');
4161% prog=Listprog{index};
4162% switch prog
4163%     case 'MenuCivX'
4164%         set(handles.thresh_patch1,'Visible','off')
4165%         set(handles.thresh_text1,'Visible','off')
4166%         set(handles.num_MaxDiff,'Visible','off')
4167%         set(handles.title_MaxDiff,'Visible','off')
4168%         set(handles.num_Rho,'Style','edit')
4169%         set(handles.num_Rho,'String','1')
4170%         set(handles.BATCH,'Enable','on')
4171%     case 'CivAll'
4172%         if get(handles.CheckPatch1,'Value')
4173%             set(handles.thresh_patch1,'Visible','on')
4174%             set(handles.thresh_text1,'Visible','on')
4175%         end
4176%         set(handles.num_Rho,'Style','edit')
4177%         set(handles.num_Rho,'String','1')
4178%         set(handles.BATCH,'Enable','on')
4179%     case 'CivUvmat'
4180%       
4181% end
4182
4183%------------------------------------------------------------------------
4184function cmd=cmd_civ1(filename,Param)
4185%------------------------------------------------------------------------
4186%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4187%changes : filename_cmx -> filename ( no extension )
4188cmd='';
4189errormsg=''; %default
4190filename=regexprep(filename,'.nc',''); %file name for the result
4191if isequal(Param.Civ1.Dt,0)
4192    Param.Civ1.Dt=1 ;%case of 'displacement' mode
4193end
4194Param.Civ1.ImageA=regexprep(Param.Civ1.ImageA,'.png','');
4195Param.Civ1.ImageB=regexprep(Param.Civ1.ImageB,'.png','');
4196fid=fopen([filename '.civ1.cmx'],'w');
4197if isequal(fid,-1)
4198    display(['cmd file ' filename ' cannot be created'])
4199    return
4200end
4201fprintf(fid,['##############   CMX file' '\n' ]);
4202fprintf(fid,   ['FirstImage ' regexprep(Param.Civ1.ImageA,'\\','\\\\') '\n' ]);% for windows compatibility
4203fprintf(fid,   ['LastImage  ' regexprep(Param.Civ1.ImageB,'\\','\\\\') '\n' ]);% for windows compatibility
4204fprintf(fid,  ['XX' '\n' ]);
4205if isfield(Param.Civ1,'Mask')
4206    fprintf(fid,  ['Mask ' 'y' '\n' ]);
4207    fprintf(fid,  ['MaskName ' regexprep(Param.Civ1.Mask,'\\','\\\\') '\n' ]);
4208else
4209    fprintf(fid,  ['Mask ' 'n' '\n' ]);
4210    fprintf(fid,  ['MaskName ' 'noFile use default' '\n' ]);
4211end
4212fprintf(fid,   ['ImageSize ' num2str(Param.Civ1.ImageWidth) ' ' num2str(Param.Civ1.ImageHeight) '\n' ]);   %VERIFIER CAS GENERAL ?
4213fprintf(fid,   ['CorrelationBoxesSize ' num2str(Param.Civ1.Bx) ' ' num2str(Param.Civ1.By) '\n' ]);
4214fprintf(fid,   ['SearchBoxeSize ' num2str(Param.Civ1.Searchx) ' ' num2str(Param.Civ1.Searchy) '\n' ]);
4215fprintf(fid,   ['RO ' num2str(Param.Civ1.Rho) '\n' ]);
4216if isfield(Param.Civ1,'Grid')
4217    fprintf(fid,   ['GridSpacing ' '25' ' ' '25' '\n' ]);
4218else
4219    fprintf(fid,   ['GridSpacing ' num2str(Param.Civ1.Dx) ' ' num2str(Param.Civ1.Dy) '\n' ]);
4220end
4221fprintf(fid,   ['XX 1.0' '\n' ]);
4222fprintf(fid,   ['Dt_TO ' num2str(Param.Civ1.Dt) ' ' num2str(Param.Civ1.Time) '\n' ]);
4223fprintf(fid,  ['PixCmXY ' '1' ' ' '1' '\n' ]);
4224fprintf(fid,  ['XX 1' '\n' ]);
4225fprintf(fid,   ['ShiftXY ' num2str(Param.Civ1.Shiftx) ' '  num2str(Param.Civ1.Shifty) '\n' ]);
4226if isfield(Param.Civ1,'Grid')
4227    fprintf(fid,  ['Grid ' 'y' '\n' ]);
4228    fprintf(fid,   ['GridName ' regexprep(Param.Civ1.Grid,'\\','\\\\') '\n' ]);
4229else
4230    fprintf(fid,  ['Grid ' 'n' '\n' ]);
4231    fprintf(fid,   ['GridName ' 'noFile use default' '\n' ]);
4232end
4233fprintf(fid,   ['XX 85' '\n' ]);
4234fprintf(fid,   ['XX 1.0' '\n' ]);
4235fprintf(fid,   ['XX 1.0' '\n' ]);
4236fprintf(fid,   ['Hart 1' '\n' ]);
4237fprintf(fid,  [ 'DecimalShift 0' '\n' ]);
4238fprintf(fid,   ['Deformation 0' '\n' ]);
4239fprintf(fid,  ['CorrelationMin 0' '\n' ]);
4240fprintf(fid,   ['IntensityMin 0' '\n' ]);
4241if ~isfield(Param.Civ1,'MinIma')% Image threshold not activated
4242    fprintf(fid,  ['SeuilImage n' '\n' ]);
4243    fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);%not used in principle
4244else% Image threshold  activated
4245    if isempty(Param.Civ1.MaxIma)||isnan(Param.Civ1.MaxIma)
4246        Param.Civ1.MaxIma=2^Param.Civ1.ImageBitDepth;%take the max image value as upper bound by default
4247    end
4248    fprintf(fid,  ['SeuilImage y' '\n' ]);
4249    fprintf(fid,   ['SeuilImageValues ' num2str(Param.Civ1.MinIma) ' ' num2str(Param.Civ1.MaxIma) '\n' ]);
4250end
4251fprintf(fid,   ['ImageToUse ' Param.Civ1.term_a ' ' Param.Civ1.term_b '\n' ]); % VERIFIER ?
4252fprintf(fid,   ['ImageUsedBefore null null' '\n' ]);
4253fclose(fid);
4254
4255if(isunix) %unix (or Mac) system
4256    cmd=['cp -f ' filename '.civ1.cmx ' filename '.cmx \n '];% the cmx file gives the name to the nc file
4257    cmd=[cmd Param.xml.Civ1Bin ' -f ' filename '.cmx >' filename '.civ1.log \n ' ]; % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx
4258    cmd=[cmd 'rm ' filename '.cmx'];
4259else %Windows system
4260    filename=regexprep(filename,'\\','\\\\');
4261    cmd=['copy /Y "' filename '.civ1.cmx" "' filename '.cmx" \n '];
4262    cmd=[cmd '"' regexprep(Param.xml.Civ1Bin,'\\','\\\\')...
4263        '" -f "' filename '.cmx" >"' filename '.civ1.log" \n ' ]; % redirect standard output to the log file
4264    cmd=[cmd 'del "' filename '.cmx"'];
4265end
4266
4267
4268function cmd=cmd_fix(filename,Param,fixname)
4269%%
4270switch fixname
4271    case 'Fix1'
4272        fi2_value=num2str(Param.(fixname).CheckF2);
4273    case 'Fix2'
4274        fi2_value=num2str(Param.(fixname).CheckF4);%need to understand why...
4275end
4276filename=regexprep(filename,'.nc','');
4277MaskName_string='';%default
4278% if Param.(fixname).CheckMask
4279%     MaskName_string=[' -maskName "' Param.(fixname).Mask '"'];
4280% end
4281MaxVel_string='';%default
4282if ~isempty(Param.(fixname).MaxVel)
4283    MaxVel_string=[' -threshV ' num2str(Param.(fixname).MaxVel)];
4284end
4285if isunix
4286    cmd=[Param.xml.FixBin ' -f ' filename '.nc -fi1 ' num2str(Param.(fixname).CheckFmin2) ...
4287        ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ...
4288        ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string...
4289        ' >' filename '.' lower(fixname) '.log 2>&1'];
4290else
4291    cmd=['"' Param.xml.FixBin '" -f "' filename '.nc" -fi1 ' num2str(Param.(fixname).CheckFmin2)...
4292        ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ...
4293        ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string...
4294        ' > "' filename '.' lower(fixname) '.log"'];
4295    cmd=regexprep(cmd,'\\','\\\\');
4296end
4297
4298
4299function cmd=cmd_patch(filename,Param,patchname)
4300%% ------------------------------------------------------------------------
4301filename=regexprep(filename,'.nc','');
4302if isunix
4303    cmd=[Param.xml.PatchBin...
4304        ' -f ' filename '.nc -m ' num2str(Param.(patchname).Nx)...
4305        ' -n ' num2str(Param.(patchname).Ny) ' -ro ' num2str(Param.(patchname).SmoothingParam)...
4306        ' -nopt ' num2str(Param.(patchname).SubdomainSize) ...
4307        '  > ' filename '.' lower(patchname) '.log 2>&1']; % redirect standard output to the log file
4308else
4309    cmd=['"' Param.xml.PatchBin...
4310        '" -f "' filename '.nc" -m ' num2str(Param.(patchname).Nx)...
4311        ' -n ' num2str(Param.(patchname).Ny) ' -ro ' num2str(Param.(patchname).SmoothingParam)...
4312        ' -nopt ' num2str(Param.(patchname).SubdomainSize)...
4313        '  > "' filename '.' lower(patchname) '.log" 2>&1']; % redirect standard output to the log file
4314    cmd=regexprep(cmd,'\\','\\\\');
4315end
4316
4317%------------------------------------------------------------------------
4318% --- CheckCiv2  CheckCiv2  CheckCiv2 CheckCiv2
4319function cmd=cmd_civ2(filename,Param)
4320%------------------------------------------------------------------------
4321%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4322% global civ2Bin sge%name of the executable for checkciv1 calculation
4323filename=regexprep(filename,'.nc','');
4324if isequal(Param.Civ2.Dt,'0')
4325    Param.Civ2.Dt='1' ;%case of 'displacement' mode
4326end
4327Param.Civ2.ImageA=regexprep(Param.Civ2.ImageA,'.png','');
4328Param.Civ2.ImageB=regexprep(Param.Civ2.ImageB,'.png','');% bug : .png appears two times ?
4329[fid,errormsg]=fopen([filename '.civ2.cmx'],'w');
4330if isequal(fid,-1)
4331    msgbox_uvmat('ERROR',errormsg)
4332    cmd='';
4333    return
4334end
4335fprintf(fid,['##############   CMX file' '\n' ]);
4336fprintf(fid,   ['FirstImage ' regexprep(Param.Civ2.ImageA,'\\','\\\\') '\n' ]);% for windows compatibility
4337fprintf(fid,   ['LastImage  ' regexprep(Param.Civ2.ImageB,'\\','\\\\') '\n' ]);% for windows compatibility
4338fprintf(fid,  ['XX' '\n' ]);
4339if isfield(Param.Civ2,'Mask')
4340    fprintf(fid,  ['Mask ' 'y' '\n' ]);
4341    fprintf(fid,  ['MaskName ' regexprep(Param.Civ2.Mask,'\\','\\\\') '\n' ]);
4342else
4343    fprintf(fid,  ['Mask ' 'n' '\n' ]);
4344    fprintf(fid,  ['MaskName ' 'noFile use default' '\n' ]);
4345end
4346% fprintf(fid, ['Mask ' Param.Civ2.MaskFlag '\n' ]);
4347% fprintf(fid, ['MaskName ' regexprep(Param.Civ2.MaskName,'\\','\\\\') '\n' ]);% for windows compatibility
4348fprintf(fid,   ['ImageSize ' num2str(Param.Civ2.ImageWidth) ' ' num2str(Param.Civ2.ImageHeight) '\n' ]); 
4349% fprintf(fid, ['ImageSize ' num2str(Param.Civ2.npx) ' ' num2str(Param.Civ2.npy) '\n' ]);   %VERIFIER CAS GENERAL ?
4350fprintf(fid, ['CorrelationBoxesSize ' num2str(Param.Civ2.Bx) ' ' num2str(Param.Civ2.By) '\n' ]);
4351fprintf(fid, ['SearchBoxeSize ' num2str(Param.Civ2.Bx) ' ' num2str(Param.Civ2.By) '\n']);
4352fprintf(fid, ['RO ' num2str(Param.Civ2.Rho) '\n']);
4353if isfield(Param.Civ2,'Grid')
4354    fprintf(fid,   ['GridSpacing ' '25' ' ' '25' '\n' ]);
4355else
4356    fprintf(fid,   ['GridSpacing ' num2str(Param.Civ2.Dx) ' ' num2str(Param.Civ2.Dy) '\n' ]);
4357end
4358% fprintf(fid, ['GridSpacing ' num2str(Param.Civ2.Dx) ' ' num2str(Param.Civ2.Dy) '\n']);
4359fprintf(fid, ['XX 1.0' '\n' ]);
4360fprintf(fid, ['Dt_TO ' num2str(Param.Civ2.Dt) ' ' num2str(Param.Civ2.Time) '\n' ]);
4361fprintf(fid, ['PixCmXY ' '1' ' ' '1' '\n' ]);
4362fprintf(fid, ['XX 1' '\n' ]);
4363fprintf(fid, 'ShiftXY 0 0\n');
4364if isfield(Param.Civ2,'Grid')
4365    fprintf(fid,  ['Grid ' 'y' '\n' ]);
4366    fprintf(fid,   ['GridName ' regexprep(Param.Civ2.Grid,'\\','\\\\') '\n' ]);
4367else
4368    fprintf(fid,  ['Grid ' 'n' '\n' ]);
4369    fprintf(fid,   ['GridName ' 'noFile use default' '\n' ]);
4370end
4371% fprintf(fid, ['Grid ' Param.Civ2.GridFlag '\n' ]);
4372% fprintf(fid, ['GridName ' regexprep(Param.Civ2.GridName,'\\','\\\\') '\n']);
4373fprintf(fid, ['XX 85' '\n' ]);
4374fprintf(fid, ['XX 1.0' '\n' ]);
4375fprintf(fid, ['XX 1.0' '\n' ]);
4376fprintf(fid, ['Hart 1' '\n' ]);
4377fprintf(fid, ['DecimalShift ' num2str(Param.Civ2.CheckDecimal) '\n']);
4378fprintf(fid, ['Deformation ' num2str(Param.Civ2.CheckDeformation) '\n']);
4379fprintf(fid,  ['CorrelationMin 0' '\n' ]);
4380fprintf(fid,   ['IntensityMin 0' '\n' ]);
4381
4382if ~isfield(Param.Civ2,'MinIma')% Image threshold not activated
4383    fprintf(fid,  ['SeuilImage n' '\n' ]);
4384    fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);%not used in principle
4385else% Image threshold  activated
4386    if isempty(Param.Civ2.MaxIma)||isnan(Param.Civ2.MaxIma)
4387        Param.Civ2.MaxIma=2^Param.Civ2.ImageBitDepth;%take the max image value as upper bound by default
4388    end
4389    fprintf(fid,  ['SeuilImage y' '\n' ]);
4390    fprintf(fid,   ['SeuilImageValues ' num2str(Param.Civ2.MinIma) ' ' num2str(Param.Civ2.MaxIma) '\n' ]);
4391end
4392fprintf(fid,   ['ImageToUse ' Param.Civ2.term_a ' ' Param.Civ2.term_b '\n' ]); % VERIFIER ?
4393fprintf(fid, ['ImageUsedBefore ' regexprep(Param.Civ2.filename_nc1,'\\','\\\\') '\n']);
4394fclose(fid);
4395
4396if(isunix)
4397    cmd=['cp -f ' filename '.civ2.cmx ' filename '.cmx\n'...
4398        Param.xml.Civ2Bin ' -f ' filename  '.cmx >' filename '.civ2.log \n '... % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx
4399        'rm ' filename '.cmx \n'];%rename .cmx as .checkciv2.cmx, the result file is named [filename '.nc'] by CIVx
4400else
4401    filename=regexprep(filename,'\\','\\\\');
4402    cmd=['copy /Y "' filename '.civ2.cmx" "' filename '.cmx" \n'...
4403        '"' regexprep(Param.xml.Civ2Bin,'\\','\\\\') '" -f "' filename  '.cmx" >"' filename '.civ2.log" \n'...
4404        'del "' filename '.cmx" \n'];
4405end
4406
4407%------------------------------------------------------------------------
4408% --- CheckCiv1  Unified: TO ABADON
4409function xml_civ1_parameters=CIV1_CMD_Unified(filename,namelog,par)
4410%------------------------------------------------------------------------
4411%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4412%global CivBin%name of the executable for checkciv1 calculation
4413
4414civ1.image1=par.ImageA;
4415civ1.image2=par.ImageB;
4416civ1.imageSize_X=par.npx;
4417civ1.imageSize_Y=par.npy;
4418civ1.outputFileName=[filename '.nc'];
4419civ1.correlationBoxesSize_X=par.ibx;
4420civ1.correlationBoxesSize_Y=par.iby;
4421civ1.searchBoxesSize_X=par.isx;
4422civ1.searchBoxesSize_Y=par.isy;
4423civ1.globalShift_X=par.shiftx;
4424civ1.globalShift_Y=par.shifty;
4425civ1.ro=par.rho;
4426civ1.hart='y';
4427if isequal(par.gridflag,'y')
4428    civ1.grid=par.gridname;
4429else
4430    civ1.grid='n';
4431    civ1.gridSpacing_X=par.dx;
4432    civ1.gridSpacing_Y=par.dy;
4433end
4434if isequal(par.maskflag,'y')
4435    civ1.mask=par.maskname;
4436end
4437civ1.dt=par.Dt;
4438civ1.unit='pixel';
4439civ1.absolut_time_T0=par.Time;
4440civ1.pixcmx='1';
4441civ1.pixcmy='1';
4442civ1.convectFlow='n';
4443
4444xml_civ1_parameters=civ1;
4445
4446%------------------------------------------------------------------------
4447% --- CheckCiv2  Unified: TO ABADON
4448function civ2=CIV2_CMD_Unified(filename,namelog,par)
4449%------------------------------------------------------------------------
4450%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4451%global CivBin%name of the executable for checkciv1 calculation
4452
4453filename=regexprep(filename,'.nc','');
4454
4455civ2.image1=par.ImageA;
4456civ2.image2=par.ImageB;
4457civ2.imageSize_X=par.npx;
4458civ2.imageSize_Y=par.npy;
4459civ2.inputFileName=[par.filename_nc1 '.nc'];
4460civ2.outputFileName=[filename '.nc'];
4461civ2.correlationBoxesSize_X=par.ibx;
4462civ2.correlationBoxesSize_Y=par.iby;
4463civ2.ro=par.rho;
4464%checkciv2.decimalShift=par.CheckDecimal;
4465%checkciv2.CheckDeformation=par.CheckDeformation;
4466if isequal(par.decimal,'1')
4467    civ2.decimalShift='y';
4468else
4469    civ2.decimalShift='n';
4470end
4471if isequal(par.deformation,'1')
4472    civ2.deformation='y';
4473else
4474    civ2.deformation='n';
4475end
4476if isequal(par.gridflag,'y')
4477    civ2.grid=par.gridname;
4478else
4479    civ2.grid='n';
4480    civ2.gridSpacing_X=par.dx;
4481    civ2.gridSpacing_Y=par.dy;
4482end
4483civ2.gridSpacing_X='10';
4484civ2.gridSpacing_Y='10';%NOTE: faut mettre gridSpacing pourque ca tourne, meme si c'est la grille qui est utilisee
4485if isequal(par.maskflag,'y')
4486    civ2.mask=par.maskname;
4487else
4488    civ2.mask='n';
4489end
4490civ2.dt=par.Dt;
4491civ2.unit='pixel';
4492civ2.absolut_time_T0=par.Time;
4493civ2.pixcmx='1';
4494civ2.pixcmy='1';
4495civ2.convectFlow='n';
4496
4497
4498% --- Executes on button press in TestPatch1.
4499function TestPatch1_Callback(hObject, eventdata, handles)
4500set(handles.TestPatch1,'BackgroundColor',[1 1 0])
4501drawnow
4502if get(handles.TestPatch1,'Value')
4503    ref_i=str2double(get(handles.ref_i,'String'));
4504    if strcmp(get(handles.ref_j,'Visible'),'on')
4505        ref_j=str2double(get(handles.ref_j,'String'));
4506    else
4507        ref_j=1;%default
4508    end
4509    [filecell,i1,i21,j1,j2,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,file_ref_fix1,file_ref_fix2]=...
4510        set_civ_filenames(handles,ref_i,ref_j,[0 0 1 0 0 0]);
4511   
4512    Data.ListVarName={'ny','nx','A'};
4513    Data.VarDimName= {'ny','nx',{'ny','nx'}};
4514   
4515    param_patch1=read_GUI(handles.Patch1);
4516    param_patch1.CivFile=filecell.nc.civ1{1};
4517    Param.Patch1=param_patch1;
4518    for irho=1:7
4519        [Data,errormsg]=civ_matlab(Param);% get the grid of x, y positions set for PIV
4520        if ~isempty(errormsg)
4521            msgbox_uvmat('ERROR',errormsg)
4522            return
4523        end
4524        SmoothingParam(irho)=Param.Patch1.SmoothingParam;
4525        Data.Civ1_U_Diff=Data.Civ1_U_Diff(Data.Civ1_FF==0);
4526        Data.Civ1_V_Diff=Data.Civ1_V_Diff(Data.Civ1_FF==0);
4527        DiffVel(irho)=sqrt(mean(Data.Civ1_U_Diff.*Data.Civ1_U_Diff+Data.Civ1_V_Diff.*Data.Civ1_V_Diff))
4528        NbSites(irho)=Data.Civ1_NbSites/numel(Data.Civ1_U_Diff);
4529        Param.Patch1.SmoothingParam=2*Param.Patch1.SmoothingParam;
4530    end
4531    figure
4532    plot(SmoothingParam,DiffVel,'b',SmoothingParam,NbSites,'r')
4533    set(handles.TestPatch1,'BackgroundColor',[1 0 0])
4534else
4535    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
4536    if ~isempty(corrfig)
4537        delete(corrfig)
4538    end
4539    hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
4540    if ~isempty(hview_field)
4541        delete(hview_field)
4542    end
4543end
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