source: trunk/src/civ.m @ 315

Last change on this file since 315 was 315, checked in by sommeria, 9 years ago

many corrections, use of the new GUI civ with mask, grid and the new matlab civ1 and fix
pivlab now included in civ_matlab which contains all matlab subfunctions for civ.

File size: 176.6 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 03-Dec-2011 16:08:25
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
139ind_opening=1;%default
140browse.incr_pair=[0 0]; %default
141menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)';
142    '*.xml',  '.xml files '; ...
143    '*.civ',  '.civ files '; ...
144    '*.png','.png image files'; ...
145    '*.jpg',' jpeg image files'; ...
146    '*.tif','.tif image files'; ...
147    '*.avi;*.AVI','.avi movie files'; ...
148    '*.nc','.netcdf files'; ...
149    '*.*',  'All Files (*.*)'};
150[FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file',oldfile);
151fileinput=[PathName FileName];%complete file name
152sizf=size(fileinput);
153if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
154
155%% prepare the GUI with parameters from the input file if opened from uvmat
156errormsg=display_file_name(handles,fileinput);
157if ~isempty(errormsg)
158    msgbox_uvmat('ERROR',erromsg)
159end
160
161[path,name,ext]=fileparts(fileinput);
162testeditxml=0;
163if isequal(ext,'.xml')
164    testeditxml=1;
165    t_browse=xmltree(fileinput);
166    head_element=get(t_browse,1);
167    if isfield(head_element,'name')&& isequal(head_element.name,'ImaDoc')
168        testeditxml=0;
169    end
170end
171if testeditxml==1 || isequal(ext,'.xls')
172    heditxml=editxml({fileinput});
173    set(heditxml,'Tag','browser')
174    waitfor(heditxml,'Tag','idle')
175    if ~ishandle(heditxml)
176        return
177    end
178    attr=findobj(get(heditxml,'children'),'Tag','CurrentAttributes');
179    set(handles.browse,'UserData',fileinput)% store for future opening with browser
180    fileinput=get(attr,'UserData');
181    if ~exist(fileinput,'file')
182        return
183    end
184end
185[RootPath,RootFile,str1,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fileinput);
186% filebase=fullfile(RootPath,RootFile);
187num_i1=str2double(str1);
188if isnan(num_i1),num_i1=1;end
189num_i2=str2double(str2);
190if isnan(num_i2),num_i2=num_i1;end
191num_j1=stra2num(str_a);
192if isnan(num_j1),num_j1=1;end
193num_j2=stra2num(str_b);
194if isnan(num_j2),num_j2=num_j1;end
195if isequal(get(handles.ListCompareMode,'Value'),1)
196    browse=[];%initialisation
197else
198    browse=get(handlesRootName,'UserData');
199end
200browse.num_i1=num_i1;
201browse.num_i2=num_i2;
202browse.num_j1=num_j1;
203browse.num_j2=num_j2;
204if length(ext)>1 && (~isempty(imformats(ext(2:end)))||strcmpi(ext,'.avi'));%if an image file has been opened by uvmat
205    browse.nom_type_ima=nom_type;
206    browse.ext_ima=ext;
207    set(handles.ImaExt,'String',ext)
208end
209set(handles.ImaDoc,'String',ext);
210
211set(handles.RootName,'UserData',browse);% store information from browser
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')
270% set(handles.num_MaxDiff,'Visible','off')
271% set(handles.thresh_text2,'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')
283if get(handles.CheckPatch1,'Value')
284    set(handles.thresh_patch1,'Visible','on')
285    set(handles.thresh_text1,'Visible','on')
286end
287if get(handles.CheckPatch2,'Value')
288    set(handles.num_MaxDiff,'Visible','on')
289    set(handles.thresh_text2,'Visible','on')
290end
291set(handles.num_Rho,'Style','popupmenu')
292set(handles.num_Rho,'Value',1)
293set(handles.num_Rho,'String',{'1';'2'})
294set(handles.BATCH,'Enable','off')
295
296% -----------------------------------------------------------------------
297% --- Open the help html file
298function MenuHelp_Callback(hObject, eventdata, handles)
299% -----------------------------------------------------------------------
300path_civ=fileparts(which ('civ'));
301helpfile=fullfile(path_civ,'uvmat_doc','uvmat_doc.html');
302if isempty(dir(helpfile))
303    msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
304else
305    addpath (fullfile(path_civ,'uvmat_doc'))
306    web([helpfile '#civ'])
307end
308
309%------------------------------------------------------------------------
310% --- Function activated when a new filebase (image series) is introduced
311function RootName_Callback(hObject, eventdata, handles)
312%------------------------------------------------------------------------
313filebase=get(handles.RootName,'String');
314errormsg=display_file_name(handles,filebase);
315if ~isempty(errormsg)
316    msgbox_uvmat('ERROR',erromsg)
317end
318
319%------------------------------------------------------------------------
320% --- general function activated for an input file series
321function errormsg=display_file_name(handles,fileinput)
322%------------------------------------------------------------------------
323set(handles.ListCompareMode,'Visible','on')
324errormsg='';%default empty error message
325
326%% enable RUN, BATCH button and 'status' display
327set(handles.RUN, 'Enable','On')
328set(handles.RUN,'BackgroundColor',[1 0 0])%set RUN button to red color
329set(handles.BATCH,'Enable','On')
330set(handles.BATCH,'BackgroundColor',[1 0 0])%set BATCH button to red color
331if isfield(handles,'status')
332    set(handles.status,'Value',0);       %suppress the 'status' display
333    status_Callback([], [], handles)
334end
335
336%% determine nomenclature types and extension of the input files
337ext_ima='';%default
338nom_type_ima='';%default
339nom_type_nc='';
340[RootPath,FileName,i1_str,i2_str,j1_str,j2_str,ext_input,nom_type_input,subdir]=name2display(fileinput);
341RootName=fullfile(RootPath,FileName);
342set(handles.RootName,'String',RootName)
343set(handles.RootName,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
344i1=str2double(i1_str);
345i2=str2double(i2_str);
346j1=str2double(j1_str);
347j2=str2double(j2_str);
348num_ref_i=i1;%efaulmt ref index
349num_ref_j=j1;
350browse.incr_pair=[0 0];%default
351
352% form=imformats(ext_input(2:end));
353if ~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
354    ext_ima=ext_input;
355    nom_type_ima=nom_type_input;
356else %case of netcdf input file, look for corresponding images
357    nom_type_nc=nom_type_input;
358    if ~isnan(i2)
359        num_ref_i=floor((num_ref_i+i2)/2);% reference image number corresponding to the file
360        browse.incr_pair(1)=i2-i1;
361        browse.incr_pair(2)=0;
362    end
363    %TODO: read the image name in the netcdf file (if documented)
364    %look for double image series '_i_j'
365    dirima=dir([RootName '_' i1_str '_' j1_str '.*']);
366    if isempty(dirima)
367        % look for images series  with sub marker '_'
368        dirima=dir([RootName '_*' i1_str  '.*']);
369        if isempty(dirima)
370            % look for other images series
371            dirima=dir([RootName '*' i1_str '.*']);
372            if isempty(dirima)
373                % look for other images series witth letter appendix
374                appendix=char(96+j1_str);
375                dirima=dir([RootName '*' i1_str appendix '.*']);
376            end
377        end
378    end
379    for ilist=1:numel(dirima)
380        [pp,ff,i1_str,i2_str,j1_str,j2_str,ext_list,nom_type_list]=name2display(dirima(ilist).name);
381        form=imformats(ext_list(2:end));
382        if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
383            ext_ima=ext_list;
384            nom_type_ima=nom_type_list;
385            i1=str2double(i1_str);
386            j1=str2double(j1_str);
387            i2=str2double(i2_str);
388            j2=str2double(j2_str);         
389            % set the range of fields (1:1 by default) and selected pair
390            if isequal(i2,i1)||isnan(i2)
391                num_ref_i=i1;
392            else
393                num_ref_i=floor((i1+i2)/2);
394                browse.incr_pair(1)=i2-i1;
395                browse.incr_pair(2)=0;
396            end
397            if isequal(j1,j2)||isnan(j2)
398                if isnan(j1)
399                    num_ref_j=1;
400                else
401                    num_ref_j=j1;
402                end
403            else
404                num_ref_j=floor((j1+j2)/2);
405                browse.incr_pair(2)=j2-j1;
406            end
407            break
408        end
409    end
410end
411
412%% look for an image documentation file
413ext_imadoc='';%default
414if exist([RootName '.xml'],'file')
415    ext_imadoc='.xml';
416elseif exist([RootName '.civxml'],'file')
417    ext_imadoc='.civxml';
418elseif exist([RootName '.civ'],'file')
419    ext_imadoc='.civ';
420elseif exist([RootName '.avi'],'file')
421    ext_imadoc='.avi';
422elseif exist([RootName '.AVI'],'file')
423    ext_imadoc='.AVI';
424end
425set(handles.ImaDoc,'String',ext_imadoc)% display the extension name for the image documentation file used
426set(handles.ImaDoc,'BackgroundColor',[1 1 0])
427drawnow
428%%%%%%%%   read image documentation file  %%%%%%%%%%%%%%%%%%%%%%%%%%%
429mode=''; %default
430time=[];
431TimeUnit='frame'; %default
432CoordUnit='px';%default
433pxcmx_search=[];%default
434pxcmy_search=[];%default
435if isequal(ext_imadoc,'.civxml')%TO ABANDON
436    [nbfield,nbfield2,time]=read_civxml([RootName '.civxml']);
437    mode='pair j1-j2';
438    if isempty(nom_type_ima)% dtermine types by default if not already selected by browser or uvmat
439        nom_type_ima='_i_j';
440    end
441elseif isequal(ext_imadoc,'.xml')
442    [XmlData,warntext]=imadoc2struct([RootName '.xml']);
443    ext_ima_read=[];
444    nom_type_read=[];
445    if isfield(XmlData,'Heading')&&isfield(XmlData.Heading','ImageName')&&ischar(XmlData.Heading.ImageName)% get image nom type and extension from the xml file
446        [PP,FF,fc,str2,str_a,str_b,ext_ima_read,nom_type_read]=name2display(XmlData.Heading.ImageName);
447        fullname=fullfile(fileparts(RootName),XmlData.Heading.ImageName); %full name (including path) of the first image defined by the xmle file,
448        if ~exist(fullname,'file')
449            msgbox_uvmat('WARNING',['FirstImage ' fullname ' defined in the xml file does not exist'])
450        end
451    end
452    if isfield(XmlData,'Time')
453        time=XmlData.Time;
454        nbfield=size(time,1);
455        nbfield2=size(time,2);
456        %transform .Time to a column vector if it is a line vector thenomenclature uses a single index: correct possible bug in xml
457        if isequal(nbfield,1) && ~isequal(nbfield2,1)% .Time is a line vector
458            if numel(nom_type_read)>=2 && isempty(regexp(nom_type_read(2:end),'\D','once'))
459                time=time';
460                nbfield=nbfield2;
461                nbfield2=1;
462            end
463        end
464    end
465    if isfield(XmlData,'TimeUnit')
466        TimeUnit=XmlData.TimeUnit;
467    end
468    pxcmx_search=1;
469    pxcmy_search=1;
470    if isfield(XmlData,'GeometryCalib')
471        tsai=XmlData.GeometryCalib;
472        if isfield(tsai,'f') && isfield(tsai,'Tz') && isfield(tsai,'dpx') && isfield(tsai,'dpy')&& isfield(tsai,'R')
473            rot2D=tsai.R(1:2,[1,2]);
474            pxcmx_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpx);
475            pxcmy_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpy);
476        end
477        if isfield(tsai,'CoordUnit')
478            CoordUnit=tsai.CoordUnit;
479        end
480    end
481elseif strcmp(ext_imadoc,'.civ')% case of .civ image documentation file
482    [error,time,TimeUnit,mode,npx,npy]=read_imatext([RootName '.civ']);
483    if error==2, msgbox_uvmat('WARNING',['no file ' RootName '.civ']);
484    elseif error==1, msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file');
485    end
486    nom_type_ima='001a';
487elseif strcmpi(ext_imadoc,'.avi')
488    nom_type_ima='*';
489    ext_ima=ext_imadoc;
490    set(handles.ListPairMode,'Value',1);
491    set(handles.ListPairMode,'String',{'series(Di)'})
492    dt=0.04;%default
493    if exist([RootName ext_imadoc],'file')==2
494        info=aviinfo([RootName ext_imadoc]);%read infos on the avi movie
495        dt=1/info.FramesPerSecond;%time interval between successive frames
496        nbfield=info.NumFrames;%number of frames
497    end
498    time=(dt*(0:nbfield-1))';%list of image times
499end
500if isempty(time)
501    set(handles.ImaDoc,'String',''); %xml file not used for timing
502end
503set(handles.ImaDoc,'BackgroundColor',[1 1 1])% set display box to yellow color
504
505
506%% timing display
507%show the reference image edit box if relevant (not needed for movies or in the absence of time information
508if ~isempty(time)
509    if size(time,1)+size(time,2)>=3 % if there are at least two time values to define dt
510        nbfield=size(time,1);
511        nbfield2=size(time,2);
512        set(handles.ImaDoc,'UserData',time); %store the set of times
513        set(handles.dt_unit,'String',['dt in m' TimeUnit]);
514        set(handles.TimeUnit,'String',TimeUnit);
515        set(handles.nb_field,'String',num2str(nbfield));
516        set(handles.nb_field2,'String',num2str(nbfield2));
517    end
518end
519set(handles.CoordUnit,'String',CoordUnit)
520set(handles.SearchRange,'UserData',[pxcmx_search pxcmy_search]);
521set(handles.ImaExt,'String',ext_ima)
522set(handles.ref_i,'String',num2str(num_ref_i))
523set(handles.first_i,'String',num2str(num_ref_i));
524set(handles.last_i,'String',num2str(num_ref_i));%
525set(handles.ref_j,'String',num2str(num_ref_j))
526set(handles.first_j,'String',num2str(num_ref_j));
527set(handles.last_j,'String',num2str(num_ref_j));%
528
529%% set the civ options depending on the input file content
530ind_opening=0;%default
531if isequal(ext_input,'.nc')
532    browse.nom_type_nc=nom_type_input;
533    ind_opening=2;% propose 'fix' as the default option
534    Data=nc2struct(fileinput,'ListGlobalAttribute','CivStage','absolut_time_T0','fix','patch','civ2','fix2');
535    if isfield(Data,'Txt')
536        msgbox_uvmat('ERROR',Data.Txt)
537        return
538    end
539    if ~isempty(Data.CivStage)%test for civ files
540        ind_opening=Data.CivStage;
541        set(handles.ListPairMode,'Value',3)
542    end
543end
544ListOptions={'CheckCiv1', 'CheckFix1' 'CheckPatch1', 'CheckCiv2', 'CheckFix2', 'CheckPatch2'};
545for index = 1:ind_opening
546    set(handles.(ListOptions{index}),'value',0)
547end
548for index = ind_opening+1
549    set(handles.(ListOptions{index}),'value',1)
550end
551update_CivOptions(handles)
552
553
554%%  set the menus of image pairs and default selection for civ   %%%%%%%%%%%%%%%%%%%
555test_ima_i=numel(nom_type_ima)>1 && isempty(regexp(nom_type_ima(2:end),'\D','once'));%images with single indexing
556if test_ima_i || isequal(nom_type_nc,'_i1-i2')||~(exist('nbfield2','var')&&(nbfield2~=1))
557    set(handles.ListPairMode,'Value',1)
558    set(handles.ListPairMode,'String',{'series(Di)'})   
559elseif (nbfield==1)% simple series in j
560    set(handles.ListPairMode,'Value',1)
561    set(handles.ListPairMode,'String',{'series(Dj)'})
562else
563    set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)';'series(Di)'})%multiple choice
564    if nbfield2 <= 10
565        set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' for small burst
566    end
567end
568
569%% update the subdirectory display
570listot=dir(RootPath);%directory of RootPath
571idir=0;
572listdir={''};%default
573% get the list of existing civ subdirectories in the path of theinput root  file
574for ilist=1:length(listot)
575    if listot(ilist).isdir
576        name=listot(ilist).name;
577        if ~isequal(name,'.') && ~isequal(name,'..')
578            idir=idir+1;
579            listdir{idir,1}=listot(ilist).name;
580        end
581    end
582end
583Value=find(strcmp(subdir,listdir));%search the index of subdir in the cell listdir
584if isempty(Value)% if the input subdir is not found
585    ValueCiv1=get(handles.ListSubdirCiv1,'Value');%read the currrently selected dir name
586    if ValueCiv1>numel(listdir)
587        ValueCiv1=1;
588    end
589    set(handles.txt_SubdirCiv1,'String',listdir{ValueCiv1})
590    ValueCiv2=get(handles.ListSubdirCiv2,'Value');
591    if ValueCiv2>numel(listdir)
592        ValueCiv2=1;
593    end
594    set(handles.txt_SubdirCiv2,'String',listdir{ValueCiv2})
595else
596    ValueCiv1=Value;
597    ValueCiv2=Value;
598     set(handles.txt_SubdirCiv1,'String',listdir{Value})
599     set(handles.txt_SubdirCiv2,'String',listdir{Value})
600end
601set(handles.ListSubdirCiv1,'Value',ValueCiv1)
602set(handles.ListSubdirCiv2,'Value',ValueCiv2)
603set(handles.ListSubdirCiv1,'String',[listdir;'new...'])
604set(handles.ListSubdirCiv2,'String',[listdir;'new...'])
605if isempty(listdir)
606    set(handles.txt_SubdirCiv1,'String','CIV')
607    set(handles.txt_SubdirCiv2,'String','CIV')
608end
609
610%% store info
611browse.nom_type_ima=nom_type_ima;
612set(handles.RootName,'UserData',browse)% store the nomenclature type
613
614%% list the possible index pairs, depending on the option set in ListPairMode
615ListPairMode_Callback([], [], handles)
616
617%% store the root input filename for future opening
618profil_perso=fullfile(prefdir,'uvmat_perso.mat');
619% RootPath=fileparts(RootName);
620if exist(profil_perso,'file')
621    save (profil_perso,'RootPath','-append'); %store the root name for future opening of uvmat
622else
623    txt=ver('MATLAB');
624    Release=txt.Release;
625    relnumb=str2double(Release(3:4));
626    if relnumb >= 14
627        save (profil_perso,'RootPath','-V6'); %store the root name for future opening of uvmat
628    else
629        save (profil_perso,'RootPath'); %store the root name for future opening of uvmat
630    end
631end
632set(handles.RootName,'BackgroundColor',[1 1 1])
633
634%------------------------------------------------------------------------
635% --- Executes on carriage return on the subdir checkciv1 edit window
636function txt_SubdirCiv1_Callback(hObject, eventdata, handles)
637%------------------------------------------------------------------------
638subdir=get(handles.txt_SubdirCiv1,'String');
639menu_str=get(handles.ListSubdirCiv1,'String');% read the list of subdirectories for update
640ichoice=find(strcmp(subdir,menu_str),1);
641if isempty(ichoice)
642    ilist=numel(menu_str); %select 'new...' in the menu
643else
644    ilist=ichoice;
645end
646set(handles.ListSubdirCiv1,'Value',ilist)% select the selected subdir in the menu
647if get(handles.CheckCiv1,'Value')% if Civ1 is performed
648    set(handles.txt_SubdirCiv2,'String',subdir);% set by default civ2 directory the same as civ1
649    set(handles.ListSubdirCiv2,'Value',ilist)
650else % if Civ1 data already exist
651    find_netcpair_civ1(handles); %update the list of available pairs from netcdf files in the new directory
652end
653
654%------------------------------------------------------------------------
655% --- Executes on carriage return on the subdir checkciv1 edit window
656function txt_SubdirCiv2_Callback(hObject, eventdata, handles)
657%------------------------------------------------------------------------
658subdir=get(handles.txt_SubdirCiv1,'String');
659menu_str=get(handles.ListSubdirCiv2,'String');% read the list of subdirectories for update
660ichoice=find(strcmp(subdir,menu_str),1);
661if isempty(ichoice)
662    ilist=numel(menu_str); %select 'new...' in the menu
663else
664    ilist=ichoice;
665end
666set(handles.ListSubdirCiv2,'Value',ilist)% select the selected subdir in the menu
667%update the list of available pairs from netcdf files in the new directory
668if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
669    find_netcpair_civ2(handles);
670end
671
672%------------------------------------------------------------------------
673% --- Executes on button press in CheckCiv1.
674function CheckCiv1_Callback(hObject, eventdata, handles)
675%------------------------------------------------------------------------
676update_CivOptions(handles)
677
678%------------------------------------------------------------------------
679% --- Executes on button press in CheckFix1.
680function CheckFix1_Callback(hObject, eventdata, handles)
681%------------------------------------------------------------------------
682update_CivOptions(handles)
683
684%------------------------------------------------------------------------
685% --- Executes on button press in CheckPatch1.
686function CheckPatch1_Callback(hObject, eventdata, handles)
687%------------------------------------------------------------------------
688update_CivOptions(handles)
689
690%------------------------------------------------------------------------
691% --- Executes on button press in CheckCiv2.
692function CheckCiv2_Callback(hObject, eventdata, handles)
693%------------------------------------------------------------------------
694update_CivOptions(handles)
695
696%------------------------------------------------------------------------
697% --- Executes on button press in CheckFix2.
698function CheckFix2_Callback(hObject, eventdata, handles)
699%------------------------------------------------------------------------
700update_CivOptions(handles)
701
702%------------------------------------------------------------------------
703% --- Executes on button press in CheckPatch2.
704function CheckPatch2_Callback(hObject, eventdata, handles)
705%------------------------------------------------------------------------
706update_CivOptions(handles)
707
708%------------------------------------------------------------------------
709% --- activated by any checkbox controling the selection of Civ1,Fix1,Patch1,Civ2,Fix2,Patch2
710function update_CivOptions(handles)
711%------------------------------------------------------------------------
712checkbox=zeros(1,6);
713checkbox(1)=get(handles.CheckCiv1,'Value');
714checkbox(2)=get(handles.CheckFix1,'Value');
715checkbox(3)=get(handles.CheckPatch1,'Value');
716checkbox(4)=get(handles.CheckCiv2,'Value');
717checkbox(5)=get(handles.CheckFix2,'Value');
718checkbox(6)=get(handles.CheckPatch2,'Value');
719ind_selected=find(checkbox,1);
720if ~isempty(ind_selected)
721  RootName=get(handles.RootName,'String');
722    if isempty(RootName)
723         msgbox_uvmat('ERROR','Please open an image or PIV .nc file with the upper bar menu Open/Browse...')
724        return
725    end
726end
727set(handles.PairIndices,'Visible','on')
728set(handles.txt_SubdirCiv1,'Visible','on')
729set(handles.ListSubdirCiv1,'Visible','on')
730find_netcpair_civ1(handles) % select the available netcdf files
731if max(checkbox(4:6))% case of civ2 pair choice needed
732    set(handles.TitlePairCiv2,'Visible','on')
733    set(handles.TitleSubdirCiv2,'Visible','on')
734    set(handles.txt_SubdirCiv2,'Visible','on')
735    set(handles.ListSubdirCiv2,'Visible','on')
736    set(handles.ListPairCiv2,'Visible','on')
737    find_netcpair_civ2(handles) % select the available netcdf files
738else
739    set(handles.TitleSubdirCiv2,'Visible','off')
740    set(handles.txt_SubdirCiv2,'Visible','off')
741    set(handles.ListSubdirCiv2,'Visible','off')
742    set(handles.ListPairCiv2,'Visible','off')
743end
744options={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'};
745for ilist=1:length(options)
746    if checkbox(ilist)
747        set(handles.(options{ilist}),'Visible','on')
748    else
749        set(handles.(options{ilist}),'Visible','off')
750    end
751end
752
753%------------------------------------------------------------------------
754% --- Executes on button press in RUN: processing on local computer
755function RUN_Callback(hObject, eventdata, handles)
756%------------------------------------------------------------------------
757set(handles.RUN, 'Enable','Off')
758set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
759batch=0;
760errormsg=launch_jobs(hObject, eventdata, handles,batch);
761set(handles.RUN, 'Enable','On')
762set(handles.RUN,'BackgroundColor',[1 0 0])
763
764% start status callback to visualise results
765if ~isempty(errormsg)
766    display(errormsg)
767    msgbox_uvmat('ERROR',errormsg)
768elseif  isfield(handles,'status') %&& ~isequal(get(handles.ListPairMode,'Value'),3)
769    set(handles.status,'Value',1);%suppress status display
770    status_Callback(hObject, eventdata, handles)
771end
772
773%------------------------------------------------------------------------
774% --- Executes on button press in BATCH: remote processing
775function BATCH_Callback(hObject, eventdata, handles)
776% -----------------------------------------------------------------------
777set(handles.BATCH, 'Enable','Off')
778set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])
779batch=1;
780errormsg=launch_jobs(hObject, eventdata, handles, batch);
781set(handles.BATCH, 'Enable','On')
782set(handles.BATCH,'BackgroundColor',[1 0 0])
783
784% start status callback to visualise results
785if ~isempty(errormsg)
786    display(errormsg)
787    msgbox_uvmat('ERROR',errormsg)
788elseif isfield(handles,'status')
789    set(handles.status,'Value',1);%suppress status display
790    status_Callback(hObject, eventdata, handles)
791end
792
793%-------------------------------------------------------------------
794% --- Executes on button press in status.
795function status_Callback(hObject, eventdata, handles)
796%-------------------------------------------------------------------
797val=get(handles.status,'Value');
798if val==0
799    set(handles.status,'BackgroundColor',[0 1 0])
800    hfig=findobj(allchild(0),'name','civ_status');
801    if ~isempty(hfig)
802        delete(hfig)
803    end
804    return
805end
806set(handles.status,'BackgroundColor',[1 1 0])
807drawnow
808listtype={'civ1','fix1','patch1','civ2','fix2','patch2'};
809Param.CheckCiv1=get(handles.CheckCiv1,'Value');
810Param.CheckFix1=get(handles.CheckFix1,'Value');
811Param.CheckPatch1=get(handles.CheckPatch1,'Value');
812Param.CheckCiv2=get(handles.CheckCiv2,'Value');
813Param.CheckFix2=get(handles.CheckFix2,'Value');
814Param.CheckPatch2=get(handles.CheckPatch2,'Value');
815box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2];
816
817option_civ=find(box_test,1,'last');%last selected option (non-zero index of box_test)
818filecell=get(handles.civ,'UserData');%retrieve the list of output files expected for PIV
819test_new=0;
820if ~isfield(filecell,'nc')
821    test_new=1;
822    [ref_i,ref_j,errormsg]=find_ref_indices(handles);
823    if ~isempty(errormsg)
824        msgbox_uvmat('ERROR',errormsg)
825        return
826    end
827    filecell=set_civ_filenames(handles,ref_i,ref_j,box_test);%determine the output file expected from the GUI status
828end
829if ~isequal(box_test(4:6),[0 0 0])
830    civ_files=filecell.nc.civ2;%case of civ2 operations
831else
832    civ_files=filecell.nc.civ1;
833end
834[root,filename,ext]=fileparts(civ_files{1});
835[rootroot,subdir,extdir]=fileparts(root);
836hfig=findobj(allchild(0),'name','civ_status');
837if isempty(hfig)
838    hfig=figure('DeleteFcn',@stop_status);
839    set(hfig,'name','civ_status')
840    hlist=uicontrol('Style','listbox','Units','normalized', 'Position',[0.05 0.09 0.9 0.71], 'Callback', @open_view_field,'tag','list');
841    uicontrol('Style','edit','Units','normalized', 'Position', [0.05 0.87 0.9 0.1],'tag','msgbox','Max',2,'String','checking files...');
842    uicontrol('Style','frame','Units','normalized', 'Position', [0.05 0.81 0.9 0.05]);
843    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);
844    BarPosition=[0.05 0.81 0.01 0.05];
845    hwaitbar=uicontrol('Style','frame','Units','normalized', 'Position',BarPosition ,'BackgroundColor',[1 0 0],'tag','waitbar');
846    drawnow
847end
848% datnum=[];
849Tabchar={};
850nbfiles=numel(civ_files);
851count=0;
852testrecent=0;
853while count<nbfiles
854    count=0;
855    datnum=zeros(1,nbfiles);
856    for ifile=1:nbfiles
857        detect=exist(civ_files{ifile},'file'); % check the existence of the file
858        option=0;
859        if detect==0
860            option_str='not created';
861        else
862            datfile=dir(civ_files{ifile});
863            if isfield(datfile,'datenum')
864                datnum(ifile)=datfile.datenum;%only available in recent matlab versions
865                testrecent=1;
866            end
867            filefound(ifile)={datfile.name};
868            lastfield='';
869            % check the content  netcdf file
870            Data=nc2struct(civ_files{ifile},'ListGlobalAttribute','patch2','fix2','civ2','patch','fix');
871            if ~isempty(Data.patch2) && isequal(Data.patch2,1)
872                option=6;
873                option_str='patch2';
874            elseif ~isempty(Data.fix2) && isequal(Data.fix2,1)
875                option=5;
876                option_str='fix2';
877            elseif ~isempty(Data.civ2) && isequal(Data.civ2,1);
878                option=4;
879                option_str='civ2';
880            elseif ~isempty(Data.patch) && isequal(Data.patch,1);
881                option=3;
882                option_str='patch1';
883            elseif ~isempty(Data.fix) && isequal(Data.fix,1);
884                option=2;
885                option_str='fix1';
886            else
887                option=1;
888                option_str='civ1';
889            end
890        end
891        if option >= option_civ
892            count=count+1;
893        end
894        [rr,filename,ext]=fileparts(civ_files{ifile});
895        Tabchar{ifile,1}=[fullfile([subdir extdir],filename) ext  '...' option_str];
896    end
897    datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
898    if isempty(datnum)
899        if testrecent
900            message='no civ result created yet';
901        else
902            message='';
903        end
904    else
905        datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
906        [first,ind]=min(datnum);
907        [last,indlast]=max(datnum);
908        if test_new
909            message='existing file status, no processing launched yet';
910        else
911        message={[num2str(count) ' file(s) done over ' num2str(nbfiles)] ;['oldest modification:  ' cell2mat(filefound(ind)) ' : ' datestr(first)];...
912            ['latest modification:  ' cell2mat(filefound(indlast)) ' : ' datestr(last)]};
913        end
914    end
915    hfig=findobj(allchild(0),'name','civ_status');
916    if isempty(hfig)% the status list has been deleted
917        return
918    else
919        hlist=findobj(hfig,'tag','list');
920        hmsgbox=findobj(hfig,'tag','msgbox');
921        hwaitbar=findobj(hfig,'tag','waitbar');
922        set(hlist,'String',Tabchar)
923        set(hmsgbox,'String', message)
924        if count>0 && ~test_new
925            BarPosition(3)=0.9*count/nbfiles;
926            set(hwaitbar,'Position',BarPosition)
927        end
928    end
929    set(hlist,'UserData',rootroot)
930    if count<10||(nbfiles-count)<10
931    pause(.5)% wait 0.5 seconds for next check
932    else
933        pause(10)% wait 10 seconds for next check
934    end
935end
936
937%------------------------------------------------------------------------
938% --- Main lauch command, called by RUN and BATCH
939function errormsg=launch_jobs(hObject, eventdata, handles, batch)
940%-----------------------------------------------------------------------
941errormsg='';%default
942
943%% read the input parameters from the  GUI civ
944Param=read_GUI(handles.civ);
945
946%% check the selected list of operations:
947operations={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'};
948box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2];
949index_first=find(box_test==1,1);
950if isempty(index_first)
951    errormsg='no selected operation';
952    return
953end
954index_last=find(box_test==1,1,'last');
955box_used=box_test(index_first : index_last);
956[box_missing,ind_missing]=min(box_used);
957if isequal(box_missing,0); %there is a missing step in the sequence of operations
958    errormsg=['missing' cell2mat(operations(ind_missing))];
959    return
960end
961
962%% check mask if selecetd
963%could be included in get_mask callback ?
964if isequal(get(handles.CheckMask,'Value'),1)
965    maskname=get(handles.txt_Mask,'String');
966    if ~exist(maskname,'file')
967        get_mask_civ1_Callback(hObject, eventdata, handles);
968    end
969end
970if isequal(get(handles.CheckMask,'Value'),1)
971    maskname=get(handles.txt_Mask,'String');
972    if ~exist(maskname,'file')
973        get_mask_fix1_Callback(hObject, eventdata, handles);
974    end
975end
976if isequal(get(handles.CheckMask,'Value'),1)
977    maskname=get(handles.txt_Mask,'String');
978    if ~exist(maskname,'file')
979        get_mask_civ2_Callback(hObject, eventdata, handles);
980    end
981end
982if isequal(get(handles.CheckMask,'Value'),1)
983    maskname=get(handles.txt_Mask,'String');
984    if ~exist(maskname,'file')
985        get_mask_fix2_Callback(hObject, eventdata, handles);
986    end
987end
988
989%% reinitialise status callback
990if isfield(handles,'status')
991    set(handles.status,'Value',0);%suppress status display
992    status_Callback(hObject, eventdata, handles)
993end
994
995%% read the PARAM.xml file to get the binaries (and batch_mode if batch)
996path_civ=fileparts(which('civ')); %path to the source directory of uvmat
997xmlfile='PARAM.xml';
998if exist(xmlfile,'file')% search parameter xml file in the whole matlab path
999    t=xmltree(xmlfile);
1000    s=convert(t);
1001else
1002    errormsg=['no file ' xmlfile];
1003    return
1004end
1005test_interp=0; %eviter les variables test_ (LG)
1006if batch
1007    if isfield(s,'BatchParam')
1008        Param.xml=s.BatchParam;
1009        if isfield(Param.xml,'BatchMode')
1010            batch_mode=Param.xml.BatchMode;
1011            if ~ismember(batch_mode,{'sge','oar'})
1012                errormsg=['batch mode ' batch_mode ' not supported by UVMAT'];
1013                return
1014            end
1015        end
1016    else
1017        errormsg='no batch civ binaries defined in PARAM.xml';
1018        return
1019    end
1020else % run
1021    if isfield(s,'RunParam')
1022        Param.xml=s.RunParam;
1023    else
1024        msgbox_uvmat('ERROR','no run civ binaries defined in PARAM.xml')
1025        return
1026    end
1027end
1028
1029%% check batch mode supported
1030if batch
1031    switch batch_mode
1032        case 'sge'
1033            test_command='qstat';
1034        case 'oar'
1035            test_command='oarstat';
1036    end   
1037    [s,w]=system(test_command);
1038    if ~isequal(s,0)
1039        msgbox_uvmat('ERROR',[batch_mode ' batch system not available'])
1040        return
1041    end
1042end
1043
1044%% check if the binaries exist
1045if isequal(get(handles.MenuMatlab,'checked'),'on')
1046    CivMode='Matlab';
1047else
1048    CivMode='CivX';
1049end
1050binary_list={};
1051switch CivMode
1052    case 'CivX'
1053        binary_list={'Civ1Bin','Civ2Bin','PatchBin','FixBin'};
1054    case 'CivAll'
1055        binary_list={'Civ'};
1056    case 'Matlab'
1057        if batch
1058            % vérifier MenuMatlab installé sur le cluster
1059            % difficile a faire a priori
1060        end         
1061end
1062for bin_name=binary_list %loop on the list of binaries
1063    if isfield(Param.xml,bin_name{1})% bin_name{1} =current name in the list
1064        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
1065            fullname=fullfile(path_civ,Param.xml.(bin_name{1}));
1066            if exist(fullname,'file')
1067                Param.xml.(bin_name{1})=fullname;
1068            else
1069                msgbox_uvmat('ERROR',['Binary ' Param.xml.(bin_name{1}) ' defined in PARAM.xml does not exist'])
1070                return
1071            end
1072        else
1073            [path,name,ext]=fileparts(Param.xml.(bin_name{1}));
1074            currentdir=pwd;
1075            cd(path);
1076            binpath=pwd;%path of the binary
1077            Param.xml.(bin_name{1})=fullfile(binpath,[name ext]);
1078            cd(currentdir);
1079        end
1080       
1081    end
1082end
1083display('files OK, processing...')
1084
1085%% set the list of files and check them
1086display('checking the files...')
1087[ref_i,ref_j,errormsg]=find_ref_indices(handles);
1088if ~isempty(errormsg)
1089    return
1090end
1091[filecell,i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,xx,yy,compare]=...
1092    set_civ_filenames(handles,ref_i,ref_j,box_test);
1093Rootbat=fileparts(filecell.nc.civ1{1,1});%output netcdf file (without extention)
1094set(handles.civ,'UserData',filecell);%store for futur use of status callback
1095if isempty(filecell)% (error message displayed in fct set_civ_filenames)
1096    return
1097end
1098nbfield=numel(i1_civ1);
1099nbslice=numel(j1_civ1);
1100
1101%% MAIN LOOP
1102time=get(handles.ImaDoc,'UserData'); %get the set of times
1103batch_file_list=[];
1104 
1105for ifile=1:nbfield
1106    for j=1:nbslice
1107        % initiate system command
1108        switch CivMode
1109            case 'CivX'
1110                if isunix % check: necessaire aussi en RUN?
1111                    cmd=['#!/bin/bash \n '...
1112                        '#$ -cwd \n '...
1113                        'hostname && date \n '...
1114                        'umask 002 \n'];%allow writting access to created files for user group
1115                else
1116                    cmd=[];
1117                end
1118            case 'CivAll'
1119                CivAllxml=xmltree;% xml contents,  all parameters
1120                CivAllCmd='';
1121                CivAllxml=set(CivAllxml,1,'name','CivDoc');
1122        end
1123           
1124        % define output file name
1125        if Param.CheckCiv2==1 || Param.CheckFix2==1 || Param.CheckPatch2==1
1126            OutputFile=filecell.nc.civ2{ifile,j};
1127        else
1128            OutputFile=filecell.nc.civ1{ifile,j};
1129        end
1130        OutputFile=regexprep(OutputFile,'.nc','');
1131       
1132        if Param.CheckCiv1
1133            % read image-dependent parameters
1134            Param.Civ1.ImageA=filecell.ima1.civ1{ifile,j};
1135            Param.Civ1.ImageB=filecell.ima2.civ1{ifile,j};
1136            if size(time,1)>=i2_civ1(ifile) && size(time,2)>=j2_civ1(j)
1137                Param.Civ1.Dt=(time(i2_civ1(ifile),j2_civ1(j))-time(i1_civ1(ifile),j1_civ1(j)));
1138                Param.Civ1.Time=((time(i2_civ1(ifile),j2_civ1(j))+time(i1_civ1(ifile),j1_civ1(j)))/2);
1139            else
1140                Param.Civ1.Dt=1;
1141                Param.Civ1.Time=0;
1142            end
1143            Param.Civ1.term_a=num2stra(j1_civ1(j),nom_type_nc);%UTILITE?
1144            Param.Civ1.term_b=num2stra(j2_civ1(j),nom_type_nc);%   
1145            ImageInfo=imfinfo(filecell.ima1.civ1{1,1});%read the first image to get the size
1146            Param.Civ1.ImageWidth=ImageInfo.Width;
1147            Param.Civ1.ImageHeight=ImageInfo.Height;
1148            Param.Civ1.ImageBitDepth=ImageInfo.BitDepth;
1149            % read mask parameters
1150            if Param.Civ1.CheckMask % the lines below should be changed with the new gui
1151                if ~exist(Param.Civ1.Mask,'file')
1152                    maskbase=[filecell.filebase '_' Param.Civ1.Mask]; %
1153                    nbslice_mask=str2double(Param.Civ1.Mask(1:end-4)); %
1154                    i1_mask=mod(i1_civ1(ifile)-1,nbslice_mask)+1;
1155                    Param.Civ1.Mask=name_generator(maskbase,i1_mask,1,'.png','_i');
1156                end
1157            end
1158            % read grid parameters
1159            if Param.Civ1.CheckGrid
1160                if numel(Param.Civ1.Grid)>=4 && isequal(Param.Civ1.Grid(end-3:end),'grid')
1161                    nbslice_grid=str2double(Param.Civ1.Grid(1:end-4)); %
1162                    if ~isnan(nbslice_grid)
1163                        i1_grid=mod(i1_civ1(ifile)-1,nbslice_grid)+1;
1164                        Param.Civ1.Grid=[filecell.filebase '_' name_generator(Param.Civ1.Grid,i1_grid,1,'.grid','_i')];
1165                        if ~exist(Param.Civ1.GridName,'file')
1166                            msgbox_uvmat('ERROR','grid file absent for civ1')
1167                        end
1168                    elseif ~exist(Param.Civ1.Grid,'file')
1169                        msgbox_uvmat('ERROR','grid file absent for civ1')
1170                    end
1171                end
1172            end
1173           
1174            % send command
1175            switch CivMode
1176                case 'CivX'
1177                    cmd=[cmd...
1178                        cmd_civ1(filecell.nc.civ1{ifile,j},Param) '\n'];
1179                case 'CivAll'
1180                    CivAllCmd=[CivAllCmd ' civ1 '];
1181                    str=CIV1_CMD_Unified(filecell.nc.civ1{ifile,j},'',Param.Civ1);
1182                    fieldnames=fields(str);
1183                    [CivAllxml,uid_civ1]=add(CivAllxml,1,'element','civ1');
1184                    for ilist=1:length(fieldnames)
1185                        val=eval(['str.' fieldnames{ilist}]);
1186                        if ischar(val)
1187                            [CivAllxml,uid_t]=add(CivAllxml,uid_civ1,'element',fieldnames{ilist});
1188                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1189                        end
1190                    end
1191            end
1192        end
1193       
1194        if Param.CheckFix1
1195            switch CivMode
1196                case 'CivX'
1197                    cmd=[cmd...
1198                        cmd_fix(filecell.nc.civ1{ifile,j},Param,'Fix1') '\n'];
1199                case 'CivAll'%to abandon
1200                    fix1.inputFileName=filecell.nc.civ1{ifile,j} ;
1201                    fix1.fi1=num2str(param.fix1.flagindex1(1));
1202                    fix1.fi2=num2str(param.fix1.flagindex1(2));
1203                    fix1.fi3=num2str(param.fix1.flagindex1(3));
1204                    fix1.threshC=num2str(param.fix1.thresh_vecC1);
1205                    fix1.threshV=num2str(param.fix1.thresh_vel1);
1206                    fieldnames=fields(fix1);
1207                    [CivAllxml,uid_fix1]=add(CivAllxml,1,'element','fix1');
1208                    for ilist=1:length(fieldnames)
1209                        val=eval(['fix1.' fieldnames{ilist}]);
1210                        if ischar(val)
1211                            [CivAllxml,uid_t]=add(CivAllxml,uid_fix1,'element',fieldnames{ilist});
1212                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1213                        end
1214                    end
1215                    CivAllCmd=[CivAllCmd ' fix1 '];
1216            end
1217        end
1218       
1219        %CheckPatch1
1220        if Param.CheckPatch1==1
1221            switch CivMode
1222                case 'CivX'
1223                    cmd=[cmd...
1224                        cmd_patch(filecell.nc.civ1{ifile,j},Param,'Patch1') '\n'];
1225                case 'CivAll'
1226                    patch1.inputFileName=filecell.nc.civ1{ifile,j} ;
1227                    patch1.nopt=subdomain_patch1;
1228                    patch1.maxdiff=thresh_patch1;
1229                    patch1.ro=rho_patch1;
1230                    test_grid=get(handles.get_gridpatch1,'Value');
1231                    if test_grid
1232                        patch1.gridflag='y';
1233                        gridname=get(handles.grid_patch1,'String');
1234                        if isequal(gridname(end-3:end),'grid')
1235                            nbslice_grid=str2double(gridname(1:end-4)); %
1236                            if ~isnan(nbslice_grid)
1237                                i1_grid=mod(i1_civ1(ifile)-1,nbslice_grid)+1;
1238                                patch1.gridPatch=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')];
1239                                if ~exist(patch1.gridPatch,'file')
1240                                    msgbox_uvmat('ERROR','grid file absent for patch1')
1241                                end
1242                            elseif exist(gridname,'file')
1243                                patch1.gridPatch=gridname;
1244                            else
1245                                msgbox_uvmat('ERROR','grid file absent for patch1')
1246                            end
1247                        end
1248                    else
1249                        patch1.gridPatch='none';
1250                        patch1.gridflag='n';
1251                        patch1.m=nx_patch1;
1252                        patch1.n=ny_patch1;
1253                    end
1254                    patch1.convectFlow='n';
1255                    fieldnames=fields(patch1);
1256                    [CivAllxml,uid_patch1]=add(CivAllxml,1,'element','patch1');
1257                    for ilist=1:length(fieldnames)
1258                        val=eval(['patch1.' fieldnames{ilist}]);
1259                        if ischar(val)
1260                            [CivAllxml,uid_t]=add(CivAllxml,uid_patch1,'element',fieldnames{ilist});
1261                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1262                        end
1263                    end
1264                    CivAllCmd=[CivAllCmd ' patch1 '];
1265            end
1266        end
1267        if Param.CheckCiv2==1
1268            Param.Civ2.ImageA=filecell.ima1.civ2{ifile,j};
1269            Param.Civ2.ImageB=filecell.ima2.civ2{ifile,j};
1270            if size(time,1)>=i2_civ2(ifile) && size(time,2)>=j2_civ2(j)
1271                Param.Civ2.Dt=num2str(time(i2_civ2(ifile),j2_civ2(j))-time(i1_civ2(ifile),j1_civ2(j)));
1272                Param.Civ2.Time=num2str((time(i2_civ2(ifile),j2_civ2(j))+time(i1_civ2(ifile),j1_civ2(j)))/2);
1273            else
1274                Param.Civ2.Dt=1;
1275                Param.Civ2.Time=0;
1276            end
1277            Param.Civ2.term_a=num2stra(j1_civ2(j),nom_type_nc);
1278            Param.Civ2.term_b=num2stra(j2_civ2(j),nom_type_nc);
1279            Param.Civ2.filename_nc1=filecell.nc.civ1{ifile,j};
1280            Param.Civ2.filename_nc1(end-2:end)=[]; % remove '.nc'
1281           
1282            % mask
1283            if Param.Civ2.CheckMask
1284                if ~exist(Param.Civ2.Mask,'file')
1285                    maskbase=[filecell.filebase '_' Param.Civ2.Mask]; %
1286                    nbslice_mask=str2double(Param.Civ2.Mask(1:end-4)); %
1287                    i1_mask=mod(i1_civ2(ifile)-1,nbslice_mask)+1;
1288                    Param.Civ2.Mask=name_generator(maskbase,i1_mask,1,'.png','_i');
1289                end
1290            end
1291            %grid
1292            if Param.Civ2.CheckGrid
1293                if numel(Param.Civ2.Grid)>=4 && isequal(Param.Civ2.Grid(end-3:end),'grid')
1294                    nbslice_grid=str2double(Param.Civ2.Grid(1:end-4)); %
1295                    if ~isnan(nbslice_grid)
1296                        i1_grid=mod(i1_civ2(ifile)-1,nbslice_grid)+1;
1297                        Param.Civ2.Grid=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')];
1298                    end
1299                end
1300            end
1301            ImageInfo=imfinfo(filecell.ima1.civ2{1,1});%read the first image to get the size
1302            Param.Civ2.ImageWidth=ImageInfo.Width;
1303            Param.Civ2.ImageHeight=ImageInfo.Height;
1304            Param.Civ2.ImageBitDepth=ImageInfo.BitDepth;
1305            % TODO: case of movie   
1306            switch CivMode
1307                case 'CivX'
1308                    cmd=[cmd...
1309                        cmd_civ2(filecell.nc.civ2{ifile,j},Param) '\n'];
1310                case 'CivAll'
1311                    CivAllCmd=[CivAllCmd ' civ2 '];
1312                    str=CIV2_CMD_Unified(filecell.nc.civ2{ifile,j},'',Param.Civ2);
1313                    fieldnames=fields(str);
1314                    [CivAllxml,uid_civ2]=add(CivAllxml,1,'element','civ2');
1315                    for ilist=1:length(fieldnames)
1316                        val=eval(['str.' fieldnames{ilist}]);
1317                        if ischar(val)
1318                            [CivAllxml,uid_t]=add(CivAllxml,uid_civ2,'element',fieldnames{ilist});
1319                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1320                        end
1321                    end
1322            end
1323        end
1324       
1325        % CheckFix2
1326        if Param.CheckFix2==1
1327            switch CivMode
1328                case 'CivX'
1329                    cmd=[cmd...
1330                        cmd_fix(filecell.nc.civ2{ifile,j},Param,'Fix2') '\n'];
1331                case 'CivAll'
1332                    fix2.inputFileName=filecell.nc.civ2{ifile,j} ;
1333                    fix2.fi1=num2str(flagindex2(1));
1334                    fix2.fi2=num2str(flagindex2(2));
1335                    fix2.fi3=num2str(flagindex2(3));
1336                    fix2.threshC=num2str(thresh_vec2C);
1337                    fix2.threshV=num2str(thresh_vel2);
1338                    fieldnames=fields(fix2);
1339                    [CivAllxml,uid_fix2]=add(CivAllxml,1,'element','fix2');
1340                    for ilist=1:length(fieldnames)
1341                        val=eval(['fix2.' fieldnames{ilist}]);
1342                        if ischar(val)
1343                            [CivAllxml,uid_t]=add(CivAllxml,uid_fix2,'element',fieldnames{ilist});
1344                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1345                        end
1346                    end
1347                    CivAllCmd=[CivAllCmd ' fix2 '];
1348            end
1349        end
1350       
1351        %CheckPatch2
1352        if Param.CheckPatch2==1
1353           
1354            switch CivMode
1355               
1356                case 'CivX'
1357                    cmd=[cmd...
1358                        cmd_patch(filecell.nc.civ1{ifile,j},Param,'Patch2') '\n'];
1359                   
1360                case 'CivAll'
1361                    patch2.inputFileName=filecell.nc.civ1{ifile,j} ;
1362                    patch2.nopt=subdomain_patch2;
1363                    patch2.maxdiff=thresh_patch2;
1364                    patch2.ro=rho_patch2;
1365                    test_grid=get(handles.get_gridpatch2,'Value');
1366                    if test_grid
1367                        patch2.gridflag='y';
1368                        gridname=get(handles.grid_patch2,'String');
1369                        if isequal(gridname(end-3:end),'grid')
1370                            nbslice_grid=str2double(gridname(1:end-4)); %
1371                            if ~isnan(nbslice_grid)
1372                                i1_grid=mod(i1_civ2(ifile)-1,nbslice_grid)+1;
1373                                patch2.gridPatch=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')];
1374                                if ~exist(patch2.gridPatch,'file')
1375                                    msgbox_uvmat('ERROR','grid file absent for patch2')
1376                                end
1377                            elseif exist(gridname,'file')
1378                                patch2.gridPatch=gridname;
1379                            else
1380                                msgbox_uvmat('ERROR','grid file absent for patch2')
1381                            end
1382                        end
1383                    else
1384                        patch2.gridPatch='none';
1385                        patch2.gridflag='n';
1386                        patch2.m=nx_patch2;
1387                        patch2.n=ny_patch2;
1388                    end
1389                    patch2.convectFlow='n';
1390                    fieldnames=fields(patch2);
1391                    [CivAllxml,uid_patch2]=add(CivAllxml,1,'element','patch2');
1392                    for ilist=1:length(fieldnames)
1393                        val=eval(['patch2.' fieldnames{ilist}]);
1394                        if ischar(val)
1395                            [CivAllxml,uid_t]=add(CivAllxml,uid_patch2,'element',fieldnames{ilist});
1396                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1397                        end
1398                    end
1399                    CivAllCmd=[CivAllCmd ' patch2 '];
1400            end
1401        end
1402       
1403        switch CivMode
1404           
1405            case {'CivX','CivAll'}
1406                if isequal(CivMode,'CivAll')
1407                    save(CivAllxml,[OutputFile '.xml']);
1408                    cmd=[cmd sparam.CivBin ' -f ' OutputFile '.xml '  CivAllCmd ' >' OutputFile '.log' '\n'];
1409                end             
1410                % create the .bat file used in run or batch
1411                filename_bat=[OutputFile '.bat'];
1412                [fid,message]=fopen(filename_bat,'w');
1413                if isequal(fid,-1)
1414                    msgbox_uvmat('ERROR', ['creation of .bat file: ' message])
1415                    return
1416                end
1417                fprintf(fid,cmd);
1418                fclose(fid);           
1419                if isunix
1420                    system(['chmod +x ' filename_bat]);
1421                end             
1422                batch_file_list{length(batch_file_list)+1}=filename_bat;
1423               
1424            case 'Matlab'
1425                drawnow
1426                if ~strcmp(compare,'stereo PIV')
1427                    [Data,erromsg]=civ_matlab(Param,filecell.nc.civ1{ifile,j});
1428                    if isempty(errormsg)
1429                        display([filecell.nc.civ1{ifile,j} ' written'])
1430                    else
1431                        msgbox_uvmat('ERROR',errormsg)
1432                    end                 
1433                end
1434        end
1435    end
1436end
1437
1438if batch 
1439    switch batch_mode   
1440       
1441        case 'sge'
1442            for p=1:length(batch_file_list)
1443                cmd=['!qsub -p ' pvalue ' -q civ.q -e ' flname '.errors -o ' flname '.log' ' ' batch_file_list{p}];
1444                display(cmd);eval(cmd);
1445            end           
1446        case 'oar_old'
1447                for p=1:length(batch_file_list)
1448                    oar_command=['!oarsub -n CIVX -q nicejob '...
1449                   '-E ' regexprep(batch_file_list{p},'.bat','.errors') ' -O ' regexprep(batch_file_list{p},'.bat','.log ')...
1450                    '-l "/core=1+{type = ''smalljob''}/licence=1,walltime=00:60:00"   ' batch_file_list{p}];
1451                display(oar_command);eval(oar_command);
1452                end               
1453        case 'oar'
1454           
1455            oar_modes={'oar-dispatch','mpilauncher'};
1456            text={'Batch processing on servcalcul3 LEGI';...
1457                'Please choose one of the followint modes';...
1458                '* oar-dispatch : jobs in a container';...
1459                '* mpilauncher : one single job using several cores';...
1460                '**********************************'...
1461                };
1462            [S,v]=listdlg('PromptString',text,'ListString',oar_modes,...
1463                'SelectionMode','single','ListSize',[400 100],'Name','LEGI job mode');
1464            switch oar_modes{S}
1465               
1466                case 'oar-dispatch' %oar-dispatch.pl
1467                    filename_joblist=fullfile(Rootbat,'job_list.txt');
1468                    fid=fopen(filename_joblist,'w');
1469                    walltime_onejob=600;%seconds
1470                    for p=1:length(batch_file_list)
1471                        oar_command=['oarsub -n CIVX '...
1472                            '-E ' regexprep(batch_file_list{p},'\.bat\>','.errors') ' -O ' regexprep(batch_file_list{p},'\.bat\>','.log ')...
1473                            '-l "/core=1,walltime=' datestr(walltime_onejob/86400,13) '"   ' batch_file_list{p}];
1474                        fprintf(fid,[oar_command '\n']);
1475                    end
1476                    fclose(fid);
1477                    ncores=36;
1478                    oar_command=['oarsub -t container -n civx-container '...
1479                        '-l /core=' num2str(ncores)...
1480                        ',walltime=' datestr(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,13)...
1481                        ' "oar-dispatch -f ' filename_joblist '"'];
1482                    filename_oarcommand=fullfile(Rootbat,'oar_command');
1483                    fid=fopen(filename_oarcommand,'w');
1484                    fprintf(fid,[oar_command '\n']);
1485                    fclose(fid);
1486                    display(oar_command);
1487                    eval(['! . ' filename_oarcommand])
1488                case 'mpilauncher'
1489                    filename_joblist=fullfile(Rootbat,'job_list.txt');
1490                    fid=fopen(filename_joblist,'w');
1491                   
1492                    for p=1:length(batch_file_list)
1493                        fprintf(fid,[batch_file_list{p} '\n']);
1494                    end
1495                    fclose(fid)
1496                    text_oarscript=[...
1497                        '#!/bin/bash \n'...
1498                        '#OAR -n Mylauncher \n'...
1499                        '#OAR -l node=4/core=5,walltime=0:15:00 \n'...
1500                        '#OAR -E stderrfile.log \n'...
1501                        '#OAR -O stdoutfile.log \n'...
1502                        '# ========================================================= \n'...
1503                        '# This simple program launch a multinode parallel OpenMPI mpilauncher \n'...
1504                        '# application for coriolis PIV post-processing. \n'...
1505                        '# OAR uses oarshmost wrapper to propagate the user environement. \n'...
1506                        '# This wrapper assert that the user has the same environment on all the \n'...
1507                        '# allocated nodes (basic behavior needed by most MPI applications).  \n'...
1508                        '# \n'...
1509                        '# REQUIREMENT: \n'...
1510                        '# the oarshmost wrapper should be installed in $HOME/bin directory. \n'...
1511                        '# If a different location is used, change the line following the comment "Bidouille" \n'...
1512                        '# ========================================================= \n'...
1513                        '#   USER should only modify these 2 lines  \n'...
1514                        'WORKDIR=' pwd ' \n'...
1515                        'COMMANDE="mpilauncher  -f ' filename_joblist '" \n'...
1516                        '# ========================================================= \n'...
1517                        '# DO NOT MODIFY the FOLOWING LINES. (or be carefull) \n'...
1518                        'echo "job starting on: "`hostname` \n'...
1519                        'MPINODES="-host `tr [\\\\\\n] [,] <$OAR_NODEFILE |sed -e "s/,$/ /"`" \n'...
1520                        'NCPUS=`cat $OAR_NODEFILE |wc -l` \n'...
1521                        '#========== Bidouille ============== \n'...
1522                        'export OMPI_MCA_plm_rsh_agent=oar-envsh \n'...%                     'cd $WORKDIR \n'...
1523                        'CMD="mpirun -np $NCPUS -wdir $WORKDIR $MPINODES $COMMANDE" \n'...
1524                        'echo "I run: $CMD"  \n'...
1525                        '$CMD \n'...
1526                        'echo "job ending" \n'...
1527                        ];
1528                    %                 oarsub -S ./oar.sub
1529                    filename_oarscript=fullfile(Rootbat,'oar_command');
1530                    fid=fopen(filename_oarscript,'w');
1531                    fprintf(fid,[text_oarscript]);
1532                    fclose(fid);
1533                    eval(['!chmod +x  ' filename_oarscript]);
1534                    eval(['!oarsub -S ' filename_oarscript]);
1535            end
1536    end
1537else
1538    if ~isequal(CivMode,'Matlab')
1539        filename_superbat=fullfile(Rootbat,'job_list.bat');
1540        fid=fopen(filename_superbat,'w');
1541        if fid==-1
1542            msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat])
1543            return
1544        end
1545        for p=1:length(batch_file_list)
1546            if isunix
1547                fprintf(fid,['sh ' batch_file_list{p} '\n']);
1548            else
1549                fprintf(fid,['@call "' regexprep(filename_bat,'\\','\\\\') '"' '\n']);
1550            end
1551        end
1552        fclose(fid);
1553        if(isunix)
1554            system(['chmod +x ' filename_superbat]);
1555        end
1556        system([filename_superbat ' &']);% execute main commmand
1557    end
1558end
1559
1560
1561%% save interface state
1562if isfield(filecell,'nc')
1563    if isfield(filecell.nc,'civ2')
1564        fileresu=filecell.nc.civ2{1,1};
1565    else
1566        fileresu=filecell.nc.civ1{1,1};
1567    end
1568end
1569[RootPath,RootFile,field_count,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fileresu);
1570namedoc=fullfile(RootPath,subdir,RootFile);
1571detect=1;
1572while detect==1
1573    namefigfull=[namedoc '.fig'];
1574    hh=dir(namefigfull);
1575    if ~isempty(hh)
1576        detect=1;
1577        namedoc=[namedoc '.0'];
1578    else
1579        detect=0;
1580    end
1581end
1582saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER  .xml)
1583
1584%Save info in personal profile (initiate browser next time) TODO
1585MenuFile={};
1586dir_perso=prefdir;
1587profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1588if exist(profil_perso,'file')
1589    hh=load (profil_perso);
1590      if isfield(hh,'MenuFile')
1591          MenuFile=hh.MenuFile;
1592      end
1593      if isfield(filecell.nc,'civ2')
1594          MenuFile=[filecell.nc.civ2{1,1}; MenuFile];
1595      else
1596           MenuFile=[filecell.nc.civ1{1,1}; MenuFile];
1597      end
1598      save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
1599else
1600    MenuFile=filecell.ima1.civ1(1,1);
1601    save (profil_perso,'MenuFile')
1602end
1603
1604%------------------------------------------------------------------------
1605% --- determine the list of reference indices of processing file
1606function [ref_i,ref_j,errormsg]=find_ref_indices(handles)
1607%------------------------------------------------------------------------
1608errormsg=''; %default error message
1609first_i=str2double(get(handles.first_i,'String'));%first index i
1610last_i=str2double(get(handles.last_i,'String'));%last index i
1611incr_i=str2double(get(handles.incr_i,'String'));% increment
1612if isequal(get(handles.first_j,'Visible'),'on')
1613    first_j=str2double(get(handles.first_j,'String'));%first index j
1614    last_j=str2double(get(handles.last_j,'String'));%last index j
1615    incr_j=str2double(get(handles.incr_j,'String'));% increment
1616else
1617    first_j=1;
1618    last_j=1;
1619    incr_j=1;
1620end
1621ref_i=first_i:incr_i:last_i;% list of i indices (reference values for each pair)
1622ref_j=first_j:incr_j:last_j;% list of j indices (reference values for each pair)
1623if isnan(first_i)||isnan(first_j)
1624    errormsg='first field number not defined';
1625elseif isnan(last_i)||isnan(last_j)
1626    errormsg='last field number not defined';
1627elseif isnan(incr_i)||isnan(incr_j)
1628    errormsg='increment in field number not defined';
1629elseif last_i < first_i || last_j < first_j
1630    errormsg='last field number must be larger than the first one';
1631end
1632
1633%------------------------------------------------------------------------
1634% --- determine the list of filenames and indices needed for launch_job
1635function [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]=...
1636    set_civ_filenames(handles,ref_i,ref_j,checkbox)
1637%------------------------------------------------------------------------
1638filecell=[];%default
1639
1640%% get the root names nomenclature and numbers
1641filebase=get(handles.RootName,'String');
1642
1643if isempty(filebase)||isequal(filebase,'')
1644    msgbox_uvmat('ERROR','please open an image with the upper menu option Open/Browse...')
1645    return
1646end
1647
1648%filebase=regexprep(filebase,'\.fsnet','fsnet');% temporary fix for cluster Coriolis
1649filecell.filebase=filebase;
1650
1651browse=get(handles.RootName,'UserData');
1652compare_list=get(handles.ListCompareMode,'String');
1653val=get(handles.ListCompareMode,'Value');
1654compare=compare_list{val};
1655if strcmp(compare,'displacement')
1656    mode='displacement';
1657else
1658    mode_list=get(handles.ListPairMode,'String');
1659    mode_value=get(handles.ListPairMode,'Value');
1660    mode=mode_list{mode_value};
1661end
1662%time=get(handles.RootName,'UserData'); %get the set of times
1663ext_ima=get(handles.ImaExt,'String');
1664nom_type_nc=browse.nom_type_nc;
1665if isfield(browse,'nom_type_ima')
1666    nom_type_ima2=browse.nom_type_ima;
1667end
1668if isempty(nom_type_ima2),nom_type_ima2='1';end; %default
1669if isempty(nom_type_nc),nom_type_nc='_i1-i2';end; %default
1670[num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=...
1671    find_pair_indices(handles,ref_i,ref_j,mode);
1672%determine the new filebase for 'displacement' ListPairMode (comparison of two series)
1673filebase_B=filebase;% root name of the second field series for stereo
1674if strcmp(compare,'displacement') || strcmp(compare,'stereo PIV')
1675%     test_disp=1;
1676    nom_type_ima1=browse.nom_type_ima_1; %nomenclature type of the second file series
1677    [Path2,Name2]=fileparts(filebase_B);
1678    Path1=Path2;
1679    Name1=get(handles.RootName_1,'String');% root name of the first field series for stereo
1680    filebase_A=fullfile(Path1,Name1);
1681    if length(Name1)>6
1682        Name1=Name1(end-5:end);
1683    end
1684    if length(Name2)>6
1685        Name2=Name2(end-5:end);
1686    end
1687    filebase_AB=fullfile(Path2,[Name2 '-' Name1]);
1688else
1689%     test_disp=0;
1690    filebase_A=filebase;
1691    nom_type_ima1=nom_type_ima2;
1692    filebase_AB=filebase;
1693end
1694if strcmp(compare,'displacement')
1695    filebase_ima1=filebase_A;
1696    filebase_ima2=filebase_B;
1697    filebase_nc=filebase_AB; %root name for the result of civ2
1698else
1699    filebase_ima1=filebase_B;
1700    filebase_ima2=filebase_B;
1701    filebase_nc=filebase_B;
1702end
1703
1704%determine reference files for fix:
1705file_ref_fix1={};%default
1706file_ref_fix2={};
1707nbfield=length(num1_civ1);
1708nbslice=length(num_a_civ1);
1709if checkbox(2)==1% fix1 performed
1710    ref=get(handles.ref_fix1,'UserData');%read data on the ref file stored by get_ref_fix1_Callback
1711    if ~isempty(ref)
1712        first_i=str2double(get(handles.first_i,'String'));
1713        last_i=str2double(get(handles.last_i,'String'));
1714        incr_i=str2double(get(handles.incr_i,'String'));
1715        first_j=str2double(get(handles.first_j,'String'));
1716        last_j=str2double(get(handles.last_j,'String'));
1717        incr_j=str2double(get(handles.incr_j,'String'));
1718        num_i_ref=first_i:incr_i:last_i;
1719        num_j_ref=first_j:incr_j:last_j;
1720        if isequal(mode,'displacement')
1721            num_i1=num_i_ref;
1722            num_i2=num_i_ref;
1723            num_j1=num_j_ref;
1724            num_j2=num_j_ref;
1725        elseif isequal(mode,'pair j1-j2')% isequal(mode,'st_pair j1-j2')
1726            num_i1=num_i_ref;
1727            num_i2=num_i1;
1728            num_j1=ref.num_a*ones(size(num_i_ref));
1729            num_j2=ref.num_b*ones(size(num_i_ref));
1730        elseif isequal(mode,'series(Di)') % isequal(mode,'st_series(Di)')
1731            delta1=floor((ref.num2-ref.num1)/2);
1732            delta2=ceil((ref.num2-ref.num1)/2);
1733            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
1734            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
1735            if isempty(ref.num_a)
1736                ref.num_a=1;
1737            end
1738            num_j1=ref.num_a*ones(size(num_i1));
1739            num_j2=num_j1;
1740        elseif isequal(mode,'series(Dj)')%| isequal(mode,'st_series(Dj)')
1741            delta1=floor((ref.num_b-ref.num_a)/2);
1742            delta2=ceil((ref.num_b-ref.num_a)/2);
1743            num_i1=ref.num1*ones(size(num_i_ref));
1744            num_i2=num_i1;
1745            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
1746            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
1747        end
1748        for ifile=1:nbfield
1749            for j=1:nbslice
1750                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);%
1751                file_ref_fix1(ifile,j)={file_ref};
1752                if ~exist(file_ref,'file')
1753                    msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix1'])
1754                    filecell=[];
1755                    return
1756                end
1757            end
1758        end
1759    end
1760end
1761
1762%determine reference files for checkfix2:
1763if checkbox(5)==1% fix2 performed
1764    ref=get(handles.ref_fix2,'UserData');
1765    if ~isempty(ref)
1766        first_i=str2double(get(handles.first_i,'String'));
1767        last_i=str2double(get(handles.last_i,'String'));
1768        incr_i=str2double(get(handles.incr_i,'String'));
1769        first_j=str2double(get(handles.first_j,'String'));
1770        last_j=str2double(get(handles.last_j,'String'));
1771        incr_j=str2double(get(handles.incr_j,'String'));
1772        num_i_ref=first_i:incr_i:last_i;
1773        num_j_ref=first_j:incr_j:last_j;
1774        if isequal(mode,'displacement')
1775            num_i1=num_i_ref;
1776            num_i2=num_i_ref;
1777            num_j1=num_j_ref;
1778            num_j2=num_j_ref;
1779        elseif isequal(mode,'pair j1-j2')
1780            num_i1=num_i_ref;
1781            num_i2=num_i1;
1782            num_j1=ref.num_a;
1783            num_j2=ref.num_b;
1784        elseif isequal(mode,'series(Di)')
1785            delta1=floor((ref.num2-ref.num1)/2);
1786            delta2=ceil((ref.num2-ref.num1)/2);
1787            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
1788            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
1789            num_j1=ref.num_a*ones(size(num_i1));
1790            num_j2=num_j1;
1791        elseif isequal(mode,'series(Dj)')
1792            delta1=floor((ref.num_b-ref.num_a)/2);
1793            delta2=ceil((ref.num_b-ref.num_a)/2);
1794            num_i1=ref.num1*ones(size(num_i_ref));
1795            num_i2=num_i1;
1796            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
1797            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
1798        end
1799        for ifile=1:nbfield
1800            for j=1:nbslice
1801                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);%
1802                file_ref_fix2(ifile,j)={file_ref};
1803                if ~exist(file_ref,'file')
1804                    msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix2'])
1805                    filecell={};
1806                    return
1807                end
1808            end
1809        end
1810    end
1811end
1812
1813%check dir
1814subdir_civ1=get(handles.txt_SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf output data
1815subdir_civ2=get(handles.txt_SubdirCiv2,'String');
1816if isequal(subdir_civ1,''),subdir_civ1='CIV'; end% put default subdir
1817if isequal(subdir_civ2,''),subdir_civ2=subdir_civ1; end% put default subdir
1818% currentdir=pwd;%store the current working directory
1819[Path_ima,Name]=fileparts(filebase);%Path of the image files (.civ)
1820if ~exist(Path_ima,'dir')
1821    msgbox_uvmat('ERROR',['path to images ' Path_ima ' not found'])
1822    filecell={};
1823    return
1824end
1825[xx,message]=fileattrib(Path_ima);
1826if ~isempty(message) && ~isequal(message.UserWrite,1)
1827    msgbox_uvmat('ERROR',['No writting access to ' Path_ima])
1828    filecell={};
1829%     cd(currentdir);
1830    return
1831end
1832
1833%check the existence of the netcdf and image files involved
1834% %%%%%%%%%%%%  case CheckCiv1 activated   %%%%%%%%%%%%%
1835if checkbox(1)==1;
1836    detect=1;
1837    vers=0;
1838    subdir_civ1_new=subdir_civ1;
1839    while detect==1 %create a new subdir if the netcdf files already exist
1840        for ifile=1:nbfield
1841            for j=1:nbslice
1842                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);
1843                detect=exist(filename,'file')==2;
1844                if detect% if a netcdf file already exists
1845                    indstr=regexp(subdir_civ1_new,'\D');
1846                    if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number
1847                        vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1;
1848                        subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)];
1849                    else
1850                        vers=vers+1;
1851                        subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) '_' num2str(vers)];       
1852                    end
1853                    subdir_civ2=subdir_civ1_new;
1854                    break
1855                end
1856                filecell.nc.civ1(ifile,j)={filename};
1857            end
1858            if detect% if a netcdf file already exists
1859                break
1860            end
1861        end
1862 
1863        %create the new txt_SubdirCiv1
1864        if ~exist(fullfile(Path_ima,subdir_civ1_new),'dir')
1865%             cd(Path_ima);         
1866            [xx,msg1]=mkdir(fullfile(Path_ima,subdir_civ1_new));
1867
1868            if ~strcmp(msg1,'')
1869                msgbox_uvmat('ERROR',['cannot create ' subdir_civ1_new ': ' msg1])%error message for directory creation
1870                filecell={};
1871                return
1872            elseif isunix         
1873                [xx,msg2] = fileattrib(fullfile(Path_ima,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g)
1874                if ~strcmp(msg2,'')
1875                    msgbox_uvmat('ERROR',['pb of permission for  ' fullfile(Path_ima,subdir_civ1_new) ': ' msg2])%error message for directory creation
1876                    filecell={};
1877                    return
1878                end
1879            end
1880%             cd(currentdir);
1881        end
1882        if strcmp(compare,'stereo PIV')&&(strcmp(mode,'pair j1-j2')||strcmp(mode,'series(Dj)')||strcmp(mode,'series(Di)'))%check second nc series
1883            for ifile=1:nbfield
1884                for j=1:nbslice
1885                    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);%
1886                    detect=exist(filename,'file')==2;
1887                    if detect% if a netcdf file already exists
1888                       indstr=regexp(subdir_civ1_new,'\D');
1889                       if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number
1890                           vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1;
1891                           subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)];
1892                       else
1893                           vers=vers+1;
1894                           subdir_civ1_new=[subdir_civ1_new '_' num2str(vers)];
1895                       end
1896                       subdir_civ2=subdir_civ1;
1897                       break
1898                    end
1899                    filecell.ncA.civ1(ifile,j)={filename};
1900                end
1901                if detect% if a netcdf file already exists
1902                    break
1903                end
1904            end
1905            %create the new txt_SubdirCiv1
1906            if ~exist(fullfile(Path_ima,subdir_civ1_new),'dir')
1907%                    cd(Path_ima);         
1908                [xx,msg1]=mkdir(fullfile(Path_ima,subdir_civ1_new));
1909%                             cd(currentdir);
1910                if ~strcmp(msg1,'')
1911                    msgbox_uvmat('ERROR',['cannot create ' subdir_civ1_new ': ' msg1])
1912%                     cd(currentdir)
1913                    filecell={};
1914                    return
1915                else
1916                    [xx,msg2] = fileattrib(fullfile(Path_ima,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g)
1917                    if ~strcmp(msg2,'')
1918                        msgbox_uvmat('ERROR',['pb of permission for ' subdir_civ1_new ': ' msg2])%error message for directory creation
1919%                         cd(currentdir)
1920                        filecell={};
1921                        return
1922                    end
1923                end
1924            end
1925        end
1926    end
1927    subdir_civ1=subdir_civ1_new;
1928    % get image names
1929    for ifile=1:nbfield
1930        for j=1:nbslice
1931            filename=name_generator(filebase_ima1, num1_civ1(ifile),num_a_civ1(j),ext_ima,nom_type_ima1);
1932            idetect(j)=exist(filename,'file')==2;
1933            filecell.ima1.civ1(ifile,j)={filename}; %first image
1934            filename=name_generator(filebase_ima2, num2_civ1(ifile),num_b_civ1(j),ext_ima,nom_type_ima2);
1935            idetect_1(j)=exist(filename,'file')==2;
1936            filecell.ima2.civ1(ifile,j)={filename};%second image
1937        end
1938        [idetectmin,indexj]=min(idetect);
1939        if idetectmin==0,
1940            msgbox_uvmat('ERROR',[filecell.ima1.civ1{ifile,indexj} ' not found'])
1941            filecell={};
1942           % cd(currentdir)
1943            return
1944        end
1945        [idetectmin,indexj]=min(idetect_1);
1946        if idetectmin==0,
1947            msgbox_uvmat('ERROR',[filecell.ima2.civ1{ifile,indexj} ' not found'])
1948            filecell={};
1949            %cd(currentdir)
1950            return
1951        end
1952    end
1953    if strcmp(compare,'stereo PIV') && (strcmp(mode,'pair j1-j2') || strcmp(mode,'series(Dj)') || strcmp(mode,'series(Di)'))
1954        for ifile=1:nbfield
1955            for j=1:nbslice
1956                filename=name_generator(filebase_A, num1_civ1(ifile),num_a_civ1(j),ext_ima,nom_type_ima1);
1957                idetect(j)=exist(filename,'file')==2;
1958                filecell.imaA1.civ1(ifile,j)={filename} ;%first image
1959                filename=name_generator(filebase_A, num2_civ1(ifile),num_b_civ1(j),ext_ima,nom_type_ima2);
1960                idetect_1(j)=exist(filename,'file')==2;
1961                filecell.imaA2.civ1(ifile,j)={filename};%second image
1962            end
1963            [idetectmin,indexj]=min(idetect);
1964            if idetectmin==0,
1965                msgbox_uvmat('ERROR',[filecell.imaA1.civ1{ifile,indexj} ' not found'])
1966                filecell={};
1967               % cd(currentdir)
1968                return
1969            end
1970            [idetectmin,indexj]=min(idetect_1);
1971            if idetectmin==0,
1972                msgbox_uvmat('ERROR',[filecell.imaA2.civ1{ifile,indexj} ' not found'])
1973                filecell={};
1974               % cd(currentdir)
1975                return
1976            end
1977        end
1978    end
1979   
1980    %%%%%%%%%%%%%  checkfix1 or checkpatch1 activated but no checkciv1   %%%%%%%%%%%%%
1981elseif (checkbox(2)==1 || checkbox(3)==1);
1982    for ifile=1:nbfield
1983        for j=1:nbslice
1984            filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',...
1985                nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
1986            detect=exist(filename,'file')==2;
1987            if detect==0
1988                msgbox_uvmat('ERROR',[filename ' not found'])
1989                filecell={};
1990               % cd(currentdir)
1991                return
1992            end
1993            filecell.nc.civ1(ifile,j)={filename};
1994        end
1995    end
1996    if strcmp(compare,'stereo PIV')
1997        for ifile=1:nbfield
1998            for j=1:nbslice
1999                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);%
2000                filecell.ncA.civ1(ifile,j)={filename};
2001                if ~exist(filename,'file')
2002                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2003                    set(handles.RUN, 'Enable','On')
2004                    set(handles.RUN,'BackgroundColor',[1 0 0])
2005                    filecell={};
2006                    %cd(currentdir)
2007                    return
2008                end
2009            end
2010        end
2011    end
2012end
2013
2014%%%%%%%%%%%%%  if checkciv2 performed with pairs different than checkciv1  %%%%%%%%%%%%%
2015testdiff=0;
2016if (checkbox(4)==1)&&...
2017        ((get(handles.ListPairCiv1,'Value')~=get(handles.ListPairCiv2,'Value'))||~strcmp(subdir_civ2,subdir_civ1))
2018    testdiff=1;
2019    detect=1;
2020    vers=0;
2021    subdir_civ2_new=subdir_civ2;
2022    while detect==1 %create a new subdir if the netcdf files already exist
2023        for ifile=1:nbfield
2024            for j=1:nbslice
2025                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);%
2026                detect=exist(filename,'file')==2;
2027                if detect% if a netcdf file already exists
2028                    indstr=regexp(subdir_civ2,'\D');
2029                    if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2030                        vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2031                        subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2032                    else
2033                        vers=vers+1;
2034                        subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2035                    end
2036                    break
2037                end
2038                filecell.nc.civ2(ifile,j)={filename};
2039            end
2040            if detect% if a netcdf file already exists
2041                break
2042            end
2043        end
2044        %create the new subdir_civ2_new
2045        if ~exist(fullfile(Path_ima,subdir_civ2_new),'dir')
2046            [xx,m2]=mkdir(fullfile(Path_ima,subdir_civ2_new));
2047            [xx,msg2] = fileattrib(fullfile(Path_ima,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g)
2048            if ~isequal(m2,'')
2049                msgbox_uvmat('ERROR',['cannot create ' fullfile(Path_ima,subdir_civ2_new) ': ' m2])
2050                filecell={};
2051               % cd(currentdir)
2052                return
2053            end
2054        end
2055        if strcmp(compare,'stereo PIV')%check second nc series
2056            for ifile=1:nbfield
2057                for j=1:nbslice
2058                    filename=name_generator(filebase_A,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2059                        nom_type_nc,1,num2_civ2(ifile),num_b_civ1(j),subdir_civ2_new);%
2060                    detect=exist(filename,'file')==2;
2061                    if detect% if a netcdf file already exists
2062                        indstr=regexp(subdir_civ2,'\D');
2063                        if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2064                           vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2065                           subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2066                        else
2067                           vers=vers+1;
2068                           subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2069                        end
2070                        break
2071                    end
2072                    filecell.ncA.civ2(ifile,j)={filename};
2073                end
2074                if detect% if a netcdf file already exists
2075                    break
2076                end
2077            end
2078            subdir_civ2=subdir_civ2_new;
2079            %create the new txt_SubdirCiv1
2080            if ~exist(fullfile(Path_ima,subdir_civ2_new),'dir')
2081                [xx,m2]=mkdir(subdir_civ2_new);
2082                 [xx,msg2] = fileattrib(fullfile(Path_ima,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g)
2083                if ~isequal(m2,'')
2084                    msgbox_uvmat('ERROR', ['cannot create ' fullfile(Path_ima,subdir_civ2_new) ': ' m2])%error message for directory creation
2085                  %  cd(currentdir)
2086                    filecell={};
2087                    return
2088                end
2089            end
2090        end
2091    end
2092    subdir_civ2=subdir_civ2_new;
2093end
2094%cd(currentdir);%come back to the current working directory
2095
2096%%%%%%%%%%%%%  if checkciv2 results are obtained or used  %%%%%%%%%%%%%
2097if checkbox(4)==1 || checkbox(5)==1 || checkbox(6)==1 %civ2
2098    %check source netcdf file of checkciv1 estimates
2099    if checkbox(1)==0; %no civ1 performed
2100        for ifile=1:nbfield
2101            for j=1:nbslice
2102                filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',...
2103                    nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
2104                filecell.nc.civ1(ifile,j)={filename};% name of the civ1 file
2105                if ~exist(filename,'file')
2106                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2107                    filecell={};
2108                    return
2109                end
2110                if ~testdiff % civ2 or patch2 are written in the same file as civ1
2111                    if checkbox(4)==0 ; %check the existence of civ2 if it is not calculated
2112                        Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2');
2113                        if ~isempty(Data.CivStage) && Data.CivStage<4 %test for civ files
2114                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2115                            filecell=[];
2116                            return
2117                        elseif isempty(Data.civ2)||isequal(Data.civ2,0)
2118                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2119                            filecell=[];
2120                            return
2121                        end
2122                    elseif checkbox(3)==0; %check the existence of patch if it is not calculated
2123                        Data=nc2struct(filename,'ListGlobalAttribute','CivStage','patch');
2124                        if ~isempty(Data.CivStage)
2125                            if Data.CivStage<3 %test for civ files
2126                                msgbox_uvmat('ERROR',['no patch data in ' filename])
2127                                filecell=[];
2128                                return
2129                            end
2130                        elseif isempty(Data.patch)||isequal(Data.patch,0)
2131                            msgbox_uvmat('ERROR',['no patch data in ' filename])
2132                            filecell=[];
2133                            return
2134                        end
2135                    end
2136                end
2137            end
2138        end
2139        if strcmp(compare,'stereo PIV')
2140            for ifile=1:nbfield
2141                for j=1:nbslice
2142                    filename=name_generator(filebase_A,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2143                        nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
2144                    filecell.ncA.civ2(ifile,j)={filename};
2145                    if ~exist(filename,'file')
2146                        msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2147                        set(handles.RUN, 'Enable','On')
2148                        set(handles.RUN,'BackgroundColor',[1 0 0])
2149                        return
2150                    end
2151                end
2152            end
2153        end
2154    end
2155   
2156    detect=1;
2157    %     while detect==1%creates a new subdir if the netcdf files already contain checkciv2 data
2158    for ifile=1:nbfield
2159        for j=1:nbslice
2160            filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2161                nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);
2162            detect=exist(filename,'file')==2;
2163            filecell.nc.civ2(ifile,j)={filename};
2164        end
2165    end
2166    %get first image names for checkciv2
2167    if checkbox(1)==1 && isequal(num1_civ1,num1_civ2) && isequal(num_a_civ1,num_a_civ2)
2168        filecell.ima1.civ2=filecell.ima1.civ1;
2169    elseif checkbox(4)==1
2170        for ifile=1:nbfield
2171            for j=1:nbslice
2172                filename=name_generator(filebase_ima1, num1_civ2(ifile),num_a_civ2(j),ext_ima,nom_type_ima1);
2173                idetect_2(j)=exist(filename,'file')==2;
2174                filecell.ima1.civ2(ifile,j)={filename};%first image
2175            end
2176            [idetectmin,indexj]=min(idetect_2);
2177            if idetectmin==0,
2178                msgbox_uvmat('ERROR',['input image ' filecell.ima1.civ2{ifile,indexj} ' not found'])
2179                filecell=[];
2180                return
2181            end
2182        end
2183    end
2184   
2185    %get second image names for checkciv2
2186    if checkbox(1)==1 && isequal(num2_civ1,num2_civ2) && isequal(num_b_civ1,num_b_civ2)
2187        filecell.ima2.civ2=filecell.ima2.civ1;
2188    elseif checkbox(4)==1
2189        for ifile=1:nbfield
2190            for j=1:nbslice
2191                filename=name_generator(filebase_ima2, num2_civ2(ifile),num_b_civ2(j),ext_ima,nom_type_ima2);
2192                idetect_3(j)=exist(filename,'file')==2;
2193                filecell.ima2.civ2(ifile,j)={filename};%first image
2194            end
2195            [idetectmin,indexj]=min(idetect_3);
2196            if idetectmin==0,
2197                msgbox_uvmat('ERROR',['input image ' filecell.ima2.civ2{ifile,indexj} ' not found'])
2198                filecell=[];
2199                return
2200            end
2201        end
2202    end
2203end
2204if (checkbox(5) || checkbox(6)) && ~checkbox(4)  % need to read an existing netcdf civ2 file
2205    if ~testdiff
2206        filecell.nc.civ2=filecell.nc.civ1;% file already checked
2207    else     % check the civ2 files
2208        for ifile=1:nbfield
2209            for j=1:nbslice
2210                filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2211                    nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
2212                filecell.nc.civ2(ifile,j)={filename};
2213                if ~exist(filename,'file')
2214                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2215                    filecell=[];
2216                    return
2217                else
2218                    Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2');
2219                    if ~isempty(Data.CivStage) && Data.CivStage<4 %test for civ files
2220                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2221                            filecell=[];
2222                            return
2223                    elseif isempty(Data.civ2)||isequal(Data.civ2,0)
2224                        msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2225                        filecell=[];
2226                        return
2227                    end
2228                end
2229            end
2230        end
2231    end
2232end
2233
2234%%%%%%%%%%%%%  if stereo fields are calculated by PATCH %%%%%%%%%%%%%
2235if strcmp(compare,'stereo PIV')
2236    if  checkbox(3) && isequal(get(handles.test_stereo1,'Value'),1)
2237        for ifile=1:nbfield
2238            for j=1:nbslice
2239                filename=name_generator(filebase_AB,num1_civ1(ifile),num_a_civ1(j),'.nc',...
2240                    nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
2241                filecell.st(ifile,j)={filename};
2242            end
2243        end
2244    end
2245    if  checkbox(6) && isequal(get(handles.CheckStereo,'Value'),1)
2246        for ifile=1:nbfield
2247            for j=1:nbslice
2248                filename=name_generator(filebase_AB,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2249                    nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
2250                filecell.st(ifile,j)={filename};
2251            end
2252        end
2253    end
2254end
2255set(handles.txt_SubdirCiv1,'String',subdir_civ1);%update the edit box
2256set(handles.txt_SubdirCiv2,'String',subdir_civ2);%update the edit box
2257browse.nom_type_nc=nom_type_nc;
2258set(handles.RootName,'UserData',browse); %update the nomenclature type for uvmat
2259
2260
2261%COPY IMAGES TO THE FORMAT .png IF NEEDED
2262if isequal(nom_type_ima1,'*')%case of movie files
2263    nom_type_imanew1='_i';
2264else
2265    nom_type_imanew1=nom_type_ima1;
2266end
2267if isequal(nom_type_ima2,'*')%case of movie files
2268    nom_type_imanew2='_i';
2269else
2270    nom_type_imanew2=nom_type_ima2;
2271end
2272if ~isequal(ext_ima,'.png')
2273    %%type of image file
2274    type_ima1='none';%default
2275    movieobject1=[];%default
2276    if strcmpi(ext_ima,'.avi')
2277        hhh=which('mmreader');
2278        if ~isequal(hhh,'')&& mmreader.isPlatformSupported()% if the mmreader function is found (recent version of matlab)
2279            type_ima1='movie';
2280            movieobject1=mmreader([filebase_ima2 ext_ima]);
2281        else
2282            type_ima1='avi';
2283        end
2284    elseif ischar(ext_ima) && ~isempty(ext_ima(2:end))
2285        form=imformats(ext_ima(2:end));
2286        if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2287            if isequal(nom_type_ima1,'*');
2288                type_ima1='multimage';%image series in a single image file
2289            else
2290                type_ima1='image';
2291            end
2292        end
2293    end
2294    type_ima2='none';%default
2295    movieobject2=[];
2296    if strcmpi(ext_ima,'.avi')
2297        hhh=which('mmreader');
2298        if ~isequal(hhh,'')&& mmreader.isPlatformSupported()% if the mmreader function is found (recent version of matlab)
2299            type_ima2='movie';
2300            movieobject2=mmreader([filebase_ima2 ext_ima]);
2301        else
2302            type_ima2='avi';
2303        end
2304    elseif ischar(ext_ima) && ~isempty(ext_ima(2:end))
2305        form=imformats(ext_ima(2:end));
2306        if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2307            if isequal(nom_type_ima1,'*');
2308                type_ima2='multimage';%image series in a single image file
2309            else
2310                type_ima2='image';
2311            end
2312        end
2313    end
2314    %npxy=get(handles.ImaExt,'UserData');
2315    % %     if numel(npxy)<2
2316    %
2317    %         filename=name_generator(filebase_ima1,num1_civ1(1),num_a_civ1(1),ImaExt,nom_type_ima1);
2318    %         A=imread(filename);
2319    %         npxy=size(A);
2320    % %     end
2321    %     npy=npxy(1);
2322    %     npx=npxy(2);
2323    if checkbox(1) %if civ1 is performed
2324        h = waitbar(0,'copy images to the .png format for civ1');% display a wait bar
2325        for ifile=1:nbfield
2326            waitbar(ifile/nbfield);
2327            for j=1:nbslice
2328                filename=name_generator(filebase_ima1,num1_civ1(ifile),num_a_civ1(j),'.png',nom_type_imanew1);
2329                if ~exist(filename,'file')
2330                    A=read_image(filecell.ima1.civ1{ifile,j},type_ima1,num1_civ1(ifile),movieobject1);
2331                    imwrite(A,filename,'BitDepth',16);
2332                end
2333                filecell.ima1.civ1(ifile,j)={filename};
2334                filename=name_generator(filebase_ima2, num2_civ1(ifile),num_b_civ1(j),'.png',nom_type_imanew2);
2335                if ~exist(filename,'file')
2336                    A=read_image(filecell.ima2.civ1{ifile,j},type_ima2,num2_civ1(ifile),movieobject2);
2337                    imwrite(A,filename,'BitDepth',16);
2338                end
2339                filecell.ima2.civ1(ifile,j)={filename};
2340            end
2341        end
2342        close(h)
2343    end
2344    if checkbox(4) %if civ2 is performed
2345        h = waitbar(0,'copy images to the .png format for civ2');% display a wait bar
2346        for ifile=1:nbfield
2347            waitbar(ifile/nbfield);
2348            for j=1:nbslice
2349                filename=name_generator(filebase_ima1,num1_civ2(ifile),num_a_civ2(j),'.png',nom_type_imanew1);
2350                if ~exist(filename,'file')
2351                    A=read_image(cell2mat(filecell.ima1.civ2(ifile,j)),type_ima2,num1_civ2(ifile));
2352                    imwrite(A,filename,'BitDepth',16);
2353                end
2354                filecell.ima1.civ2(ifile,j)={filename};
2355                filename=name_generator(filebase_ima2, num2_civ2(ifile),num_b_civ2(j),'.png',nom_type_imanew2);
2356                if ~exist(filename,'file')
2357                    A=read_image(cell2mat(filecell.ima2.civ2(ifile,j)),type_ima2,num2_civ2(ifile));
2358                    imwrite(A,filename,'BitDepth',16);
2359                end
2360                filecell.ima2.civ2(ifile,j)={filename};
2361            end
2362        end
2363        close(h);
2364    end
2365end
2366
2367%------------------------------------------------------------------------
2368% --- determine the list of index pairs of processing file
2369function [num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=...
2370    find_pair_indices(handles,ref_i,ref_j,mode)
2371%------------------------------------------------------------------------
2372
2373list_civ1=get(handles.ListPairCiv1,'String');
2374index_civ1=get(handles.ListPairCiv1,'Value');
2375str_civ1=list_civ1{index_civ1};%string defining the image pairs for civ1
2376if isempty(str_civ1)||isequal(str_civ1,'')
2377    msgbox_uvmat('ERROR','no image pair selected for civ1')
2378    return
2379end
2380list_civ2=get(handles.ListPairCiv2,'String');
2381index_civ2=get(handles.ListPairCiv2,'Value');
2382if index_civ2>length(list_civ2)
2383    list_civ2=list_civ1;
2384    index_civ2=index_civ1;
2385end
2386str_civ2=list_civ2{index_civ2};%string defining the image pairs for civ2
2387
2388if isequal (mode,'series(Di)')
2389    lastfield=str2double(get(handles.nb_field,'String'));
2390    num1_civ1=ref_i-floor(index_civ1/2)*ones(size(ref_i));% set of first image numbers
2391    num2_civ1=ref_i+ceil(index_civ1/2)*ones(size(ref_i));
2392    num_a_civ1=ref_j;
2393    num_b_civ1=ref_j;
2394    num1_civ2=ref_i-floor(index_civ2/2)*ones(size(ref_i));
2395    num2_civ2=ref_i+ceil(index_civ2/2)*ones(size(ref_i));
2396    num_a_civ2=ref_j;
2397    num_b_civ2=ref_j;   
2398   
2399    % adjust the first and last field number
2400    lastfield=str2double(get(handles.nb_field,'String'));
2401    if isnan(lastfield)
2402        indsel=find((num1_civ1 >= 1)&(num1_civ2 >= 1));
2403    else
2404        indsel=find((num2_civ1 <= lastfield)&(num2_civ2 <= lastfield)&(num1_civ1 >= 1)&(num1_civ2 >= 1));
2405    end
2406    if length(indsel)>=1
2407        firstind=indsel(1);
2408        lastind=indsel(end);
2409        set(handles.first_i,'String',num2str(ref_i(firstind)))%update the display of first and last fields
2410        set(handles.last_i,'String',num2str(ref_i(lastind)))
2411        ref_i=ref_i(indsel);
2412        num1_civ1=num1_civ1(indsel);
2413        num1_civ2=num1_civ2(indsel);
2414        num2_civ1=num2_civ1(indsel);
2415        num2_civ2=num2_civ2(indsel);
2416    end
2417elseif isequal (mode,'series(Dj)')
2418    lastfield_j=str2double(get(handles.nb_field2,'String'));
2419    num1_civ1=ref_i;% set of first image numbers
2420    num2_civ1=ref_i;
2421    num_a_civ1=ref_j-floor(index_civ1/2)*ones(size(ref_j));
2422    num_b_civ1=ref_j+ceil(index_civ1/2)*ones(size(ref_j));
2423    num1_civ2=ref_i;
2424    num2_civ2=ref_i;
2425    num_a_civ2=ref_j-floor(index_civ2/2)*ones(size(ref_j));
2426    num_b_civ2=ref_j+ceil(index_civ2/2)*ones(size(ref_j));
2427    % adjust the first and last field number
2428    if isnan(lastfield_j)
2429        indsel=find((num_a_civ1 >= 1)&(num_a_civ2 >= 1));
2430    else
2431        indsel=find((num_b_civ1 <= lastfield_j)&(num_b_civ2 <= lastfield_j)&(num_a_civ1 >= 1)&(num_a_civ2 >= 1));
2432    end
2433    if length(indsel)>=1
2434        firstind=indsel(1);
2435        lastind=indsel(end);
2436        set(handles.first_j,'String',num2str(ref_j(firstind)))%update the display of first and last fields
2437        set(handles.last_j,'String',num2str(ref_j(lastind)))
2438        ref_j=ref_j(indsel);
2439        num_a_civ1=num_a_civ1(indsel);
2440        num_b_civ1=num_b_civ1(indsel);
2441        num_a_civ2=num_a_civ2(indsel);
2442        num_b_civ2=num_b_civ2(indsel);
2443    end
2444elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)
2445    displ_num=get(handles.ListPairCiv1,'UserData');
2446    num1_civ1=ref_i;
2447    num2_civ1=ref_i;
2448    num_a_civ1=displ_num(1,index_civ1);
2449    num_b_civ1=displ_num(2,index_civ1);
2450    num1_civ2=ref_i;
2451    num2_civ2=ref_i;
2452    num_a_civ2=displ_num(1,index_civ2);
2453    num_b_civ2=displ_num(2,index_civ2);
2454elseif isequal(mode,'displacement')
2455    num1_civ1=ref_i;
2456    num2_civ1=ref_i;
2457    num_a_civ1=ref_j;
2458    num_b_civ1=ref_j;
2459    num1_civ2=ref_i;
2460    num2_civ2=ref_i;
2461    num_a_civ2=ref_j;
2462    num_b_civ2=ref_j;
2463end
2464
2465%------------------------------------------------------------------------
2466% --- Executes on button press in ListCompareMode.
2467function ListCompareMode_Callback(hObject, eventdata, handles)
2468%------------------------------------------------------------------------
2469test=get(handles.ListCompareMode,'Value');
2470if test==2 || test==3 % case 'dispalcemen' or 'stereo PIV'
2471    filebase=get(handles.RootName,'String');
2472    browse=get(handlesRootName,'Userdata');
2473    browse.nom_type_ima1=browse.nom_type_ima;
2474    set(handlesRootName,'UserData',browse);
2475    set(handles.sub_txt,'Visible','on')
2476    set(handles.RootName_1,'Visible','On');%mkes the second file input window visible
2477    mode_store=get(handles.ListPairMode,'String');%get the present 'mode'
2478    set(handles.ListCompareMode,'UserData',mode_store);%store the mode display
2479    set(handles.ListPairMode,'Visible','off')
2480    if test==2
2481        set(handles.ListPairMode,'Visible','off')
2482        set(handles.ListPairMode,'Value',1) % mode 'civX' selected by default
2483    else
2484        set(handles.ListPairMode,'Visible','on')
2485        set(handles.ListPairMode,'Value',3) % mode 'Matlab' selected for stereo
2486    end
2487   
2488    %% menuopen an image file with the browser
2489    ind_opening=1;%default
2490    browse.incr_pair=[0 0]; %default
2491    oldfile=get(handles.RootName,'String');
2492     menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)';
2493       '*.xml',  '.xml files '; ...
2494        '*.civ',  '.civ files '; ...
2495        '*.png','.png image files'; ...
2496        '*.jpg',' jpeg image files'; ...
2497        '*.tif','.tif image files'; ...
2498        '*.avi;*.AVI','.avi movie files'; ...
2499        '*.nc','.netcdf files'; ...
2500        '*.*',  'All Files (*.*)'};
2501    [FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file of the second series',oldfile);
2502    fileinput=[PathName FileName];%complete file name
2503    sizf=size(fileinput);
2504    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
2505    [path,name,ext]=fileparts(fileinput);
2506    [path1]=fileparts(filebase);
2507    if isunix
2508        [status,path]=system(['readlink ' path]);
2509        [status,path1]=system(['readlink ' path1]);% look for the true path in case of symbolic paths
2510    end
2511    if ~strcmp(path1,path)
2512        msgbox_uvmat('ERROR','The second image series must be in the same directory as the first one')
2513        return
2514     end
2515%     set(handles.RootName_1,'String',name);
2516    [RootPath,RootFile,field_count,str2,str_a,str_b,xx,nom_type,subdir]=name2display(name);
2517    set(handles.RootName_1,'String',RootFile);
2518    browse=get(handlesRootName,'UserData');
2519    browse.nom_type_ima_1=nom_type;
2520    set(handlesRootName,'UserData',browse)
2521   
2522    %check image extension
2523    if ~strcmp(ext,get(handles.ImaExt,'String'))
2524        msgbox_uvmat('ERROR','The second image series must have the same extension name as the first one')
2525        return
2526    end
2527   
2528    %% check coincidence of image sizes
2529%     ref_i=get(handles.ref_i,'string');
2530%     ref_j=get(handles.ref_j,'string');
2531%     [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]);
2532%     A=imread(filecell.ima1.checkciv1{1});
2533%     A_1=imread(fileinput);
2534%     npxy=size(A);
2535%     npxy_1=size(A_1);
2536%     if ~isequal(size(A),size(A_1))
2537%         msgbox_uvmat('ERROR','The two input image series do not have the same size')
2538%         return
2539%     end
2540else
2541    set(handles.ListPairMode,'Visible','on')
2542    set(handles.RootName_1,'Visible','Off');
2543    set(handles.sub_txt,'Visible','off')
2544    set(handles.RootName_1,'String',[]);
2545    mode_store=get(handles.ListCompareMode,'UserData');
2546    set(handles.ListPairMode,'Value',1)
2547    set(handles.ListPairMode,'String',mode_store)
2548    set(handles.test_stereo1,'Value',0)
2549    set(handles.CheckStereo,'Value',0)
2550    set(handles.ListPairMode,'Value',1) % mode 'civX' selected by default
2551end
2552if test==3 && get(handles.CheckPatch1,'Value')
2553    set(handles.test_stereo1,'Visible','on')
2554else
2555    set(handles.test_stereo1,'Visible','off')
2556end
2557if test==3 && get(handles.CheckPatch2,'Value')
2558    set(handles.CheckStereo,'Visible','on')
2559else
2560    set(handles.CheckStereo,'Visible','off')
2561end
2562mode_Callback(hObject, eventdata, handles)
2563
2564
2565%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2566% Callbacks in the uipanel Pair Indices
2567%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2568%------------------------------------------------------------------------
2569% --- Executes on button press in ListPairMode.
2570function ListPairMode_Callback(hObject, eventdata, handles)
2571%------------------------------------------------------------------------
2572compare_list=get(handles.ListCompareMode,'String');
2573val=get(handles.ListCompareMode,'Value');
2574compare=compare_list{val};
2575if strcmp(compare,'displacement')
2576    mode='displacement';
2577else
2578    mode_list=get(handles.ListPairMode,'String');
2579    if ischar(mode_list)
2580        mode_list={mode_list};
2581    end
2582    mode_value=get(handles.ListPairMode,'Value');
2583    mode=mode_list{mode_value};
2584end
2585displ_num=[];%default
2586ref_i=str2double(get(handles.ref_i,'String'));
2587% last_i=str2num(get(handles.last_i,'String'));
2588time=get(handles.ImaDoc,'UserData'); %get the set of times
2589siztime=size(time);
2590nbfield=siztime(1);
2591nbfield2=siztime(2);
2592indchosen=1;  %%first pair selected by default
2593%displ_num used to define the indices of the civ pairs
2594% in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices
2595% are relative to the reference indices ref_i and ref_j respectively.
2596if isequal(mode,'pair j1-j2')%| isequal(mode,'st_pair j1-j2')
2597    dt=1;
2598    displ='';
2599    index=0;
2600    numlist_a=[];
2601    numlist_B=[];
2602    %get all the time intervals in bursts
2603    displ_dt=1;%default
2604    nbfield2=min(nbfield2,10);%limitate the number of pairs to 10x10
2605    for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'pair j1-j2' mode
2606        for numod_b=(numod_a+1):nbfield2
2607            index=index+1;
2608            numlist_a(index)=numod_a;
2609            numlist_b(index)=numod_b;
2610            if ~isempty(time)
2611                dt(numod_a,numod_b)=time(ref_i,numod_b)-time(ref_i,numod_a);%first time interval dt
2612                displ_dt(index)=dt(numod_a,numod_b);
2613            else
2614                displ_dt(index)=1;
2615            end
2616        end
2617    end
2618    [dtsort,indsort]=sort(displ_dt);
2619    if ~isempty(numlist_a)
2620        displ_num(1,:)=numlist_a(indsort);
2621        displ_num(2,:)=numlist_b(indsort);
2622    end
2623    displ_num(3,:)=0;
2624    displ_num(4,:)=0;
2625    set(handles.jtext,'Visible','Off')
2626    set(handles.first_j,'Visible','Off')
2627    set(handles.last_j,'Visible','Off')
2628    set(handles.incr_j,'Visible','Off')
2629    set(handles.nb_field2,'Visible','Off')
2630    set(handles.ref_j,'Visible','Off')
2631elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)')
2632    index=1:200;
2633    displ_num(1,index)=-floor(index/2);
2634    displ_num(2,index)=ceil(index/2);
2635    displ_num(3:4,index)=zeros(2,200);
2636%     for index=1:min(nbfield2-1,200)
2637%         displ_num(1,index)=-floor(index/2);
2638%         displ_num(2,index)=ceil(index/2);
2639%         displ_num(3,index)=0;
2640%         displ_num(4,index)=0;
2641%     end
2642    set(handles.jtext,'Visible','On')
2643    set(handles.first_j,'Visible','On')
2644    set(handles.last_j,'Visible','On')
2645    set(handles.incr_j,'Visible','On')
2646    set(handles.nb_field2,'Visible','On')
2647    set(handles.ref_j,'Visible','On')
2648    if nbfield > 1
2649        set(handles.itext,'Visible','On')
2650        set(handles.first_i,'Visible','On')
2651        set(handles.last_i,'Visible','On')
2652        set(handles.incr_i,'Visible','On')
2653        set(handles.nb_field,'Visible','On')
2654        set(handles.ref_i,'Visible','On')
2655    else
2656        set(handles.itext,'Visible','Off')
2657        set(handles.first_i,'Visible','Off')
2658        set(handles.last_i,'Visible','Off')
2659        set(handles.incr_i,'Visible','Off')
2660        set(handles.nb_field,'Visible','Off')
2661        set(handles.ref_i,'Visible','Off')
2662    end
2663elseif isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)')
2664    index=1:200;
2665    displ_num(1:2,index)=zeros(2,200);
2666    displ_num(3,index)=-floor(index/2);
2667    displ_num(4,index)=ceil(index/2);
2668%     for index=1:200%min(nbfield-1,200)
2669%         displ_num(1,index)=0;
2670%         displ_num(2,index)=0;
2671%         displ_num(3,index)=-floor(index/2);
2672%         displ_num(4,index)=ceil(index/2);
2673%     end
2674    set(handles.itext,'Visible','On')
2675    set(handles.first_i,'Visible','On')
2676    set(handles.last_i,'Visible','On')
2677    set(handles.incr_i,'Visible','On')
2678    set(handles.nb_field,'Visible','On')
2679    set(handles.ref_i,'Visible','On')
2680    if nbfield2 > 1
2681        set(handles.jtext,'Visible','On')
2682        set(handles.first_j,'Visible','On')
2683        set(handles.last_j,'Visible','On')
2684        set(handles.incr_j,'Visible','On')
2685        set(handles.nb_field2,'Visible','On')
2686        set(handles.ref_j,'Visible','On')
2687    else
2688        set(handles.jtext,'Visible','Off')
2689        set(handles.first_j,'Visible','Off')
2690        set(handles.last_j,'Visible','Off')
2691        set(handles.incr_j,'Visible','Off')
2692        set(handles.nb_field2,'Visible','Off')
2693        set(handles.ref_j,'Visible','Off')
2694    end
2695elseif isequal(mode,'displacement')%the pairs have the same indices
2696    displ_num(1,1)=0;
2697    displ_num(2,1)=0;
2698    displ_num(3,1)=0;
2699    displ_num(4,1)=0;
2700    if nbfield > 1
2701        set(handles.itext,'Visible','On')
2702        set(handles.first_i,'Visible','On')
2703        set(handles.last_i,'Visible','On')
2704        set(handles.incr_i,'Visible','On')
2705        set(handles.nb_field,'Visible','On')
2706        set(handles.ref_i,'Visible','On')
2707    else
2708        set(handles.itext,'Visible','Off')
2709        set(handles.first_i,'Visible','Off')
2710        set(handles.last_i,'Visible','Off')
2711        set(handles.incr_i,'Visible','Off')
2712        set(handles.nb_field,'Visible','Off')
2713        set(handles.ref_i,'Visible','Off')
2714    end
2715    if nbfield2 > 1
2716        set(handles.jtext,'Visible','On')
2717        set(handles.first_j,'Visible','On')
2718        set(handles.last_j,'Visible','On')
2719        set(handles.incr_j,'Visible','On')
2720        set(handles.nb_field2,'Visible','On')
2721        set(handles.ref_j,'Visible','On')
2722    else
2723        set(handles.jtext,'Visible','Off')
2724        set(handles.first_j,'Visible','Off')
2725        set(handles.last_j,'Visible','Off')
2726        set(handles.incr_j,'Visible','Off')
2727        set(handles.nb_field2,'Visible','Off')
2728        set(handles.ref_j,'Visible','Off')
2729    end
2730end
2731set(handles.ListPairCiv1,'UserData',displ_num);
2732find_netcpair_civ1( handles)
2733find_netcpair_civ2(handles)
2734
2735%------------------------------------------------------------------------
2736% --- Executes on selection change in ListPairCiv1.
2737function ListPairCiv1_Callback(hObject, eventdata, handles)
2738%------------------------------------------------------------------------
2739%reproduce by default the chosen pair in the checkciv2 menu
2740list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
2741index_pair=get(handles.ListPairCiv1,'Value');
2742displ_num=get(handles.ListPairCiv1,'UserData');
2743% num_a=displ_num(1,index_pair);
2744% num_b=displ_num(2,index_pair);
2745list_pair2=get(handles.ListPairCiv2,'String');%get the menu of image pairs
2746if index_pair<=length(list_pair2)
2747    set(handles.ListPairCiv2,'Value',index_pair);
2748end
2749
2750%update first_i and last_i according to the chosen image pairs
2751mode_list=get(handles.ListPairMode,'String');
2752mode_value=get(handles.ListPairMode,'Value');
2753mode=mode_list{mode_value};
2754if isequal(mode,'series(Di)')
2755    first_i=str2double(get(handles.first_i,'String'));
2756    last_i=str2double(get(handles.last_i,'String'));
2757    incr_i=str2double(get(handles.incr_i,'String'));
2758    num1=first_i:incr_i:last_i;
2759    lastfield=str2double(get(handles.nb_field,'String'));
2760    if ~isnan(lastfield)
2761        test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ...
2762            (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield);
2763        num1=num1(test_find);
2764    end
2765    set(handles.first_i,'String',num2str(num1(1)));
2766    set(handles.last_i,'String',num2str(num1(end)));
2767elseif isequal(mode,'series(Dj)')
2768    first_j=str2double(get(handles.first_j,'String'));
2769    last_j=str2double(get(handles.last_j,'String'));
2770    incr_j=str2double(get(handles.incr_j,'String'));
2771    num_j=first_j:incr_j:last_j;
2772    lastfield2=str2double(get(handles.nb_field2,'String'));
2773    if ~isnan(lastfield2)
2774        test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
2775            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2);
2776        num1=num_j(test_find);
2777    end
2778    set(handles.first_j,'String',num2str(num1(1)));
2779    set(handles.last_j,'String',num2str(num1(end)));
2780end
2781
2782%------------------------------------------------------------------------
2783% --- Executes on selection change in ListPairCiv2.
2784function ListPairCiv2_Callback(hObject, eventdata, handles)
2785%------------------------------------------------------------------------
2786index_pair=get(handles.ListPairCiv2,'Value');%get the selected position index in the menu
2787
2788%update first_i and last_i according to the chosen image pairs
2789mode_list=get(handles.ListPairMode,'String');
2790mode_value=get(handles.ListPairMode,'Value');
2791mode=mode_list{mode_value};
2792if isequal(mode,'series(Di)')
2793    first_i=str2double(get(handles.first_i,'String'));
2794    last_i=str2double(get(handles.last_i,'String'));
2795    incr_i=str2double(get(handles.incr_i,'String'));
2796    num1=first_i:incr_i:last_i;
2797    lastfield=str2double(get(handles.nb_field,'String'));
2798    if ~isnan(lastfield)
2799        test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ...
2800            (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield);
2801        num1=num1(test_find);
2802    end
2803    set(handles.first_i,'String',num2str(num1(1)));
2804    set(handles.last_i,'String',num2str(num1(end)));
2805elseif isequal(mode,'series(Dj)')
2806    first_j=str2double(get(handles.first_j,'String'));
2807    last_j=str2double(get(handles.last_j,'String'));
2808    incr_j=str2double(get(handles.incr_j,'String'));
2809    num_j=first_j:incr_j:last_j;
2810    lastfield2=str2double(get(handles.nb_field2,'String'));
2811    if ~isnan(lastfield2)
2812        test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
2813            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2);
2814        num1=num_j(test_find);
2815    end
2816    set(handles.first_j,'String',num2str(num1(1)));
2817    set(handles.last_j,'String',num2str(num1(end)));
2818end
2819
2820%------------------------------------------------------------------------
2821function ref_i_Callback(hObject, eventdata, handles)
2822%------------------------------------------------------------------------
2823mode_list=get(handles.ListPairMode,'String');
2824mode_value=get(handles.ListPairMode,'Value');
2825mode=mode_list{mode_value};
2826find_netcpair_civ1(handles);% update the menu of pairs depending on the available netcdf files
2827if isequal(mode,'series(Di)') || ...% we do patch2 only
2828        (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
2829    find_netcpair_civ2( handles);
2830end
2831
2832%------------------------------------------------------------------------
2833function ref_j_Callback(hObject, eventdata, handles)
2834%------------------------------------------------------------------------
2835mode_list=get(handles.ListPairMode,'String');
2836mode_value=get(handles.ListPairMode,'Value');
2837mode=mode_list{mode_value};
2838if isequal(get(handles.CheckCiv1,'Value'),0)|| isequal(mode,'series(Dj)')
2839    find_netcpair_civ1(handles);% update the menu of pairs depending on the available netcdf files
2840end
2841if isequal(mode,'series(Dj)') || ...
2842        (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
2843    find_netcpair_civ2(handles);
2844end
2845%
2846%------------------------------------------------------------------------
2847% determine the menu for checkciv1 pairs depending on existing netcdf file at the middle of
2848% the field series set by first_i, incr, last_i
2849function find_netcpair_civ1(handles)
2850%------------------------------------------------------------------------
2851set(gcf,'Pointer','watch')
2852%nomenclature types
2853filebase=get(handles.RootName,'String');
2854[filepath,Nme,ext_dir]=fileparts(filebase);
2855browse=get(handles.RootName,'UserData');
2856compare_list=get(handles.ListCompareMode,'String');
2857val=get(handles.ListCompareMode,'Value');
2858compare=compare_list{val};
2859if strcmp(compare,'displacement')
2860    mode='displacement';
2861else
2862    mode_list=get(handles.ListPairMode,'String');
2863    mode_value=get(handles.ListPairMode,'Value');
2864    if isempty(mode_list)
2865        return
2866    end
2867    mode=mode_list{mode_value};
2868end
2869
2870% nomenclature type of the .nc files
2871nom_type_ima=[];%default
2872if isfield(browse,'nom_type_ima')
2873    nom_type_ima=browse.nom_type_ima;
2874end
2875
2876%determine nom_type_nc:
2877nom_type_nc=[];%default
2878if isfield(browse,'nom_type_nc')
2879    nom_type_nc=browse.nom_type_nc;
2880end
2881if isempty(nom_type_nc)
2882    [nom_type_nc]=nomtype2pair(nom_type_ima,isequal(mode,'series(Di)'),isequal(mode,'series(Dj)'));
2883end
2884browse.nom_type_nc=nom_type_nc;
2885set(handles.RootName,'UserData',browse)
2886
2887%reads .nc subdirectoy and image numbers from the interface
2888subdir_civ1=get(handles.txt_SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf data
2889ref_i=str2double(get(handles.ref_i,'String'));
2890if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
2891    ref_j=0;
2892else
2893    ref_j=str2double(get(handles.ref_j,'String'));
2894end
2895time=get(handles.ImaDoc,'UserData');%get the set of times
2896if isempty(time)
2897    time=[0 1];
2898end
2899dt_unit=1000;%default
2900displ_num=get(handles.ListPairCiv1,'UserData');
2901
2902%eliminate the first pairs inconsistent with the position
2903if isempty(displ_num)
2904    nbpair=0;
2905else
2906    nbpair=length(displ_num(1,:));%nbre of displayed pairs
2907    if  isequal(mode,'series(Di)')  %| isequal(mode,'st_series(Di)')
2908        nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index
2909    elseif  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
2910        nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index
2911    end
2912end
2913nbpair=min(200,nbpair);%limit the number of displayed pairs to 200
2914
2915%look for existing processed pairs involving the field at the middle of the series if checkciv1 will not
2916% be performed, while the result is needed for next steps.
2917displ_pair={''};
2918select=ones(size(1:nbpair));%flag for displayed pairs =1 for display
2919testpair=0;
2920
2921%% case with no Civ1 operation, netcdf files need to exist for reading
2922if ~get(handles.CheckCiv1,'Value') %
2923    if ~exist(fullfile(filepath,subdir_civ1,ext_dir),'dir')
2924        msgbox_uvmat('ERROR',['no civ1 file available: subdirectory ' subdir_civ1 ' does not exist']);
2925        set(handles.ListPairCiv1,'String',{});
2926        return
2927    end
2928    for ipair=1:nbpair
2929        filename=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,...
2930            ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1);
2931        select(ipair)=exist(filename,'file')==2;% put flag to 0 if the file does not exist
2932    end   
2933    % case of no displayed pair
2934    if isequal(select,zeros(size(1:nbpair)))
2935        if isfield(browse,'incr_pair') && ~isequal(browse.incr_pair,[0 0])
2936            num_i1=ref_i-floor(browse.incr_pair(1)/2);
2937            num_i2=ref_i+ceil(browse.incr_pair(1)/2);
2938            num_j1=ref_j-floor(browse.incr_pair(2)/2);
2939            num_j2=ref_j+ceil(browse.incr_pair(2)/2);
2940            filename=name_generator(filebase,num_i1,num_j1,'.nc',nom_type_nc,1,num_i2,num_j2,subdir_civ1);
2941            select(1)=exist(filename,'file')==2;
2942            testpair=1;
2943        else
2944            if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
2945                msgbox_uvmat('ERROR',['no civ1 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ1]);
2946            else
2947                msgbox_uvmat('ERROR',['no civ1 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ1]);
2948            end
2949            set(handles.ListPairCiv1,'String',{''});
2950            %COMPLETER CAS STEREO
2951            return
2952        end
2953    end
2954end
2955
2956%% determine the menu display in .ListPairCiv1
2957% the menu depends on the mode defined in ListPairMode_callback through the array displ_num:
2958% displ_num(1,:)=indices j1
2959% displ_num(2,:)=indices j2
2960% displ_num(3,:)=indices i1
2961% displ_num(4,:)=indices i2
2962% in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices
2963% are relative to the reference indices ref_i and ref_j respectively.
2964if isequal(mode,'series(Di)')
2965    if testpair
2966        displ_pair{1}=['Di= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
2967    else
2968        for ipair=1:nbpair
2969            if select(ipair)
2970                displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
2971                if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
2972                    dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt
2973                    displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
2974                end
2975            else
2976                displ_pair{ipair}='...'; %pair not displayed in the menu
2977            end
2978        end
2979    end
2980elseif isequal(mode,'series(Dj)')
2981    if testpair
2982        displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
2983    else
2984        for ipair=1:nbpair
2985            if select(ipair)
2986                displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
2987                if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
2988                    dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt
2989                    displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
2990                end
2991            else
2992                displ_pair{ipair}='...'; %pair not displayed in the menu
2993            end
2994        end
2995    end
2996elseif isequal(mode,'pair j1-j2')%case of pairs
2997    for ipair=1:nbpair
2998        if select(ipair)
2999            dt=time(ref_i+displ_num(4,ipair),displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),displ_num(1,ipair));%time interval dt
3000            displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ...
3001                ' :dt= ' num2str(dt*1000)];
3002        else
3003            displ_pair{ipair}='...'; %pair not displayed in the menu
3004        end
3005    end
3006elseif isequal(mode,'displacement')
3007    displ_pair={'Di=Dj=0'};
3008end
3009set(handles.ListPairCiv1,'String',displ_pair');
3010
3011%% determine the default selection in the pair menu
3012ichoice=find(select,1);% index of selected pair
3013if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
3014initial=get(handles.ListPairCiv1,'Value');%initial choice of pair
3015if initial>nbpair || (numel(select)>=initial && ~isequal(select(initial),1))
3016    set(handles.ListPairCiv1,'Value',ichoice);% first valid pair proposed by default in the menu
3017end
3018initial=get(handles.ListPairCiv2,'Value');
3019if initial>length(displ_pair')%|~isequal(select(initial),1)
3020    if ichoice <= length(displ_pair')
3021        set(handles.ListPairCiv2,'Value',ichoice);% same pair proposed by default for civ2
3022    else
3023        set(handles.ListPairCiv2,'Value',1);% same pair proposed by default for civ2
3024    end
3025end
3026set(handles.ListPairCiv2,'String',displ_pair');
3027set(gcf,'Pointer','arrow')
3028
3029%------------------------------------------------------------------------
3030% determine the menu for checkciv2 pairs depending on the existing netcdf file at the
3031%middle of the series set by first_i, incr, last_i
3032function find_netcpair_civ2(handles)
3033%------------------------------------------------------------------------
3034set(gcf,'Pointer','watch')
3035%nomenclature types
3036filebase=get(handles.RootName,'String');
3037[filepath,Nme,ext_dir]=fileparts(filebase);
3038browse=get(handles.RootName,'UserData');
3039compare_list=get(handles.ListCompareMode,'String');
3040val=get(handles.ListCompareMode,'Value');
3041compare=compare_list{val};
3042if strcmp(compare,'displacement')
3043    mode='displacement';
3044else
3045    mode_list=get(handles.ListPairMode,'String');
3046    if isempty(mode_list)
3047        msgbox_uvmat('ERROR','please enter an input image or netcdf file')
3048        return
3049    end
3050    mode_value=get(handles.ListPairMode,'Value');
3051    mode=mode_list{mode_value};
3052end
3053
3054% nomenclature type of the .nc files
3055nom_type_ima='ima_num';%default
3056if isfield(browse,'nom_type_ima')
3057    nom_type_ima=browse.nom_type_ima;
3058end
3059nom_type_nc='_i1-i2';%default
3060if isfield(browse,'nom_type_nc')
3061    nom_type_nc=browse.nom_type_nc;
3062end
3063if isequal(nom_type_ima,'png_old') || isequal(nom_type_ima,'netc_old')|| isequal(nom_type_ima,'raw_SMD')|| isequal(nom_type_nc,'netc_old')
3064    nom_type_nc='netc_old';%nom_type for the netcdf files
3065elseif isequal(nom_type_ima,'none')||isequal(nom_type_nc,'none')
3066    nom_type_nc='none';
3067elseif isequal(nom_type_ima,'avi')||isequal(nom_type_ima,'_i')||isequal(nom_type_ima,'ima_num')||isequal(nom_type_nc,'_i1-i2')
3068    nom_type_nc='_i1-i2';
3069else
3070    if  isequal(mode,'series(Di)')%|isequal(mode,'st_series(Di)')
3071        nom_type_nc='_i1-i2_j'; % PIV in volume
3072    else
3073        nom_type_nc='_i_j1-j2';
3074    end
3075end
3076browse.nom_type_nc=nom_type_nc;
3077set(handles.RootName,'UserData',browse)
3078
3079%reads .nc subdirectory and image numbers from the interface
3080subdir_civ1=get(handles.txt_SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf data
3081subdir_civ2=get(handles.txt_SubdirCiv2,'String');%subdirectory subdir_civ2 for the netcdf data
3082ref_i=str2double(get(handles.ref_i,'String'));
3083if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
3084    ref_j=0;
3085else
3086    ref_j=str2double(get(handles.ref_j,'String'));
3087end
3088time=get(handles.ImaDoc,'UserData'); %get the set of times
3089if isempty(time)
3090    time=[0 1];%default
3091end
3092displ_num=get(handles.ListPairCiv1,'UserData');
3093
3094%eliminate the first pairs inconsistent with the position
3095if isempty(displ_num)
3096    nbpair=0;
3097else
3098    nbpair=length(displ_num(1,:));%nbre of displayed pairs
3099    if  isequal(mode,'series(Di)')% | isequal(mode,'st_series(Di)')
3100        nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index
3101    elseif  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
3102        nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index
3103    end
3104end
3105nbpair=min(200,nbpair);%limit the number of displayed pairs to 200
3106
3107%% look for existing processed pairs at the reference indices if Civ1 will not
3108% be performed, while the result is needed for next steps.
3109displ_pair={''}; %default
3110select=ones(size(1:nbpair));%default =1 for numbers of displayed pairs
3111if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
3112    if ~exist(fullfile(filepath,subdir_civ2,ext_dir),'dir')
3113        errordlg(['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist'])
3114        set(handles.ListPairCiv2,'Value',1);
3115        set(handles.ListPairCiv2,'String',{''});
3116        return
3117    end
3118    for ipair=1:nbpair
3119        filename=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,...
3120            ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1);
3121        select(ipair)=exist(filename,'file')==2;
3122    end
3123    if  isequal(select,zeros(size(1:nbpair)))
3124        if isfield(browse,'incr_pair')
3125            num_i1=ref_i-floor(browse.incr_pair(1)/2);
3126            num_i2=ref_i+floor((browse.incr_pair(1)+1)/2);
3127            num_j1=ref_j-floor(browse.incr_pair(2)/2);
3128            num_j2=ref_j+floor((browse.incr_pair(2)+1)/2);
3129            filename=name_generator(filebase,num_i1,num_j1,'.nc',nom_type_nc,1,num_i2,num_j2,subdir_civ2);
3130            select(1)=exist(filename,'file')==2;
3131        else
3132            if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
3133                errordlg(['no civ2 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ2])
3134            else
3135                errordlg(['no civ2 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ2])
3136            end
3137            set(handles.ListPairCiv2,'Value',1);
3138            set(handles.ListPairCiv2,'String',{''});
3139            return
3140        end
3141    end
3142end
3143if isequal(mode,'series(Di)')
3144    for ipair=1:nbpair
3145        if select(ipair)
3146            displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
3147            if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
3148                dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt
3149                displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
3150            end
3151        else
3152            displ_pair{ipair}='...'; %pair not displayed in the menu
3153        end
3154    end
3155elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)') % series on the j index
3156    for ipair=1:nbpair
3157        if select(ipair)
3158            displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
3159            if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
3160                dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt
3161                displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
3162            end
3163        else
3164            displ_pair{ipair}='...'; %pair not displayed in the menu
3165        end
3166    end
3167elseif isequal(mode,'pair j1-j2')% | isequal(mode,'st_pair j1-j2') %case of pairs
3168    for ipair=1:nbpair
3169        if select(ipair)
3170            dt=time(ref_i+displ_num(4,ipair),displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),displ_num(1,ipair));%time interval dt
3171            displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ...
3172                ' :dt= ' num2str(dt*1000)];
3173        else
3174            displ_pair{ipair}='...'; %pair not displayed in the menu
3175        end
3176    end
3177elseif isequal(mode,'displacement')
3178    displ_pair={'Di=Dj=0'};
3179end
3180val=get(handles.ListPairCiv2,'Value');
3181ichoice=find(select,1);
3182if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
3183if get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0
3184    val=ichoice;% first valid pair proposed by default in the menu
3185end
3186if val>length(displ_pair')
3187    set(handles.ListPairCiv2,'Value',1);% first valid pair proposed by default in the menu
3188else
3189    set(handles.ListPairCiv2,'Value',val);
3190end
3191set(handles.ListPairCiv2,'String',displ_pair');
3192set(gcf,'Pointer','arrow')
3193
3194%-------------------------------------------------------------------
3195% ---
3196function closeview_field(gcbo,eventdata)
3197hview_field=findobj(allchild(0),'tag','view_field');% look for view_field   
3198    if ~isempty(hview_field)
3199        delete(hview_field)
3200    end
3201   
3202   
3203%------------------------------------------------------------------------   
3204% call 'view_field.fig' to display the  field selected in the list of 'status'
3205function open_view_field(hObject, eventdata)
3206%------------------------------------------------------------------------
3207list=get(hObject,'String');
3208index=get(hObject,'Value');
3209rootroot=get(hObject,'UserData');
3210filename=list{index};
3211ind_dot=strfind(filename,'...');
3212filename=filename(1:ind_dot-1);
3213filename=fullfile(rootroot,filename);
3214delete(get(hObject,'parent'))%delete the display figure to stop the check process
3215if exist(filename,'file')%visualise the vel field if it exists
3216    uvmat(filename)
3217    set(gcbo,'Value',1)
3218end
3219
3220%------------------------------------------------------------------------   
3221% launched by pressing OK on the status figure
3222function close_GUI(hObject, eventdata)
3223%------------------------------------------------------------------------
3224    delete(gcbf)
3225   
3226%------------------------------------------------------------------------   
3227% launched by deleting the status figure
3228function stop_status(hObject, eventdata)
3229%------------------------------------------------------------------------
3230hciv=findobj(allchild(0),'tag','civ');
3231hhciv=guidata(hciv);
3232set(hhciv.status,'value',0) %reset the status uicontrol in the GUI civ
3233set(hhciv.status,'BackgroundColor',[0 1 0])
3234
3235
3236%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3237% Callbacks in the uipanel Reference Indices
3238%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3239%------------------------------------------------------------------------
3240function first_i_Callback(hObject, eventdata, handles)
3241%------------------------------------------------------------------------
3242first_i=str2double(get(handles.first_i,'String'));
3243set(handles.ref_i,'String', num2str(first_i))% reference index for pair dt = first index
3244ref_i_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
3245
3246%------------------------------------------------------------------------
3247function first_j_Callback(hObject, eventdata, handles)
3248%------------------------------------------------------------------------
3249first_j=str2num(get(handles.first_j,'String'));
3250set(handles.ref_j,'String', num2str(first_j))% reference index for pair dt = first index
3251ref_j_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
3252
3253%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3254% Callbacks in the uipanel Civ1
3255%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3256%------------------------------------------------------------------------
3257% --- Executes on button press in SearchRange: determine the search range num_Searchx,num_Searchy
3258function SearchRange_Callback(hObject, eventdata, handles)
3259%------------------------------------------------------------------------
3260%determine pair numbers
3261if strcmp(get(handles.umin,'Visible'),'off')
3262    set(handles.u_title,'Visible','on')
3263    set(handles.v_title,'Visible','on')
3264    set(handles.umin,'Visible','on')
3265    set(handles.umax,'Visible','on')
3266    set(handles.vmin,'Visible','on')
3267    set(handles.vmax,'Visible','on')
3268    set(handles.CoordUnit,'Visible','on')
3269    set(handles.TimeUnit,'Visible','on')
3270    set(handles.slash_title,'Visible','on')
3271    set(handles.min_title,'Visible','on')
3272    set(handles.max_title,'Visible','on')
3273    set(handles.unit_title,'Visible','on')
3274else
3275    get_search_range(hObject, eventdata, handles)
3276end
3277
3278%------------------------------------------------------------------------
3279% ---  determine the search range num_Searchx,num_Searchy and shift
3280function get_search_range(hObject, eventdata, handles)
3281umin=str2double(get(handles.umin,'String'));
3282umax=str2double(get(handles.umax,'String'));
3283vmin=str2double(get(handles.umin,'String'));
3284vmax=str2double(get(handles.vmax,'String'));
3285%switch min_title and max_title in case of error
3286if umax<=umin
3287    umin_old=umin;
3288    umin=umax;
3289    umax=umin_old;
3290    set(handles.umin,'String', num2str(umin))
3291    set(handles.umax,'String', num2str(umax))
3292end
3293if vmax<=vmin
3294    vmin_old=vmin;
3295    vmin=vmax;
3296    vmax=vmin_old;
3297    set(handles.vmin,'String', num2str(vmin))
3298    set(handles.vmax,'String', num2str(vmax))
3299end   
3300if ~(isnan(umin)||isnan(umax)||isnan(vmin)||isnan(vmax))
3301    list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
3302    index=get(handles.ListPairCiv1,'Value');
3303    displ_num=get(handles.ListPairCiv1,'UserData');
3304    time=get(handles.ImaDoc,'UserData'); %get the set of times
3305    pxcm_xy=get(handles.SearchRange,'UserData');
3306    pxcmx=pxcm_xy(1);
3307    pxcmy=pxcm_xy(2);
3308    mode_list=get(handles.ListPairMode,'String');
3309    mode_value=get(handles.ListPairMode,'Value');
3310    mode=mode_list{mode_value};
3311    if isequal (mode, 'series(Di)' )
3312        ref_i=str2double(get(handles.ref_i,'String'));
3313        num1=ref_i-floor(index/2);%  first image numbers
3314        num2=ref_i+ceil(index/2);
3315        num_a=1;
3316        num_b=1;
3317    elseif isequal (mode, 'series(Dj)')
3318        num1=1;
3319        num2=1;
3320        ref_j=str2double(get(handles.ref_j,'String'));
3321        num_a=ref_j-floor(index/2);%  first image numbers
3322        num_b=ref_j+ceil(index/2);
3323    elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)
3324        ref_i=str2double(get(handles.ref_i,'String'));
3325        num1=ref_i;
3326        num2=ref_i;
3327        num_a=displ_num(1,index);
3328        num_b=displ_num(2,index);
3329    end
3330    dt=time(num2,num_b)-time(num1,num_a);
3331    ibx=str2double(get(handles.num_Bx,'String'));
3332    iby=str2double(get(handles.num_By,'String'));
3333    umin=dt*pxcmx*umin;
3334    umax=dt*pxcmx*umax;
3335    vmin=dt*pxcmy*vmin;
3336    vmax=dt*pxcmy*vmax;
3337    shiftx=round((umin+umax)/2);
3338    shifty=round((vmin+vmax)/2);
3339    isx=(umax+2-shiftx)*2+ibx;
3340    isx=2*ceil(isx/2)+1;
3341    isy=(vmax+2-shifty)*2+iby;
3342    isy=2*ceil(isy/2)+1;
3343    set(handles.num_Shiftx,'String',num2str(shiftx));
3344    set(handles.num_Shifty,'String',num2str(shifty));
3345    set(handles.num_Searchx,'String',num2str(isx));
3346    set(handles.num_Searchy,'String',num2str(isy));
3347end
3348
3349%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3350% Callbacks in the uipanel Fix1
3351%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3352%------------------------------------------------------------------------
3353% --- Executes on button press in CheckMask.
3354function get_mask_fix1_Callback(hObject, eventdata, handles)
3355%------------------------------------------------------------------------
3356maskval=get(handles.CheckMask,'Value');
3357if isequal(maskval,0)
3358    set(handles.txt_Mask,'String','')
3359else
3360    mask_displ='no mask'; %default
3361    filebase=get(handles.RootName,'String');
3362    [nbslice, flag_mask]=get_mask(filebase,handles);
3363    if isequal(flag_mask,1)
3364        mask_displ=[num2str(nbslice) 'mask'];
3365    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3366        filebase_a=get(handles.RootName_1,'String');
3367        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3368        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3369            mask_displ='no mask';
3370        end
3371    end
3372    if isequal(mask_displ,'no mask')
3373        [FileName, PathName, filterindex] = uigetfile( ...
3374            {'*.png', ' (*.png)';
3375            '*.png',  '.png files '; ...
3376            '*.*', 'All Files (*.*)'}, ...
3377            'Pick a mask file *.png',filebase);
3378        mask_displ=fullfile(PathName,FileName);
3379        if ~exist(mask_displ,'file')
3380            mask_displ='no mask';
3381        end
3382    end
3383    if isequal(mask_displ,'no mask')
3384        set(handles.CheckMask,'Value',0)
3385        set(handles.CheckMask,'Value',0)
3386        set(handles.CheckMask,'Value',0)
3387    else
3388        %set(handles.CheckMask,'Value',1)
3389        set(handles.CheckMask,'Value',1)
3390    end
3391    set(handles.txt_Mask,'String',mask_displ)
3392    set(handles.txt_Mask,'String',mask_displ)
3393    set(handles.txt_Mask,'String',mask_displ)
3394end
3395
3396%------------------------------------------------------------------------
3397% --- Executes on button press in CheckMask: select box for mask option
3398function get_mask_civ2_Callback(hObject, eventdata, handles)
3399%------------------------------------------------------------------------
3400maskval=get(handles.CheckMask,'Value');
3401if isequal(maskval,0)
3402    set(handles.txt_Mask,'String','')
3403else
3404    mask_displ='no mask'; %default
3405    filebase=get(handles.RootName,'String');
3406    [nbslice, flag_mask]=get_mask(filebase,handles);
3407    if isequal(flag_mask,1)
3408        mask_displ=[num2str(nbslice) 'mask'];
3409    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3410        filebase_a=get(handles.RootName_1,'String');
3411        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3412        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3413            mask_displ='no mask';
3414        end
3415    end
3416    if isequal(mask_displ,'no mask')
3417        [FileName, PathName, filterindex] = uigetfile( ...
3418            {'*.png', ' (*.png)';
3419            '*.png',  '.png files '; ...
3420            '*.*', 'All Files (*.*)'}, ...
3421            'Pick a mask file *.png',filebase);
3422        mask_displ=fullfile(PathName,FileName);
3423        if ~exist(mask_displ,'file')
3424            mask_displ='no mask';
3425        end
3426    end
3427    if isequal(mask_displ,'no mask')
3428        set(handles.CheckMask,'Value',0)
3429        set(handles.CheckMask,'Value',0)
3430    else
3431        set(handles.CheckMask,'Value',1)
3432    end
3433    set(handles.txt_Mask,'String',mask_displ)
3434    set(handles.txt_Mask,'String',mask_displ)
3435end
3436
3437%------------------------------------------------------------------------
3438% --- Executes on button press in CheckMask.
3439function get_mask_fix2_Callback(hObject, eventdata, handles)
3440%------------------------------------------------------------------------
3441maskval=get(handles.CheckMask,'Value');
3442if isequal(maskval,0)
3443    set(handles.txt_Mask,'String','')
3444else
3445    mask_displ='no mask'; %default
3446    filebase=get(handles.RootName,'String');
3447    [nbslice, flag_mask]=get_mask(filebase,handles);
3448    if isequal(flag_mask,1)
3449        mask_displ=[num2str(nbslice) 'mask'];
3450    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3451        filebase_a=get(handles.RootName_1,'String');
3452        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3453        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3454            mask_displ='no mask';
3455        end
3456    end
3457    if isequal(mask_displ,'no mask')
3458        [FileName, PathName, filterindex] = uigetfile( ...
3459            {'*.png', ' (*.png)';
3460            '*.png',  '.png files '; ...
3461            '*.*', 'All Files (*.*)'}, ...
3462            'Pick a mask file *.png',filebase);
3463        mask_displ=fullfile(PathName,FileName);
3464        if ~exist(mask_displ,'file')
3465            mask_displ='no mask';
3466        end
3467    end
3468    if isequal(mask_displ,'no mask')
3469        set(handles.CheckMask,'Value',0)
3470    end
3471    set(handles.txt_Mask,'String',mask_displ)
3472end
3473
3474%------------------------------------------------------------------------
3475% --- function called to look for mask files
3476function [nbslice, flag_mask]=get_mask(filebase,handles)
3477%------------------------------------------------------------------------
3478%detect mask files, images with appropriate file base
3479%[filebase '_' xx 'mask'], xx=nbslice
3480%flag_mask=1 indicates detection
3481
3482flag_mask=0;%default
3483nbslice=1;
3484
3485% subdir=get(handles.txt_SubdirCiv1,'String');
3486[Path,Name]=fileparts(filebase);
3487if ~isdir(Path)
3488    msgbox_uvmat('ERROR','no path for input files')
3489    return
3490end
3491% currentdir=pwd;
3492% cd(Path);%move in the dir of the root name filebase
3493maskfiles=dir(fullfile(Path,[Name '_*mask_*.png']));%look for mask files
3494% cd(currentdir);%come back to the current working directory
3495if ~isempty(maskfiles)
3496    %     msgbox_uvmat('ERROR','no mask available, to create it use Tools/Make mask in the upper menu bar of uvmat')
3497    % else
3498    flag_mask=1;
3499    maskname=maskfiles(1).name;% take the first mask file in the list
3500    [Path2,Name,ext]=fileparts(maskname);
3501    Namedouble=double(Name);
3502    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3503    ind_mask=findstr('mask',Name);
3504    i=ind_mask-1;
3505    while val(i)==0 && i>0
3506        i=i-1;
3507    end
3508    nbslice=str2double(Name(i+1:ind_mask-1));
3509    if ~isnan(nbslice) && Name(i)=='_'
3510        flag_mask=1;
3511    else
3512        msgbox_uvmat('ERROR',['bad mask file ' Name ext ' found in ' Path2])
3513        return
3514        nbslice=1;
3515    end
3516end
3517
3518%------------------------------------------------------------------------
3519% --- function called to look for grid files
3520function [nbslice, flag_mask]=get_grid(filebase,handles)
3521%------------------------------------------------------------------------
3522flag_mask=0;%default
3523nbslice=1;
3524[Path,Name]=fileparts(filebase);
3525currentdir=pwd;
3526cd(Path);%move in the dir of the root name filebase
3527maskfiles=dir([Name '_*grid_*.grid']);%look for mask files
3528cd(currentdir);%come back to the current working directory
3529if ~isempty(maskfiles)
3530    flag_mask=1;
3531    maskname=maskfiles(1).name;% take the first mask file in the list
3532    [Path2,Name,ext]=fileparts(maskname);
3533    Namedouble=double(Name);
3534    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3535    ind_mask=findstr('grid',Name);
3536    i=ind_mask-1;
3537    while val(i)==0 && i>0
3538        i=i-1;
3539    end
3540    nbslice=str2double(Name(i+1:ind_mask-1));
3541    if ~isnan(nbslice) && Name(i)=='_'
3542        flag_mask=1;
3543    else
3544        msgbox_uvmat('ERROR',['bad grid file ' Name ext ' found in ' Path2])
3545        return
3546        nbslice=1;
3547    end
3548end
3549
3550%------------------------------------------------------------------------
3551% --- transform numbers to letters
3552function str=num2stra(num,nom_type)
3553%------------------------------------------------------------------------
3554if isempty(nom_type)
3555    str='';
3556elseif strcmp(nom_type(end),'a')
3557    str=char(96+num);
3558elseif strcmp(nom_type(end),'A')
3559    str=char(96+num);
3560elseif isempty(nom_type(2:end))%a single index
3561    str='';
3562else
3563    str=num2str(num);
3564end
3565
3566%------------------------------------------------------------------------
3567% --- Executes on button press in ListSubdirCiv1.
3568function ListSubdirCiv1_Callback(hObject, eventdata, handles)
3569%------------------------------------------------------------------------
3570list_subdir_civ1=get(handles.ListSubdirCiv1,'String');
3571val=get(handles.ListSubdirCiv1,'Value');
3572subdir=list_subdir_civ1{val};
3573if strcmp(subdir,'new...')
3574    if get(handles.CheckCiv1,'Value')
3575        subdir='CIV'; %default subdirectory
3576    else
3577        msgbox_uvmat('ERROR','select CheckCiv1 to perform a new Civ operation')
3578        return
3579    end   
3580end
3581set(handles.txt_SubdirCiv1,'String',subdir);
3582find_netcpair_civ1(handles)
3583
3584%------------------------------------------------------------------------
3585% --- Executes on button press in ListSubdirCiv2.
3586function ListSubdirCiv2_Callback(hObject, eventdata, handles)
3587%------------------------------------------------------------------------
3588list_subdir_civ2=get(handles.ListSubdirCiv2,'String');
3589val=get(handles.ListSubdirCiv2,'Value');
3590subdir=list_subdir_civ2{val};
3591if strcmp(subdir,'new...')
3592    if get(handles.CheckCiv2,'Value')
3593        subdir='CIV'; %default subdirectory
3594    else
3595        msgbox_uvmat('ERROR','select CheckCiv2 to perform a new Civ operation')
3596        return
3597    end
3598end
3599set(handles.txt_SubdirCiv2,'String',subdir);
3600
3601%------------------------------------------------------------------------
3602% --- Executes on button press in CheckGrid.
3603function CheckGrid_Callback(hObject, eventdata, handles)
3604%------------------------------------------------------------------------
3605value=get(hObject,'Value');
3606hparent=get(hObject,'parent');
3607hchildren=get(hparent,'children');
3608handle_txtbox=findobj(hchildren,'tag','txt_Grid');
3609handle_dx=findobj(hchildren,'tag','num_Dx');
3610handle_dy=findobj(hchildren,'tag','num_Dy');
3611handle_title_dx=findobj(hchildren,'tag','title_Dx');
3612handle_title_dy=findobj(hchildren,'tag','title_Dy');
3613testgrid=0;
3614filegrid='';
3615if value
3616    filebase=get(handles.RootName,'String');
3617    [nbslice, flag_grid]=get_grid(filebase,handles);% look for a grid with appropriate name
3618    if isequal(flag_grid,1)
3619        filegrid=[num2str(nbslice) 'grid'];
3620        testgrid=1;
3621    else % browse for a grid
3622        filegrid=get(hObject,'UserData');%look for previous grid name stored as UserData
3623        if exist(filegrid,'file')
3624            filebase=filegrid;
3625        end
3626        [FileName, PathName, filterindex] = uigetfile( ...
3627            {'*.grid', ' (*.grid)';
3628            '*.grid',  '.grid files '; ...
3629            '*.*', 'All Files (*.*)'}, ...
3630            'Pick a file',filebase);
3631        filegrid=fullfile(PathName,FileName);
3632        set(hObject,'UserData',filegrid);%store for future use
3633        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filegrid,'file'))
3634            testgrid=1;
3635        end
3636    end
3637end
3638if testgrid
3639    set(handle_dx,'Visible','off');
3640    set(handle_dy,'Visible','off');
3641    set(handle_title_dy,'Visible','off');
3642    set(handle_title_dx,'Visible','off');
3643    set(handle_txtbox,'Visible','on')
3644    set(handle_txtbox,'String',filegrid)
3645else
3646    set(hObject,'Value',0);
3647    set(handle_dx,'Visible','on');
3648    set(handle_dy,'Visible','on');
3649    set(handle_title_dy,'Visible','on');
3650    set(handle_title_dx,'Visible','on');
3651    set(handle_txtbox,'Visible','off')
3652end
3653
3654%% if hObject is on the checkciv1 frame, duplicate action for checkciv2 frame
3655PanelName=get(hparent,'tag')
3656if strcmp(PanelName,'Civ1')
3657    hchildren=get(handles.Civ2,'children');
3658    handle_checkbox=findobj(hchildren,'tag','CheckGrid');
3659    handle_txtbox=findobj(hchildren,'tag','txt_Grid');
3660    handle_dx=findobj(hchildren,'tag','num_Dx');
3661    handle_dy=findobj(hchildren,'tag','num_Dy');
3662    handle_title_dx=findobj(hchildren,'tag','title_Dx');
3663    handle_title_dy=findobj(hchildren,'tag','title_Dy');
3664    set(handle_checkbox,'UserData',filegrid);%store for future use
3665    if testgrid
3666        set(handle_checkbox,'Value',1);
3667        set(handle_dx,'Visible','off');
3668        set(handle_dy,'Visible','off');
3669        set(handle_title_dx,'Visible','off');
3670        set(handle_title_dy,'Visible','off');
3671        set(handle_txtbox,'Visible','on')
3672        set(handle_txtbox,'String',filegrid)
3673%     else
3674%         set(handle_checkbox,'Value',0);
3675%         set(handles.CheckGrid,'Value',0);
3676%         set(handle_dx,'Visible','on');
3677%         set(handle_dy,'Visible','on');
3678%          set(handle_title_dx,'Visible','on');
3679%         set(handle_title_dy,'Visible','on');
3680%         set(handle_txtbox,'Visible','off')
3681    end
3682end
3683%------------------------------------------------------------------------
3684% --- Executes on button press in CheckMask.
3685function CheckMask_Callback(hObject, eventdata, handles)
3686%------------------------------------------------------------------------
3687value=get(hObject,'Value');
3688hparent=get(hObject,'parent');
3689parent_tag=get(hparent,'Tag');
3690hchildren=get(hparent,'children');
3691handle_txtbox=findobj(hchildren,'tag','txt_Mask');
3692% handle_dx=findobj(hchildren,'tag','num_Dx');
3693% handle_dy=findobj(hchildren,'tag','num_Dy');
3694testmask=0;
3695if value
3696    filebase=get(handles.RootName,'String');
3697    [nbslice, flag_mask]=get_mask(filebase,handles);% look for a mask with appropriate name
3698    if isequal(flag_mask,1)
3699        filemask=[num2str(nbslice) 'mask'];
3700        testmask=1;
3701    else % browse for a mask
3702        filemask=get(hObject,'UserData');%look for previous mask name stored as UserData
3703        if exist(filemask,'file')
3704            filebase=filemask;
3705        end
3706        [FileName, PathName] = uigetfile( ...
3707            {'*.png', ' (*.png)';
3708            '*.png',  '.png files '; ...
3709            '*.*', 'All Files (*.*)'}, ...
3710            'Pick a mask file *.png',filebase);
3711        filemask=fullfile(PathName,FileName);
3712        set(hObject,'UserData',filemask);%store for future use
3713        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filemask,'file'))
3714            testmask=1;
3715        end
3716    end
3717end
3718if testmask
3719    stage=1;%default
3720    switch parent_tag
3721%         case 'Fix1'
3722%             stage=2;
3723        case 'Civ2'
3724             stage=3;
3725%         case 'Fix2'
3726%             stage=4;
3727    end
3728    set(handles.txt_Mask(stage:end),'Visible','on')
3729    set(handles.txt_Mask(stage:end),'String',filemask)
3730    set(handles.CheckMask(stage:end),'Value',1)
3731else
3732    set(hObject,'Value',0);
3733    set(handle_txtbox,'Visible','off')
3734end
3735
3736
3737% --- Executes on button press in get_gridpatch1.
3738function get_gridpatch1_Callback(hObject, eventdata, handles)
3739% hObject    handle to get_gridpatch1 (see GCBO)
3740% eventdata  reserved - to be defined in a future version of MENUMATLAB
3741% handles    structure with handles and user data (see GUIDATA)
3742
3743filebase=get(handles.RootName,'String');
3744[FileName, PathName, filterindex] = uigetfile( ...
3745    {'*.grid', ' (*.grid)';
3746    '*.grid',  '.grid files '; ...
3747    '*.*', 'All Files (*.*)'}, ...
3748    'Pick a file',filebase);
3749filegrid=fullfile(PathName,FileName);
3750set(handles.grid_patch1,'string',filegrid);
3751% set(handles.grid_patch2,'string',filegrid
3752
3753%------------------------------------------------------------------------
3754% --- Executes on button press in get_gridpatch2.
3755function get_gridpatch2_Callback(hObject, eventdata, handles)
3756%------------------------------------------------------------------------
3757
3758
3759%------------------------------------------------------------------------
3760% --- STEREO Interp
3761function cmd=RUN_STINTERP(stinterpBin,filename_A_nc,filename_B_nc,filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,xmlA,xmlB)
3762%------------------------------------------------------------------------
3763namelog=[filename_nc(1:end-3) '_stinterp.log'];
3764cmd=[stinterpBin ' -f1 ' filename_A_nc  ' -f2 ' filename_B_nc ' -f  ' filename_nc ...
3765    ' -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
3766
3767%------------------------------------------------------------------------
3768%--read images and convert them to the uint16 format used for PIV
3769function A=read_image(filename,type_ima,num,movieobject)
3770%------------------------------------------------------------------------
3771%num is the view number needed for an avi movie
3772switch type_ima
3773    case 'movie'
3774        A=read(movieobject,num);
3775    case 'avi'
3776        mov=aviread(filename,num);
3777        A=frame2im(mov(1));
3778    case 'multimage'
3779        A=imread(filename,num);
3780    case 'image'
3781        A=imread(filename);
3782end
3783siz=size(A);
3784if length(siz)==3;%color images
3785    A=sum(double(A),3);
3786    A=uint16(A);
3787end
3788
3789
3790%------------------------------------------------------------------------
3791% --- Executes on button press in get_ref_fix1.
3792function get_ref_fix1_Callback(hObject, eventdata, handles)
3793%------------------------------------------------------------------------
3794filebase=get(handles.RootName,'String');
3795[FileName, PathName, filterindex] = uigetfile( ...
3796    {'*.nc', ' (*.nc)';
3797    '*.nc',  'netcdf files '; ...
3798    '*.*', 'All Files (*.*)'}, ...
3799    'Pick a file',filebase);
3800
3801fileinput=[PathName FileName];
3802sizf=size(fileinput);
3803if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
3804[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
3805ref.filebase=fullfile(Path,File);
3806ref.num_a=stra2num(str_a);
3807ref.num_b=stra2num(str_b);
3808ref.num1=str2double(field_count);
3809ref.num2=str2double(str2);
3810browse=[];%initialisation
3811if ~isequal(ref.ext,'.nc')
3812    msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
3813    return
3814end
3815set(handles.ref_fix1,'String',[fullfile(ref.subdir,File) '....nc']);
3816set(handles.ref_fix1,'UserData',ref)
3817menu_field{1}='civ1';
3818Data=nc2struct(fileinput,[]);
3819if isfield(Data,'patch') && isequal(Data.patch,1)
3820    menu_field{2}='filter1';
3821end
3822if isfield(Data,'civ2') && isequal(Data.civ2,1)
3823    menu_field{3}='civ2';
3824end
3825if isfield(Data,'patch2') && isequal(Data.patch2,1)
3826    menu_field{4}='filter2';
3827end
3828set(handles.field_ref1,'String',menu_field);
3829set(handles.field_ref1,'Value',length(menu_field));
3830set(handles.num_MinVel,'Value',2);
3831set(handles.num_MinVel,'String','1');%default threshold
3832set(handles.ref_fix1,'Enable','on')
3833
3834%------------------------------------------------------------------------
3835% --- Executes on button press in get_ref_fix2.
3836function get_ref_fix2_Callback(hObject, eventdata, handles)
3837%------------------------------------------------------------------------
3838if isequal(get(handles.get_ref_fix2,'Value'),1)
3839    filebase=get(handles.RootName,'String');
3840    [FileName, PathName, filterindex] = uigetfile( ...
3841        {'*.nc', ' (*.nc)';
3842        '*.nc',  'netcdf files '; ...
3843        '*.*', 'All Files (*.*)'}, ...
3844        'Pick a file',filebase);
3845    fileinput=[PathName FileName];
3846    sizf=size(fileinput);
3847    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
3848    [Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
3849    ref.filebase=fullfile(Path,File);
3850    ref.num_a=stra2num(str_a);
3851    ref.num_b=stra2num(str_b);
3852    ref.num1=str2num(field_count);
3853    ref.num2=str2num(str2);
3854    browse=[];%initialisation
3855    if ~isequal(ref.ext,'.nc')
3856        msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
3857        return
3858    end
3859    set(handles.ref_fix2,'String',[fullfile(ref.subdir,File) '....nc']);
3860    set(handles.ref_fix2,'UserData',ref)
3861    menu_field{1}='civ1';
3862    Data=nc2struct(fileinput,[]);
3863    if isfield(Data,'patch') && isequal(Data.patch,1)
3864        menu_field{2}='filter1';
3865    end
3866    if isfield(Data,'civ2') && isequal(Data.civ2,1)
3867        menu_field{3}='civ2';
3868    end
3869    if isfield(Data,'patch2') && isequal(Data.patch2,1)
3870        menu_field{4}='filter2';
3871    end
3872    set(handles.field_ref2,'String',menu_field);
3873    set(handles.field_ref2,'Value',length(menu_field));
3874    set(handles.num_MinVel,'Value',2);
3875    set(handles.num_MinVel,'String','1');%default threshold
3876    set(handles.ref_fix2,'Enable','on')
3877    set(handles.ref_fix2,'Visible','on')
3878    set(handles.field_ref2,'Visible','on')
3879else
3880    set(handles.ref_fix2,'Visible','off')
3881    set(handles.field_ref2,'Visible','off')
3882end
3883
3884%------------------------------------------------------------------------
3885function ref_fix1_Callback(hObject, eventdata, handles)
3886%------------------------------------------------------------------------
3887set(handles.num_MinVel,'Value',1);
3888set(handles.field_ref1,'Value',1)
3889set(handles.field_ref1,'String',{' '})
3890set(handles.ref_fix1,'UserData',[]);
3891set(handles.ref_fix1,'String','');
3892set(handles.thresh_vel1,'String','0');
3893
3894%------------------------------------------------------------------------
3895function ref_fix2_Callback(hObject, eventdata, handles)
3896%------------------------------------------------------------------------
3897set(handles.num_MinVel,'Value',1);
3898set(handles.field_ref2,'Value',1)
3899set(handles.field_ref2,'String',{' '})
3900set(handles.ref_fix2,'UserData',[]);
3901set(handles.ref_fix2,'String','');
3902set(handles.num_MinVel,'String','0');
3903
3904%------------------------------------------------------------------------
3905% --- Executes on button press in test_stereo1.
3906function test_stereo1_Callback(hObject, eventdata, handles)
3907%------------------------------------------------------------------------
3908if isequal(get(handles.test_stereo1,'Value'),0)
3909    set(handles.subdomain_patch1,'Visible','on')
3910    set(handles.rho_patch1,'Visible','on')
3911else
3912    set(handles.subdomain_patch1,'Visible','off')
3913    set(handles.rho_patch1,'Visible','off')
3914end
3915
3916%------------------------------------------------------------------------
3917% --- Executes on button press in CheckStereo.
3918function StereoCheck_Callback(hObject, eventdata, handles)
3919%------------------------------------------------------------------------
3920if isequal(get(handles.CheckStereo,'Value'),0)
3921    set(handles.num_SubdomainSize,'Visible','on')
3922    set(handles.num_SmoothingParam,'Visible','on')
3923else
3924    set(handles.num_SubdomainSize,'Visible','off')
3925    set(handles.num_SmoothingParam,'Visible','off')
3926end
3927
3928%------------------------------------------------------------------------
3929% --- Executes on button press in TestCiv1: display image correlation function
3930function TestCiv1_Callback(hObject, eventdata, handles)
3931%------------------------------------------------------------------------
3932set(handles.TestCiv1,'BackgroundColor',[1 1 0])
3933drawnow
3934if get(handles.TestCiv1,'Value')
3935    ref_i=str2double(get(handles.ref_i,'String'));
3936    if strcmp(get(handles.ref_j,'Visible'),'on')
3937        ref_j=str2double(get(handles.ref_j,'String'));
3938    else
3939        ref_j=1;%default
3940    end
3941    [filecell,i1,i21,j1,j2,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,file_ref_fix1,file_ref_fix2]=...
3942        set_civ_filenames(handles,ref_i,ref_j,[1 0 0 0 0 0]);
3943    Data.ListVarName={'ny','nx','A'};
3944    Data.VarDimName= {'ny','nx',{'ny','nx'}};
3945    Data.A=imread(filecell.ima1.civ1{1});
3946    Data.ny=[size(Data.A,1) 1];
3947    Data.nx=[1 size(Data.A,2)];
3948    par_civ1=read_GUI(handles.Civ1);
3949    par_civ1.ImageWidth=size(Data.A,1);
3950    par_civ1.ImageHeight=size(Data.A,2);
3951    par_civ1.Mask='all';% will provide only the grid set for PIV, no image correlation
3952    Param.Civ1=par_civ1;
3953    Grid=civ_matlab(Param);% get the grid of x, y positions set for PIV
3954    hview_field=view_field(Data);
3955    set(0,'CurrentFigure',hview_field)
3956    hhview_field=guihandles(hview_field);
3957    set(hview_field,'CurrentAxes',hhview_field.axes3)
3958    ViewData=get(hview_field,'UserData');
3959    ViewData.CivHandle=handles.civ;% indicate the handle of the civ GUI in view_field
3960    ViewData.axes3.B=imread(filecell.ima2.civ1{1});%store the second image in the UserData of the GUI view_field
3961    ViewData.axes3.X=Grid.Civ1_X; %keep the set of points in memeory
3962    ViewData.axes3.Y=Grid.Civ1_Y;
3963    set(hview_field,'UserData',ViewData)
3964    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
3965    if isempty(corrfig)
3966        corrfig=figure;
3967        set(corrfig,'tag','corrfig')
3968        set(corrfig,'name','image correlation')
3969        set(corrfig,'DeleteFcn',{@closeview_field})%
3970    end
3971    set(handles.TestCiv1,'BackgroundColor',[1 0 0])
3972else
3973    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
3974    if ~isempty(corrfig)
3975        delete(corrfig)
3976    end
3977    hview_field=findobj(allchild(0),'tag','view_field');% look for view_field   
3978    if ~isempty(hview_field)
3979        delete(hview_field)
3980    end
3981end
3982
3983
3984%------------------------------------------------------------------------
3985% --- Executes on button press in CheckThreshold.
3986function CheckThreshold_Callback(hObject, eventdata, handles)
3987%------------------------------------------------------------------------
3988huipanel=get(hObject,'parent');
3989obj(1)=findobj(huipanel,'Tag','num_MinIma');
3990obj(2)=findobj(huipanel,'Tag','num_MaxIma');
3991obj(3)=findobj(huipanel,'Tag','title_Threshold');
3992if get(hObject,'Value')
3993    set(obj,'Visible','on')
3994else
3995    set(obj,'Visible','off')
3996end
3997
3998
3999%------------------------------------------------------------------------
4000% % --- Executes on button press in ListPairMode.
4001% function CivMode_Callback(hObject, eventdata, handles)
4002% %------------------------------------------------------------------------
4003% Listprog=get(handles.ListPairMode,'String');
4004% index=get(handles.ListPairMode,'Value');
4005% prog=Listprog{index};
4006% switch prog
4007%     case 'MenuCivX'
4008%         set(handles.thresh_patch1,'Visible','off')
4009%         set(handles.thresh_text1,'Visible','off')
4010%         set(handles.num_MaxDiff,'Visible','off')
4011%         set(handles.thresh_text2,'Visible','off')
4012%         set(handles.num_Rho,'Style','edit')
4013%         set(handles.num_Rho,'String','1')
4014%         set(handles.BATCH,'Enable','on')
4015%     case 'CivAll'
4016%         if get(handles.CheckPatch1,'Value')
4017%             set(handles.thresh_patch1,'Visible','on')
4018%             set(handles.thresh_text1,'Visible','on')
4019%         end
4020%         set(handles.num_Rho,'Style','edit')
4021%         set(handles.num_Rho,'String','1')
4022%         set(handles.BATCH,'Enable','on')
4023%     case 'CivUvmat'
4024%       
4025% end
4026
4027%------------------------------------------------------------------------
4028function cmd=cmd_civ1(filename,Param)
4029%------------------------------------------------------------------------
4030%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4031%changes : filename_cmx -> filename ( no extension )
4032filename=regexprep(filename,'.nc',''); %file name for the result
4033if isequal(Param.Civ1.Dt,'0')
4034    Param.Civ1.Dt='1' ;%case of 'displacement' mode
4035end
4036Param.Civ1.ImageA=regexprep(Param.Civ1.ImageA,'.png','');
4037Param.Civ1.ImageB=regexprep(Param.Civ1.ImageB,'.png','');
4038fid=fopen([filename '.civ1.cmx'],'w');
4039fprintf(fid,['##############   CMX file' '\n' ]);
4040fprintf(fid,   ['FirstImage ' regexprep(Param.Civ1.ImageA,'\\','\\\\') '\n' ]);% for windows compatibility
4041fprintf(fid,   ['LastImage  ' regexprep(Param.Civ1.ImageB,'\\','\\\\') '\n' ]);% for windows compatibility
4042fprintf(fid,  ['XX' '\n' ]);
4043if isfield(Param.Civ1,'Mask')
4044    fprintf(fid,  ['Mask ' 'y' '\n' ]);
4045    fprintf(fid,  ['MaskName ' regexprep(Param.Civ1.Mask,'\\','\\\\') '\n' ]);
4046else
4047    fprintf(fid,  ['Mask ' 'n' '\n' ]);
4048    fprintf(fid,  ['MaskName ' 'noFile use default' '\n' ]);
4049end
4050fprintf(fid,   ['ImageSize ' num2str(Param.Civ1.ImageWidth) ' ' num2str(Param.Civ1.ImageHeight) '\n' ]);   %VERIFIER CAS GENERAL ?
4051fprintf(fid,   ['CorrelationBoxesSize ' num2str(Param.Civ1.Bx) ' ' num2str(Param.Civ1.By) '\n' ]);
4052fprintf(fid,   ['SearchBoxeSize ' num2str(Param.Civ1.Searchx) ' ' num2str(Param.Civ1.Searchy) '\n' ]);
4053fprintf(fid,   ['RO ' num2str(Param.Civ1.Rho) '\n' ]);
4054if isfield(Param.Civ1,'Grid')
4055    fprintf(fid,   ['GridSpacing ' '25' ' ' '25' '\n' ]);
4056else
4057    fprintf(fid,   ['GridSpacing ' num2str(Param.Civ1.Dx) ' ' num2str(Param.Civ1.Dy) '\n' ]);
4058end
4059fprintf(fid,   ['XX 1.0' '\n' ]);
4060fprintf(fid,   ['Dt_TO ' num2str(Param.Civ1.Dt) ' ' num2str(Param.Civ1.Time) '\n' ]);
4061fprintf(fid,  ['PixCmXY ' '1' ' ' '1' '\n' ]);
4062fprintf(fid,  ['XX 1' '\n' ]);
4063fprintf(fid,   ['ShiftXY ' num2str(Param.Civ1.Shiftx) ' '  num2str(Param.Civ1.Shifty) '\n' ]);
4064if isfield(Param.Civ1,'Grid')
4065    fprintf(fid,  ['Grid ' 'y' '\n' ]);
4066    fprintf(fid,   ['GridName ' regexprep(Param.Civ1.Grid,'\\','\\\\') '\n' ]);
4067else
4068    fprintf(fid,  ['Grid ' 'n' '\n' ]);
4069    fprintf(fid,   ['GridName ' 'noFile use default' '\n' ]);
4070end
4071fprintf(fid,   ['XX 85' '\n' ]);
4072fprintf(fid,   ['XX 1.0' '\n' ]);
4073fprintf(fid,   ['XX 1.0' '\n' ]);
4074fprintf(fid,   ['Hart 1' '\n' ]);
4075fprintf(fid,  [ 'DecimalShift 0' '\n' ]);
4076fprintf(fid,   ['Deformation 0' '\n' ]);
4077fprintf(fid,  ['CorrelationMin 0' '\n' ]);
4078fprintf(fid,   ['IntensityMin 0' '\n' ]);
4079if ~isfield(Param.Civ1,'MinIma')% Image threshold not activated
4080    fprintf(fid,  ['SeuilImage n' '\n' ]);
4081    fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);%not used in principle
4082else% Image threshold  activated
4083    if isempty(Param.Civ1.MaxIma)||isnan(Param.Civ1.MaxIma)
4084        Param.Civ1.MaxIma=2^Param.Civ1.ImageBitDepth;%take the max image value as upper bound by default
4085    end
4086    fprintf(fid,  ['SeuilImage y' '\n' ]);
4087    fprintf(fid,   ['SeuilImageValues ' num2str(Param.Civ1.MinIma) ' ' num2str(Param.Civ1.MaxIma) '\n' ]);
4088end
4089fprintf(fid,   ['ImageToUse ' Param.Civ1.term_a ' ' Param.Civ1.term_b '\n' ]); % VERIFIER ?
4090fprintf(fid,   ['ImageUsedBefore null null' '\n' ]);
4091fclose(fid);
4092
4093if(isunix) %unix (or Mac) system
4094    cmd=['cp -f ' filename '.civ1.cmx ' filename '.cmx \n '];% the cmx file gives the name to the nc file
4095    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
4096    cmd=[cmd 'rm ' filename '.cmx'];
4097else %Windows system
4098    filename=regexprep(filename,'\\','\\\\');
4099    cmd=['copy /Y "' filename '.civ1.cmx" "' filename '.cmx" \n '];
4100    cmd=[cmd '"' regexprep(Param.xml.Civ1Bin,'\\','\\\\')...
4101        '" -f "' filename '.cmx" >"' filename '.civ1.log" \n ' ]; % redirect standard output to the log file
4102    cmd=[cmd 'del "' filename '.cmx"'];
4103end
4104
4105
4106function cmd=cmd_fix(filename,Param,fixname)
4107%%
4108switch fixname
4109    case 'Fix1'
4110        fi2_value=num2str(Param.(fixname).CheckF2);
4111    case 'Fix2'
4112        fi2_value=num2str(Param.(fixname).CheckF4);%need to understand why...
4113end
4114filename=regexprep(filename,'.nc','');
4115MaskName_string='';%default
4116if Param.(fixname).CheckMask
4117    MaskName_string=[' -maskName "' Param.(fixname).MaskName '"'];
4118end
4119MaxVel_string='';%default
4120if ~isempty(Param.(fixname).MaxVel)
4121    MaxVel_string=[' -threshV ' num2str(Param.(fixname).MaxVel)];
4122end
4123if isunix
4124    cmd=[Param.xml.FixBin ' -f ' filename '.nc -fi1 ' num2str(Param.(fixname).CheckFmin2) ...
4125        ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ...
4126        ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string...
4127        ' >' filename '.' lower(fixname) '.log 2>&1'];
4128else
4129    cmd=['"' Param.xml.FixBin '" -f "' filename '.nc" -fi1 ' num2str(Param.(fixname).CheckFmin2)...
4130        ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ...
4131        ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string...
4132        ' > "' filename '.' lower(fixname) '.log"'];
4133    cmd=regexprep(cmd,'\\','\\\\');
4134end
4135
4136
4137function cmd=cmd_patch(filename,Param,patchname)
4138%% ------------------------------------------------------------------------
4139filename=regexprep(filename,'.nc','');
4140if isunix
4141    cmd=[Param.xml.PatchBin...
4142        ' -f ' filename '.nc -m ' num2str(Param.(patchname).Nx)...
4143        ' -n ' num2str(Param.(patchname).Ny) ' -ro ' num2str(Param.(patchname).SmoothingParam)...
4144        ' -nopt ' num2str(Param.(patchname).SubdomainSize) ...
4145        '  > ' filename '.' lower(patchname) '.log 2>&1']; % redirect standard output to the log file
4146else
4147    cmd=['"' Param.xml.PatchBin...
4148        '" -f "' filename '.nc" -m ' num2str(Param.(patchname).Nx)...
4149        ' -n ' num2str(Param.(patchname).Ny) ' -ro ' num2str(Param.(patchname).SmoothingParam)...
4150        ' -nopt ' num2str(Param.(patchname).SubdomainSize)...
4151        '  > "' filename '.' lower(patchname) '.log" 2>&1']; % redirect standard output to the log file
4152    cmd=regexprep(cmd,'\\','\\\\');
4153end
4154
4155%------------------------------------------------------------------------
4156% --- CheckCiv2  CheckCiv2  CheckCiv2 CheckCiv2
4157function cmd=cmd_civ2(filename,Param)
4158%------------------------------------------------------------------------
4159%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4160% global civ2Bin sge%name of the executable for checkciv1 calculation
4161filename=regexprep(filename,'.nc','');
4162if isequal(Param.Civ2.Dt,'0')
4163    Param.Civ2.Dt='1' ;%case of 'displacement' mode
4164end
4165Param.Civ2.ImageA=regexprep(Param.Civ2.ImageA,'.png','');
4166Param.Civ2.ImageB=regexprep(Param.Civ2.ImageB,'.png','');% bug : .png appears two times ?
4167[fid,errormsg]=fopen([filename '.civ2.cmx'],'w');
4168if isequal(fid,-1)
4169    msgbox_uvmat('ERROR',errormsg)
4170    cmd='';
4171    return
4172end
4173fprintf(fid,['##############   CMX file' '\n' ]);
4174fprintf(fid,   ['FirstImage ' regexprep(Param.Civ2.ImageA,'\\','\\\\') '\n' ]);% for windows compatibility
4175fprintf(fid,   ['LastImage  ' regexprep(Param.Civ2.ImageB,'\\','\\\\') '\n' ]);% for windows compatibility
4176fprintf(fid,  ['XX' '\n' ]);
4177if isfield(Param.Civ2,'Mask')
4178    fprintf(fid,  ['Mask ' 'y' '\n' ]);
4179    fprintf(fid,  ['MaskName ' regexprep(Param.Civ2.Mask,'\\','\\\\') '\n' ]);
4180else
4181    fprintf(fid,  ['Mask ' 'n' '\n' ]);
4182    fprintf(fid,  ['MaskName ' 'noFile use default' '\n' ]);
4183end
4184% fprintf(fid, ['Mask ' Param.Civ2.MaskFlag '\n' ]);
4185% fprintf(fid, ['MaskName ' regexprep(Param.Civ2.MaskName,'\\','\\\\') '\n' ]);% for windows compatibility
4186fprintf(fid,   ['ImageSize ' num2str(Param.Civ2.ImageWidth) ' ' num2str(Param.Civ2.ImageHeight) '\n' ]); 
4187% fprintf(fid, ['ImageSize ' num2str(Param.Civ2.npx) ' ' num2str(Param.Civ2.npy) '\n' ]);   %VERIFIER CAS GENERAL ?
4188fprintf(fid, ['CorrelationBoxesSize ' num2str(Param.Civ2.Bx) ' ' num2str(Param.Civ2.By) '\n' ]);
4189fprintf(fid, ['SearchBoxeSize ' num2str(Param.Civ2.Bx) ' ' num2str(Param.Civ2.By) '\n']);
4190fprintf(fid, ['RO ' num2str(Param.Civ2.Rho) '\n']);
4191if isfield(Param.Civ2,'Grid')
4192    fprintf(fid,   ['GridSpacing ' '25' ' ' '25' '\n' ]);
4193else
4194    fprintf(fid,   ['GridSpacing ' num2str(Param.Civ2.Dx) ' ' num2str(Param.Civ2.Dy) '\n' ]);
4195end
4196% fprintf(fid, ['GridSpacing ' num2str(Param.Civ2.Dx) ' ' num2str(Param.Civ2.Dy) '\n']);
4197fprintf(fid, ['XX 1.0' '\n' ]);
4198fprintf(fid, ['Dt_TO ' num2str(Param.Civ2.Dt) ' ' num2str(Param.Civ2.Time) '\n' ]);
4199fprintf(fid, ['PixCmXY ' '1' ' ' '1' '\n' ]);
4200fprintf(fid, ['XX 1' '\n' ]);
4201fprintf(fid, 'ShiftXY 0 0\n');
4202if isfield(Param.Civ2,'Grid')
4203    fprintf(fid,  ['Grid ' 'y' '\n' ]);
4204    fprintf(fid,   ['GridName ' regexprep(Param.Civ2.Grid,'\\','\\\\') '\n' ]);
4205else
4206    fprintf(fid,  ['Grid ' 'n' '\n' ]);
4207    fprintf(fid,   ['GridName ' 'noFile use default' '\n' ]);
4208end
4209% fprintf(fid, ['Grid ' Param.Civ2.GridFlag '\n' ]);
4210% fprintf(fid, ['GridName ' regexprep(Param.Civ2.GridName,'\\','\\\\') '\n']);
4211fprintf(fid, ['XX 85' '\n' ]);
4212fprintf(fid, ['XX 1.0' '\n' ]);
4213fprintf(fid, ['XX 1.0' '\n' ]);
4214fprintf(fid, ['Hart 1' '\n' ]);
4215fprintf(fid, ['DecimalShift ' num2str(Param.Civ2.CheckDecimal) '\n']);
4216fprintf(fid, ['Deformation ' num2str(Param.Civ2.CheckDeformation) '\n']);
4217fprintf(fid,  ['CorrelationMin 0' '\n' ]);
4218fprintf(fid,   ['IntensityMin 0' '\n' ]);
4219
4220if ~isfield(Param.Civ2,'MinIma')% Image threshold not activated
4221    fprintf(fid,  ['SeuilImage n' '\n' ]);
4222    fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);%not used in principle
4223else% Image threshold  activated
4224    if isempty(Param.Civ2.MaxIma)||isnan(Param.Civ2.MaxIma)
4225        Param.Civ2.MaxIma=2^Param.Civ2.ImageBitDepth;%take the max image value as upper bound by default
4226    end
4227    fprintf(fid,  ['SeuilImage y' '\n' ]);
4228    fprintf(fid,   ['SeuilImageValues ' num2str(Param.Civ2.MinIma) ' ' num2str(Param.Civ2.MaxIma) '\n' ]);
4229end
4230fprintf(fid,   ['ImageToUse ' Param.Civ2.term_a ' ' Param.Civ2.term_b '\n' ]); % VERIFIER ?
4231fprintf(fid, ['ImageUsedBefore ' regexprep(Param.Civ2.filename_nc1,'\\','\\\\') '\n']);
4232fclose(fid);
4233
4234if(isunix)
4235    cmd=['cp -f ' filename '.civ2.cmx ' filename '.cmx\n'...
4236        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
4237        'rm ' filename '.cmx \n'];%rename .cmx as .checkciv2.cmx, the result file is named [filename '.nc'] by CIVx
4238else
4239    filename=regexprep(filename,'\\','\\\\');
4240    cmd=['copy /Y "' filename '.civ2.cmx" "' filename '.cmx" \n'...
4241        '"' regexprep(Param.xml.Civ2Bin,'\\','\\\\') '" -f "' filename  '.cmx" >"' filename '.civ2.log" \n'...
4242        'del "' filename '.cmx" \n'];
4243end
4244
4245%------------------------------------------------------------------------
4246% --- CheckCiv1  Unified: TO ABADON
4247function xml_civ1_parameters=CIV1_CMD_Unified(filename,namelog,par)
4248%------------------------------------------------------------------------
4249%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4250%global CivBin%name of the executable for checkciv1 calculation
4251
4252civ1.image1=par.ImageA;
4253civ1.image2=par.ImageB;
4254civ1.imageSize_X=par.npx;
4255civ1.imageSize_Y=par.npy;
4256civ1.outputFileName=[filename '.nc'];
4257civ1.correlationBoxesSize_X=par.ibx;
4258civ1.correlationBoxesSize_Y=par.iby;
4259civ1.searchBoxesSize_X=par.isx;
4260civ1.searchBoxesSize_Y=par.isy;
4261civ1.globalShift_X=par.shiftx;
4262civ1.globalShift_Y=par.shifty;
4263civ1.ro=par.rho;
4264civ1.hart='y';
4265if isequal(par.gridflag,'y')
4266    civ1.grid=par.gridname;
4267else
4268    civ1.grid='n';
4269    civ1.gridSpacing_X=par.dx;
4270    civ1.gridSpacing_Y=par.dy;
4271end
4272if isequal(par.maskflag,'y')
4273    civ1.mask=par.maskname;
4274end
4275civ1.dt=par.Dt;
4276civ1.unit='pixel';
4277civ1.absolut_time_T0=par.Time;
4278civ1.pixcmx='1';
4279civ1.pixcmy='1';
4280civ1.convectFlow='n';
4281
4282xml_civ1_parameters=civ1;
4283
4284%------------------------------------------------------------------------
4285% --- CheckCiv2  Unified: TO ABADON
4286function civ2=CIV2_CMD_Unified(filename,namelog,par)
4287%------------------------------------------------------------------------
4288%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4289%global CivBin%name of the executable for checkciv1 calculation
4290
4291filename=regexprep(filename,'.nc','');
4292
4293civ2.image1=par.ImageA;
4294civ2.image2=par.ImageB;
4295civ2.imageSize_X=par.npx;
4296civ2.imageSize_Y=par.npy;
4297civ2.inputFileName=[par.filename_nc1 '.nc'];
4298civ2.outputFileName=[filename '.nc'];
4299civ2.correlationBoxesSize_X=par.ibx;
4300civ2.correlationBoxesSize_Y=par.iby;
4301civ2.ro=par.rho;
4302%checkciv2.decimalShift=par.CheckDecimal;
4303%checkciv2.CheckDeformation=par.CheckDeformation;
4304if isequal(par.decimal,'1')
4305    civ2.decimalShift='y';
4306else
4307    civ2.decimalShift='n';
4308end
4309if isequal(par.deformation,'1')
4310    civ2.deformation='y';
4311else
4312    civ2.deformation='n';
4313end
4314if isequal(par.gridflag,'y')
4315    civ2.grid=par.gridname;
4316else
4317    civ2.grid='n';
4318    civ2.gridSpacing_X=par.dx;
4319    civ2.gridSpacing_Y=par.dy;
4320end
4321civ2.gridSpacing_X='10';
4322civ2.gridSpacing_Y='10';%NOTE: faut mettre gridSpacing pourque ca tourne, meme si c'est la grille qui est utilisee
4323if isequal(par.maskflag,'y')
4324    civ2.mask=par.maskname;
4325else
4326    civ2.mask='n';
4327end
4328civ2.dt=par.Dt;
4329civ2.unit='pixel';
4330civ2.absolut_time_T0=par.Time;
4331civ2.pixcmx='1';
4332civ2.pixcmy='1';
4333civ2.convectFlow='n';
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