source: trunk/src/civ.m @ 326

Last change on this file since 326 was 326, checked in by sommeria, 12 years ago

bug corrected in patch matlab. regexrep introduced in uvmat

File size: 180.3 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 04-Dec-2011 18:52:13
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(handles.RootName,'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')
270set(handles.num_MaxDiff,'Visible','off')
271set(handles.title_MaxDiff,'Visible','off')
272set(handles.num_Rho,'Style','edit')
273set(handles.num_Rho,'String','1')
274set(handles.BATCH,'Enable','on')
275% -----------------------------------------------------------------------
276
277% -----------------------------------------------------------------------
278% --- Prepare the GUI for the Matlab PIV program
279function MenuMatlab_Callback(hObject, eventdata, handles)
280% -----------------------------------------------------------------------
281set(handles.MenuMatlab,'checked','on')
282set(handles.MenuCivX,'checked','off')
283% if get(handles.CheckPatch1,'Value')
284set(handles.num_MaxDiff,'Visible','on')
285set(handles.title_MaxDiff,'Visible','on')
286
287% end
288set(handles.num_Rho,'Style','popupmenu')
289set(handles.num_Rho,'Value',1)
290set(handles.num_Rho,'String',{'1';'2'})
291% set(handles.BATCH,'Enable','off')
292
293% -----------------------------------------------------------------------
294% --- Open the help html file
295function MenuHelp_Callback(hObject, eventdata, handles)
296% -----------------------------------------------------------------------
297path_civ=fileparts(which ('civ'));
298helpfile=fullfile(path_civ,'uvmat_doc','uvmat_doc.html');
299if isempty(dir(helpfile))
300    msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
301else
302    addpath (fullfile(path_civ,'uvmat_doc'))
303    web([helpfile '#civ'])
304end
305
306%------------------------------------------------------------------------
307% --- Function activated when a new filebase (image series) is introduced
308function RootName_Callback(hObject, eventdata, handles)
309%------------------------------------------------------------------------
310filebase=get(handles.RootName,'String');
311errormsg=display_file_name(handles,filebase);
312if ~isempty(errormsg)
313    msgbox_uvmat('ERROR',erromsg)
314end
315
316%------------------------------------------------------------------------
317% --- general function activated for an input file series
318function errormsg=display_file_name(handles,fileinput)
319%------------------------------------------------------------------------
320set(handles.ListCompareMode,'Visible','on')
321errormsg='';%default empty error message
322
323%% enable RUN, BATCH button and 'status' display
324set(handles.RUN, 'Enable','On')
325set(handles.RUN,'BackgroundColor',[1 0 0])%set RUN button to red color
326set(handles.BATCH,'Enable','On')
327set(handles.BATCH,'BackgroundColor',[1 0 0])%set BATCH button to red color
328if isfield(handles,'status')
329    set(handles.status,'Value',0);       %suppress the 'status' display
330    status_Callback([], [], handles)
331end
332
333%% determine nomenclature types and extension of the input files
334ext_ima='';%default
335nom_type_ima='';%default
336nom_type_nc='';
337[RootPath,FileName,i1_str,i2_str,j1_str,j2_str,ext_input,nom_type_input,subdir]=name2display(fileinput);
338RootName=fullfile(RootPath,FileName);
339set(handles.RootName,'String',RootName)
340set(handles.RootName,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
341i1=str2double(i1_str);
342i2=str2double(i2_str);
343j1=str2double(j1_str);
344j2=str2double(j2_str);
345num_ref_i=i1;%efaulmt ref index
346num_ref_j=j1;
347browse=get(handles.RootName,'UserData');
348browse.incr_pair=[0 0];%default
349
350% form=imformats(ext_input(2:end));
351if ~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
352    ext_ima=ext_input;
353    nom_type_ima=nom_type_input;
354else %case of netcdf input file, look for corresponding images
355    nom_type_nc=nom_type_input;
356    if ~isnan(i2)
357        num_ref_i=floor((num_ref_i+i2)/2);% reference image number corresponding to the file
358        browse.incr_pair(1)=i2-i1;
359        browse.incr_pair(2)=0;
360    end
361    %TODO: read the image name in the netcdf file (if documented)
362    %look for double image series '_i_j'
363    dirima=dir([RootName '_' i1_str '_' j1_str '.*']);
364    if isempty(dirima)
365        % look for images series  with sub marker '_'
366        dirima=dir([RootName '_*' i1_str  '.*']);
367        if isempty(dirima)
368            % look for other images series
369            dirima=dir([RootName '*' i1_str '.*']);
370            if isempty(dirima)
371                % look for other images series witth letter appendix
372                appendix=char(96+j1_str);
373                dirima=dir([RootName '*' i1_str appendix '.*']);
374            end
375        end
376    end
377    for ilist=1:numel(dirima)
378        [pp,ff,i1_str,i2_str,j1_str,j2_str,ext_list,nom_type_list]=name2display(dirima(ilist).name);
379        form=imformats(ext_list(2:end));
380        if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
381            ext_ima=ext_list;
382            nom_type_ima=nom_type_list;
383            i1=str2double(i1_str);
384            j1=str2double(j1_str);
385            i2=str2double(i2_str);
386            j2=str2double(j2_str);         
387            % set the range of fields (1:1 by default) and selected pair
388            if isequal(i2,i1)||isnan(i2)
389                num_ref_i=i1;
390            else
391                num_ref_i=floor((i1+i2)/2);
392                browse.incr_pair(1)=i2-i1;
393                browse.incr_pair(2)=0;
394            end
395            if isequal(j1,j2)||isnan(j2)
396                if isnan(j1)
397                    num_ref_j=1;
398                else
399                    num_ref_j=j1;
400                end
401            else
402                num_ref_j=floor((j1+j2)/2);
403                browse.incr_pair(2)=j2-j1;
404            end
405            break
406        end
407    end
408end
409
410%% look for an image documentation file
411ext_imadoc='';%default
412if exist([RootName '.xml'],'file')
413    ext_imadoc='.xml';
414elseif exist([RootName '.civxml'],'file')
415    ext_imadoc='.civxml';
416elseif exist([RootName '.civ'],'file')
417    ext_imadoc='.civ';
418elseif exist([RootName '.avi'],'file')
419    ext_imadoc='.avi';
420elseif exist([RootName '.AVI'],'file')
421    ext_imadoc='.AVI';
422end
423set(handles.ImaDoc,'String',ext_imadoc)% display the extension name for the image documentation file used
424set(handles.ImaDoc,'BackgroundColor',[1 1 0])
425drawnow
426%%%%%%%%   read image documentation file  %%%%%%%%%%%%%%%%%%%%%%%%%%%
427mode=''; %default
428time=[];
429TimeUnit='frame'; %default
430CoordUnit='px';%default
431pxcmx_search=[];%default
432pxcmy_search=[];%default
433if isequal(ext_imadoc,'.civxml')%TO ABANDON
434    [nbfield,nbfield2,time]=read_civxml([RootName '.civxml']);
435    mode='pair j1-j2';
436    if isempty(nom_type_ima)% dtermine types by default if not already selected by browser or uvmat
437        nom_type_ima='_i_j';
438    end
439elseif isequal(ext_imadoc,'.xml')
440    [XmlData,warntext]=imadoc2struct([RootName '.xml']);
441    ext_ima_read=[];
442    nom_type_read=[];
443    if isfield(XmlData,'Heading')&&isfield(XmlData.Heading','ImageName')&&ischar(XmlData.Heading.ImageName)% get image nom type and extension from the xml file
444        [PP,FF,fc,str2,str_a,str_b,ext_ima_read,nom_type_read]=name2display(XmlData.Heading.ImageName);
445        fullname=fullfile(fileparts(RootName),XmlData.Heading.ImageName); %full name (including path) of the first image defined by the xmle file,
446        if ~exist(fullname,'file')
447            msgbox_uvmat('WARNING',['FirstImage ' fullname ' defined in the xml file does not exist'])
448        end
449    end
450    if isfield(XmlData,'Time')
451        time=XmlData.Time;
452        nbfield=size(time,1);
453        nbfield2=size(time,2);
454        %transform .Time to a column vector if it is a line vector thenomenclature uses a single index: correct possible bug in xml
455        if isequal(nbfield,1) && ~isequal(nbfield2,1)% .Time is a line vector
456            if numel(nom_type_read)>=2 && isempty(regexp(nom_type_read(2:end),'\D','once'))
457                time=time';
458                nbfield=nbfield2;
459                nbfield2=1;
460            end
461        end
462    end
463    if isfield(XmlData,'TimeUnit')
464        TimeUnit=XmlData.TimeUnit;
465    end
466    pxcmx_search=1;
467    pxcmy_search=1;
468    if isfield(XmlData,'GeometryCalib')
469        tsai=XmlData.GeometryCalib;
470        if isfield(tsai,'f') && isfield(tsai,'Tz') && isfield(tsai,'dpx') && isfield(tsai,'dpy')&& isfield(tsai,'R')
471            rot2D=tsai.R(1:2,[1,2]);
472            pxcmx_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpx);
473            pxcmy_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpy);
474        end
475        if isfield(tsai,'CoordUnit')
476            CoordUnit=tsai.CoordUnit;
477        end
478    end
479elseif strcmp(ext_imadoc,'.civ')% case of .civ image documentation file
480    [error,time,TimeUnit,mode,npx,npy]=read_imatext([RootName '.civ']);
481    if error==2, msgbox_uvmat('WARNING',['no file ' RootName '.civ']);
482    elseif error==1, msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file');
483    end
484    nom_type_ima='001a';
485elseif strcmpi(ext_imadoc,'.avi')
486    nom_type_ima='*';
487    ext_ima=ext_imadoc;
488    set(handles.ListPairMode,'Value',1);
489    set(handles.ListPairMode,'String',{'series(Di)'})
490    dt=0.04;%default
491    if exist([RootName ext_imadoc],'file')==2
492        info=aviinfo([RootName ext_imadoc]);%read infos on the avi movie
493        dt=1/info.FramesPerSecond;%time interval between successive frames
494        nbfield=info.NumFrames;%number of frames
495    end
496    time=(dt*(0:nbfield-1))';%list of image times
497end
498if isempty(time)
499    set(handles.ImaDoc,'String',''); %xml file not used for timing
500end
501set(handles.ImaDoc,'BackgroundColor',[1 1 1])% set display box to yellow color
502
503
504%% timing display
505%show the reference image edit box if relevant (not needed for movies or in the absence of time information
506if ~isempty(time)
507    if size(time,1)+size(time,2)>=3 % if there are at least two time values to define dt
508        nbfield=size(time,1);
509        nbfield2=size(time,2);
510        set(handles.ImaDoc,'UserData',time); %store the set of times
511        set(handles.dt_unit,'String',['dt in m' TimeUnit]);
512        set(handles.TimeUnit,'String',TimeUnit);
513        set(handles.nb_field,'String',num2str(nbfield));
514        set(handles.nb_field2,'String',num2str(nbfield2));
515    end
516end
517set(handles.CoordUnit,'String',CoordUnit)
518set(handles.SearchRange,'UserData',[pxcmx_search pxcmy_search]);
519set(handles.ImaExt,'String',ext_ima)
520set(handles.ref_i,'String',num2str(num_ref_i))
521set(handles.first_i,'String',num2str(num_ref_i));
522set(handles.last_i,'String',num2str(num_ref_i));%
523set(handles.ref_j,'String',num2str(num_ref_j))
524set(handles.first_j,'String',num2str(num_ref_j));
525set(handles.last_j,'String',num2str(num_ref_j));%
526
527%% set the civ options depending on the input file content
528ind_opening=0;%default
529if isequal(ext_input,'.nc')
530    browse.nom_type_nc=nom_type_input;
531    ind_opening=2;% propose 'fix' as the default option
532    Data=nc2struct(fileinput,'ListGlobalAttribute','CivStage','absolut_time_T0','fix','patch','civ2','fix2');
533    if isfield(Data,'Txt')
534        msgbox_uvmat('ERROR',Data.Txt)
535        return
536    end
537    if ~isempty(Data.CivStage)%test for civ files
538        ind_opening=Data.CivStage;
539        set(handles.ListPairMode,'Value',3)
540    end
541end
542ListOptions={'CheckCiv1', 'CheckFix1' 'CheckPatch1', 'CheckCiv2', 'CheckFix2', 'CheckPatch2'};
543for index = 1:ind_opening
544    set(handles.(ListOptions{index}),'value',0)
545end
546for index = ind_opening+1
547    set(handles.(ListOptions{index}),'value',1)
548end
549update_CivOptions(handles)
550
551
552%%  set the menus of image pairs and default selection for civ   %%%%%%%%%%%%%%%%%%%
553test_ima_i=numel(nom_type_ima)>1 && isempty(regexp(nom_type_ima(2:end),'\D','once'));%images with single indexing
554if test_ima_i || isequal(nom_type_nc,'_i1-i2')||~(exist('nbfield2','var')&&(nbfield2~=1))
555    set(handles.ListPairMode,'Value',1)
556    set(handles.ListPairMode,'String',{'series(Di)'})   
557elseif (nbfield==1)% simple series in j
558    set(handles.ListPairMode,'Value',1)
559    set(handles.ListPairMode,'String',{'series(Dj)'})
560else
561    set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)';'series(Di)'})%multiple choice
562    if nbfield2 <= 10
563        set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' for small burst
564    end
565end
566
567%% update the subdirectory display
568listot=dir(RootPath);%directory of RootPath
569idir=0;
570listdir={''};%default
571% get the list of existing civ subdirectories in the path of theinput root  file
572for ilist=1:length(listot)
573    if listot(ilist).isdir
574        name=listot(ilist).name;
575        if ~isequal(name,'.') && ~isequal(name,'..')
576            idir=idir+1;
577            listdir{idir,1}=listot(ilist).name;
578        end
579    end
580end
581Value=find(strcmp(subdir,listdir));%search the index of subdir in the cell listdir
582if isempty(Value)% if the input subdir is not found
583    ValueCiv1=get(handles.ListSubdirCiv1,'Value');%read the currrently selected dir name
584    if ValueCiv1>numel(listdir)
585        ValueCiv1=1;
586    end
587    set(handles.txt_SubdirCiv1,'String',listdir{ValueCiv1})
588    ValueCiv2=get(handles.ListSubdirCiv2,'Value');
589    if ValueCiv2>numel(listdir)
590        ValueCiv2=1;
591    end
592    set(handles.txt_SubdirCiv2,'String',listdir{ValueCiv2})
593else
594    ValueCiv1=Value;
595    ValueCiv2=Value;
596     set(handles.txt_SubdirCiv1,'String',listdir{Value})
597     set(handles.txt_SubdirCiv2,'String',listdir{Value})
598end
599set(handles.ListSubdirCiv1,'Value',ValueCiv1)
600set(handles.ListSubdirCiv2,'Value',ValueCiv2)
601set(handles.ListSubdirCiv1,'String',[listdir;'new...'])
602set(handles.ListSubdirCiv2,'String',[listdir;'new...'])
603if isempty(listdir)
604    set(handles.txt_SubdirCiv1,'String','CIV')
605    set(handles.txt_SubdirCiv2,'String','CIV')
606end
607
608%% store info
609browse.nom_type_ima=nom_type_ima;
610set(handles.RootName,'UserData',browse)% store the nomenclature type
611
612%% list the possible index pairs, depending on the option set in ListPairMode
613ListPairMode_Callback([], [], handles)
614
615%% store the root input filename for future opening
616profil_perso=fullfile(prefdir,'uvmat_perso.mat');
617% RootPath=fileparts(RootName);
618if exist(profil_perso,'file')
619    save (profil_perso,'RootPath','-append'); %store the root name for future opening of uvmat
620else
621    txt=ver('MATLAB');
622    Release=txt.Release;
623    relnumb=str2double(Release(3:4));
624    if relnumb >= 14
625        save (profil_perso,'RootPath','-V6'); %store the root name for future opening of uvmat
626    else
627        save (profil_perso,'RootPath'); %store the root name for future opening of uvmat
628    end
629end
630set(handles.RootName,'BackgroundColor',[1 1 1])
631
632%------------------------------------------------------------------------
633% --- Executes on carriage return on the subdir checkciv1 edit window
634function txt_SubdirCiv1_Callback(hObject, eventdata, handles)
635%------------------------------------------------------------------------
636subdir=get(handles.txt_SubdirCiv1,'String');
637menu_str=get(handles.ListSubdirCiv1,'String');% read the list of subdirectories for update
638ichoice=find(strcmp(subdir,menu_str),1);
639if isempty(ichoice)
640    ilist=numel(menu_str); %select 'new...' in the menu
641else
642    ilist=ichoice;
643end
644set(handles.ListSubdirCiv1,'Value',ilist)% select the selected subdir in the menu
645if get(handles.CheckCiv1,'Value')% if Civ1 is performed
646    set(handles.txt_SubdirCiv2,'String',subdir);% set by default civ2 directory the same as civ1
647    set(handles.ListSubdirCiv2,'Value',ilist)
648else % if Civ1 data already exist
649    find_netcpair_civ1(handles); %update the list of available pairs from netcdf files in the new directory
650end
651
652%------------------------------------------------------------------------
653% --- Executes on carriage return on the subdir checkciv1 edit window
654function txt_SubdirCiv2_Callback(hObject, eventdata, handles)
655%------------------------------------------------------------------------
656subdir=get(handles.txt_SubdirCiv1,'String');
657menu_str=get(handles.ListSubdirCiv2,'String');% read the list of subdirectories for update
658ichoice=find(strcmp(subdir,menu_str),1);
659if isempty(ichoice)
660    ilist=numel(menu_str); %select 'new...' in the menu
661else
662    ilist=ichoice;
663end
664set(handles.ListSubdirCiv2,'Value',ilist)% select the selected subdir in the menu
665%update the list of available pairs from netcdf files in the new directory
666if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
667    find_netcpair_civ2(handles);
668end
669
670%------------------------------------------------------------------------
671% --- Executes on button press in CheckCiv1.
672function CheckCiv1_Callback(hObject, eventdata, handles)
673%------------------------------------------------------------------------
674update_CivOptions(handles)
675
676%------------------------------------------------------------------------
677% --- Executes on button press in CheckFix1.
678function CheckFix1_Callback(hObject, eventdata, handles)
679%------------------------------------------------------------------------
680update_CivOptions(handles)
681
682%------------------------------------------------------------------------
683% --- Executes on button press in CheckPatch1.
684function CheckPatch1_Callback(hObject, eventdata, handles)
685%------------------------------------------------------------------------
686update_CivOptions(handles)
687
688%------------------------------------------------------------------------
689% --- Executes on button press in CheckCiv2.
690function CheckCiv2_Callback(hObject, eventdata, handles)
691%------------------------------------------------------------------------
692update_CivOptions(handles)
693
694%------------------------------------------------------------------------
695% --- Executes on button press in CheckFix2.
696function CheckFix2_Callback(hObject, eventdata, handles)
697%------------------------------------------------------------------------
698update_CivOptions(handles)
699
700%------------------------------------------------------------------------
701% --- Executes on button press in CheckPatch2.
702function CheckPatch2_Callback(hObject, eventdata, handles)
703%------------------------------------------------------------------------
704update_CivOptions(handles)
705
706%------------------------------------------------------------------------
707% --- activated by any checkbox controling the selection of Civ1,Fix1,Patch1,Civ2,Fix2,Patch2
708function update_CivOptions(handles)
709%------------------------------------------------------------------------
710checkbox=zeros(1,6);
711checkbox(1)=get(handles.CheckCiv1,'Value');
712checkbox(2)=get(handles.CheckFix1,'Value');
713checkbox(3)=get(handles.CheckPatch1,'Value');
714checkbox(4)=get(handles.CheckCiv2,'Value');
715checkbox(5)=get(handles.CheckFix2,'Value');
716checkbox(6)=get(handles.CheckPatch2,'Value');
717ind_selected=find(checkbox,1);
718if ~isempty(ind_selected)
719  RootName=get(handles.RootName,'String');
720    if isempty(RootName)
721         msgbox_uvmat('ERROR','Please open an image or PIV .nc file with the upper bar menu Open/Browse...')
722        return
723    end
724end
725set(handles.PairIndices,'Visible','on')
726set(handles.txt_SubdirCiv1,'Visible','on')
727set(handles.ListSubdirCiv1,'Visible','on')
728find_netcpair_civ1(handles) % select the available netcdf files
729if max(checkbox(4:6))% case of civ2 pair choice needed
730    set(handles.TitlePairCiv2,'Visible','on')
731    set(handles.TitleSubdirCiv2,'Visible','on')
732    set(handles.txt_SubdirCiv2,'Visible','on')
733    set(handles.ListSubdirCiv2,'Visible','on')
734    set(handles.ListPairCiv2,'Visible','on')
735    find_netcpair_civ2(handles) % select the available netcdf files
736else
737    set(handles.TitleSubdirCiv2,'Visible','off')
738    set(handles.txt_SubdirCiv2,'Visible','off')
739    set(handles.ListSubdirCiv2,'Visible','off')
740    set(handles.ListPairCiv2,'Visible','off')
741end
742options={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'};
743for ilist=1:length(options)
744    if checkbox(ilist)
745        set(handles.(options{ilist}),'Visible','on')
746    else
747        set(handles.(options{ilist}),'Visible','off')
748    end
749end
750
751%------------------------------------------------------------------------
752% --- Executes on button press in RUN: processing on local computer
753function RUN_Callback(hObject, eventdata, handles)
754%------------------------------------------------------------------------
755set(handles.RUN, 'Enable','Off')
756set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
757batch=0;
758errormsg=launch_jobs(hObject, eventdata, handles,batch);
759set(handles.RUN, 'Enable','On')
760set(handles.RUN,'BackgroundColor',[1 0 0])
761
762% start status callback to visualise results
763if ~isempty(errormsg)
764    display(errormsg)
765    msgbox_uvmat('ERROR',errormsg)
766elseif  isfield(handles,'status') %&& ~isequal(get(handles.ListPairMode,'Value'),3)
767    set(handles.status,'Value',1);%suppress status display
768    status_Callback(hObject, eventdata, handles)
769end
770
771%------------------------------------------------------------------------
772% --- Executes on button press in BATCH: remote processing
773function BATCH_Callback(hObject, eventdata, handles)
774% -----------------------------------------------------------------------
775set(handles.BATCH, 'Enable','Off')
776set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])
777batch=1;
778errormsg=launch_jobs(hObject, eventdata, handles, batch);
779set(handles.BATCH, 'Enable','On')
780set(handles.BATCH,'BackgroundColor',[1 0 0])
781
782% start status callback to visualise results
783if ~isempty(errormsg)
784    display(errormsg)
785    msgbox_uvmat('ERROR',errormsg)
786elseif isfield(handles,'status')
787    set(handles.status,'Value',1);%suppress status display
788    status_Callback(hObject, eventdata, handles)
789end
790
791%-------------------------------------------------------------------
792% --- Executes on button press in status.
793function status_Callback(hObject, eventdata, handles)
794%-------------------------------------------------------------------
795val=get(handles.status,'Value');
796if val==0
797    set(handles.status,'BackgroundColor',[0 1 0])
798    hfig=findobj(allchild(0),'name','civ_status');
799    if ~isempty(hfig)
800        delete(hfig)
801    end
802    return
803end
804set(handles.status,'BackgroundColor',[1 1 0])
805drawnow
806listtype={'civ1','fix1','patch1','civ2','fix2','patch2'};
807Param.CheckCiv1=get(handles.CheckCiv1,'Value');
808Param.CheckFix1=get(handles.CheckFix1,'Value');
809Param.CheckPatch1=get(handles.CheckPatch1,'Value');
810Param.CheckCiv2=get(handles.CheckCiv2,'Value');
811Param.CheckFix2=get(handles.CheckFix2,'Value');
812Param.CheckPatch2=get(handles.CheckPatch2,'Value');
813box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2];
814
815option_civ=find(box_test,1,'last');%last selected option (non-zero index of box_test)
816filecell=get(handles.civ,'UserData');%retrieve the list of output files expected for PIV
817test_new=0;
818if ~isfield(filecell,'nc')
819    test_new=1;
820    [ref_i,ref_j,errormsg]=find_ref_indices(handles);
821    if ~isempty(errormsg)
822        msgbox_uvmat('ERROR',errormsg)
823        return
824    end
825    filecell=set_civ_filenames(handles,ref_i,ref_j,box_test);%determine the output file expected from the GUI status
826end
827if ~isequal(box_test(4:6),[0 0 0])
828    civ_files=filecell.nc.civ2;%case of civ2 operations
829else
830    civ_files=filecell.nc.civ1;
831end
832[root,filename,ext]=fileparts(civ_files{1});
833[rootroot,subdir,extdir]=fileparts(root);
834hfig=findobj(allchild(0),'name','civ_status');
835if isempty(hfig)
836    hfig=figure('DeleteFcn',@stop_status);
837    set(hfig,'name','civ_status')
838    hlist=uicontrol('Style','listbox','Units','normalized', 'Position',[0.05 0.09 0.9 0.71], 'Callback', @open_view_field,'tag','list');
839    uicontrol('Style','edit','Units','normalized', 'Position', [0.05 0.87 0.9 0.1],'tag','msgbox','Max',2,'String','checking files...');
840    uicontrol('Style','frame','Units','normalized', 'Position', [0.05 0.81 0.9 0.05]);
841    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);
842    BarPosition=[0.05 0.81 0.01 0.05];
843    hwaitbar=uicontrol('Style','frame','Units','normalized', 'Position',BarPosition ,'BackgroundColor',[1 0 0],'tag','waitbar');
844    drawnow
845end
846% datnum=[];
847Tabchar={};
848nbfiles=numel(civ_files);
849count=0;
850testrecent=0;
851while count<nbfiles
852    count=0;
853    datnum=zeros(1,nbfiles);
854    for ifile=1:nbfiles
855        detect=exist(civ_files{ifile},'file'); % check the existence of the file
856        option=0;
857        if detect==0
858            option_str='not created';
859        else
860            datfile=dir(civ_files{ifile});
861            if isfield(datfile,'datenum')
862                datnum(ifile)=datfile.datenum;%only available in recent matlab versions
863                testrecent=1;
864            end
865            filefound(ifile)={datfile.name};
866            lastfield='';
867            % check the content  netcdf file
868            Data=nc2struct(civ_files{ifile},'ListGlobalAttribute','CivStage','patch2','fix2','civ2','patch','fix');
869            option_list={'civ1','fix1','patch1','civ2','fix2','patch2'};
870            if ~isempty(Data.CivStage)
871                option=Data.CivStage;
872            else
873                if ~isempty(Data.patch2) && isequal(Data.patch2,1)
874                    option=6;
875                    %                 option_str='patch2';
876                elseif ~isempty(Data.fix2) && isequal(Data.fix2,1)
877                    option=5;
878                    %                 option_str='fix2';
879                elseif ~isempty(Data.civ2) && isequal(Data.civ2,1);
880                    option=4;
881                    %                 option_str='civ2';
882                elseif ~isempty(Data.patch) && isequal(Data.patch,1);
883                    option=3;
884                    %                 option_str='patch1';
885                elseif ~isempty(Data.fix) && isequal(Data.fix,1);
886                    option=2;
887                    %                 option_str='fix1';
888                else
889                    option=1;
890                    %                 option_str='civ1';
891                end
892            end
893            option_str=option_list{option};
894        end
895        if option >= option_civ
896            count=count+1;
897        end
898        [rr,filename,ext]=fileparts(civ_files{ifile});
899        Tabchar{ifile,1}=[fullfile([subdir extdir],filename) ext  '...' option_str];
900    end
901    datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
902    if isempty(datnum)
903        if testrecent
904            message='no civ result created yet';
905        else
906            message='';
907        end
908    else
909        datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
910        [first,ind]=min(datnum);
911        [last,indlast]=max(datnum);
912        if test_new
913            message='existing file status, no processing launched yet';
914        else
915        message={[num2str(count) ' file(s) done over ' num2str(nbfiles)] ;['oldest modification:  ' cell2mat(filefound(ind)) ' : ' datestr(first)];...
916            ['latest modification:  ' cell2mat(filefound(indlast)) ' : ' datestr(last)]};
917        end
918    end
919    hfig=findobj(allchild(0),'name','civ_status');
920    if isempty(hfig)% the status list has been deleted
921        return
922    else
923        hlist=findobj(hfig,'tag','list');
924        hmsgbox=findobj(hfig,'tag','msgbox');
925        hwaitbar=findobj(hfig,'tag','waitbar');
926        set(hlist,'String',Tabchar)
927        set(hmsgbox,'String', message)
928        if count>0 && ~test_new
929            BarPosition(3)=0.9*count/nbfiles;
930            set(hwaitbar,'Position',BarPosition)
931        end
932    end
933    set(hlist,'UserData',rootroot)
934    if count<10||(nbfiles-count)<10
935    pause(.5)% wait 0.5 seconds for next check
936    else
937        pause(10)% wait 10 seconds for next check
938    end
939end
940
941%------------------------------------------------------------------------
942% --- Main lauch command, called by RUN and BATCH
943function errormsg=launch_jobs(hObject, eventdata, handles, batch)
944%-----------------------------------------------------------------------
945errormsg='';%default
946
947%% read the input parameters from the  GUI civ
948Param=read_GUI(handles.civ);
949
950%% check the selected list of operations:
951operations={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'};
952box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2];
953index_first=find(box_test==1,1);
954if isempty(index_first)
955    errormsg='no selected operation';
956    return
957end
958index_last=find(box_test==1,1,'last');
959box_used=box_test(index_first : index_last);
960[box_missing,ind_missing]=min(box_used);
961if isequal(box_missing,0); %there is a missing step in the sequence of operations
962    errormsg=['missing' cell2mat(operations(ind_missing))];
963    return
964end
965
966%% check mask if selecetd
967%could be included in get_mask callback ?
968if isequal(get(handles.CheckMask,'Value'),1)
969    maskname=get(handles.txt_Mask,'String');
970    if ~exist(maskname,'file')
971        get_mask_civ1_Callback(hObject, eventdata, handles);
972    end
973end
974if isequal(get(handles.CheckMask,'Value'),1)
975    maskname=get(handles.txt_Mask,'String');
976    if ~exist(maskname,'file')
977        get_mask_fix1_Callback(hObject, eventdata, handles);
978    end
979end
980if isequal(get(handles.CheckMask,'Value'),1)
981    maskname=get(handles.txt_Mask,'String');
982    if ~exist(maskname,'file')
983        get_mask_civ2_Callback(hObject, eventdata, handles);
984    end
985end
986if isequal(get(handles.CheckMask,'Value'),1)
987    maskname=get(handles.txt_Mask,'String');
988    if ~exist(maskname,'file')
989        get_mask_fix2_Callback(hObject, eventdata, handles);
990    end
991end
992
993%% reinitialise status callback
994if isfield(handles,'status')
995    set(handles.status,'Value',0);%suppress status display
996    status_Callback(hObject, eventdata, handles)
997end
998
999%% read the PARAM.xml file to get the binaries (and batch_mode if batch)
1000path_civ=fileparts(which('civ')); %path to the source directory of uvmat
1001xmlfile='PARAM.xml';
1002if exist(xmlfile,'file')% search parameter xml file in the whole matlab path
1003    t=xmltree(xmlfile);
1004    s=convert(t);
1005else
1006    errormsg=['no file ' xmlfile];
1007    return
1008end
1009test_interp=0; %eviter les variables test_ (LG)
1010if batch
1011    if isfield(s,'BatchParam')
1012        Param.xml=s.BatchParam;
1013        if isfield(Param.xml,'BatchMode')
1014            batch_mode=Param.xml.BatchMode;
1015            if ~ismember(batch_mode,{'sge','oar'})
1016                errormsg=['batch mode ' batch_mode ' not supported by UVMAT'];
1017                return
1018            end
1019        end
1020    else
1021        errormsg='no batch civ binaries defined in PARAM.xml';
1022        return
1023    end
1024else % run
1025    if isfield(s,'RunParam')
1026        Param.xml=s.RunParam;
1027    else
1028        msgbox_uvmat('ERROR','no run civ binaries defined in PARAM.xml')
1029        return
1030    end
1031end
1032
1033%% check batch mode supported
1034if batch
1035    switch batch_mode
1036        case 'sge'
1037            test_command='qstat';
1038        case 'oar'
1039            test_command='oarstat';
1040    end   
1041    [s,w]=system(test_command);
1042    if ~isequal(s,0)
1043        msgbox_uvmat('ERROR',[batch_mode ' batch system not available'])
1044        return
1045    end
1046end
1047
1048%% check if the binaries exist
1049if isequal(get(handles.MenuMatlab,'checked'),'on')
1050    CivMode='Matlab';
1051else
1052    CivMode='CivX';
1053end
1054binary_list={};
1055switch CivMode
1056    case 'CivX'
1057        binary_list={'Civ1Bin','Civ2Bin','PatchBin','FixBin'};
1058    case 'CivAll'
1059        binary_list={'Civ'};
1060    case 'Matlab'
1061        if batch
1062            % vérifier MenuMatlab installé sur le cluster
1063            % difficile a faire a priori
1064        end         
1065end
1066for bin_name=binary_list %loop on the list of binaries
1067    if isfield(Param.xml,bin_name{1})% bin_name{1} =current name in the list
1068        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
1069            fullname=fullfile(path_civ,Param.xml.(bin_name{1}));
1070            if exist(fullname,'file')
1071                Param.xml.(bin_name{1})=fullname;
1072            else
1073                msgbox_uvmat('ERROR',['Binary ' Param.xml.(bin_name{1}) ' defined in PARAM.xml does not exist'])
1074                return
1075            end
1076        else
1077            [path,name,ext]=fileparts(Param.xml.(bin_name{1}));
1078            currentdir=pwd;
1079            cd(path);
1080            binpath=pwd;%path of the binary
1081            Param.xml.(bin_name{1})=fullfile(binpath,[name ext]);
1082            cd(currentdir);
1083        end
1084       
1085    end
1086end
1087display('files OK, processing...')
1088
1089%% set the list of files and check them
1090display('checking the files...')
1091[ref_i,ref_j,errormsg]=find_ref_indices(handles);
1092if ~isempty(errormsg)
1093    return
1094end
1095[filecell,i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,xx,yy,compare]=...
1096    set_civ_filenames(handles,ref_i,ref_j,box_test);
1097Rootbat=fileparts(filecell.nc.civ1{1,1});%output netcdf file (without extention)
1098set(handles.civ,'UserData',filecell);%store for futur use of status callback
1099if isempty(filecell)% (error message displayed in fct set_civ_filenames)
1100    return
1101end
1102nbfield=numel(i1_civ1);
1103nbslice=numel(j1_civ1);
1104
1105%% MAIN LOOP
1106time=get(handles.ImaDoc,'UserData'); %get the set of times
1107batch_file_list=[];%should be renamed file_list, can be used for xml or bash files
1108 
1109for ifile=1:nbfield
1110    for j=1:nbslice
1111        % initiate system command
1112        switch CivMode
1113            case 'CivX'
1114                if isunix % check: necessaire aussi en RUN?
1115                    cmd=['#!/bin/bash \n '...
1116                        '#$ -cwd \n '...
1117                        'hostname && date \n '...
1118                        'umask 002 \n'];%allow writting access to created files for user group
1119                else
1120                    cmd=[];
1121                end
1122            case 'CivAll'
1123                CivAllxml=xmltree;% xml contents,  all parameters
1124                CivAllCmd='';
1125                CivAllxml=set(CivAllxml,1,'name','CivDoc');
1126        end
1127           
1128        % define output file name
1129        if Param.CheckCiv2==1 || Param.CheckFix2==1 || Param.CheckPatch2==1
1130            OutputFile=filecell.nc.civ2{ifile,j};
1131        else
1132            OutputFile=filecell.nc.civ1{ifile,j};
1133        end
1134        OutputFile=regexprep(OutputFile,'.nc','');
1135       
1136        if Param.CheckCiv1
1137            % read image-dependent parameters
1138            Param.Civ1.ImageA=filecell.ima1.civ1{ifile,j};
1139            Param.Civ1.ImageB=filecell.ima2.civ1{ifile,j};
1140            if size(time,1)>=i2_civ1(ifile) && size(time,2)>=j2_civ1(j)
1141                Param.Civ1.Dt=(time(i2_civ1(ifile),j2_civ1(j))-time(i1_civ1(ifile),j1_civ1(j)));
1142                Param.Civ1.Time=((time(i2_civ1(ifile),j2_civ1(j))+time(i1_civ1(ifile),j1_civ1(j)))/2);
1143            else
1144                Param.Civ1.Dt=1;
1145                Param.Civ1.Time=0;
1146            end
1147            Param.Civ1.term_a=num2stra(j1_civ1(j),nom_type_nc);%UTILITE?
1148            Param.Civ1.term_b=num2stra(j2_civ1(j),nom_type_nc);%   
1149            ImageInfo=imfinfo(filecell.ima1.civ1{1,1});%read the first image to get the size
1150            Param.Civ1.ImageWidth=ImageInfo.Width;
1151            Param.Civ1.ImageHeight=ImageInfo.Height;
1152            Param.Civ1.ImageBitDepth=ImageInfo.BitDepth;
1153            % read mask parameters
1154            if Param.Civ1.CheckMask % the lines below should be changed with the new gui
1155                if ~exist(Param.Civ1.Mask,'file')
1156                    maskbase=[filecell.filebase '_' Param.Civ1.Mask]; %
1157                    nbslice_mask=str2double(Param.Civ1.Mask(1:end-4)); %
1158                    i1_mask=mod(i1_civ1(ifile)-1,nbslice_mask)+1;
1159                    Param.Civ1.Mask=name_generator(maskbase,i1_mask,1,'.png','_i');
1160                end
1161            end
1162            % read grid parameters
1163            if Param.Civ1.CheckGrid
1164                if numel(Param.Civ1.Grid)>=4 && isequal(Param.Civ1.Grid(end-3:end),'grid')
1165                    nbslice_grid=str2double(Param.Civ1.Grid(1:end-4)); %
1166                    if ~isnan(nbslice_grid)
1167                        i1_grid=mod(i1_civ1(ifile)-1,nbslice_grid)+1;
1168                        Param.Civ1.Grid=[filecell.filebase '_' name_generator(Param.Civ1.Grid,i1_grid,1,'.grid','_i')];
1169                        if ~exist(Param.Civ1.GridName,'file')
1170                            msgbox_uvmat('ERROR','grid file absent for civ1')
1171                        end
1172                    elseif ~exist(Param.Civ1.Grid,'file')
1173                        msgbox_uvmat('ERROR','grid file absent for civ1')
1174                    end
1175                end
1176            end
1177           
1178            % send command
1179            switch CivMode
1180                case 'CivX'
1181                    cmd=[cmd...
1182                        cmd_civ1(filecell.nc.civ1{ifile,j},Param) '\n'];
1183                    if ~isempty(errormsg)
1184                        msgbox_uvmat('ERROR',errormsg)
1185                        return
1186                    end
1187                case 'CivAll'
1188                    CivAllCmd=[CivAllCmd ' civ1 '];
1189                    str=CIV1_CMD_Unified(filecell.nc.civ1{ifile,j},'',Param.Civ1);
1190                    fieldnames=fields(str);
1191                    [CivAllxml,uid_civ1]=add(CivAllxml,1,'element','civ1');
1192                    for ilist=1:length(fieldnames)
1193                        val=eval(['str.' fieldnames{ilist}]);
1194                        if ischar(val)
1195                            [CivAllxml,uid_t]=add(CivAllxml,uid_civ1,'element',fieldnames{ilist});
1196                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1197                        end
1198                    end
1199            end
1200        end
1201       
1202        if Param.CheckFix1
1203            switch CivMode
1204                case 'CivX'
1205                    cmd=[cmd...
1206                        cmd_fix(filecell.nc.civ1{ifile,j},Param,'Fix1') '\n'];
1207                case 'CivAll'%to abandon
1208                    fix1.inputFileName=filecell.nc.civ1{ifile,j} ;
1209                    fix1.fi1=num2str(param.fix1.flagindex1(1));
1210                    fix1.fi2=num2str(param.fix1.flagindex1(2));
1211                    fix1.fi3=num2str(param.fix1.flagindex1(3));
1212                    fix1.threshC=num2str(param.fix1.thresh_vecC1);
1213                    fix1.threshV=num2str(param.fix1.thresh_vel1);
1214                    fieldnames=fields(fix1);
1215                    [CivAllxml,uid_fix1]=add(CivAllxml,1,'element','fix1');
1216                    for ilist=1:length(fieldnames)
1217                        val=eval(['fix1.' fieldnames{ilist}]);
1218                        if ischar(val)
1219                            [CivAllxml,uid_t]=add(CivAllxml,uid_fix1,'element',fieldnames{ilist});
1220                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1221                        end
1222                    end
1223                    CivAllCmd=[CivAllCmd ' fix1 '];
1224            end
1225        end
1226       
1227        %CheckPatch1
1228        if Param.CheckPatch1==1
1229            switch CivMode
1230                case 'CivX'
1231                    cmd=[cmd...
1232                        cmd_patch(filecell.nc.civ1{ifile,j},Param,'Patch1') '\n'];
1233                case 'CivAll'
1234                    patch1.inputFileName=filecell.nc.civ1{ifile,j} ;
1235                    patch1.nopt=subdomain_patch1;
1236                    patch1.maxdiff=thresh_patch1;
1237                    patch1.ro=rho_patch1;
1238                    test_grid=get(handles.get_gridpatch1,'Value');
1239                    if test_grid
1240                        patch1.gridflag='y';
1241                        gridname=get(handles.grid_patch1,'String');
1242                        if isequal(gridname(end-3:end),'grid')
1243                            nbslice_grid=str2double(gridname(1:end-4)); %
1244                            if ~isnan(nbslice_grid)
1245                                i1_grid=mod(i1_civ1(ifile)-1,nbslice_grid)+1;
1246                                patch1.gridPatch=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')];
1247                                if ~exist(patch1.gridPatch,'file')
1248                                    msgbox_uvmat('ERROR','grid file absent for patch1')
1249                                end
1250                            elseif exist(gridname,'file')
1251                                patch1.gridPatch=gridname;
1252                            else
1253                                msgbox_uvmat('ERROR','grid file absent for patch1')
1254                            end
1255                        end
1256                    else
1257                        patch1.gridPatch='none';
1258                        patch1.gridflag='n';
1259                        patch1.m=nx_patch1;
1260                        patch1.n=ny_patch1;
1261                    end
1262                    patch1.convectFlow='n';
1263                    fieldnames=fields(patch1);
1264                    [CivAllxml,uid_patch1]=add(CivAllxml,1,'element','patch1');
1265                    for ilist=1:length(fieldnames)
1266                        val=eval(['patch1.' fieldnames{ilist}]);
1267                        if ischar(val)
1268                            [CivAllxml,uid_t]=add(CivAllxml,uid_patch1,'element',fieldnames{ilist});
1269                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1270                        end
1271                    end
1272                    CivAllCmd=[CivAllCmd ' patch1 '];
1273            end
1274        end
1275        if Param.CheckCiv2==1
1276            Param.Civ2.ImageA=filecell.ima1.civ2{ifile,j};
1277            Param.Civ2.ImageB=filecell.ima2.civ2{ifile,j};
1278            if size(time,1)>=i2_civ2(ifile) && size(time,2)>=j2_civ2(j)
1279                Param.Civ2.Dt=num2str(time(i2_civ2(ifile),j2_civ2(j))-time(i1_civ2(ifile),j1_civ2(j)));
1280                Param.Civ2.Time=num2str((time(i2_civ2(ifile),j2_civ2(j))+time(i1_civ2(ifile),j1_civ2(j)))/2);
1281            else
1282                Param.Civ2.Dt=1;
1283                Param.Civ2.Time=0;
1284            end
1285            Param.Civ2.term_a=num2stra(j1_civ2(j),nom_type_nc);
1286            Param.Civ2.term_b=num2stra(j2_civ2(j),nom_type_nc);
1287            Param.Civ2.filename_nc1=filecell.nc.civ1{ifile,j};
1288            Param.Civ2.filename_nc1(end-2:end)=[]; % remove '.nc'
1289           
1290            % mask
1291            if Param.Civ2.CheckMask
1292                if ~exist(Param.Civ2.Mask,'file')
1293                    maskbase=[filecell.filebase '_' Param.Civ2.Mask]; %
1294                    nbslice_mask=str2double(Param.Civ2.Mask(1:end-4)); %
1295                    i1_mask=mod(i1_civ2(ifile)-1,nbslice_mask)+1;
1296                    Param.Civ2.Mask=name_generator(maskbase,i1_mask,1,'.png','_i');
1297                end
1298            end
1299            %grid
1300            if Param.Civ2.CheckGrid
1301                if numel(Param.Civ2.Grid)>=4 && isequal(Param.Civ2.Grid(end-3:end),'grid')
1302                    nbslice_grid=str2double(Param.Civ2.Grid(1:end-4)); %
1303                    if ~isnan(nbslice_grid)
1304                        i1_grid=mod(i1_civ2(ifile)-1,nbslice_grid)+1;
1305                        Param.Civ2.Grid=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')];
1306                    end
1307                end
1308            end
1309            ImageInfo=imfinfo(filecell.ima1.civ2{1,1});%read the first image to get the size
1310            Param.Civ2.ImageWidth=ImageInfo.Width;
1311            Param.Civ2.ImageHeight=ImageInfo.Height;
1312            Param.Civ2.ImageBitDepth=ImageInfo.BitDepth;
1313            % TODO: case of movie   
1314            switch CivMode
1315                case 'CivX'
1316                    cmd=[cmd...
1317                        cmd_civ2(filecell.nc.civ2{ifile,j},Param) '\n'];
1318                case 'CivAll'
1319                    CivAllCmd=[CivAllCmd ' civ2 '];
1320                    str=CIV2_CMD_Unified(filecell.nc.civ2{ifile,j},'',Param.Civ2);
1321                    fieldnames=fields(str);
1322                    [CivAllxml,uid_civ2]=add(CivAllxml,1,'element','civ2');
1323                    for ilist=1:length(fieldnames)
1324                        val=eval(['str.' fieldnames{ilist}]);
1325                        if ischar(val)
1326                            [CivAllxml,uid_t]=add(CivAllxml,uid_civ2,'element',fieldnames{ilist});
1327                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1328                        end
1329                    end
1330            end
1331        end
1332       
1333        % CheckFix2
1334        if Param.CheckFix2==1
1335            switch CivMode
1336                case 'CivX'
1337                    cmd=[cmd...
1338                        cmd_fix(filecell.nc.civ2{ifile,j},Param,'Fix2') '\n'];
1339                case 'CivAll'
1340                    fix2.inputFileName=filecell.nc.civ2{ifile,j} ;
1341                    fix2.fi1=num2str(flagindex2(1));
1342                    fix2.fi2=num2str(flagindex2(2));
1343                    fix2.fi3=num2str(flagindex2(3));
1344                    fix2.threshC=num2str(thresh_vec2C);
1345                    fix2.threshV=num2str(thresh_vel2);
1346                    fieldnames=fields(fix2);
1347                    [CivAllxml,uid_fix2]=add(CivAllxml,1,'element','fix2');
1348                    for ilist=1:length(fieldnames)
1349                        val=eval(['fix2.' fieldnames{ilist}]);
1350                        if ischar(val)
1351                            [CivAllxml,uid_t]=add(CivAllxml,uid_fix2,'element',fieldnames{ilist});
1352                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1353                        end
1354                    end
1355                    CivAllCmd=[CivAllCmd ' fix2 '];
1356            end
1357        end
1358       
1359        %CheckPatch2
1360        if Param.CheckPatch2==1
1361           
1362            switch CivMode
1363               
1364                case 'CivX'
1365                    cmd=[cmd...
1366                        cmd_patch(filecell.nc.civ1{ifile,j},Param,'Patch2') '\n'];
1367                   
1368                case 'CivAll'
1369                    patch2.inputFileName=filecell.nc.civ1{ifile,j} ;
1370                    patch2.nopt=subdomain_patch2;
1371                    patch2.maxdiff=thresh_patch2;
1372                    patch2.ro=rho_patch2;
1373                    test_grid=get(handles.get_gridpatch2,'Value');
1374                    if test_grid
1375                        patch2.gridflag='y';
1376                        gridname=get(handles.grid_patch2,'String');
1377                        if isequal(gridname(end-3:end),'grid')
1378                            nbslice_grid=str2double(gridname(1:end-4)); %
1379                            if ~isnan(nbslice_grid)
1380                                i1_grid=mod(i1_civ2(ifile)-1,nbslice_grid)+1;
1381                                patch2.gridPatch=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')];
1382                                if ~exist(patch2.gridPatch,'file')
1383                                    msgbox_uvmat('ERROR','grid file absent for patch2')
1384                                end
1385                            elseif exist(gridname,'file')
1386                                patch2.gridPatch=gridname;
1387                            else
1388                                msgbox_uvmat('ERROR','grid file absent for patch2')
1389                            end
1390                        end
1391                    else
1392                        patch2.gridPatch='none';
1393                        patch2.gridflag='n';
1394                        patch2.m=nx_patch2;
1395                        patch2.n=ny_patch2;
1396                    end
1397                    patch2.convectFlow='n';
1398                    fieldnames=fields(patch2);
1399                    [CivAllxml,uid_patch2]=add(CivAllxml,1,'element','patch2');
1400                    for ilist=1:length(fieldnames)
1401                        val=eval(['patch2.' fieldnames{ilist}]);
1402                        if ischar(val)
1403                            [CivAllxml,uid_t]=add(CivAllxml,uid_patch2,'element',fieldnames{ilist});
1404                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1405                        end
1406                    end
1407                    CivAllCmd=[CivAllCmd ' patch2 '];
1408            end
1409        end
1410       
1411        switch CivMode
1412           
1413            case {'CivX','CivAll'}
1414                if isequal(CivMode,'CivAll')
1415                    save(CivAllxml,[OutputFile '.xml']);
1416                    cmd=[cmd sparam.CivBin ' -f ' OutputFile '.xml '  CivAllCmd ' >' OutputFile '.log' '\n'];
1417                end             
1418                % create the .bat file used in run or batch
1419                filename_bat=[OutputFile '.bat'];
1420                [fid,message]=fopen(filename_bat,'w');
1421                if isequal(fid,-1)
1422                    msgbox_uvmat('ERROR', ['creation of .bat file: ' message])
1423                    return
1424                end
1425                fprintf(fid,cmd);
1426                fclose(fid);           
1427                if isunix
1428                    system(['chmod +x ' filename_bat]);
1429                end             
1430                batch_file_list{length(batch_file_list)+1}=filename_bat;
1431               
1432            case 'Matlab'
1433                drawnow
1434                if ~strcmp(compare,'stereo PIV')
1435                    filename_xml=[OutputFile '.civ.xml'];
1436                    t=struct2xml(Param);
1437                    save(t,filename_xml)
1438                    if batch   
1439                        path_civ=fileparts(which('civ'));
1440                        filename_bat=[OutputFile '.bat'];
1441                        [fid,message]=fopen(filename_bat,'w');
1442                        if isequal(fid,-1)
1443                            msgbox_uvmat('ERROR', ['creation of .bat file: ' message])
1444                            return
1445                        end
1446                        fprintf(fid,['/opt/matlab/R2011a/bin/matlab -nodisplay -nosplash -r "cd(''' path_civ ''');'...
1447                            'civ_matlab(''' filename_xml ''',''' OutputFile '.nc'');exit"']);
1448                        fclose(fid);
1449                        if isunix
1450                            system(['chmod +x ' filename_bat]);
1451                        end
1452                        batch_file_list{length(batch_file_list)+1}=filename_bat;
1453                    else
1454                        [Data,erromsg]=civ_matlab(Param,filecell.nc.civ1{ifile,j});
1455                        if isempty(errormsg)
1456                            display([filecell.nc.civ1{ifile,j} ' written'])
1457                        else
1458                            msgbox_uvmat('ERROR',errormsg)
1459                        end
1460                    end
1461                end
1462        end
1463    end
1464end
1465
1466if batch 
1467    switch batch_mode   
1468       
1469        case 'sge'
1470            for p=1:length(batch_file_list)
1471                cmd=['!qsub -p ' pvalue ' -q civ.q -e ' flname '.errors -o ' flname '.log' ' ' batch_file_list{p}];
1472                display(cmd);eval(cmd);
1473            end           
1474        case 'oar_old'
1475                for p=1:length(batch_file_list)
1476                    oar_command=['!oarsub -n CIVX -q nicejob '...
1477                   '-E ' regexprep(batch_file_list{p},'.bat','.errors') ' -O ' regexprep(batch_file_list{p},'.bat','.log ')...
1478                    '-l "/core=1+{type = ''smalljob''}/licence=1,walltime=00:60:00"   ' batch_file_list{p}];
1479                display(oar_command);eval(oar_command);
1480                end               
1481        case 'oar'
1482           
1483            oar_modes={'oar-dispatch','mpilauncher'};
1484            text={'Batch processing on servcalcul3 LEGI';...
1485                'Please choose one of the followint modes';...
1486                '* oar-dispatch : jobs in a container';...
1487                '* mpilauncher : one single job using several cores';...
1488                '**********************************'...
1489                };
1490            [S,v]=listdlg('PromptString',text,'ListString',oar_modes,...
1491                'SelectionMode','single','ListSize',[400 100],'Name','LEGI job mode');
1492            switch oar_modes{S}
1493               
1494                case 'oar-dispatch' %oar-dispatch.pl
1495                    walltime_onejob=600;%seconds
1496                    filename_joblist=fullfile(Rootbat,'job_list.txt');
1497                    fid=fopen(filename_joblist,'w');
1498                    for p=1:length(batch_file_list)
1499                        oar_command=['oarsub -n CIVX '...
1500                            '-E ' regexprep(batch_file_list{p},'\.bat\>','.errors') ' -O ' regexprep(batch_file_list{p},'\.bat\>','.log ')...
1501                            '-l "/core=1,walltime=' datestr(walltime_onejob/86400,13) '"   ' batch_file_list{p}];
1502                        fprintf(fid,[oar_command '\n']);
1503                    end
1504                    fclose(fid);
1505                    ncores=36;
1506                    oar_command=['oarsub -t container -n civx-container '...
1507                        '-l /core=' num2str(ncores)...
1508                        ',walltime=' datestr(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,13)...
1509                        ' "oar-dispatch -f ' filename_joblist '"'];
1510                    filename_oarcommand=fullfile(Rootbat,'oar_command');
1511                    fid=fopen(filename_oarcommand,'w');
1512                    fprintf(fid,[oar_command '\n']);
1513                    fclose(fid);
1514                    display(oar_command);
1515                    eval(['! . ' filename_oarcommand])
1516                case 'mpilauncher'
1517                    filename_joblist=fullfile(Rootbat,'job_list.txt');
1518                    fid=fopen(filename_joblist,'w');
1519                   
1520                    for p=1:length(batch_file_list)
1521                        fprintf(fid,[batch_file_list{p} '\n']);
1522                    end
1523                    fclose(fid)
1524                    text_oarscript=[...
1525                        '#!/bin/bash \n'...
1526                        '#OAR -n Mylauncher \n'...
1527                        '#OAR -l node=4/core=5,walltime=0:15:00 \n'...
1528                        '#OAR -E stderrfile.log \n'...
1529                        '#OAR -O stdoutfile.log \n'...
1530                        '# ========================================================= \n'...
1531                        '# This simple program launch a multinode parallel OpenMPI mpilauncher \n'...
1532                        '# application for coriolis PIV post-processing. \n'...
1533                        '# OAR uses oarshmost wrapper to propagate the user environement. \n'...
1534                        '# This wrapper assert that the user has the same environment on all the \n'...
1535                        '# allocated nodes (basic behavior needed by most MPI applications).  \n'...
1536                        '# \n'...
1537                        '# REQUIREMENT: \n'...
1538                        '# the oarshmost wrapper should be installed in $HOME/bin directory. \n'...
1539                        '# If a different location is used, change the line following the comment "Bidouille" \n'...
1540                        '# ========================================================= \n'...
1541                        '#   USER should only modify these 2 lines  \n'...
1542                        'WORKDIR=' pwd ' \n'...
1543                        'COMMANDE="mpilauncher  -f ' filename_joblist '" \n'...
1544                        '# ========================================================= \n'...
1545                        '# DO NOT MODIFY the FOLOWING LINES. (or be carefull) \n'...
1546                        'echo "job starting on: "`hostname` \n'...
1547                        'MPINODES="-host `tr [\\\\\\n] [,] <$OAR_NODEFILE |sed -e "s/,$/ /"`" \n'...
1548                        'NCPUS=`cat $OAR_NODEFILE |wc -l` \n'...
1549                        '#========== Bidouille ============== \n'...
1550                        'export OMPI_MCA_plm_rsh_agent=oar-envsh \n'...%                     'cd $WORKDIR \n'...
1551                        'CMD="mpirun -np $NCPUS -wdir $WORKDIR $MPINODES $COMMANDE" \n'...
1552                        'echo "I run: $CMD"  \n'...
1553                        '$CMD \n'...
1554                        'echo "job ending" \n'...
1555                        ];
1556                    %                 oarsub -S ./oar.sub
1557                    filename_oarscript=fullfile(Rootbat,'oar_command');
1558                    fid=fopen(filename_oarscript,'w');
1559                    fprintf(fid,[text_oarscript]);
1560                    fclose(fid);
1561                    eval(['!chmod +x  ' filename_oarscript]);
1562                    eval(['!oarsub -S ' filename_oarscript]);
1563            end
1564    end
1565else
1566    if ~isequal(CivMode,'Matlab')
1567        filename_superbat=fullfile(Rootbat,'job_list.bat');
1568        fid=fopen(filename_superbat,'w');
1569        if fid==-1
1570            msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat])
1571            return
1572        end
1573        for p=1:length(batch_file_list)
1574            if isunix
1575                fprintf(fid,['sh ' batch_file_list{p} '\n']);
1576            else
1577                fprintf(fid,['@call "' regexprep(filename_bat,'\\','\\\\') '"' '\n']);
1578            end
1579        end
1580        fclose(fid);
1581        if(isunix)
1582            system(['chmod +x ' filename_superbat]);
1583        end
1584        system([filename_superbat ' &']);% execute main commmand
1585    end
1586end
1587
1588
1589%% save interface state
1590if isfield(filecell,'nc')
1591    if isfield(filecell.nc,'civ2')
1592        fileresu=filecell.nc.civ2{1,1};
1593    else
1594        fileresu=filecell.nc.civ1{1,1};
1595    end
1596end
1597[RootPath,RootFile,field_count,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fileresu);
1598namedoc=fullfile(RootPath,subdir,RootFile);
1599detect=1;
1600while detect==1
1601    namefigfull=[namedoc '.fig'];
1602    hh=dir(namefigfull);
1603    if ~isempty(hh)
1604        detect=1;
1605        namedoc=[namedoc '.0'];
1606    else
1607        detect=0;
1608    end
1609end
1610saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER  .xml)
1611
1612%Save info in personal profile (initiate browser next time) TODO
1613MenuFile={};
1614dir_perso=prefdir;
1615profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1616if exist(profil_perso,'file')
1617    hh=load (profil_perso);
1618      if isfield(hh,'MenuFile')
1619          MenuFile=hh.MenuFile;
1620      end
1621      if isfield(filecell.nc,'civ2')
1622          MenuFile=[filecell.nc.civ2{1,1}; MenuFile];
1623      else
1624           MenuFile=[filecell.nc.civ1{1,1}; MenuFile];
1625      end
1626      save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
1627else
1628    MenuFile=filecell.ima1.civ1(1,1);
1629    save (profil_perso,'MenuFile')
1630end
1631
1632%------------------------------------------------------------------------
1633% --- determine the list of reference indices of processing file
1634function [ref_i,ref_j,errormsg]=find_ref_indices(handles)
1635%------------------------------------------------------------------------
1636errormsg=''; %default error message
1637first_i=str2double(get(handles.first_i,'String'));%first index i
1638last_i=str2double(get(handles.last_i,'String'));%last index i
1639incr_i=str2double(get(handles.incr_i,'String'));% increment
1640if isequal(get(handles.first_j,'Visible'),'on')
1641    first_j=str2double(get(handles.first_j,'String'));%first index j
1642    last_j=str2double(get(handles.last_j,'String'));%last index j
1643    incr_j=str2double(get(handles.incr_j,'String'));% increment
1644else
1645    first_j=1;
1646    last_j=1;
1647    incr_j=1;
1648end
1649ref_i=first_i:incr_i:last_i;% list of i indices (reference values for each pair)
1650ref_j=first_j:incr_j:last_j;% list of j indices (reference values for each pair)
1651if isnan(first_i)||isnan(first_j)
1652    errormsg='first field number not defined';
1653elseif isnan(last_i)||isnan(last_j)
1654    errormsg='last field number not defined';
1655elseif isnan(incr_i)||isnan(incr_j)
1656    errormsg='increment in field number not defined';
1657elseif last_i < first_i || last_j < first_j
1658    errormsg='last field number must be larger than the first one';
1659end
1660
1661%------------------------------------------------------------------------
1662% --- determine the list of filenames and indices needed for launch_job
1663function [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]=...
1664    set_civ_filenames(handles,ref_i,ref_j,checkbox)
1665%------------------------------------------------------------------------
1666filecell=[];%default
1667
1668%% get the root names nomenclature and numbers
1669filebase=get(handles.RootName,'String');
1670
1671if isempty(filebase)||isequal(filebase,'')
1672    msgbox_uvmat('ERROR','please open an image with the upper menu option Open/Browse...')
1673    return
1674end
1675
1676%filebase=regexprep(filebase,'\.fsnet','fsnet');% temporary fix for cluster Coriolis
1677filecell.filebase=filebase;
1678
1679browse=get(handles.RootName,'UserData');
1680compare_list=get(handles.ListCompareMode,'String');
1681val=get(handles.ListCompareMode,'Value');
1682compare=compare_list{val};
1683if strcmp(compare,'displacement')
1684    mode='displacement';
1685else
1686    mode_list=get(handles.ListPairMode,'String');
1687    mode_value=get(handles.ListPairMode,'Value');
1688    mode=mode_list{mode_value};
1689end
1690%time=get(handles.RootName,'UserData'); %get the set of times
1691ext_ima=get(handles.ImaExt,'String');
1692nom_type_nc=browse.nom_type_nc;
1693if isfield(browse,'nom_type_ima')
1694    nom_type_ima2=browse.nom_type_ima;
1695end
1696if isempty(nom_type_ima2),nom_type_ima2='1';end; %default
1697if isempty(nom_type_nc),nom_type_nc='_i1-i2';end; %default
1698[num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=...
1699    find_pair_indices(handles,ref_i,ref_j,mode);
1700%determine the new filebase for 'displacement' ListPairMode (comparison of two series)
1701filebase_B=filebase;% root name of the second field series for stereo
1702if strcmp(compare,'displacement') || strcmp(compare,'stereo PIV')
1703%     test_disp=1;
1704    nom_type_ima1=browse.nom_type_ima_1; %nomenclature type of the second file series
1705    [Path2,Name2]=fileparts(filebase_B);
1706    Path1=Path2;
1707    Name1=get(handles.RootName_1,'String');% root name of the first field series for stereo
1708    filebase_A=fullfile(Path1,Name1);
1709    if length(Name1)>6
1710        Name1=Name1(end-5:end);
1711    end
1712    if length(Name2)>6
1713        Name2=Name2(end-5:end);
1714    end
1715    filebase_AB=fullfile(Path2,[Name2 '-' Name1]);
1716else
1717%     test_disp=0;
1718    filebase_A=filebase;
1719    nom_type_ima1=nom_type_ima2;
1720    filebase_AB=filebase;
1721end
1722if strcmp(compare,'displacement')
1723    filebase_ima1=filebase_A;
1724    filebase_ima2=filebase_B;
1725    filebase_nc=filebase_AB; %root name for the result of civ2
1726else
1727    filebase_ima1=filebase_B;
1728    filebase_ima2=filebase_B;
1729    filebase_nc=filebase_B;
1730end
1731
1732%determine reference files for fix:
1733file_ref_fix1={};%default
1734file_ref_fix2={};
1735nbfield=length(num1_civ1);
1736nbslice=length(num_a_civ1);
1737if checkbox(2)==1% fix1 performed
1738    ref=get(handles.ref_fix1,'UserData');%read data on the ref file stored by get_ref_fix1_Callback
1739    if ~isempty(ref)
1740        first_i=str2double(get(handles.first_i,'String'));
1741        last_i=str2double(get(handles.last_i,'String'));
1742        incr_i=str2double(get(handles.incr_i,'String'));
1743        first_j=str2double(get(handles.first_j,'String'));
1744        last_j=str2double(get(handles.last_j,'String'));
1745        incr_j=str2double(get(handles.incr_j,'String'));
1746        num_i_ref=first_i:incr_i:last_i;
1747        num_j_ref=first_j:incr_j:last_j;
1748        if isequal(mode,'displacement')
1749            num_i1=num_i_ref;
1750            num_i2=num_i_ref;
1751            num_j1=num_j_ref;
1752            num_j2=num_j_ref;
1753        elseif isequal(mode,'pair j1-j2')% isequal(mode,'st_pair j1-j2')
1754            num_i1=num_i_ref;
1755            num_i2=num_i1;
1756            num_j1=ref.num_a*ones(size(num_i_ref));
1757            num_j2=ref.num_b*ones(size(num_i_ref));
1758        elseif isequal(mode,'series(Di)') % isequal(mode,'st_series(Di)')
1759            delta1=floor((ref.num2-ref.num1)/2);
1760            delta2=ceil((ref.num2-ref.num1)/2);
1761            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
1762            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
1763            if isempty(ref.num_a)
1764                ref.num_a=1;
1765            end
1766            num_j1=ref.num_a*ones(size(num_i1));
1767            num_j2=num_j1;
1768        elseif isequal(mode,'series(Dj)')%| isequal(mode,'st_series(Dj)')
1769            delta1=floor((ref.num_b-ref.num_a)/2);
1770            delta2=ceil((ref.num_b-ref.num_a)/2);
1771            num_i1=ref.num1*ones(size(num_i_ref));
1772            num_i2=num_i1;
1773            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
1774            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
1775        end
1776        for ifile=1:nbfield
1777            for j=1:nbslice
1778                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);%
1779                file_ref_fix1(ifile,j)={file_ref};
1780                if ~exist(file_ref,'file')
1781                    msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix1'])
1782                    filecell=[];
1783                    return
1784                end
1785            end
1786        end
1787    end
1788end
1789
1790%determine reference files for checkfix2:
1791if checkbox(5)==1% fix2 performed
1792    ref=get(handles.ref_fix2,'UserData');
1793    if ~isempty(ref)
1794        first_i=str2double(get(handles.first_i,'String'));
1795        last_i=str2double(get(handles.last_i,'String'));
1796        incr_i=str2double(get(handles.incr_i,'String'));
1797        first_j=str2double(get(handles.first_j,'String'));
1798        last_j=str2double(get(handles.last_j,'String'));
1799        incr_j=str2double(get(handles.incr_j,'String'));
1800        num_i_ref=first_i:incr_i:last_i;
1801        num_j_ref=first_j:incr_j:last_j;
1802        if isequal(mode,'displacement')
1803            num_i1=num_i_ref;
1804            num_i2=num_i_ref;
1805            num_j1=num_j_ref;
1806            num_j2=num_j_ref;
1807        elseif isequal(mode,'pair j1-j2')
1808            num_i1=num_i_ref;
1809            num_i2=num_i1;
1810            num_j1=ref.num_a;
1811            num_j2=ref.num_b;
1812        elseif isequal(mode,'series(Di)')
1813            delta1=floor((ref.num2-ref.num1)/2);
1814            delta2=ceil((ref.num2-ref.num1)/2);
1815            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
1816            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
1817            num_j1=ref.num_a*ones(size(num_i1));
1818            num_j2=num_j1;
1819        elseif isequal(mode,'series(Dj)')
1820            delta1=floor((ref.num_b-ref.num_a)/2);
1821            delta2=ceil((ref.num_b-ref.num_a)/2);
1822            num_i1=ref.num1*ones(size(num_i_ref));
1823            num_i2=num_i1;
1824            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
1825            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
1826        end
1827        for ifile=1:nbfield
1828            for j=1:nbslice
1829                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);%
1830                file_ref_fix2(ifile,j)={file_ref};
1831                if ~exist(file_ref,'file')
1832                    msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix2'])
1833                    filecell={};
1834                    return
1835                end
1836            end
1837        end
1838    end
1839end
1840
1841%check dir
1842subdir_civ1=get(handles.txt_SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf output data
1843subdir_civ2=get(handles.txt_SubdirCiv2,'String');
1844if isequal(subdir_civ1,''),subdir_civ1='CIV'; end% put default subdir
1845if isequal(subdir_civ2,''),subdir_civ2=subdir_civ1; end% put default subdir
1846% currentdir=pwd;%store the current working directory
1847[Path_ima,Name]=fileparts(filebase);%Path of the image files (.civ)
1848if ~exist(Path_ima,'dir')
1849    msgbox_uvmat('ERROR',['path to images ' Path_ima ' not found'])
1850    filecell={};
1851    return
1852end
1853[xx,message]=fileattrib(Path_ima);
1854if ~isempty(message) && ~isequal(message.UserWrite,1)
1855    msgbox_uvmat('ERROR',['No writting access to ' Path_ima])
1856    filecell={};
1857%     cd(currentdir);
1858    return
1859end
1860
1861%check the existence of the netcdf and image files involved
1862% %%%%%%%%%%%%  case CheckCiv1 activated   %%%%%%%%%%%%%
1863if checkbox(1)==1;
1864    detect=1;
1865    vers=0;
1866    subdir_civ1_new=subdir_civ1;
1867    while detect==1 %create a new subdir if the netcdf files already exist
1868        for ifile=1:nbfield
1869            for j=1:nbslice
1870                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);
1871                detect=exist(filename,'file')==2;
1872                if detect% if a netcdf file already exists
1873                    indstr=regexp(subdir_civ1_new,'\D');
1874                    if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number
1875                        vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1;
1876                        subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)];
1877                    else
1878                        vers=vers+1;
1879                        subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) '_' num2str(vers)];       
1880                    end
1881                    subdir_civ2=subdir_civ1_new;
1882                    break
1883                end
1884                filecell.nc.civ1(ifile,j)={filename};
1885            end
1886            if detect% if a netcdf file already exists
1887                break
1888            end
1889        end
1890 
1891        %create the new txt_SubdirCiv1
1892        if ~exist(fullfile(Path_ima,subdir_civ1_new),'dir')
1893%             cd(Path_ima);         
1894            [xx,msg1]=mkdir(fullfile(Path_ima,subdir_civ1_new));
1895
1896            if ~strcmp(msg1,'')
1897                msgbox_uvmat('ERROR',['cannot create ' subdir_civ1_new ': ' msg1])%error message for directory creation
1898                filecell={};
1899                return
1900            elseif isunix         
1901                [xx,msg2] = fileattrib(fullfile(Path_ima,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g)
1902                if ~strcmp(msg2,'')
1903                    msgbox_uvmat('ERROR',['pb of permission for  ' fullfile(Path_ima,subdir_civ1_new) ': ' msg2])%error message for directory creation
1904                    filecell={};
1905                    return
1906                end
1907            end
1908%             cd(currentdir);
1909        end
1910        if strcmp(compare,'stereo PIV')&&(strcmp(mode,'pair j1-j2')||strcmp(mode,'series(Dj)')||strcmp(mode,'series(Di)'))%check second nc series
1911            for ifile=1:nbfield
1912                for j=1:nbslice
1913                    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);%
1914                    detect=exist(filename,'file')==2;
1915                    if detect% if a netcdf file already exists
1916                       indstr=regexp(subdir_civ1_new,'\D');
1917                       if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number
1918                           vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1;
1919                           subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)];
1920                       else
1921                           vers=vers+1;
1922                           subdir_civ1_new=[subdir_civ1_new '_' num2str(vers)];
1923                       end
1924                       subdir_civ2=subdir_civ1;
1925                       break
1926                    end
1927                    filecell.ncA.civ1(ifile,j)={filename};
1928                end
1929                if detect% if a netcdf file already exists
1930                    break
1931                end
1932            end
1933            %create the new txt_SubdirCiv1
1934            if ~exist(fullfile(Path_ima,subdir_civ1_new),'dir')
1935%                    cd(Path_ima);         
1936                [xx,msg1]=mkdir(fullfile(Path_ima,subdir_civ1_new));
1937%                             cd(currentdir);
1938                if ~strcmp(msg1,'')
1939                    msgbox_uvmat('ERROR',['cannot create ' subdir_civ1_new ': ' msg1])
1940%                     cd(currentdir)
1941                    filecell={};
1942                    return
1943                else
1944                    [xx,msg2] = fileattrib(fullfile(Path_ima,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g)
1945                    if ~strcmp(msg2,'')
1946                        msgbox_uvmat('ERROR',['pb of permission for ' subdir_civ1_new ': ' msg2])%error message for directory creation
1947%                         cd(currentdir)
1948                        filecell={};
1949                        return
1950                    end
1951                end
1952            end
1953        end
1954    end
1955    subdir_civ1=subdir_civ1_new;
1956    % get image names
1957    for ifile=1:nbfield
1958        for j=1:nbslice
1959            filename=name_generator(filebase_ima1, num1_civ1(ifile),num_a_civ1(j),ext_ima,nom_type_ima1);
1960            idetect(j)=exist(filename,'file')==2;
1961            filecell.ima1.civ1(ifile,j)={filename}; %first image
1962            filename=name_generator(filebase_ima2, num2_civ1(ifile),num_b_civ1(j),ext_ima,nom_type_ima2);
1963            idetect_1(j)=exist(filename,'file')==2;
1964            filecell.ima2.civ1(ifile,j)={filename};%second image
1965        end
1966        [idetectmin,indexj]=min(idetect);
1967        if idetectmin==0,
1968            msgbox_uvmat('ERROR',[filecell.ima1.civ1{ifile,indexj} ' not found'])
1969            filecell={};
1970           % cd(currentdir)
1971            return
1972        end
1973        [idetectmin,indexj]=min(idetect_1);
1974        if idetectmin==0,
1975            msgbox_uvmat('ERROR',[filecell.ima2.civ1{ifile,indexj} ' not found'])
1976            filecell={};
1977            %cd(currentdir)
1978            return
1979        end
1980    end
1981    if strcmp(compare,'stereo PIV') && (strcmp(mode,'pair j1-j2') || strcmp(mode,'series(Dj)') || strcmp(mode,'series(Di)'))
1982        for ifile=1:nbfield
1983            for j=1:nbslice
1984                filename=name_generator(filebase_A, num1_civ1(ifile),num_a_civ1(j),ext_ima,nom_type_ima1);
1985                idetect(j)=exist(filename,'file')==2;
1986                filecell.imaA1.civ1(ifile,j)={filename} ;%first image
1987                filename=name_generator(filebase_A, num2_civ1(ifile),num_b_civ1(j),ext_ima,nom_type_ima2);
1988                idetect_1(j)=exist(filename,'file')==2;
1989                filecell.imaA2.civ1(ifile,j)={filename};%second image
1990            end
1991            [idetectmin,indexj]=min(idetect);
1992            if idetectmin==0,
1993                msgbox_uvmat('ERROR',[filecell.imaA1.civ1{ifile,indexj} ' not found'])
1994                filecell={};
1995               % cd(currentdir)
1996                return
1997            end
1998            [idetectmin,indexj]=min(idetect_1);
1999            if idetectmin==0,
2000                msgbox_uvmat('ERROR',[filecell.imaA2.civ1{ifile,indexj} ' not found'])
2001                filecell={};
2002               % cd(currentdir)
2003                return
2004            end
2005        end
2006    end
2007   
2008    %%%%%%%%%%%%%  checkfix1 or checkpatch1 activated but no checkciv1   %%%%%%%%%%%%%
2009elseif (checkbox(2)==1 || checkbox(3)==1);
2010    for ifile=1:nbfield
2011        for j=1:nbslice
2012            filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',...
2013                nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
2014            detect=exist(filename,'file')==2;
2015            if detect==0
2016                msgbox_uvmat('ERROR',[filename ' not found'])
2017                filecell={};
2018               % cd(currentdir)
2019                return
2020            end
2021            filecell.nc.civ1(ifile,j)={filename};
2022        end
2023    end
2024    if strcmp(compare,'stereo PIV')
2025        for ifile=1:nbfield
2026            for j=1:nbslice
2027                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);%
2028                filecell.ncA.civ1(ifile,j)={filename};
2029                if ~exist(filename,'file')
2030                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2031                    set(handles.RUN, 'Enable','On')
2032                    set(handles.RUN,'BackgroundColor',[1 0 0])
2033                    filecell={};
2034                    %cd(currentdir)
2035                    return
2036                end
2037            end
2038        end
2039    end
2040end
2041
2042%%%%%%%%%%%%%  if checkciv2 performed with pairs different than checkciv1  %%%%%%%%%%%%%
2043testdiff=0;
2044if (checkbox(4)==1)&&...
2045        ((get(handles.ListPairCiv1,'Value')~=get(handles.ListPairCiv2,'Value'))||~strcmp(subdir_civ2,subdir_civ1))
2046    testdiff=1;
2047    detect=1;
2048    vers=0;
2049    subdir_civ2_new=subdir_civ2;
2050    while detect==1 %create a new subdir if the netcdf files already exist
2051        for ifile=1:nbfield
2052            for j=1:nbslice
2053                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);%
2054                detect=exist(filename,'file')==2;
2055                if detect% if a netcdf file already exists
2056                    indstr=regexp(subdir_civ2,'\D');
2057                    if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2058                        vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2059                        subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2060                    else
2061                        vers=vers+1;
2062                        subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2063                    end
2064                    break
2065                end
2066                filecell.nc.civ2(ifile,j)={filename};
2067            end
2068            if detect% if a netcdf file already exists
2069                break
2070            end
2071        end
2072        %create the new subdir_civ2_new
2073        if ~exist(fullfile(Path_ima,subdir_civ2_new),'dir')
2074            [xx,m2]=mkdir(fullfile(Path_ima,subdir_civ2_new));
2075            [xx,msg2] = fileattrib(fullfile(Path_ima,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g)
2076            if ~isequal(m2,'')
2077                msgbox_uvmat('ERROR',['cannot create ' fullfile(Path_ima,subdir_civ2_new) ': ' m2])
2078                filecell={};
2079               % cd(currentdir)
2080                return
2081            end
2082        end
2083        if strcmp(compare,'stereo PIV')%check second nc series
2084            for ifile=1:nbfield
2085                for j=1:nbslice
2086                    filename=name_generator(filebase_A,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2087                        nom_type_nc,1,num2_civ2(ifile),num_b_civ1(j),subdir_civ2_new);%
2088                    detect=exist(filename,'file')==2;
2089                    if detect% if a netcdf file already exists
2090                        indstr=regexp(subdir_civ2,'\D');
2091                        if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2092                           vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2093                           subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2094                        else
2095                           vers=vers+1;
2096                           subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2097                        end
2098                        break
2099                    end
2100                    filecell.ncA.civ2(ifile,j)={filename};
2101                end
2102                if detect% if a netcdf file already exists
2103                    break
2104                end
2105            end
2106            subdir_civ2=subdir_civ2_new;
2107            %create the new txt_SubdirCiv1
2108            if ~exist(fullfile(Path_ima,subdir_civ2_new),'dir')
2109                [xx,m2]=mkdir(subdir_civ2_new);
2110                 [xx,msg2] = fileattrib(fullfile(Path_ima,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g)
2111                if ~isequal(m2,'')
2112                    msgbox_uvmat('ERROR', ['cannot create ' fullfile(Path_ima,subdir_civ2_new) ': ' m2])%error message for directory creation
2113                  %  cd(currentdir)
2114                    filecell={};
2115                    return
2116                end
2117            end
2118        end
2119    end
2120    subdir_civ2=subdir_civ2_new;
2121end
2122%cd(currentdir);%come back to the current working directory
2123
2124%%%%%%%%%%%%%  if checkciv2 results are obtained or used  %%%%%%%%%%%%%
2125if checkbox(4)==1 || checkbox(5)==1 || checkbox(6)==1 %civ2
2126    %check source netcdf file of checkciv1 estimates
2127    if checkbox(1)==0; %no civ1 performed
2128        for ifile=1:nbfield
2129            for j=1:nbslice
2130                filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',...
2131                    nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
2132                filecell.nc.civ1(ifile,j)={filename};% name of the civ1 file
2133                if ~exist(filename,'file')
2134                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2135                    filecell={};
2136                    return
2137                end
2138                if ~testdiff % civ2 or patch2 are written in the same file as civ1
2139                    if checkbox(4)==0 ; %check the existence of civ2 if it is not calculated
2140                        Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2');
2141                        if ~isempty(Data.CivStage) && Data.CivStage<4 %test for civ files
2142                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2143                            filecell=[];
2144                            return
2145                        elseif isempty(Data.civ2)||isequal(Data.civ2,0)
2146                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2147                            filecell=[];
2148                            return
2149                        end
2150                    elseif checkbox(3)==0; %check the existence of patch if it is not calculated
2151                        Data=nc2struct(filename,'ListGlobalAttribute','CivStage','patch');
2152                        if ~isempty(Data.CivStage)
2153                            if Data.CivStage<3 %test for civ files
2154                                msgbox_uvmat('ERROR',['no patch data in ' filename])
2155                                filecell=[];
2156                                return
2157                            end
2158                        elseif isempty(Data.patch)||isequal(Data.patch,0)
2159                            msgbox_uvmat('ERROR',['no patch data in ' filename])
2160                            filecell=[];
2161                            return
2162                        end
2163                    end
2164                end
2165            end
2166        end
2167        if strcmp(compare,'stereo PIV')
2168            for ifile=1:nbfield
2169                for j=1:nbslice
2170                    filename=name_generator(filebase_A,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2171                        nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
2172                    filecell.ncA.civ2(ifile,j)={filename};
2173                    if ~exist(filename,'file')
2174                        msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2175                        set(handles.RUN, 'Enable','On')
2176                        set(handles.RUN,'BackgroundColor',[1 0 0])
2177                        return
2178                    end
2179                end
2180            end
2181        end
2182    end
2183   
2184    detect=1;
2185    %     while detect==1%creates a new subdir if the netcdf files already contain checkciv2 data
2186    for ifile=1:nbfield
2187        for j=1:nbslice
2188            filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2189                nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);
2190            detect=exist(filename,'file')==2;
2191            filecell.nc.civ2(ifile,j)={filename};
2192        end
2193    end
2194    %get first image names for checkciv2
2195    if checkbox(1)==1 && isequal(num1_civ1,num1_civ2) && isequal(num_a_civ1,num_a_civ2)
2196        filecell.ima1.civ2=filecell.ima1.civ1;
2197    elseif checkbox(4)==1
2198        for ifile=1:nbfield
2199            for j=1:nbslice
2200                filename=name_generator(filebase_ima1, num1_civ2(ifile),num_a_civ2(j),ext_ima,nom_type_ima1);
2201                idetect_2(j)=exist(filename,'file')==2;
2202                filecell.ima1.civ2(ifile,j)={filename};%first image
2203            end
2204            [idetectmin,indexj]=min(idetect_2);
2205            if idetectmin==0,
2206                msgbox_uvmat('ERROR',['input image ' filecell.ima1.civ2{ifile,indexj} ' not found'])
2207                filecell=[];
2208                return
2209            end
2210        end
2211    end
2212   
2213    %get second image names for checkciv2
2214    if checkbox(1)==1 && isequal(num2_civ1,num2_civ2) && isequal(num_b_civ1,num_b_civ2)
2215        filecell.ima2.civ2=filecell.ima2.civ1;
2216    elseif checkbox(4)==1
2217        for ifile=1:nbfield
2218            for j=1:nbslice
2219                filename=name_generator(filebase_ima2, num2_civ2(ifile),num_b_civ2(j),ext_ima,nom_type_ima2);
2220                idetect_3(j)=exist(filename,'file')==2;
2221                filecell.ima2.civ2(ifile,j)={filename};%first image
2222            end
2223            [idetectmin,indexj]=min(idetect_3);
2224            if idetectmin==0,
2225                msgbox_uvmat('ERROR',['input image ' filecell.ima2.civ2{ifile,indexj} ' not found'])
2226                filecell=[];
2227                return
2228            end
2229        end
2230    end
2231end
2232if (checkbox(5) || checkbox(6)) && ~checkbox(4)  % need to read an existing netcdf civ2 file
2233    if ~testdiff
2234        filecell.nc.civ2=filecell.nc.civ1;% file already checked
2235    else     % check the civ2 files
2236        for ifile=1:nbfield
2237            for j=1:nbslice
2238                filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2239                    nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
2240                filecell.nc.civ2(ifile,j)={filename};
2241                if ~exist(filename,'file')
2242                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2243                    filecell=[];
2244                    return
2245                else
2246                    Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2');
2247                    if ~isempty(Data.CivStage) && Data.CivStage<4 %test for civ files
2248                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2249                            filecell=[];
2250                            return
2251                    elseif isempty(Data.civ2)||isequal(Data.civ2,0)
2252                        msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2253                        filecell=[];
2254                        return
2255                    end
2256                end
2257            end
2258        end
2259    end
2260end
2261
2262%%%%%%%%%%%%%  if stereo fields are calculated by PATCH %%%%%%%%%%%%%
2263if strcmp(compare,'stereo PIV')
2264    if  checkbox(3) && isequal(get(handles.test_stereo1,'Value'),1)
2265        for ifile=1:nbfield
2266            for j=1:nbslice
2267                filename=name_generator(filebase_AB,num1_civ1(ifile),num_a_civ1(j),'.nc',...
2268                    nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
2269                filecell.st(ifile,j)={filename};
2270            end
2271        end
2272    end
2273    if  checkbox(6) && isequal(get(handles.CheckStereo,'Value'),1)
2274        for ifile=1:nbfield
2275            for j=1:nbslice
2276                filename=name_generator(filebase_AB,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2277                    nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
2278                filecell.st(ifile,j)={filename};
2279            end
2280        end
2281    end
2282end
2283set(handles.txt_SubdirCiv1,'String',subdir_civ1);%update the edit box
2284set(handles.txt_SubdirCiv2,'String',subdir_civ2);%update the edit box
2285browse.nom_type_nc=nom_type_nc;
2286set(handles.RootName,'UserData',browse); %update the nomenclature type for uvmat
2287
2288
2289%COPY IMAGES TO THE FORMAT .png IF NEEDED
2290if isequal(nom_type_ima1,'*')%case of movie files
2291    nom_type_imanew1='_i';
2292else
2293    nom_type_imanew1=nom_type_ima1;
2294end
2295if isequal(nom_type_ima2,'*')%case of movie files
2296    nom_type_imanew2='_i';
2297else
2298    nom_type_imanew2=nom_type_ima2;
2299end
2300if ~isequal(ext_ima,'.png')
2301    %%type of image file
2302    type_ima1='none';%default
2303    movieobject1=[];%default
2304    if strcmpi(ext_ima,'.avi')
2305        hhh=which('mmreader');
2306        if ~isequal(hhh,'')&& mmreader.isPlatformSupported()% if the mmreader function is found (recent version of matlab)
2307            type_ima1='movie';
2308            movieobject1=mmreader([filebase_ima2 ext_ima]);
2309        else
2310            type_ima1='avi';
2311        end
2312    elseif ischar(ext_ima) && ~isempty(ext_ima(2:end))
2313        form=imformats(ext_ima(2:end));
2314        if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2315            if isequal(nom_type_ima1,'*');
2316                type_ima1='multimage';%image series in a single image file
2317            else
2318                type_ima1='image';
2319            end
2320        end
2321    end
2322    type_ima2='none';%default
2323    movieobject2=[];
2324    if strcmpi(ext_ima,'.avi')
2325        hhh=which('mmreader');
2326        if ~isequal(hhh,'')&& mmreader.isPlatformSupported()% if the mmreader function is found (recent version of matlab)
2327            type_ima2='movie';
2328            movieobject2=mmreader([filebase_ima2 ext_ima]);
2329        else
2330            type_ima2='avi';
2331        end
2332    elseif ischar(ext_ima) && ~isempty(ext_ima(2:end))
2333        form=imformats(ext_ima(2:end));
2334        if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2335            if isequal(nom_type_ima1,'*');
2336                type_ima2='multimage';%image series in a single image file
2337            else
2338                type_ima2='image';
2339            end
2340        end
2341    end
2342    %npxy=get(handles.ImaExt,'UserData');
2343    % %     if numel(npxy)<2
2344    %
2345    %         filename=name_generator(filebase_ima1,num1_civ1(1),num_a_civ1(1),ImaExt,nom_type_ima1);
2346    %         A=imread(filename);
2347    %         npxy=size(A);
2348    % %     end
2349    %     npy=npxy(1);
2350    %     npx=npxy(2);
2351    if checkbox(1) %if civ1 is performed
2352        h = waitbar(0,'copy images to the .png format for civ1');% display a wait bar
2353        for ifile=1:nbfield
2354            waitbar(ifile/nbfield);
2355            for j=1:nbslice
2356                filename=name_generator(filebase_ima1,num1_civ1(ifile),num_a_civ1(j),'.png',nom_type_imanew1);
2357                if ~exist(filename,'file')
2358                    A=read_image(filecell.ima1.civ1{ifile,j},type_ima1,num1_civ1(ifile),movieobject1);
2359                    imwrite(A,filename,'BitDepth',16);
2360                end
2361                filecell.ima1.civ1(ifile,j)={filename};
2362                filename=name_generator(filebase_ima2, num2_civ1(ifile),num_b_civ1(j),'.png',nom_type_imanew2);
2363                if ~exist(filename,'file')
2364                    A=read_image(filecell.ima2.civ1{ifile,j},type_ima2,num2_civ1(ifile),movieobject2);
2365                    imwrite(A,filename,'BitDepth',16);
2366                end
2367                filecell.ima2.civ1(ifile,j)={filename};
2368            end
2369        end
2370        close(h)
2371    end
2372    if checkbox(4) %if civ2 is performed
2373        h = waitbar(0,'copy images to the .png format for civ2');% display a wait bar
2374        for ifile=1:nbfield
2375            waitbar(ifile/nbfield);
2376            for j=1:nbslice
2377                filename=name_generator(filebase_ima1,num1_civ2(ifile),num_a_civ2(j),'.png',nom_type_imanew1);
2378                if ~exist(filename,'file')
2379                    A=read_image(cell2mat(filecell.ima1.civ2(ifile,j)),type_ima2,num1_civ2(ifile));
2380                    imwrite(A,filename,'BitDepth',16);
2381                end
2382                filecell.ima1.civ2(ifile,j)={filename};
2383                filename=name_generator(filebase_ima2, num2_civ2(ifile),num_b_civ2(j),'.png',nom_type_imanew2);
2384                if ~exist(filename,'file')
2385                    A=read_image(cell2mat(filecell.ima2.civ2(ifile,j)),type_ima2,num2_civ2(ifile));
2386                    imwrite(A,filename,'BitDepth',16);
2387                end
2388                filecell.ima2.civ2(ifile,j)={filename};
2389            end
2390        end
2391        close(h);
2392    end
2393end
2394
2395%------------------------------------------------------------------------
2396% --- determine the list of index pairs of processing file
2397function [num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=...
2398    find_pair_indices(handles,ref_i,ref_j,mode)
2399%------------------------------------------------------------------------
2400
2401list_civ1=get(handles.ListPairCiv1,'String');
2402index_civ1=get(handles.ListPairCiv1,'Value');
2403str_civ1=list_civ1{index_civ1};%string defining the image pairs for civ1
2404if isempty(str_civ1)||isequal(str_civ1,'')
2405    msgbox_uvmat('ERROR','no image pair selected for civ1')
2406    return
2407end
2408list_civ2=get(handles.ListPairCiv2,'String');
2409index_civ2=get(handles.ListPairCiv2,'Value');
2410if index_civ2>length(list_civ2)
2411    list_civ2=list_civ1;
2412    index_civ2=index_civ1;
2413end
2414str_civ2=list_civ2{index_civ2};%string defining the image pairs for civ2
2415
2416if isequal (mode,'series(Di)')
2417    lastfield=str2double(get(handles.nb_field,'String'));
2418    num1_civ1=ref_i-floor(index_civ1/2)*ones(size(ref_i));% set of first image numbers
2419    num2_civ1=ref_i+ceil(index_civ1/2)*ones(size(ref_i));
2420    num_a_civ1=ref_j;
2421    num_b_civ1=ref_j;
2422    num1_civ2=ref_i-floor(index_civ2/2)*ones(size(ref_i));
2423    num2_civ2=ref_i+ceil(index_civ2/2)*ones(size(ref_i));
2424    num_a_civ2=ref_j;
2425    num_b_civ2=ref_j;   
2426   
2427    % adjust the first and last field number
2428    lastfield=str2double(get(handles.nb_field,'String'));
2429    if isnan(lastfield)
2430        indsel=find((num1_civ1 >= 1)&(num1_civ2 >= 1));
2431    else
2432        indsel=find((num2_civ1 <= lastfield)&(num2_civ2 <= lastfield)&(num1_civ1 >= 1)&(num1_civ2 >= 1));
2433    end
2434    if length(indsel)>=1
2435        firstind=indsel(1);
2436        lastind=indsel(end);
2437        set(handles.first_i,'String',num2str(ref_i(firstind)))%update the display of first and last fields
2438        set(handles.last_i,'String',num2str(ref_i(lastind)))
2439        ref_i=ref_i(indsel);
2440        num1_civ1=num1_civ1(indsel);
2441        num1_civ2=num1_civ2(indsel);
2442        num2_civ1=num2_civ1(indsel);
2443        num2_civ2=num2_civ2(indsel);
2444    end
2445elseif isequal (mode,'series(Dj)')
2446    lastfield_j=str2double(get(handles.nb_field2,'String'));
2447    num1_civ1=ref_i;% set of first image numbers
2448    num2_civ1=ref_i;
2449    num_a_civ1=ref_j-floor(index_civ1/2)*ones(size(ref_j));
2450    num_b_civ1=ref_j+ceil(index_civ1/2)*ones(size(ref_j));
2451    num1_civ2=ref_i;
2452    num2_civ2=ref_i;
2453    num_a_civ2=ref_j-floor(index_civ2/2)*ones(size(ref_j));
2454    num_b_civ2=ref_j+ceil(index_civ2/2)*ones(size(ref_j));
2455    % adjust the first and last field number
2456    if isnan(lastfield_j)
2457        indsel=find((num_a_civ1 >= 1)&(num_a_civ2 >= 1));
2458    else
2459        indsel=find((num_b_civ1 <= lastfield_j)&(num_b_civ2 <= lastfield_j)&(num_a_civ1 >= 1)&(num_a_civ2 >= 1));
2460    end
2461    if length(indsel)>=1
2462        firstind=indsel(1);
2463        lastind=indsel(end);
2464        set(handles.first_j,'String',num2str(ref_j(firstind)))%update the display of first and last fields
2465        set(handles.last_j,'String',num2str(ref_j(lastind)))
2466        ref_j=ref_j(indsel);
2467        num_a_civ1=num_a_civ1(indsel);
2468        num_b_civ1=num_b_civ1(indsel);
2469        num_a_civ2=num_a_civ2(indsel);
2470        num_b_civ2=num_b_civ2(indsel);
2471    end
2472elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)
2473    displ_num=get(handles.ListPairCiv1,'UserData');
2474    num1_civ1=ref_i;
2475    num2_civ1=ref_i;
2476    num_a_civ1=displ_num(1,index_civ1);
2477    num_b_civ1=displ_num(2,index_civ1);
2478    num1_civ2=ref_i;
2479    num2_civ2=ref_i;
2480    num_a_civ2=displ_num(1,index_civ2);
2481    num_b_civ2=displ_num(2,index_civ2);
2482elseif isequal(mode,'displacement')
2483    num1_civ1=ref_i;
2484    num2_civ1=ref_i;
2485    num_a_civ1=ref_j;
2486    num_b_civ1=ref_j;
2487    num1_civ2=ref_i;
2488    num2_civ2=ref_i;
2489    num_a_civ2=ref_j;
2490    num_b_civ2=ref_j;
2491end
2492
2493%------------------------------------------------------------------------
2494% --- Executes on button press in ListCompareMode.
2495function ListCompareMode_Callback(hObject, eventdata, handles)
2496%------------------------------------------------------------------------
2497test=get(handles.ListCompareMode,'Value');
2498if test==2 || test==3 % case 'displacement' or 'stereo PIV'
2499    filebase=get(handles.RootName,'String');
2500    browse=get(handles.RootName,'Userdata');
2501    browse.nom_type_ima1=browse.nom_type_ima;
2502    set(handles.RootName,'UserData',browse);
2503    set(handles.sub_txt,'Visible','on')
2504    set(handles.RootName_1,'Visible','On');%mkes the second file input window visible
2505    mode_store=get(handles.ListPairMode,'String');%get the present 'mode'
2506    set(handles.ListCompareMode,'UserData',mode_store);%store the mode display
2507    set(handles.ListPairMode,'Visible','off')
2508    if test==2
2509        set(handles.ListPairMode,'Visible','off')
2510        set(handles.ListPairMode,'Value',1) % mode 'civX' selected by default
2511    else
2512        set(handles.ListPairMode,'Visible','on')
2513        set(handles.ListPairMode,'Value',3) % mode 'Matlab' selected for stereo
2514    end
2515   
2516    %% menuopen an image file with the browser
2517    ind_opening=1;%default
2518    browse.incr_pair=[0 0]; %default
2519    oldfile=get(handles.RootName,'String');
2520     menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)';
2521       '*.xml',  '.xml files '; ...
2522        '*.civ',  '.civ files '; ...
2523        '*.png','.png image files'; ...
2524        '*.jpg',' jpeg image files'; ...
2525        '*.tif','.tif image files'; ...
2526        '*.avi;*.AVI','.avi movie files'; ...
2527        '*.nc','.netcdf files'; ...
2528        '*.*',  'All Files (*.*)'};
2529    [FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file of the second series',oldfile);
2530    fileinput=[PathName FileName];%complete file name
2531    sizf=size(fileinput);
2532    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
2533    [path,name,ext]=fileparts(fileinput);
2534    [path1]=fileparts(filebase);
2535    if isunix
2536        [status,path]=system(['readlink ' path]);
2537        [status,path1]=system(['readlink ' path1]);% look for the true path in case of symbolic paths
2538    end
2539    if ~strcmp(path1,path)
2540        msgbox_uvmat('ERROR','The second image series must be in the same directory as the first one')
2541        return
2542     end
2543%     set(handles.RootName_1,'String',name);
2544    [RootPath,RootFile,field_count,str2,str_a,str_b,xx,nom_type,subdir]=name2display(name);
2545    set(handles.RootName_1,'String',RootFile);
2546    browse=get(handles.RootName,'UserData');
2547    browse.nom_type_ima_1=nom_type;
2548    set(handles.RootName,'UserData',browse)
2549   
2550    %check image extension
2551    if ~strcmp(ext,get(handles.ImaExt,'String'))
2552        msgbox_uvmat('ERROR','The second image series must have the same extension name as the first one')
2553        return
2554    end
2555   
2556    %% check coincidence of image sizes
2557%     ref_i=get(handles.ref_i,'string');
2558%     ref_j=get(handles.ref_j,'string');
2559%     [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]);
2560%     A=imread(filecell.ima1.checkciv1{1});
2561%     A_1=imread(fileinput);
2562%     npxy=size(A);
2563%     npxy_1=size(A_1);
2564%     if ~isequal(size(A),size(A_1))
2565%         msgbox_uvmat('ERROR','The two input image series do not have the same size')
2566%         return
2567%     end
2568else
2569    set(handles.ListPairMode,'Visible','on')
2570    set(handles.RootName_1,'Visible','Off');
2571    set(handles.sub_txt,'Visible','off')
2572    set(handles.RootName_1,'String',[]);
2573    mode_store=get(handles.ListCompareMode,'UserData');
2574    set(handles.ListPairMode,'Value',1)
2575    set(handles.ListPairMode,'String',mode_store)
2576%     set(handles.test_stereo1,'Value',0)
2577    set(handles.CheckStereo,'Value',0)
2578    set(handles.ListPairMode,'Value',1) % mode 'civX' selected by default
2579end
2580if test==3 && get(handles.CheckPatch1,'Value')
2581    set(handles.CheckStereo,'Visible','on')
2582else
2583    set(handles.CheckStereo,'Visible','off')
2584end
2585if test==3 && get(handles.CheckPatch2,'Value')
2586    set(handles.CheckStereo,'Visible','on')
2587else
2588    set(handles.CheckStereo,'Visible','off')
2589end
2590ListPairMode_Callback(hObject, eventdata, handles)
2591
2592
2593%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2594% Callbacks in the uipanel Pair Indices
2595%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2596%------------------------------------------------------------------------
2597% --- Executes on button press in ListPairMode.
2598function ListPairMode_Callback(hObject, eventdata, handles)
2599%------------------------------------------------------------------------
2600compare_list=get(handles.ListCompareMode,'String');
2601val=get(handles.ListCompareMode,'Value');
2602compare=compare_list{val};
2603if strcmp(compare,'displacement')
2604    mode='displacement';
2605else
2606    mode_list=get(handles.ListPairMode,'String');
2607    if ischar(mode_list)
2608        mode_list={mode_list};
2609    end
2610    mode_value=get(handles.ListPairMode,'Value');
2611    mode=mode_list{mode_value};
2612end
2613displ_num=[];%default
2614ref_i=str2double(get(handles.ref_i,'String'));
2615% last_i=str2num(get(handles.last_i,'String'));
2616time=get(handles.ImaDoc,'UserData'); %get the set of times
2617siztime=size(time);
2618nbfield=siztime(1);
2619nbfield2=siztime(2);
2620indchosen=1;  %%first pair selected by default
2621%displ_num used to define the indices of the civ pairs
2622% in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices
2623% are relative to the reference indices ref_i and ref_j respectively.
2624if isequal(mode,'pair j1-j2')%| isequal(mode,'st_pair j1-j2')
2625    dt=1;
2626    displ='';
2627    index=0;
2628    numlist_a=[];
2629    numlist_B=[];
2630    %get all the time intervals in bursts
2631    displ_dt=1;%default
2632    nbfield2=min(nbfield2,10);%limitate the number of pairs to 10x10
2633    for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'pair j1-j2' mode
2634        for numod_b=(numod_a+1):nbfield2
2635            index=index+1;
2636            numlist_a(index)=numod_a;
2637            numlist_b(index)=numod_b;
2638            if ~isempty(time)
2639                dt(numod_a,numod_b)=time(ref_i,numod_b)-time(ref_i,numod_a);%first time interval dt
2640                displ_dt(index)=dt(numod_a,numod_b);
2641            else
2642                displ_dt(index)=1;
2643            end
2644        end
2645    end
2646    [dtsort,indsort]=sort(displ_dt);
2647    if ~isempty(numlist_a)
2648        displ_num(1,:)=numlist_a(indsort);
2649        displ_num(2,:)=numlist_b(indsort);
2650    end
2651    displ_num(3,:)=0;
2652    displ_num(4,:)=0;
2653    set(handles.jtext,'Visible','Off')
2654    set(handles.first_j,'Visible','Off')
2655    set(handles.last_j,'Visible','Off')
2656    set(handles.incr_j,'Visible','Off')
2657    set(handles.nb_field2,'Visible','Off')
2658    set(handles.ref_j,'Visible','Off')
2659elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)')
2660    index=1:200;
2661    displ_num(1,index)=-floor(index/2);
2662    displ_num(2,index)=ceil(index/2);
2663    displ_num(3:4,index)=zeros(2,200);
2664%     for index=1:min(nbfield2-1,200)
2665%         displ_num(1,index)=-floor(index/2);
2666%         displ_num(2,index)=ceil(index/2);
2667%         displ_num(3,index)=0;
2668%         displ_num(4,index)=0;
2669%     end
2670    set(handles.jtext,'Visible','On')
2671    set(handles.first_j,'Visible','On')
2672    set(handles.last_j,'Visible','On')
2673    set(handles.incr_j,'Visible','On')
2674    set(handles.nb_field2,'Visible','On')
2675    set(handles.ref_j,'Visible','On')
2676    if nbfield > 1
2677        set(handles.itext,'Visible','On')
2678        set(handles.first_i,'Visible','On')
2679        set(handles.last_i,'Visible','On')
2680        set(handles.incr_i,'Visible','On')
2681        set(handles.nb_field,'Visible','On')
2682        set(handles.ref_i,'Visible','On')
2683    else
2684        set(handles.itext,'Visible','Off')
2685        set(handles.first_i,'Visible','Off')
2686        set(handles.last_i,'Visible','Off')
2687        set(handles.incr_i,'Visible','Off')
2688        set(handles.nb_field,'Visible','Off')
2689        set(handles.ref_i,'Visible','Off')
2690    end
2691elseif isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)')
2692    index=1:200;
2693    displ_num(1:2,index)=zeros(2,200);
2694    displ_num(3,index)=-floor(index/2);
2695    displ_num(4,index)=ceil(index/2);
2696%     for index=1:200%min(nbfield-1,200)
2697%         displ_num(1,index)=0;
2698%         displ_num(2,index)=0;
2699%         displ_num(3,index)=-floor(index/2);
2700%         displ_num(4,index)=ceil(index/2);
2701%     end
2702    set(handles.itext,'Visible','On')
2703    set(handles.first_i,'Visible','On')
2704    set(handles.last_i,'Visible','On')
2705    set(handles.incr_i,'Visible','On')
2706    set(handles.nb_field,'Visible','On')
2707    set(handles.ref_i,'Visible','On')
2708    if nbfield2 > 1
2709        set(handles.jtext,'Visible','On')
2710        set(handles.first_j,'Visible','On')
2711        set(handles.last_j,'Visible','On')
2712        set(handles.incr_j,'Visible','On')
2713        set(handles.nb_field2,'Visible','On')
2714        set(handles.ref_j,'Visible','On')
2715    else
2716        set(handles.jtext,'Visible','Off')
2717        set(handles.first_j,'Visible','Off')
2718        set(handles.last_j,'Visible','Off')
2719        set(handles.incr_j,'Visible','Off')
2720        set(handles.nb_field2,'Visible','Off')
2721        set(handles.ref_j,'Visible','Off')
2722    end
2723elseif isequal(mode,'displacement')%the pairs have the same indices
2724    displ_num(1,1)=0;
2725    displ_num(2,1)=0;
2726    displ_num(3,1)=0;
2727    displ_num(4,1)=0;
2728    if nbfield > 1 || nbfield==0
2729        set(handles.itext,'Visible','On')
2730        set(handles.first_i,'Visible','On')
2731        set(handles.last_i,'Visible','On')
2732        set(handles.incr_i,'Visible','On')
2733        set(handles.nb_field,'Visible','On')
2734        set(handles.ref_i,'Visible','On')
2735    else
2736        set(handles.itext,'Visible','Off')
2737        set(handles.first_i,'Visible','Off')
2738        set(handles.last_i,'Visible','Off')
2739        set(handles.incr_i,'Visible','Off')
2740        set(handles.nb_field,'Visible','Off')
2741        set(handles.ref_i,'Visible','Off')
2742    end
2743    if nbfield2 > 1
2744        set(handles.jtext,'Visible','On')
2745        set(handles.first_j,'Visible','On')
2746        set(handles.last_j,'Visible','On')
2747        set(handles.incr_j,'Visible','On')
2748        set(handles.nb_field2,'Visible','On')
2749        set(handles.ref_j,'Visible','On')
2750    else
2751        set(handles.jtext,'Visible','Off')
2752        set(handles.first_j,'Visible','Off')
2753        set(handles.last_j,'Visible','Off')
2754        set(handles.incr_j,'Visible','Off')
2755        set(handles.nb_field2,'Visible','Off')
2756        set(handles.ref_j,'Visible','Off')
2757    end
2758end
2759set(handles.ListPairCiv1,'UserData',displ_num);
2760find_netcpair_civ1( handles)
2761find_netcpair_civ2(handles)
2762
2763%------------------------------------------------------------------------
2764% --- Executes on selection change in ListPairCiv1.
2765function ListPairCiv1_Callback(hObject, eventdata, handles)
2766%------------------------------------------------------------------------
2767%reproduce by default the chosen pair in the checkciv2 menu
2768list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
2769index_pair=get(handles.ListPairCiv1,'Value');
2770displ_num=get(handles.ListPairCiv1,'UserData');
2771% num_a=displ_num(1,index_pair);
2772% num_b=displ_num(2,index_pair);
2773list_pair2=get(handles.ListPairCiv2,'String');%get the menu of image pairs
2774if index_pair<=length(list_pair2)
2775    set(handles.ListPairCiv2,'Value',index_pair);
2776end
2777
2778%update first_i and last_i according to the chosen image pairs
2779mode_list=get(handles.ListPairMode,'String');
2780mode_value=get(handles.ListPairMode,'Value');
2781mode=mode_list{mode_value};
2782if isequal(mode,'series(Di)')
2783    first_i=str2double(get(handles.first_i,'String'));
2784    last_i=str2double(get(handles.last_i,'String'));
2785    incr_i=str2double(get(handles.incr_i,'String'));
2786    num1=first_i:incr_i:last_i;
2787    lastfield=str2double(get(handles.nb_field,'String'));
2788    if ~isnan(lastfield)
2789        test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ...
2790            (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield);
2791        num1=num1(test_find);
2792    end
2793    set(handles.first_i,'String',num2str(num1(1)));
2794    set(handles.last_i,'String',num2str(num1(end)));
2795elseif isequal(mode,'series(Dj)')
2796    first_j=str2double(get(handles.first_j,'String'));
2797    last_j=str2double(get(handles.last_j,'String'));
2798    incr_j=str2double(get(handles.incr_j,'String'));
2799    num_j=first_j:incr_j:last_j;
2800    lastfield2=str2double(get(handles.nb_field2,'String'));
2801    if ~isnan(lastfield2)
2802        test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
2803            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2);
2804        num1=num_j(test_find);
2805    end
2806    set(handles.first_j,'String',num2str(num1(1)));
2807    set(handles.last_j,'String',num2str(num1(end)));
2808end
2809
2810%------------------------------------------------------------------------
2811% --- Executes on selection change in ListPairCiv2.
2812function ListPairCiv2_Callback(hObject, eventdata, handles)
2813%------------------------------------------------------------------------
2814index_pair=get(handles.ListPairCiv2,'Value');%get the selected position index in the menu
2815
2816%update first_i and last_i according to the chosen image pairs
2817mode_list=get(handles.ListPairMode,'String');
2818mode_value=get(handles.ListPairMode,'Value');
2819mode=mode_list{mode_value};
2820if isequal(mode,'series(Di)')
2821    first_i=str2double(get(handles.first_i,'String'));
2822    last_i=str2double(get(handles.last_i,'String'));
2823    incr_i=str2double(get(handles.incr_i,'String'));
2824    num1=first_i:incr_i:last_i;
2825    lastfield=str2double(get(handles.nb_field,'String'));
2826    if ~isnan(lastfield)
2827        test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ...
2828            (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield);
2829        num1=num1(test_find);
2830    end
2831    set(handles.first_i,'String',num2str(num1(1)));
2832    set(handles.last_i,'String',num2str(num1(end)));
2833elseif isequal(mode,'series(Dj)')
2834    first_j=str2double(get(handles.first_j,'String'));
2835    last_j=str2double(get(handles.last_j,'String'));
2836    incr_j=str2double(get(handles.incr_j,'String'));
2837    num_j=first_j:incr_j:last_j;
2838    lastfield2=str2double(get(handles.nb_field2,'String'));
2839    if ~isnan(lastfield2)
2840        test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
2841            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2);
2842        num1=num_j(test_find);
2843    end
2844    set(handles.first_j,'String',num2str(num1(1)));
2845    set(handles.last_j,'String',num2str(num1(end)));
2846end
2847
2848%------------------------------------------------------------------------
2849function ref_i_Callback(hObject, eventdata, handles)
2850%------------------------------------------------------------------------
2851mode_list=get(handles.ListPairMode,'String');
2852mode_value=get(handles.ListPairMode,'Value');
2853mode=mode_list{mode_value};
2854find_netcpair_civ1(handles);% update the menu of pairs depending on the available netcdf files
2855if isequal(mode,'series(Di)') || ...% we do patch2 only
2856        (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
2857    find_netcpair_civ2( handles);
2858end
2859
2860%------------------------------------------------------------------------
2861function ref_j_Callback(hObject, eventdata, handles)
2862%------------------------------------------------------------------------
2863mode_list=get(handles.ListPairMode,'String');
2864mode_value=get(handles.ListPairMode,'Value');
2865mode=mode_list{mode_value};
2866if isequal(get(handles.CheckCiv1,'Value'),0)|| isequal(mode,'series(Dj)')
2867    find_netcpair_civ1(handles);% update the menu of pairs depending on the available netcdf files
2868end
2869if isequal(mode,'series(Dj)') || ...
2870        (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
2871    find_netcpair_civ2(handles);
2872end
2873%
2874%------------------------------------------------------------------------
2875% determine the menu for checkciv1 pairs depending on existing netcdf file at the middle of
2876% the field series set by first_i, incr, last_i
2877function find_netcpair_civ1(handles)
2878%------------------------------------------------------------------------
2879set(gcf,'Pointer','watch')
2880%nomenclature types
2881filebase=get(handles.RootName,'String');
2882[filepath,Nme,ext_dir]=fileparts(filebase);
2883browse=get(handles.RootName,'UserData');
2884compare_list=get(handles.ListCompareMode,'String');
2885val=get(handles.ListCompareMode,'Value');
2886compare=compare_list{val};
2887if strcmp(compare,'displacement')
2888    mode='displacement';
2889else
2890    mode_list=get(handles.ListPairMode,'String');
2891    mode_value=get(handles.ListPairMode,'Value');
2892    if isempty(mode_list)
2893        return
2894    end
2895    mode=mode_list{mode_value};
2896end
2897
2898% nomenclature type of the .nc files
2899nom_type_ima=[];%default
2900if isfield(browse,'nom_type_ima')
2901    nom_type_ima=browse.nom_type_ima;
2902end
2903
2904%determine nom_type_nc:
2905nom_type_nc=[];%default
2906if isfield(browse,'nom_type_nc')
2907    nom_type_nc=browse.nom_type_nc;
2908end
2909if isempty(nom_type_nc)
2910    [nom_type_nc]=nomtype2pair(nom_type_ima,isequal(mode,'series(Di)'),isequal(mode,'series(Dj)'));
2911end
2912browse.nom_type_nc=nom_type_nc;
2913set(handles.RootName,'UserData',browse)
2914
2915%reads .nc subdirectoy and image numbers from the interface
2916subdir_civ1=get(handles.txt_SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf data
2917ref_i=str2double(get(handles.ref_i,'String'));
2918if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
2919    ref_j=0;
2920else
2921    ref_j=str2double(get(handles.ref_j,'String'));
2922end
2923time=get(handles.ImaDoc,'UserData');%get the set of times
2924if isempty(time)
2925    time=[0 1];
2926end
2927dt_unit=1000;%default
2928displ_num=get(handles.ListPairCiv1,'UserData');
2929
2930%eliminate the first pairs inconsistent with the position
2931if isempty(displ_num)
2932    nbpair=0;
2933else
2934    nbpair=length(displ_num(1,:));%nbre of displayed pairs
2935    if  isequal(mode,'series(Di)')  %| isequal(mode,'st_series(Di)')
2936        nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index
2937    elseif  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
2938        nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index
2939    end
2940end
2941nbpair=min(200,nbpair);%limit the number of displayed pairs to 200
2942
2943%look for existing processed pairs involving the field at the middle of the series if checkciv1 will not
2944% be performed, while the result is needed for next steps.
2945displ_pair={''};
2946select=ones(size(1:nbpair));%flag for displayed pairs =1 for display
2947testpair=0;
2948
2949%% case with no Civ1 operation, netcdf files need to exist for reading
2950if ~get(handles.CheckCiv1,'Value') %
2951    if ~exist(fullfile(filepath,subdir_civ1,ext_dir),'dir')
2952        msgbox_uvmat('ERROR',['no civ1 file available: subdirectory ' subdir_civ1 ' does not exist']);
2953        set(handles.ListPairCiv1,'String',{});
2954        return
2955    end
2956    for ipair=1:nbpair
2957        filename=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,...
2958            ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1);
2959        select(ipair)=exist(filename,'file')==2;% put flag to 0 if the file does not exist
2960    end   
2961    % case of no displayed pair
2962    if isequal(select,zeros(size(1:nbpair)))
2963        if isfield(browse,'incr_pair') && ~isequal(browse.incr_pair,[0 0])
2964            num_i1=ref_i-floor(browse.incr_pair(1)/2);
2965            num_i2=ref_i+ceil(browse.incr_pair(1)/2);
2966            num_j1=ref_j-floor(browse.incr_pair(2)/2);
2967            num_j2=ref_j+ceil(browse.incr_pair(2)/2);
2968            filename=name_generator(filebase,num_i1,num_j1,'.nc',nom_type_nc,1,num_i2,num_j2,subdir_civ1);
2969            select(1)=exist(filename,'file')==2;
2970            testpair=1;
2971        else
2972            if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
2973                msgbox_uvmat('ERROR',['no civ1 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ1]);
2974            else
2975                msgbox_uvmat('ERROR',['no civ1 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ1]);
2976            end
2977            set(handles.ListPairCiv1,'String',{''});
2978            %COMPLETER CAS STEREO
2979            return
2980        end
2981    end
2982end
2983
2984%% determine the menu display in .ListPairCiv1
2985% the menu depends on the mode defined in ListPairMode_callback through the array displ_num:
2986% displ_num(1,:)=indices j1
2987% displ_num(2,:)=indices j2
2988% displ_num(3,:)=indices i1
2989% displ_num(4,:)=indices i2
2990% in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices
2991% are relative to the reference indices ref_i and ref_j respectively.
2992if isequal(mode,'series(Di)')
2993    if testpair
2994        displ_pair{1}=['Di= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
2995    else
2996        for ipair=1:nbpair
2997            if select(ipair)
2998                displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
2999                if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
3000                    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
3001                    displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
3002                end
3003            else
3004                displ_pair{ipair}='...'; %pair not displayed in the menu
3005            end
3006        end
3007    end
3008elseif isequal(mode,'series(Dj)')
3009    if testpair
3010        displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
3011    else
3012        for ipair=1:nbpair
3013            if select(ipair)
3014                displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
3015                if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
3016                    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
3017                    displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
3018                end
3019            else
3020                displ_pair{ipair}='...'; %pair not displayed in the menu
3021            end
3022        end
3023    end
3024elseif isequal(mode,'pair j1-j2')%case of pairs
3025    for ipair=1:nbpair
3026        if select(ipair)
3027            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
3028            displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ...
3029                ' :dt= ' num2str(dt*1000)];
3030        else
3031            displ_pair{ipair}='...'; %pair not displayed in the menu
3032        end
3033    end
3034elseif isequal(mode,'displacement')
3035    displ_pair={'Di=Dj=0'};
3036end
3037set(handles.ListPairCiv1,'String',displ_pair');
3038
3039%% determine the default selection in the pair menu
3040ichoice=find(select,1);% index of selected pair
3041if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
3042initial=get(handles.ListPairCiv1,'Value');%initial choice of pair
3043if initial>nbpair || (numel(select)>=initial && ~isequal(select(initial),1))
3044    set(handles.ListPairCiv1,'Value',ichoice);% first valid pair proposed by default in the menu
3045end
3046initial=get(handles.ListPairCiv2,'Value');
3047if initial>length(displ_pair')%|~isequal(select(initial),1)
3048    if ichoice <= length(displ_pair')
3049        set(handles.ListPairCiv2,'Value',ichoice);% same pair proposed by default for civ2
3050    else
3051        set(handles.ListPairCiv2,'Value',1);% same pair proposed by default for civ2
3052    end
3053end
3054set(handles.ListPairCiv2,'String',displ_pair');
3055set(gcf,'Pointer','arrow')
3056
3057%------------------------------------------------------------------------
3058% determine the menu for checkciv2 pairs depending on the existing netcdf file at the
3059%middle of the series set by first_i, incr, last_i
3060function find_netcpair_civ2(handles)
3061%------------------------------------------------------------------------
3062set(gcf,'Pointer','watch')
3063%nomenclature types
3064filebase=get(handles.RootName,'String');
3065[filepath,Nme,ext_dir]=fileparts(filebase);
3066browse=get(handles.RootName,'UserData');
3067compare_list=get(handles.ListCompareMode,'String');
3068val=get(handles.ListCompareMode,'Value');
3069compare=compare_list{val};
3070if strcmp(compare,'displacement')
3071    mode='displacement';
3072else
3073    mode_list=get(handles.ListPairMode,'String');
3074    if isempty(mode_list)
3075        msgbox_uvmat('ERROR','please enter an input image or netcdf file')
3076        return
3077    end
3078    mode_value=get(handles.ListPairMode,'Value');
3079    mode=mode_list{mode_value};
3080end
3081
3082% nomenclature type of the .nc files
3083nom_type_ima='ima_num';%default
3084if isfield(browse,'nom_type_ima')
3085    nom_type_ima=browse.nom_type_ima;
3086end
3087nom_type_nc='_i1-i2';%default
3088if isfield(browse,'nom_type_nc')
3089    nom_type_nc=browse.nom_type_nc;
3090end
3091if isequal(nom_type_ima,'png_old') || isequal(nom_type_ima,'netc_old')|| isequal(nom_type_ima,'raw_SMD')|| isequal(nom_type_nc,'netc_old')
3092    nom_type_nc='netc_old';%nom_type for the netcdf files
3093elseif isequal(nom_type_ima,'none')||isequal(nom_type_nc,'none')
3094    nom_type_nc='none';
3095elseif isequal(nom_type_ima,'avi')||isequal(nom_type_ima,'_i')||isequal(nom_type_ima,'ima_num')||isequal(nom_type_nc,'_i1-i2')
3096    nom_type_nc='_i1-i2';
3097else
3098    if  isequal(mode,'series(Di)')%|isequal(mode,'st_series(Di)')
3099        nom_type_nc='_i1-i2_j'; % PIV in volume
3100    else
3101        nom_type_nc='_i_j1-j2';
3102    end
3103end
3104browse.nom_type_nc=nom_type_nc;
3105set(handles.RootName,'UserData',browse)
3106
3107%reads .nc subdirectory and image numbers from the interface
3108subdir_civ1=get(handles.txt_SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf data
3109subdir_civ2=get(handles.txt_SubdirCiv2,'String');%subdirectory subdir_civ2 for the netcdf data
3110ref_i=str2double(get(handles.ref_i,'String'));
3111if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
3112    ref_j=0;
3113else
3114    ref_j=str2double(get(handles.ref_j,'String'));
3115end
3116time=get(handles.ImaDoc,'UserData'); %get the set of times
3117if isempty(time)
3118    time=[0 1];%default
3119end
3120displ_num=get(handles.ListPairCiv1,'UserData');
3121
3122%eliminate the first pairs inconsistent with the position
3123if isempty(displ_num)
3124    nbpair=0;
3125else
3126    nbpair=length(displ_num(1,:));%nbre of displayed pairs
3127    if  isequal(mode,'series(Di)')% | isequal(mode,'st_series(Di)')
3128        nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index
3129    elseif  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
3130        nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index
3131    end
3132end
3133nbpair=min(200,nbpair);%limit the number of displayed pairs to 200
3134
3135%% look for existing processed pairs at the reference indices if Civ1 will not
3136% be performed, while the result is needed for next steps.
3137displ_pair={''}; %default
3138select=ones(size(1:nbpair));%default =1 for numbers of displayed pairs
3139if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
3140    if ~exist(fullfile(filepath,subdir_civ2,ext_dir),'dir')
3141        errordlg(['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist'])
3142        set(handles.ListPairCiv2,'Value',1);
3143        set(handles.ListPairCiv2,'String',{''});
3144        return
3145    end
3146    for ipair=1:nbpair
3147        filename=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,...
3148            ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1);
3149        select(ipair)=exist(filename,'file')==2;
3150    end
3151    if  isequal(select,zeros(size(1:nbpair)))
3152        if isfield(browse,'incr_pair')
3153            num_i1=ref_i-floor(browse.incr_pair(1)/2);
3154            num_i2=ref_i+floor((browse.incr_pair(1)+1)/2);
3155            num_j1=ref_j-floor(browse.incr_pair(2)/2);
3156            num_j2=ref_j+floor((browse.incr_pair(2)+1)/2);
3157            filename=name_generator(filebase,num_i1,num_j1,'.nc',nom_type_nc,1,num_i2,num_j2,subdir_civ2);
3158            select(1)=exist(filename,'file')==2;
3159        else
3160            if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
3161                errordlg(['no civ2 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ2])
3162            else
3163                errordlg(['no civ2 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ2])
3164            end
3165            set(handles.ListPairCiv2,'Value',1);
3166            set(handles.ListPairCiv2,'String',{''});
3167            return
3168        end
3169    end
3170end
3171if isequal(mode,'series(Di)')
3172    for ipair=1:nbpair
3173        if select(ipair)
3174            displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
3175            if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
3176                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
3177                displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
3178            end
3179        else
3180            displ_pair{ipair}='...'; %pair not displayed in the menu
3181        end
3182    end
3183elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)') % series on the j index
3184    for ipair=1:nbpair
3185        if select(ipair)
3186            displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
3187            if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
3188                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
3189                displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
3190            end
3191        else
3192            displ_pair{ipair}='...'; %pair not displayed in the menu
3193        end
3194    end
3195elseif isequal(mode,'pair j1-j2')% | isequal(mode,'st_pair j1-j2') %case of pairs
3196    for ipair=1:nbpair
3197        if select(ipair)
3198            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
3199            displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ...
3200                ' :dt= ' num2str(dt*1000)];
3201        else
3202            displ_pair{ipair}='...'; %pair not displayed in the menu
3203        end
3204    end
3205elseif isequal(mode,'displacement')
3206    displ_pair={'Di=Dj=0'};
3207end
3208val=get(handles.ListPairCiv2,'Value');
3209ichoice=find(select,1);
3210if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
3211if get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0
3212    val=ichoice;% first valid pair proposed by default in the menu
3213end
3214if val>length(displ_pair')
3215    set(handles.ListPairCiv2,'Value',1);% first valid pair proposed by default in the menu
3216else
3217    set(handles.ListPairCiv2,'Value',val);
3218end
3219set(handles.ListPairCiv2,'String',displ_pair');
3220set(gcf,'Pointer','arrow')
3221
3222%-------------------------------------------------------------------
3223% ---
3224function closeview_field(gcbo,eventdata)
3225hview_field=findobj(allchild(0),'tag','view_field');% look for view_field   
3226    if ~isempty(hview_field)
3227        delete(hview_field)
3228    end
3229   
3230   
3231%------------------------------------------------------------------------   
3232% call 'view_field.fig' to display the  field selected in the list of 'status'
3233function open_view_field(hObject, eventdata)
3234%------------------------------------------------------------------------
3235list=get(hObject,'String');
3236index=get(hObject,'Value');
3237rootroot=get(hObject,'UserData');
3238filename=list{index};
3239ind_dot=strfind(filename,'...');
3240filename=filename(1:ind_dot-1);
3241filename=fullfile(rootroot,filename);
3242delete(get(hObject,'parent'))%delete the display figure to stop the check process
3243if exist(filename,'file')%visualise the vel field if it exists
3244    uvmat(filename)
3245    set(gcbo,'Value',1)
3246end
3247
3248%------------------------------------------------------------------------   
3249% launched by pressing OK on the status figure
3250function close_GUI(hObject, eventdata)
3251%------------------------------------------------------------------------
3252    delete(gcbf)
3253   
3254%------------------------------------------------------------------------   
3255% launched by deleting the status figure
3256function stop_status(hObject, eventdata)
3257%------------------------------------------------------------------------
3258hciv=findobj(allchild(0),'tag','civ');
3259hhciv=guidata(hciv);
3260set(hhciv.status,'value',0) %reset the status uicontrol in the GUI civ
3261set(hhciv.status,'BackgroundColor',[0 1 0])
3262
3263
3264%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3265% Callbacks in the uipanel Reference Indices
3266%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3267%------------------------------------------------------------------------
3268function first_i_Callback(hObject, eventdata, handles)
3269%------------------------------------------------------------------------
3270first_i=str2double(get(handles.first_i,'String'));
3271set(handles.ref_i,'String', num2str(first_i))% reference index for pair dt = first index
3272ref_i_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
3273
3274%------------------------------------------------------------------------
3275function first_j_Callback(hObject, eventdata, handles)
3276%------------------------------------------------------------------------
3277first_j=str2num(get(handles.first_j,'String'));
3278set(handles.ref_j,'String', num2str(first_j))% reference index for pair dt = first index
3279ref_j_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
3280
3281%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3282% Callbacks in the uipanel Civ1
3283%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3284%------------------------------------------------------------------------
3285% --- Executes on button press in SearchRange: determine the search range num_Searchx,num_Searchy
3286function SearchRange_Callback(hObject, eventdata, handles)
3287%------------------------------------------------------------------------
3288%determine pair numbers
3289if strcmp(get(handles.umin,'Visible'),'off')
3290    set(handles.u_title,'Visible','on')
3291    set(handles.v_title,'Visible','on')
3292    set(handles.umin,'Visible','on')
3293    set(handles.umax,'Visible','on')
3294    set(handles.vmin,'Visible','on')
3295    set(handles.vmax,'Visible','on')
3296    set(handles.CoordUnit,'Visible','on')
3297    set(handles.TimeUnit,'Visible','on')
3298    set(handles.slash_title,'Visible','on')
3299    set(handles.min_title,'Visible','on')
3300    set(handles.max_title,'Visible','on')
3301    set(handles.unit_title,'Visible','on')
3302else
3303    get_search_range(hObject, eventdata, handles)
3304end
3305
3306%------------------------------------------------------------------------
3307% ---  determine the search range num_Searchx,num_Searchy and shift
3308function get_search_range(hObject, eventdata, handles)
3309umin=str2double(get(handles.umin,'String'));
3310umax=str2double(get(handles.umax,'String'));
3311vmin=str2double(get(handles.umin,'String'));
3312vmax=str2double(get(handles.vmax,'String'));
3313%switch min_title and max_title in case of error
3314if umax<=umin
3315    umin_old=umin;
3316    umin=umax;
3317    umax=umin_old;
3318    set(handles.umin,'String', num2str(umin))
3319    set(handles.umax,'String', num2str(umax))
3320end
3321if vmax<=vmin
3322    vmin_old=vmin;
3323    vmin=vmax;
3324    vmax=vmin_old;
3325    set(handles.vmin,'String', num2str(vmin))
3326    set(handles.vmax,'String', num2str(vmax))
3327end   
3328if ~(isnan(umin)||isnan(umax)||isnan(vmin)||isnan(vmax))
3329    list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
3330    index=get(handles.ListPairCiv1,'Value');
3331    displ_num=get(handles.ListPairCiv1,'UserData');
3332    time=get(handles.ImaDoc,'UserData'); %get the set of times
3333    pxcm_xy=get(handles.SearchRange,'UserData');
3334    pxcmx=pxcm_xy(1);
3335    pxcmy=pxcm_xy(2);
3336    mode_list=get(handles.ListPairMode,'String');
3337    mode_value=get(handles.ListPairMode,'Value');
3338    mode=mode_list{mode_value};
3339    if isequal (mode, 'series(Di)' )
3340        ref_i=str2double(get(handles.ref_i,'String'));
3341        num1=ref_i-floor(index/2);%  first image numbers
3342        num2=ref_i+ceil(index/2);
3343        num_a=1;
3344        num_b=1;
3345    elseif isequal (mode, 'series(Dj)')
3346        num1=1;
3347        num2=1;
3348        ref_j=str2double(get(handles.ref_j,'String'));
3349        num_a=ref_j-floor(index/2);%  first image numbers
3350        num_b=ref_j+ceil(index/2);
3351    elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)
3352        ref_i=str2double(get(handles.ref_i,'String'));
3353        num1=ref_i;
3354        num2=ref_i;
3355        num_a=displ_num(1,index);
3356        num_b=displ_num(2,index);
3357    end
3358    dt=time(num2,num_b)-time(num1,num_a);
3359    ibx=str2double(get(handles.num_Bx,'String'));
3360    iby=str2double(get(handles.num_By,'String'));
3361    umin=dt*pxcmx*umin;
3362    umax=dt*pxcmx*umax;
3363    vmin=dt*pxcmy*vmin;
3364    vmax=dt*pxcmy*vmax;
3365    shiftx=round((umin+umax)/2);
3366    shifty=round((vmin+vmax)/2);
3367    isx=(umax+2-shiftx)*2+ibx;
3368    isx=2*ceil(isx/2)+1;
3369    isy=(vmax+2-shifty)*2+iby;
3370    isy=2*ceil(isy/2)+1;
3371    set(handles.num_Shiftx,'String',num2str(shiftx));
3372    set(handles.num_Shifty,'String',num2str(shifty));
3373    set(handles.num_Searchx,'String',num2str(isx));
3374    set(handles.num_Searchy,'String',num2str(isy));
3375end
3376
3377%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3378% Callbacks in the uipanel Fix1
3379%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3380%------------------------------------------------------------------------
3381% --- Executes on button press in CheckMask.
3382function get_mask_fix1_Callback(hObject, eventdata, handles)
3383%------------------------------------------------------------------------
3384maskval=get(handles.CheckMask,'Value');
3385if isequal(maskval,0)
3386    set(handles.txt_Mask,'String','')
3387else
3388    mask_displ='no mask'; %default
3389    filebase=get(handles.RootName,'String');
3390    [nbslice, flag_mask]=get_mask(filebase,handles);
3391    if isequal(flag_mask,1)
3392        mask_displ=[num2str(nbslice) 'mask'];
3393    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3394        filebase_a=get(handles.RootName_1,'String');
3395        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3396        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3397            mask_displ='no mask';
3398        end
3399    end
3400    if isequal(mask_displ,'no mask')
3401        [FileName, PathName, filterindex] = uigetfile( ...
3402            {'*.png', ' (*.png)';
3403            '*.png',  '.png files '; ...
3404            '*.*', 'All Files (*.*)'}, ...
3405            'Pick a mask file *.png',filebase);
3406        mask_displ=fullfile(PathName,FileName);
3407        if ~exist(mask_displ,'file')
3408            mask_displ='no mask';
3409        end
3410    end
3411    if isequal(mask_displ,'no mask')
3412        set(handles.CheckMask,'Value',0)
3413        set(handles.CheckMask,'Value',0)
3414        set(handles.CheckMask,'Value',0)
3415    else
3416        %set(handles.CheckMask,'Value',1)
3417        set(handles.CheckMask,'Value',1)
3418    end
3419    set(handles.txt_Mask,'String',mask_displ)
3420    set(handles.txt_Mask,'String',mask_displ)
3421    set(handles.txt_Mask,'String',mask_displ)
3422end
3423
3424%------------------------------------------------------------------------
3425% --- Executes on button press in CheckMask: select box for mask option
3426function get_mask_civ2_Callback(hObject, eventdata, handles)
3427%------------------------------------------------------------------------
3428maskval=get(handles.CheckMask,'Value');
3429if isequal(maskval,0)
3430    set(handles.txt_Mask,'String','')
3431else
3432    mask_displ='no mask'; %default
3433    filebase=get(handles.RootName,'String');
3434    [nbslice, flag_mask]=get_mask(filebase,handles);
3435    if isequal(flag_mask,1)
3436        mask_displ=[num2str(nbslice) 'mask'];
3437    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3438        filebase_a=get(handles.RootName_1,'String');
3439        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3440        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3441            mask_displ='no mask';
3442        end
3443    end
3444    if isequal(mask_displ,'no mask')
3445        [FileName, PathName, filterindex] = uigetfile( ...
3446            {'*.png', ' (*.png)';
3447            '*.png',  '.png files '; ...
3448            '*.*', 'All Files (*.*)'}, ...
3449            'Pick a mask file *.png',filebase);
3450        mask_displ=fullfile(PathName,FileName);
3451        if ~exist(mask_displ,'file')
3452            mask_displ='no mask';
3453        end
3454    end
3455    if isequal(mask_displ,'no mask')
3456        set(handles.CheckMask,'Value',0)
3457        set(handles.CheckMask,'Value',0)
3458    else
3459        set(handles.CheckMask,'Value',1)
3460    end
3461    set(handles.txt_Mask,'String',mask_displ)
3462    set(handles.txt_Mask,'String',mask_displ)
3463end
3464
3465%------------------------------------------------------------------------
3466% --- Executes on button press in CheckMask.
3467function get_mask_fix2_Callback(hObject, eventdata, handles)
3468%------------------------------------------------------------------------
3469maskval=get(handles.CheckMask,'Value');
3470if isequal(maskval,0)
3471    set(handles.txt_Mask,'String','')
3472else
3473    mask_displ='no mask'; %default
3474    filebase=get(handles.RootName,'String');
3475    [nbslice, flag_mask]=get_mask(filebase,handles);
3476    if isequal(flag_mask,1)
3477        mask_displ=[num2str(nbslice) 'mask'];
3478    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3479        filebase_a=get(handles.RootName_1,'String');
3480        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3481        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3482            mask_displ='no mask';
3483        end
3484    end
3485    if isequal(mask_displ,'no mask')
3486        [FileName, PathName, filterindex] = uigetfile( ...
3487            {'*.png', ' (*.png)';
3488            '*.png',  '.png files '; ...
3489            '*.*', 'All Files (*.*)'}, ...
3490            'Pick a mask file *.png',filebase);
3491        mask_displ=fullfile(PathName,FileName);
3492        if ~exist(mask_displ,'file')
3493            mask_displ='no mask';
3494        end
3495    end
3496    if isequal(mask_displ,'no mask')
3497        set(handles.CheckMask,'Value',0)
3498    end
3499    set(handles.txt_Mask,'String',mask_displ)
3500end
3501
3502%------------------------------------------------------------------------
3503% --- function called to look for mask files
3504function [nbslice, flag_mask]=get_mask(filebase,handles)
3505%------------------------------------------------------------------------
3506%detect mask files, images with appropriate file base
3507%[filebase '_' xx 'mask'], xx=nbslice
3508%flag_mask=1 indicates detection
3509
3510flag_mask=0;%default
3511nbslice=1;
3512
3513% subdir=get(handles.txt_SubdirCiv1,'String');
3514[Path,Name]=fileparts(filebase);
3515if ~isdir(Path)
3516    msgbox_uvmat('ERROR','no path for input files')
3517    return
3518end
3519% currentdir=pwd;
3520% cd(Path);%move in the dir of the root name filebase
3521maskfiles=dir(fullfile(Path,[Name '_*mask_*.png']));%look for mask files
3522% cd(currentdir);%come back to the current working directory
3523if ~isempty(maskfiles)
3524    %     msgbox_uvmat('ERROR','no mask available, to create it use Tools/Make mask in the upper menu bar of uvmat')
3525    % else
3526    flag_mask=1;
3527    maskname=maskfiles(1).name;% take the first mask file in the list
3528    [Path2,Name,ext]=fileparts(maskname);
3529    Namedouble=double(Name);
3530    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3531    ind_mask=findstr('mask',Name);
3532    i=ind_mask-1;
3533    while val(i)==0 && i>0
3534        i=i-1;
3535    end
3536    nbslice=str2double(Name(i+1:ind_mask-1));
3537    if ~isnan(nbslice) && Name(i)=='_'
3538        flag_mask=1;
3539    else
3540        msgbox_uvmat('ERROR',['bad mask file ' Name ext ' found in ' Path2])
3541        return
3542        nbslice=1;
3543    end
3544end
3545
3546%------------------------------------------------------------------------
3547% --- function called to look for grid files
3548function [nbslice, flag_mask]=get_grid(filebase,handles)
3549%------------------------------------------------------------------------
3550flag_mask=0;%default
3551nbslice=1;
3552[Path,Name]=fileparts(filebase);
3553currentdir=pwd;
3554cd(Path);%move in the dir of the root name filebase
3555maskfiles=dir([Name '_*grid_*.grid']);%look for mask files
3556cd(currentdir);%come back to the current working directory
3557if ~isempty(maskfiles)
3558    flag_mask=1;
3559    maskname=maskfiles(1).name;% take the first mask file in the list
3560    [Path2,Name,ext]=fileparts(maskname);
3561    Namedouble=double(Name);
3562    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3563    ind_mask=findstr('grid',Name);
3564    i=ind_mask-1;
3565    while val(i)==0 && i>0
3566        i=i-1;
3567    end
3568    nbslice=str2double(Name(i+1:ind_mask-1));
3569    if ~isnan(nbslice) && Name(i)=='_'
3570        flag_mask=1;
3571    else
3572        msgbox_uvmat('ERROR',['bad grid file ' Name ext ' found in ' Path2])
3573        return
3574        nbslice=1;
3575    end
3576end
3577
3578%------------------------------------------------------------------------
3579% --- transform numbers to letters
3580function str=num2stra(num,nom_type)
3581%------------------------------------------------------------------------
3582if isempty(nom_type)
3583    str='';
3584elseif strcmp(nom_type(end),'a')
3585    str=char(96+num);
3586elseif strcmp(nom_type(end),'A')
3587    str=char(96+num);
3588elseif isempty(nom_type(2:end))%a single index
3589    str='';
3590else
3591    str=num2str(num);
3592end
3593
3594%------------------------------------------------------------------------
3595% --- Executes on button press in ListSubdirCiv1.
3596function ListSubdirCiv1_Callback(hObject, eventdata, handles)
3597%------------------------------------------------------------------------
3598list_subdir_civ1=get(handles.ListSubdirCiv1,'String');
3599val=get(handles.ListSubdirCiv1,'Value');
3600subdir=list_subdir_civ1{val};
3601if strcmp(subdir,'new...')
3602    if get(handles.CheckCiv1,'Value')
3603        subdir='CIV'; %default subdirectory
3604    else
3605        msgbox_uvmat('ERROR','select CheckCiv1 to perform a new Civ operation')
3606        return
3607    end   
3608end
3609set(handles.txt_SubdirCiv1,'String',subdir);
3610find_netcpair_civ1(handles)
3611
3612%------------------------------------------------------------------------
3613% --- Executes on button press in ListSubdirCiv2.
3614function ListSubdirCiv2_Callback(hObject, eventdata, handles)
3615%------------------------------------------------------------------------
3616list_subdir_civ2=get(handles.ListSubdirCiv2,'String');
3617val=get(handles.ListSubdirCiv2,'Value');
3618subdir=list_subdir_civ2{val};
3619if strcmp(subdir,'new...')
3620    if get(handles.CheckCiv2,'Value')
3621        subdir='CIV'; %default subdirectory
3622    else
3623        msgbox_uvmat('ERROR','select CheckCiv2 to perform a new Civ operation')
3624        return
3625    end
3626end
3627set(handles.txt_SubdirCiv2,'String',subdir);
3628
3629%------------------------------------------------------------------------
3630% --- Executes on button press in CheckGrid.
3631function CheckGrid_Callback(hObject, eventdata, handles)
3632%------------------------------------------------------------------------
3633value=get(hObject,'Value');
3634hparent=get(hObject,'parent');
3635hchildren=get(hparent,'children');
3636handle_txtbox=findobj(hchildren,'tag','txt_Grid');
3637handle_dx=findobj(hchildren,'tag','num_Dx');
3638handle_dy=findobj(hchildren,'tag','num_Dy');
3639handle_title_dx=findobj(hchildren,'tag','title_Dx');
3640handle_title_dy=findobj(hchildren,'tag','title_Dy');
3641testgrid=0;
3642filegrid='';
3643if value
3644    filebase=get(handles.RootName,'String');
3645    [nbslice, flag_grid]=get_grid(filebase,handles);% look for a grid with appropriate name
3646    if isequal(flag_grid,1)
3647        filegrid=[num2str(nbslice) 'grid'];
3648        testgrid=1;
3649    else % browse for a grid
3650        filegrid=get(hObject,'UserData');%look for previous grid name stored as UserData
3651        if exist(filegrid,'file')
3652            filebase=filegrid;
3653        end
3654        [FileName, PathName, filterindex] = uigetfile( ...
3655            {'*.grid', ' (*.grid)';
3656            '*.grid',  '.grid files '; ...
3657            '*.*', 'All Files (*.*)'}, ...
3658            'Pick a file',filebase);
3659        filegrid=fullfile(PathName,FileName);
3660        set(hObject,'UserData',filegrid);%store for future use
3661        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filegrid,'file'))
3662            testgrid=1;
3663        end
3664    end
3665end
3666if testgrid
3667    set(handle_dx,'Visible','off');
3668    set(handle_dy,'Visible','off');
3669    set(handle_title_dy,'Visible','off');
3670    set(handle_title_dx,'Visible','off');
3671    set(handle_txtbox,'Visible','on')
3672    set(handle_txtbox,'String',filegrid)
3673else
3674    set(hObject,'Value',0);
3675    set(handle_dx,'Visible','on');
3676    set(handle_dy,'Visible','on');
3677    set(handle_title_dy,'Visible','on');
3678    set(handle_title_dx,'Visible','on');
3679    set(handle_txtbox,'Visible','off')
3680end
3681
3682%% if hObject is on the checkciv1 frame, duplicate action for checkciv2 frame
3683PanelName=get(hparent,'tag');
3684if strcmp(PanelName,'Civ1')
3685    hchildren=get(handles.Civ2,'children');
3686    handle_checkbox=findobj(hchildren,'tag','CheckGrid');
3687    handle_txtbox=findobj(hchildren,'tag','txt_Grid');
3688    handle_dx=findobj(hchildren,'tag','num_Dx');
3689    handle_dy=findobj(hchildren,'tag','num_Dy');
3690    handle_title_dx=findobj(hchildren,'tag','title_Dx');
3691    handle_title_dy=findobj(hchildren,'tag','title_Dy');
3692    set(handle_checkbox,'UserData',filegrid);%store for future use
3693    if testgrid
3694        set(handle_checkbox,'Value',1);
3695        set(handle_dx,'Visible','off');
3696        set(handle_dy,'Visible','off');
3697        set(handle_title_dx,'Visible','off');
3698        set(handle_title_dy,'Visible','off');
3699        set(handle_txtbox,'Visible','on')
3700        set(handle_txtbox,'String',filegrid)
3701%     else
3702%         set(handle_checkbox,'Value',0);
3703%         set(handles.CheckGrid,'Value',0);
3704%         set(handle_dx,'Visible','on');
3705%         set(handle_dy,'Visible','on');
3706%          set(handle_title_dx,'Visible','on');
3707%         set(handle_title_dy,'Visible','on');
3708%         set(handle_txtbox,'Visible','off')
3709    end
3710end
3711%------------------------------------------------------------------------
3712% --- Executes on button press in CheckMask.
3713function CheckMask_Callback(hObject, eventdata, handles)
3714%------------------------------------------------------------------------
3715value=get(hObject,'Value');
3716hparent=get(hObject,'parent');
3717parent_tag=get(hparent,'Tag');
3718hchildren=get(hparent,'children');
3719handle_txtbox=findobj(hchildren,'tag','txt_Mask');
3720% handle_dx=findobj(hchildren,'tag','num_Dx');
3721% handle_dy=findobj(hchildren,'tag','num_Dy');
3722testmask=0;
3723if value
3724    filebase=get(handles.RootName,'String');
3725    [nbslice, flag_mask]=get_mask(filebase,handles);% look for a mask with appropriate name
3726    if isequal(flag_mask,1)
3727        filemask=[num2str(nbslice) 'mask'];
3728        testmask=1;
3729    else % browse for a mask
3730        filemask=get(hObject,'UserData');%look for previous mask name stored as UserData
3731        if exist(filemask,'file')
3732            filebase=filemask;
3733        end
3734        [FileName, PathName] = uigetfile( ...
3735            {'*.png', ' (*.png)';
3736            '*.png',  '.png files '; ...
3737            '*.*', 'All Files (*.*)'}, ...
3738            'Pick a mask file *.png',filebase);
3739        filemask=fullfile(PathName,FileName);
3740        set(hObject,'UserData',filemask);%store for future use
3741        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filemask,'file'))
3742            testmask=1;
3743        end
3744    end
3745end
3746if testmask
3747%     stage=4;%default
3748    if strcmp(parent_tag,'Civ1')
3749            set(handles.txt_Mask,'Visible','on')
3750        set(handles.txt_Mask,'String',filemask)
3751    set(handles.CheckMask,'Value',1)
3752    end
3753%     switch parent_tag
3754% %         case 'Fix1'
3755% %             stage=2;
3756%         case 'Civ2'
3757%              stage=3;
3758% %         case 'Fix2'
3759% %             stage=4;
3760%     end
3761%     set(handles.txt_Mask(stage:end),'Visible','on')
3762%     set(handles.txt_Mask(stage:end),'String',filemask)
3763%     set(handles.CheckMask(stage:end),'Value',1)
3764else
3765    set(hObject,'Value',0);
3766    set(handle_txtbox,'Visible','off')
3767end
3768
3769
3770% --- Executes on button press in get_gridpatch1.
3771function get_gridpatch1_Callback(hObject, eventdata, handles)
3772% hObject    handle to get_gridpatch1 (see GCBO)
3773% eventdata  reserved - to be defined in a future version of MENUMATLAB
3774% handles    structure with handles and user data (see GUIDATA)
3775
3776filebase=get(handles.RootName,'String');
3777[FileName, PathName, filterindex] = uigetfile( ...
3778    {'*.grid', ' (*.grid)';
3779    '*.grid',  '.grid files '; ...
3780    '*.*', 'All Files (*.*)'}, ...
3781    'Pick a file',filebase);
3782filegrid=fullfile(PathName,FileName);
3783set(handles.grid_patch1,'string',filegrid);
3784% set(handles.grid_patch2,'string',filegrid
3785
3786%------------------------------------------------------------------------
3787% --- Executes on button press in get_gridpatch2.
3788function get_gridpatch2_Callback(hObject, eventdata, handles)
3789%------------------------------------------------------------------------
3790
3791
3792%------------------------------------------------------------------------
3793% --- STEREO Interp
3794function cmd=RUN_STINTERP(stinterpBin,filename_A_nc,filename_B_nc,filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,xmlA,xmlB)
3795%------------------------------------------------------------------------
3796namelog=[filename_nc(1:end-3) '_stinterp.log'];
3797cmd=[stinterpBin ' -f1 ' filename_A_nc  ' -f2 ' filename_B_nc ' -f  ' filename_nc ...
3798    ' -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
3799
3800%------------------------------------------------------------------------
3801%--read images and convert them to the uint16 format used for PIV
3802function A=read_image(filename,type_ima,num,movieobject)
3803%------------------------------------------------------------------------
3804%num is the view number needed for an avi movie
3805switch type_ima
3806    case 'movie'
3807        A=read(movieobject,num);
3808    case 'avi'
3809        mov=aviread(filename,num);
3810        A=frame2im(mov(1));
3811    case 'multimage'
3812        A=imread(filename,num);
3813    case 'image'
3814        A=imread(filename);
3815end
3816siz=size(A);
3817if length(siz)==3;%color images
3818    A=sum(double(A),3);
3819    A=uint16(A);
3820end
3821
3822
3823%------------------------------------------------------------------------
3824% --- Executes on button press in get_ref_fix1.
3825function get_ref_fix1_Callback(hObject, eventdata, handles)
3826%------------------------------------------------------------------------
3827filebase=get(handles.RootName,'String');
3828[FileName, PathName, filterindex] = uigetfile( ...
3829    {'*.nc', ' (*.nc)';
3830    '*.nc',  'netcdf files '; ...
3831    '*.*', 'All Files (*.*)'}, ...
3832    'Pick a file',filebase);
3833
3834fileinput=[PathName FileName];
3835sizf=size(fileinput);
3836if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
3837[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
3838ref.filebase=fullfile(Path,File);
3839ref.num_a=stra2num(str_a);
3840ref.num_b=stra2num(str_b);
3841ref.num1=str2double(field_count);
3842ref.num2=str2double(str2);
3843browse=[];%initialisation
3844if ~isequal(ref.ext,'.nc')
3845    msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
3846    return
3847end
3848set(handles.ref_fix1,'String',[fullfile(ref.subdir,File) '....nc']);
3849set(handles.ref_fix1,'UserData',ref)
3850menu_field{1}='civ1';
3851Data=nc2struct(fileinput,[]);
3852if isfield(Data,'patch') && isequal(Data.patch,1)
3853    menu_field{2}='filter1';
3854end
3855if isfield(Data,'civ2') && isequal(Data.civ2,1)
3856    menu_field{3}='civ2';
3857end
3858if isfield(Data,'patch2') && isequal(Data.patch2,1)
3859    menu_field{4}='filter2';
3860end
3861set(handles.field_ref1,'String',menu_field);
3862set(handles.field_ref1,'Value',length(menu_field));
3863set(handles.num_MinVel,'Value',2);
3864set(handles.num_MinVel,'String','1');%default threshold
3865set(handles.ref_fix1,'Enable','on')
3866
3867%------------------------------------------------------------------------
3868% --- Executes on button press in get_ref_fix2.
3869function get_ref_fix2_Callback(hObject, eventdata, handles)
3870%------------------------------------------------------------------------
3871if isequal(get(handles.get_ref_fix2,'Value'),1)
3872    filebase=get(handles.RootName,'String');
3873    [FileName, PathName, filterindex] = uigetfile( ...
3874        {'*.nc', ' (*.nc)';
3875        '*.nc',  'netcdf files '; ...
3876        '*.*', 'All Files (*.*)'}, ...
3877        'Pick a file',filebase);
3878    fileinput=[PathName FileName];
3879    sizf=size(fileinput);
3880    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
3881    [Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
3882    ref.filebase=fullfile(Path,File);
3883    ref.num_a=stra2num(str_a);
3884    ref.num_b=stra2num(str_b);
3885    ref.num1=str2num(field_count);
3886    ref.num2=str2num(str2);
3887    browse=[];%initialisation
3888    if ~isequal(ref.ext,'.nc')
3889        msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
3890        return
3891    end
3892    set(handles.ref_fix2,'String',[fullfile(ref.subdir,File) '....nc']);
3893    set(handles.ref_fix2,'UserData',ref)
3894    menu_field{1}='civ1';
3895    Data=nc2struct(fileinput,[]);
3896    if isfield(Data,'patch') && isequal(Data.patch,1)
3897        menu_field{2}='filter1';
3898    end
3899    if isfield(Data,'civ2') && isequal(Data.civ2,1)
3900        menu_field{3}='civ2';
3901    end
3902    if isfield(Data,'patch2') && isequal(Data.patch2,1)
3903        menu_field{4}='filter2';
3904    end
3905    set(handles.field_ref2,'String',menu_field);
3906    set(handles.field_ref2,'Value',length(menu_field));
3907    set(handles.num_MinVel,'Value',2);
3908    set(handles.num_MinVel,'String','1');%default threshold
3909    set(handles.ref_fix2,'Enable','on')
3910    set(handles.ref_fix2,'Visible','on')
3911    set(handles.field_ref2,'Visible','on')
3912else
3913    set(handles.ref_fix2,'Visible','off')
3914    set(handles.field_ref2,'Visible','off')
3915end
3916
3917%------------------------------------------------------------------------
3918function ref_fix1_Callback(hObject, eventdata, handles)
3919%------------------------------------------------------------------------
3920set(handles.num_MinVel,'Value',1);
3921set(handles.field_ref1,'Value',1)
3922set(handles.field_ref1,'String',{' '})
3923set(handles.ref_fix1,'UserData',[]);
3924set(handles.ref_fix1,'String','');
3925set(handles.thresh_vel1,'String','0');
3926
3927%------------------------------------------------------------------------
3928function ref_fix2_Callback(hObject, eventdata, handles)
3929%------------------------------------------------------------------------
3930set(handles.num_MinVel,'Value',1);
3931set(handles.field_ref2,'Value',1)
3932set(handles.field_ref2,'String',{' '})
3933set(handles.ref_fix2,'UserData',[]);
3934set(handles.ref_fix2,'String','');
3935set(handles.num_MinVel,'String','0');
3936
3937%------------------------------------------------------------------------
3938% --- Executes on button press in test_stereo1.
3939function test_stereo1_Callback(hObject, eventdata, handles)
3940%------------------------------------------------------------------------
3941if isequal(get(handles.test_stereo1,'Value'),0)
3942    set(handles.subdomain_patch1,'Visible','on')
3943    set(handles.rho_patch1,'Visible','on')
3944else
3945    set(handles.subdomain_patch1,'Visible','off')
3946    set(handles.rho_patch1,'Visible','off')
3947end
3948
3949%------------------------------------------------------------------------
3950% --- Executes on button press in CheckStereo.
3951function StereoCheck_Callback(hObject, eventdata, handles)
3952%------------------------------------------------------------------------
3953if isequal(get(handles.CheckStereo,'Value'),0)
3954    set(handles.num_SubdomainSize,'Visible','on')
3955    set(handles.num_SmoothingParam,'Visible','on')
3956else
3957    set(handles.num_SubdomainSize,'Visible','off')
3958    set(handles.num_SmoothingParam,'Visible','off')
3959end
3960
3961%------------------------------------------------------------------------
3962% --- Executes on button press in TestCiv1: display image correlation function
3963function TestCiv1_Callback(hObject, eventdata, handles)
3964%------------------------------------------------------------------------
3965set(handles.TestCiv1,'BackgroundColor',[1 1 0])
3966drawnow
3967if get(handles.TestCiv1,'Value')
3968    ref_i=str2double(get(handles.ref_i,'String'));
3969    if strcmp(get(handles.ref_j,'Visible'),'on')
3970        ref_j=str2double(get(handles.ref_j,'String'));
3971    else
3972        ref_j=1;%default
3973    end
3974    [filecell,i1,i21,j1,j2,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,file_ref_fix1,file_ref_fix2]=...
3975        set_civ_filenames(handles,ref_i,ref_j,[1 0 0 0 0 0]);
3976    Data.ListVarName={'ny','nx','A'};
3977    Data.VarDimName= {'ny','nx',{'ny','nx'}};
3978    Data.A=imread(filecell.ima1.civ1{1});
3979    Data.ny=[size(Data.A,1) 1];
3980    Data.nx=[1 size(Data.A,2)];
3981    par_civ1=read_GUI(handles.Civ1);
3982    par_civ1.ImageWidth=size(Data.A,1);
3983    par_civ1.ImageHeight=size(Data.A,2);
3984    par_civ1.Mask='all';% will provide only the grid set for PIV, no image correlation
3985    Param.Civ1=par_civ1;
3986    Grid=civ_matlab(Param);% get the grid of x, y positions set for PIV
3987    hview_field=view_field(Data);
3988    set(0,'CurrentFigure',hview_field)
3989    hhview_field=guihandles(hview_field);
3990    set(hview_field,'CurrentAxes',hhview_field.axes3)
3991    ViewData=get(hview_field,'UserData');
3992    ViewData.CivHandle=handles.civ;% indicate the handle of the civ GUI in view_field
3993    ViewData.axes3.B=imread(filecell.ima2.civ1{1});%store the second image in the UserData of the GUI view_field
3994    ViewData.axes3.X=Grid.Civ1_X; %keep the set of points in memeory
3995    ViewData.axes3.Y=Grid.Civ1_Y;
3996    set(hview_field,'UserData',ViewData)
3997    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
3998    if isempty(corrfig)
3999        corrfig=figure;
4000        set(corrfig,'tag','corrfig')
4001        set(corrfig,'name','image correlation')
4002        set(corrfig,'DeleteFcn',{@closeview_field})%
4003    end
4004    set(handles.TestCiv1,'BackgroundColor',[1 0 0])
4005else
4006    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
4007    if ~isempty(corrfig)
4008        delete(corrfig)
4009    end
4010    hview_field=findobj(allchild(0),'tag','view_field');% look for view_field   
4011    if ~isempty(hview_field)
4012        delete(hview_field)
4013    end
4014end
4015
4016
4017%------------------------------------------------------------------------
4018% --- Executes on button press in CheckThreshold.
4019function CheckThreshold_Callback(hObject, eventdata, handles)
4020%------------------------------------------------------------------------
4021huipanel=get(hObject,'parent');
4022obj(1)=findobj(huipanel,'Tag','num_MinIma');
4023obj(2)=findobj(huipanel,'Tag','num_MaxIma');
4024obj(3)=findobj(huipanel,'Tag','title_Threshold');
4025if get(hObject,'Value')
4026    set(obj,'Visible','on')
4027else
4028    set(obj,'Visible','off')
4029end
4030
4031
4032%------------------------------------------------------------------------
4033% % --- Executes on button press in ListPairMode.
4034% function CivMode_Callback(hObject, eventdata, handles)
4035% %------------------------------------------------------------------------
4036% Listprog=get(handles.ListPairMode,'String');
4037% index=get(handles.ListPairMode,'Value');
4038% prog=Listprog{index};
4039% switch prog
4040%     case 'MenuCivX'
4041%         set(handles.thresh_patch1,'Visible','off')
4042%         set(handles.thresh_text1,'Visible','off')
4043%         set(handles.num_MaxDiff,'Visible','off')
4044%         set(handles.title_MaxDiff,'Visible','off')
4045%         set(handles.num_Rho,'Style','edit')
4046%         set(handles.num_Rho,'String','1')
4047%         set(handles.BATCH,'Enable','on')
4048%     case 'CivAll'
4049%         if get(handles.CheckPatch1,'Value')
4050%             set(handles.thresh_patch1,'Visible','on')
4051%             set(handles.thresh_text1,'Visible','on')
4052%         end
4053%         set(handles.num_Rho,'Style','edit')
4054%         set(handles.num_Rho,'String','1')
4055%         set(handles.BATCH,'Enable','on')
4056%     case 'CivUvmat'
4057%       
4058% end
4059
4060%------------------------------------------------------------------------
4061function cmd=cmd_civ1(filename,Param)
4062%------------------------------------------------------------------------
4063%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4064%changes : filename_cmx -> filename ( no extension )
4065cmd='';
4066errormsg=''; %default
4067filename=regexprep(filename,'.nc',''); %file name for the result
4068if isequal(Param.Civ1.Dt,'0')
4069    Param.Civ1.Dt='1' ;%case of 'displacement' mode
4070end
4071Param.Civ1.ImageA=regexprep(Param.Civ1.ImageA,'.png','');
4072Param.Civ1.ImageB=regexprep(Param.Civ1.ImageB,'.png','');
4073fid=fopen([filename '.civ1.cmx'],'w');
4074if isequal(fid,-1)
4075    display(['cmd file ' filename ' cannot be created'])
4076    return
4077end
4078fprintf(fid,['##############   CMX file' '\n' ]);
4079fprintf(fid,   ['FirstImage ' regexprep(Param.Civ1.ImageA,'\\','\\\\') '\n' ]);% for windows compatibility
4080fprintf(fid,   ['LastImage  ' regexprep(Param.Civ1.ImageB,'\\','\\\\') '\n' ]);% for windows compatibility
4081fprintf(fid,  ['XX' '\n' ]);
4082if isfield(Param.Civ1,'Mask')
4083    fprintf(fid,  ['Mask ' 'y' '\n' ]);
4084    fprintf(fid,  ['MaskName ' regexprep(Param.Civ1.Mask,'\\','\\\\') '\n' ]);
4085else
4086    fprintf(fid,  ['Mask ' 'n' '\n' ]);
4087    fprintf(fid,  ['MaskName ' 'noFile use default' '\n' ]);
4088end
4089fprintf(fid,   ['ImageSize ' num2str(Param.Civ1.ImageWidth) ' ' num2str(Param.Civ1.ImageHeight) '\n' ]);   %VERIFIER CAS GENERAL ?
4090fprintf(fid,   ['CorrelationBoxesSize ' num2str(Param.Civ1.Bx) ' ' num2str(Param.Civ1.By) '\n' ]);
4091fprintf(fid,   ['SearchBoxeSize ' num2str(Param.Civ1.Searchx) ' ' num2str(Param.Civ1.Searchy) '\n' ]);
4092fprintf(fid,   ['RO ' num2str(Param.Civ1.Rho) '\n' ]);
4093if isfield(Param.Civ1,'Grid')
4094    fprintf(fid,   ['GridSpacing ' '25' ' ' '25' '\n' ]);
4095else
4096    fprintf(fid,   ['GridSpacing ' num2str(Param.Civ1.Dx) ' ' num2str(Param.Civ1.Dy) '\n' ]);
4097end
4098fprintf(fid,   ['XX 1.0' '\n' ]);
4099fprintf(fid,   ['Dt_TO ' num2str(Param.Civ1.Dt) ' ' num2str(Param.Civ1.Time) '\n' ]);
4100fprintf(fid,  ['PixCmXY ' '1' ' ' '1' '\n' ]);
4101fprintf(fid,  ['XX 1' '\n' ]);
4102fprintf(fid,   ['ShiftXY ' num2str(Param.Civ1.Shiftx) ' '  num2str(Param.Civ1.Shifty) '\n' ]);
4103if isfield(Param.Civ1,'Grid')
4104    fprintf(fid,  ['Grid ' 'y' '\n' ]);
4105    fprintf(fid,   ['GridName ' regexprep(Param.Civ1.Grid,'\\','\\\\') '\n' ]);
4106else
4107    fprintf(fid,  ['Grid ' 'n' '\n' ]);
4108    fprintf(fid,   ['GridName ' 'noFile use default' '\n' ]);
4109end
4110fprintf(fid,   ['XX 85' '\n' ]);
4111fprintf(fid,   ['XX 1.0' '\n' ]);
4112fprintf(fid,   ['XX 1.0' '\n' ]);
4113fprintf(fid,   ['Hart 1' '\n' ]);
4114fprintf(fid,  [ 'DecimalShift 0' '\n' ]);
4115fprintf(fid,   ['Deformation 0' '\n' ]);
4116fprintf(fid,  ['CorrelationMin 0' '\n' ]);
4117fprintf(fid,   ['IntensityMin 0' '\n' ]);
4118if ~isfield(Param.Civ1,'MinIma')% Image threshold not activated
4119    fprintf(fid,  ['SeuilImage n' '\n' ]);
4120    fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);%not used in principle
4121else% Image threshold  activated
4122    if isempty(Param.Civ1.MaxIma)||isnan(Param.Civ1.MaxIma)
4123        Param.Civ1.MaxIma=2^Param.Civ1.ImageBitDepth;%take the max image value as upper bound by default
4124    end
4125    fprintf(fid,  ['SeuilImage y' '\n' ]);
4126    fprintf(fid,   ['SeuilImageValues ' num2str(Param.Civ1.MinIma) ' ' num2str(Param.Civ1.MaxIma) '\n' ]);
4127end
4128fprintf(fid,   ['ImageToUse ' Param.Civ1.term_a ' ' Param.Civ1.term_b '\n' ]); % VERIFIER ?
4129fprintf(fid,   ['ImageUsedBefore null null' '\n' ]);
4130fclose(fid);
4131
4132if(isunix) %unix (or Mac) system
4133    cmd=['cp -f ' filename '.civ1.cmx ' filename '.cmx \n '];% the cmx file gives the name to the nc file
4134    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
4135    cmd=[cmd 'rm ' filename '.cmx'];
4136else %Windows system
4137    filename=regexprep(filename,'\\','\\\\');
4138    cmd=['copy /Y "' filename '.civ1.cmx" "' filename '.cmx" \n '];
4139    cmd=[cmd '"' regexprep(Param.xml.Civ1Bin,'\\','\\\\')...
4140        '" -f "' filename '.cmx" >"' filename '.civ1.log" \n ' ]; % redirect standard output to the log file
4141    cmd=[cmd 'del "' filename '.cmx"'];
4142end
4143
4144
4145function cmd=cmd_fix(filename,Param,fixname)
4146%%
4147switch fixname
4148    case 'Fix1'
4149        fi2_value=num2str(Param.(fixname).CheckF2);
4150    case 'Fix2'
4151        fi2_value=num2str(Param.(fixname).CheckF4);%need to understand why...
4152end
4153filename=regexprep(filename,'.nc','');
4154MaskName_string='';%default
4155% if Param.(fixname).CheckMask
4156%     MaskName_string=[' -maskName "' Param.(fixname).Mask '"'];
4157% end
4158MaxVel_string='';%default
4159if ~isempty(Param.(fixname).MaxVel)
4160    MaxVel_string=[' -threshV ' num2str(Param.(fixname).MaxVel)];
4161end
4162if isunix
4163    cmd=[Param.xml.FixBin ' -f ' filename '.nc -fi1 ' num2str(Param.(fixname).CheckFmin2) ...
4164        ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ...
4165        ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string...
4166        ' >' filename '.' lower(fixname) '.log 2>&1'];
4167else
4168    cmd=['"' Param.xml.FixBin '" -f "' filename '.nc" -fi1 ' num2str(Param.(fixname).CheckFmin2)...
4169        ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ...
4170        ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string...
4171        ' > "' filename '.' lower(fixname) '.log"'];
4172    cmd=regexprep(cmd,'\\','\\\\');
4173end
4174
4175
4176function cmd=cmd_patch(filename,Param,patchname)
4177%% ------------------------------------------------------------------------
4178filename=regexprep(filename,'.nc','');
4179if isunix
4180    cmd=[Param.xml.PatchBin...
4181        ' -f ' filename '.nc -m ' num2str(Param.(patchname).Nx)...
4182        ' -n ' num2str(Param.(patchname).Ny) ' -ro ' num2str(Param.(patchname).SmoothingParam)...
4183        ' -nopt ' num2str(Param.(patchname).SubdomainSize) ...
4184        '  > ' filename '.' lower(patchname) '.log 2>&1']; % redirect standard output to the log file
4185else
4186    cmd=['"' Param.xml.PatchBin...
4187        '" -f "' filename '.nc" -m ' num2str(Param.(patchname).Nx)...
4188        ' -n ' num2str(Param.(patchname).Ny) ' -ro ' num2str(Param.(patchname).SmoothingParam)...
4189        ' -nopt ' num2str(Param.(patchname).SubdomainSize)...
4190        '  > "' filename '.' lower(patchname) '.log" 2>&1']; % redirect standard output to the log file
4191    cmd=regexprep(cmd,'\\','\\\\');
4192end
4193
4194%------------------------------------------------------------------------
4195% --- CheckCiv2  CheckCiv2  CheckCiv2 CheckCiv2
4196function cmd=cmd_civ2(filename,Param)
4197%------------------------------------------------------------------------
4198%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4199% global civ2Bin sge%name of the executable for checkciv1 calculation
4200filename=regexprep(filename,'.nc','');
4201if isequal(Param.Civ2.Dt,'0')
4202    Param.Civ2.Dt='1' ;%case of 'displacement' mode
4203end
4204Param.Civ2.ImageA=regexprep(Param.Civ2.ImageA,'.png','');
4205Param.Civ2.ImageB=regexprep(Param.Civ2.ImageB,'.png','');% bug : .png appears two times ?
4206[fid,errormsg]=fopen([filename '.civ2.cmx'],'w');
4207if isequal(fid,-1)
4208    msgbox_uvmat('ERROR',errormsg)
4209    cmd='';
4210    return
4211end
4212fprintf(fid,['##############   CMX file' '\n' ]);
4213fprintf(fid,   ['FirstImage ' regexprep(Param.Civ2.ImageA,'\\','\\\\') '\n' ]);% for windows compatibility
4214fprintf(fid,   ['LastImage  ' regexprep(Param.Civ2.ImageB,'\\','\\\\') '\n' ]);% for windows compatibility
4215fprintf(fid,  ['XX' '\n' ]);
4216if isfield(Param.Civ2,'Mask')
4217    fprintf(fid,  ['Mask ' 'y' '\n' ]);
4218    fprintf(fid,  ['MaskName ' regexprep(Param.Civ2.Mask,'\\','\\\\') '\n' ]);
4219else
4220    fprintf(fid,  ['Mask ' 'n' '\n' ]);
4221    fprintf(fid,  ['MaskName ' 'noFile use default' '\n' ]);
4222end
4223% fprintf(fid, ['Mask ' Param.Civ2.MaskFlag '\n' ]);
4224% fprintf(fid, ['MaskName ' regexprep(Param.Civ2.MaskName,'\\','\\\\') '\n' ]);% for windows compatibility
4225fprintf(fid,   ['ImageSize ' num2str(Param.Civ2.ImageWidth) ' ' num2str(Param.Civ2.ImageHeight) '\n' ]); 
4226% fprintf(fid, ['ImageSize ' num2str(Param.Civ2.npx) ' ' num2str(Param.Civ2.npy) '\n' ]);   %VERIFIER CAS GENERAL ?
4227fprintf(fid, ['CorrelationBoxesSize ' num2str(Param.Civ2.Bx) ' ' num2str(Param.Civ2.By) '\n' ]);
4228fprintf(fid, ['SearchBoxeSize ' num2str(Param.Civ2.Bx) ' ' num2str(Param.Civ2.By) '\n']);
4229fprintf(fid, ['RO ' num2str(Param.Civ2.Rho) '\n']);
4230if isfield(Param.Civ2,'Grid')
4231    fprintf(fid,   ['GridSpacing ' '25' ' ' '25' '\n' ]);
4232else
4233    fprintf(fid,   ['GridSpacing ' num2str(Param.Civ2.Dx) ' ' num2str(Param.Civ2.Dy) '\n' ]);
4234end
4235% fprintf(fid, ['GridSpacing ' num2str(Param.Civ2.Dx) ' ' num2str(Param.Civ2.Dy) '\n']);
4236fprintf(fid, ['XX 1.0' '\n' ]);
4237fprintf(fid, ['Dt_TO ' num2str(Param.Civ2.Dt) ' ' num2str(Param.Civ2.Time) '\n' ]);
4238fprintf(fid, ['PixCmXY ' '1' ' ' '1' '\n' ]);
4239fprintf(fid, ['XX 1' '\n' ]);
4240fprintf(fid, 'ShiftXY 0 0\n');
4241if isfield(Param.Civ2,'Grid')
4242    fprintf(fid,  ['Grid ' 'y' '\n' ]);
4243    fprintf(fid,   ['GridName ' regexprep(Param.Civ2.Grid,'\\','\\\\') '\n' ]);
4244else
4245    fprintf(fid,  ['Grid ' 'n' '\n' ]);
4246    fprintf(fid,   ['GridName ' 'noFile use default' '\n' ]);
4247end
4248% fprintf(fid, ['Grid ' Param.Civ2.GridFlag '\n' ]);
4249% fprintf(fid, ['GridName ' regexprep(Param.Civ2.GridName,'\\','\\\\') '\n']);
4250fprintf(fid, ['XX 85' '\n' ]);
4251fprintf(fid, ['XX 1.0' '\n' ]);
4252fprintf(fid, ['XX 1.0' '\n' ]);
4253fprintf(fid, ['Hart 1' '\n' ]);
4254fprintf(fid, ['DecimalShift ' num2str(Param.Civ2.CheckDecimal) '\n']);
4255fprintf(fid, ['Deformation ' num2str(Param.Civ2.CheckDeformation) '\n']);
4256fprintf(fid,  ['CorrelationMin 0' '\n' ]);
4257fprintf(fid,   ['IntensityMin 0' '\n' ]);
4258
4259if ~isfield(Param.Civ2,'MinIma')% Image threshold not activated
4260    fprintf(fid,  ['SeuilImage n' '\n' ]);
4261    fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);%not used in principle
4262else% Image threshold  activated
4263    if isempty(Param.Civ2.MaxIma)||isnan(Param.Civ2.MaxIma)
4264        Param.Civ2.MaxIma=2^Param.Civ2.ImageBitDepth;%take the max image value as upper bound by default
4265    end
4266    fprintf(fid,  ['SeuilImage y' '\n' ]);
4267    fprintf(fid,   ['SeuilImageValues ' num2str(Param.Civ2.MinIma) ' ' num2str(Param.Civ2.MaxIma) '\n' ]);
4268end
4269fprintf(fid,   ['ImageToUse ' Param.Civ2.term_a ' ' Param.Civ2.term_b '\n' ]); % VERIFIER ?
4270fprintf(fid, ['ImageUsedBefore ' regexprep(Param.Civ2.filename_nc1,'\\','\\\\') '\n']);
4271fclose(fid);
4272
4273if(isunix)
4274    cmd=['cp -f ' filename '.civ2.cmx ' filename '.cmx\n'...
4275        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
4276        'rm ' filename '.cmx \n'];%rename .cmx as .checkciv2.cmx, the result file is named [filename '.nc'] by CIVx
4277else
4278    filename=regexprep(filename,'\\','\\\\');
4279    cmd=['copy /Y "' filename '.civ2.cmx" "' filename '.cmx" \n'...
4280        '"' regexprep(Param.xml.Civ2Bin,'\\','\\\\') '" -f "' filename  '.cmx" >"' filename '.civ2.log" \n'...
4281        'del "' filename '.cmx" \n'];
4282end
4283
4284%------------------------------------------------------------------------
4285% --- CheckCiv1  Unified: TO ABADON
4286function xml_civ1_parameters=CIV1_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
4291civ1.image1=par.ImageA;
4292civ1.image2=par.ImageB;
4293civ1.imageSize_X=par.npx;
4294civ1.imageSize_Y=par.npy;
4295civ1.outputFileName=[filename '.nc'];
4296civ1.correlationBoxesSize_X=par.ibx;
4297civ1.correlationBoxesSize_Y=par.iby;
4298civ1.searchBoxesSize_X=par.isx;
4299civ1.searchBoxesSize_Y=par.isy;
4300civ1.globalShift_X=par.shiftx;
4301civ1.globalShift_Y=par.shifty;
4302civ1.ro=par.rho;
4303civ1.hart='y';
4304if isequal(par.gridflag,'y')
4305    civ1.grid=par.gridname;
4306else
4307    civ1.grid='n';
4308    civ1.gridSpacing_X=par.dx;
4309    civ1.gridSpacing_Y=par.dy;
4310end
4311if isequal(par.maskflag,'y')
4312    civ1.mask=par.maskname;
4313end
4314civ1.dt=par.Dt;
4315civ1.unit='pixel';
4316civ1.absolut_time_T0=par.Time;
4317civ1.pixcmx='1';
4318civ1.pixcmy='1';
4319civ1.convectFlow='n';
4320
4321xml_civ1_parameters=civ1;
4322
4323%------------------------------------------------------------------------
4324% --- CheckCiv2  Unified: TO ABADON
4325function civ2=CIV2_CMD_Unified(filename,namelog,par)
4326%------------------------------------------------------------------------
4327%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4328%global CivBin%name of the executable for checkciv1 calculation
4329
4330filename=regexprep(filename,'.nc','');
4331
4332civ2.image1=par.ImageA;
4333civ2.image2=par.ImageB;
4334civ2.imageSize_X=par.npx;
4335civ2.imageSize_Y=par.npy;
4336civ2.inputFileName=[par.filename_nc1 '.nc'];
4337civ2.outputFileName=[filename '.nc'];
4338civ2.correlationBoxesSize_X=par.ibx;
4339civ2.correlationBoxesSize_Y=par.iby;
4340civ2.ro=par.rho;
4341%checkciv2.decimalShift=par.CheckDecimal;
4342%checkciv2.CheckDeformation=par.CheckDeformation;
4343if isequal(par.decimal,'1')
4344    civ2.decimalShift='y';
4345else
4346    civ2.decimalShift='n';
4347end
4348if isequal(par.deformation,'1')
4349    civ2.deformation='y';
4350else
4351    civ2.deformation='n';
4352end
4353if isequal(par.gridflag,'y')
4354    civ2.grid=par.gridname;
4355else
4356    civ2.grid='n';
4357    civ2.gridSpacing_X=par.dx;
4358    civ2.gridSpacing_Y=par.dy;
4359end
4360civ2.gridSpacing_X='10';
4361civ2.gridSpacing_Y='10';%NOTE: faut mettre gridSpacing pourque ca tourne, meme si c'est la grille qui est utilisee
4362if isequal(par.maskflag,'y')
4363    civ2.mask=par.maskname;
4364else
4365    civ2.mask='n';
4366end
4367civ2.dt=par.Dt;
4368civ2.unit='pixel';
4369civ2.absolut_time_T0=par.Time;
4370civ2.pixcmx='1';
4371civ2.pixcmy='1';
4372civ2.convectFlow='n';
4373
4374
4375% --- Executes on button press in TestPatch1.
4376function TestPatch1_Callback(hObject, eventdata, handles)
4377set(handles.TestPatch1,'BackgroundColor',[1 1 0])
4378drawnow
4379if get(handles.TestPatch1,'Value')
4380    ref_i=str2double(get(handles.ref_i,'String'));
4381    if strcmp(get(handles.ref_j,'Visible'),'on')
4382        ref_j=str2double(get(handles.ref_j,'String'));
4383    else
4384        ref_j=1;%default
4385    end
4386    [filecell,i1,i21,j1,j2,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,file_ref_fix1,file_ref_fix2]=...
4387        set_civ_filenames(handles,ref_i,ref_j,[0 0 1 0 0 0]);
4388   
4389    Data.ListVarName={'ny','nx','A'};
4390    Data.VarDimName= {'ny','nx',{'ny','nx'}};
4391   
4392    param_patch1=read_GUI(handles.Patch1);
4393    param_patch1.CivFile=filecell.nc.civ1{1};
4394    Param.Patch1=param_patch1;
4395    for irho=1:7
4396        [Data,errormsg]=civ_matlab(Param);% get the grid of x, y positions set for PIV
4397        if ~isempty(errormsg)
4398            msgbox_uvmat('ERROR',errormsg)
4399            return
4400        end
4401        SmoothingParam(irho)=Param.Patch1.SmoothingParam;
4402        Data.Civ1_U_Diff=Data.Civ1_U_Diff(Data.Civ1_FF==0);
4403        Data.Civ1_V_Diff=Data.Civ1_V_Diff(Data.Civ1_FF==0);
4404        DiffVel(irho)=sqrt(mean(Data.Civ1_U_Diff.*Data.Civ1_U_Diff+Data.Civ1_V_Diff.*Data.Civ1_V_Diff))
4405        NbSites(irho)=Data.Civ1_NbSites/numel(Data.Civ1_U_Diff);
4406        Param.Patch1.SmoothingParam=2*Param.Patch1.SmoothingParam;
4407    end
4408    figure
4409    plot(SmoothingParam,DiffVel,'b',SmoothingParam,NbSites,'r')
4410    set(handles.TestPatch1,'BackgroundColor',[1 0 0])
4411else
4412    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
4413    if ~isempty(corrfig)
4414        delete(corrfig)
4415    end
4416    hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
4417    if ~isempty(hview_field)
4418        delete(hview_field)
4419    end
4420end
4421
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