source: trunk/src/civ.m @ 438

Last change on this file since 438 was 438, checked in by sommeria, 13 years ago

improvement of the civ GUI (order of elements)
improvement of netcdf file input

File size: 192.1 KB
Line 
1
2%'civ': function associated with the interface 'civ.fig' for PIV, spline interpolation and stereo PIV (patch)
3%------------------------------------------------------------------------
4%  provides an interface for the software menucivx
5% function varargout = civ(varargin)
6% provides an interface for the software menucivx
7%
8%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
9%  Copyright Joel Sommeria, 2011, LEGI / CNRS-UJF-INPG, sommeria@legi.grenoble-inp.fr
10%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11%     This file is part of the toolbox UVMAT.
12%
13%     UVMAT is free software; you can redistribute it and/or modify
14%     it under the terms of the GNU General Public License as published by
15%     the Free Software Foundation; either version 2 of the License, or
16%     (at your option) any later version.
17%
18%     UVMAT is distributed in the hope that it will be useful,
19%     but WITHOUT ANY WARRANTY; without even the implied warranty of
20%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
21%     GNU General Public License (file UVMAT/COPYING.txt) for more details.
22%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
23function varargout = civ(varargin)
24%TODO: search range
25
26% Last Modified by GUIDE v2.5 03-Jun-2012 22:16:42
27% Begin initialization code - DO NOT EDIT
28gui_Singleton = 1;
29gui_State = struct('gui_Name',       mfilename, ...
30    'gui_Singleton',  gui_Singleton, ...
31    'gui_OpeningFcn', @civ_OpeningFcn, ...
32    'gui_OutputFcn',  @civ_OutputFcn, ...
33    'gui_LayoutFcn',  [] , ...
34    'gui_Callback',   []);
35if nargin && ischar(varargin{1}) && ~isempty(regexp(varargin{1},'_Callback$','once'))
36    gui_State.gui_Callback = str2func(varargin{1});
37end
38
39if nargout
40    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
41else
42    gui_mainfcn(gui_State, varargin{:});
43end
44% End initialization code - DO NOT EDIT
45
46%------------------------------------------------------------------------
47% --- Executes just before civ is made visible.
48function civ_OpeningFcn(hObject, eventdata, handles, fileinput)
49%------------------------------------------------------------------------
50% This function has no output args, see OutputFcn.
51
52%% General settings
53handles.output = hObject;
54guidata(hObject, handles); % Update handles structure
55set(hObject,'WindowButtonDownFcn',{'mouse_down'}) % allows mouse action with right button (zoom for uicontrol display)
56
57%% Adjust the GUI according to the binaries available in PARAM.xml
58path_civ=fileparts(which('civ')); %path to civ
59addpath (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)
60errormsg=[];%default error message
61xmlfile='PARAM.xml';
62if exist(xmlfile,'file')
63    try
64        t=xmltree(xmlfile);
65        sparam=convert(t);
66    catch ME
67        errormsg={' Unable to read the file PARAM.xml defining the civx binaries:';ME.message};
68    end
69else
70    errormsg=[xmlfile ' not found: path to civx binaries undefined'];
71end
72if ~isempty(errormsg)
73    msgbox_uvmat('WARNING',errormsg);
74end
75test_batch=0;%default: ,no batch mode available
76if isfield(sparam,'BatchParam') && isfield(sparam.BatchParam,'BatchMode')
77    test_batch=strcmp(sparam.BatchParam.BatchMode,'sge'); %sge is currently the only implemented batch mod
78end
79if test_batch==0
80    set(handles.BATCH,'Enable','off')% put the BATCH button in grey (unactivated)
81    set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])% put the BATCH button in grey (unactivated)
82end
83if isfield(sparam.RunParam,'CivBin')
84    if ~exist(sparam.RunParam.CivBin,'file')
85        sparam.RunParam.CivBin=fullfile(path_civ,sparam.RunParam.CivBin);
86    end
87else
88    sparam.RunParam.CivBin='';
89end
90
91%% load the list of previously browsed files in the upper bar menu Open/
92dir_perso=prefdir; % path to the directory .matlab for personal data
93profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmauvmat_perso.mat' in .matlab
94if exist(profil_perso,'file')
95    h=load (profil_perso);
96    if isfield(h,'MenuFile')
97        for ifile=1:min(length(h.MenuFile),5)
98            eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',h.MenuFile{ifile});'])
99        end
100    end
101end
102
103%% prepare the GUI with parameters from the input file if opened from uvmat
104if exist('fileinput','var')% && isfield(param,'RootName') && ~isempty(param.RootName)
105    set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
106    errormsg=display_file_name(handles,fileinput);
107    if ~isempty(errormsg)
108        msgbox_uvmat('ERROR',errormsg)
109    end
110    set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
111end
112
113%------------------------------------------------------------------------
114% --- Outputs from this function are returned to the command line.
115function varargout = civ_OutputFcn(hObject, eventdata, handles)
116%------------------------------------------------------------------------
117% Get default command line output from handles structure
118varargout{1} = handles.output;
119
120%------------------------------------------------------------------------
121% --- Function activated by the Open/Browse... option in the upper menu bar.
122function MenuBrowse_Callback(hObject, eventdata, handles)
123%------------------------------------------------------------------------
124%% get the current input root file name to initiate the browser
125filebase=get(handles.RootPath,'String');
126oldfile=''; %default
127if isempty(filebase)|| isequal(filebase,'')%loads the previously stored root file name
128    dir_perso=prefdir;
129    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
130    if exist(profil_perso,'file')
131        h=load (profil_perso);
132        if isfield(h,'filebase')&& ischar(h.filebase)
133            oldfile=h.filebase;
134        end
135        if isfield(h,'RootPath') && ischar(h.RootPath)
136            oldfile=h.RootPath;
137        end
138    end
139else
140    oldfile=filebase;
141end
142
143%% get the new input file with the browser
144menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)';
145    '*.xml',  '.xml files '; ...
146    '*.civ',  '.civ files '; ...
147    '*.png','.png image files'; ...
148    '*.jpg',' jpeg image files'; ...
149    '*.tif','.tif image files'; ...
150    '*.avi;*.AVI','.avi movie files'; ...
151    '*.nc','.netcdf files'; ...
152    '*.*',  'All Files (*.*)'};
153[FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file',oldfile);
154fileinput=[PathName FileName];%complete file name
155sizf=size(fileinput);
156if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
157
158%% case of the xml file opened as input (TODO: check and see whether it is useful)
159[path,name,ext]=fileparts(fileinput);
160testeditxml=0;
161% if isequal(ext,'.xml')
162%     testeditxml=1;
163%     t_browse=xmltree(fileinput);
164%     head_element=get(t_browse,1);
165%     if isfield(head_element,'name')&& isequal(head_element.name,'ImaDoc')
166%         testeditxml=0;
167%     end
168% end
169% if testeditxml==1 || isequal(ext,'.xls')
170%     heditxml=editxml({fileinput});
171%     set(heditxml,'Tag','browser')
172%     waitfor(heditxml,'Tag','idle')
173%     if ~ishandle(heditxml)
174%         return
175%     end
176%     attr=findobj(get(heditxml,'children'),'Tag','CurrentAttributes');
177%     set(handles.browse,'UserData',fileinput)% store for future opening with browser
178%     fileinput=get(attr,'UserData');
179%     if ~exist(fileinput,'file')
180%         return
181%     end
182% end
183[tild,tild,tild,i1,i2,j1,j2,FileExt,NomType]=fileparts_uvmat(fileinput);
184
185%% prepare the GUI with parameters from the input file
186set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
187errormsg=display_file_name(handles,fileinput);
188if ~isempty(errormsg)
189    msgbox_uvmat('ERROR',erromsg)
190end
191set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
192
193%------------------------------------------------------------------------
194% --- Open again the file whose name has been recorded in MenuFile_1
195function MenuFile_1_Callback(hObject, eventdata, handles)
196%------------------------------------------------------------------------
197set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
198fileinput=get(handles.MenuFile_1,'Label');
199errormsg=display_file_name(handles,fileinput);
200if ~isempty(errormsg)
201    msgbox_uvmat('ERROR',errormsg)
202end
203set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
204
205% -----------------------------------------------------------------------
206% --- Open again the file whose name has been recorded in MenuFile_2
207function MenuFile_2_Callback(hObject, eventdata, handles)
208%------------------------------------------------------------------------
209set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
210fileinput=get(handles.MenuFile_2,'Label');
211errormsg=display_file_name(handles,fileinput);
212if ~isempty(errormsg)
213    msgbox_uvmat('ERROR',errormsg)
214end
215set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
216
217% -----------------------------------------------------------------------
218% --- Open again the file whose name has been recorded in MenuFile_3
219function MenuFile_3_Callback(hObject, eventdata, handles)
220%------------------------------------------------------------------------
221set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
222fileinput=get(handles.MenuFile_3,'Label');
223errormsg=display_file_name(handles,fileinput);
224if ~isempty(errormsg)
225    msgbox_uvmat('ERROR',errormsg)
226end
227set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
228
229% -----------------------------------------------------------------------
230% --- Open again the file whose name has been recorded in MenuFile_4
231function MenuFile_4_Callback(hObject, eventdata, handles)
232%------------------------------------------------------------------------
233set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
234fileinput=get(handles.MenuFile_4,'Label');
235errormsg=display_file_name(handles,fileinput);
236if ~isempty(errormsg)
237    msgbox_uvmat('ERROR',errormsg)
238end
239set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
240
241% -----------------------------------------------------------------------
242% --- Open again the file whose name has been recorded in MenuFile_5
243function MenuFile_5_Callback(hObject, eventdata, handles)
244%------------------------------------------------------------------------
245set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
246fileinput=get(handles.MenuFile_5,'Label');
247errormsg=display_file_name(handles,fileinput);
248if ~isempty(errormsg)
249    msgbox_uvmat('ERROR',errormsg)
250end
251set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
252
253% -----------------------------------------------------------------------
254% -----------------------------------------------------------------------
255% --- Open the help html file
256function MenuHelp_Callback(hObject, eventdata, handles)
257% -----------------------------------------------------------------------
258path_civ=fileparts(which ('civ'));
259helpfile=fullfile(path_civ,'uvmat_doc','uvmat_doc.html');
260if isempty(dir(helpfile))
261    msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
262else
263    addpath (fullfile(path_civ,'uvmat_doc'))
264    web([helpfile '#civ'])
265end
266
267%------------------------------------------------------------------------
268% --- Function activated when a new filebase (image series) is introduced
269function RootPath_Callback(hObject, eventdata, handles)
270%------------------------------------------------------------------------
271set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
272RootPath=get(handles.RootPath,'String');
273SubdirImages=get(handles.SubdirImages,'String');
274RootFile=get(handles.RootFile,'String');
275ref_i=str2num(get(handles.ref_i,'String'));
276ref_j=str2num(get(handles.ref_j,'String'));
277NomType=get(handles.NomType,'String');
278ImaExt=get(handles.ImaExt,'String');
279fileinput=fullfile_uvmat(RootPath,SubdirImages,RootFile,ImaExt,NomType,ref_i,[],ref_j);
280errormsg=display_file_name(handles,fileinput);
281if ~isempty(errormsg)
282    msgbox_uvmat('ERROR',errormsg)
283end
284set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
285
286%------------------------------------------------------------------------
287% --- general function activated for an input file series
288function errormsg=display_file_name(handles,fileinput)
289%------------------------------------------------------------------------
290set(handles.ListCompareMode,'Visible','on')
291errormsg='';%default empty error message
292drawnow
293
294%% enable RUN, BATCH button and 'status' display
295set(handles.RUN, 'Enable','On')
296set(handles.RUN,'BackgroundColor',[1 0 0])%set RUN button to red color
297set(handles.BATCH,'Enable','On')
298set(handles.BATCH,'BackgroundColor',[1 0 0])%set BATCH button to red color
299if isfield(handles,'status')
300    set(handles.status,'Value',0);       %suppress the 'status' display
301    status_Callback([], [], handles)
302end
303
304%% determine nomenclature types and extension of the input files
305[RootPath,SubDir,RootFile,i1,i2,j1,j2,ExtInput,NomTypeInput]=fileparts_uvmat(fileinput);
306NomTypeNc='';%default
307
308%% case of xml file as input, read the civ parameters
309ind_opening=0;%default
310if strcmp(ExtInput,'.xml')
311    Param=xml2struct(fileinput);
312    fill_GUI(Param,handles);%fill the GUI with the parameters retrieved from the xml file
313    return
314end
315
316%% case of netcdf file as input, get the civ processing stage and look for a coresponding image
317if strcmp(ExtInput,'.nc')
318    NomTypeNc=NomTypeInput;
319    if isempty(regexp(NomTypeInput,'[ab|AB|-]'))
320        set(handles.ListCompareMode,'Value',2) %mode displacement advised if the nomencalture does not involve index pairs
321      %  [RootPath,SubDir]=fileparts(RootPath);
322        set(handles.RootFile_1,'Visible','On');
323    else
324        set(handles.ListCompareMode,'Value',1)
325        set(handles.RootFile_1,'Visible','Off');
326    end
327    Data=nc2struct(fileinput,'ListGlobalAttribute','Conventions','absolut_time_T0','CivStage','Civ2_ImageA','Civ1_ImageA','Civ2_ImageB','Civ1_ImageB','fix','patch','civ2','fix2');
328    if isfield(Data,'Txt')
329        errormsg=Data.Txt;
330        return
331    end
332    % settings for  new civ data,
333    if strcmp(Data.Conventions,'uvmat/civdata')% case of new civ data,
334        set(handles.ListProgram,'Value',2) %select civ/Matlab by default
335        ListProgram_Callback([],[], handles)
336        if ~isempty(Data.CivStage)%test for civ files
337            ind_opening=Data.CivStage;
338        end
339        if  ~isempty(Data.Civ2_ImageB)%get the corresponding input image in the netcdf file
340            imageinput=Data.Civ2_ImageB;
341            [tild,ImaName,ImaExt]=fileparts(Data.Civ2_ImageA);
342            set(handles.RootFile_1,'String',[ImaName ImaExt])
343        elseif ~isempty(Data.Civ1_ImageB)
344            imageinput=Data.Civ1_ImageB;
345            [tild,ImaName,ImaExt]=fileparts(Data.Civ1_ImageA);
346            set(handles.RootFile_1,'String',[ImaName ImaExt])
347        end
348        % settings for civx data,
349    elseif ~isempty(Data.absolut_time_T0')% case of  civx data,
350        set(handles.ListProgram,'Value',1) %select Cix by default
351        ListProgram_Callback([],[], handles)
352        if ~isempty(Data.fix2)
353            ind_opening=5;
354        elseif ~isempty(Data.civ2)
355            ind_opening=4;
356        elseif ~isempty(Data.patch)
357            ind_opening=3;
358        elseif ~isempty(Data.fix)
359            ind_opening=2;
360        end
361    else
362        errormsg='the input netcdf file is not civ data';
363        return
364    end
365    % look for the corresponding input images
366    check_letter=~isempty(regexp(NomTypeInput,'[ab|AB]$','once'));%detect pair label by letter
367    NomTypeIma=NomTypeInput;
368    if check_letter
369        NomTypeIma=NomTypeInput(1:end-1);
370    else
371        r=regexp(NomTypeIma,'.-(?<num2>\d+)$','names');
372        if ~isempty(r)
373            NomTypeIma=regexprep(NomTypeIma,['-' r.num2],'');
374        end
375        r=regexp(NomTypeIma,'.-(?<num2>\d+)','names');
376        if ~isempty(r)
377            NomTypeIma=regexprep(NomTypeIma,['-' r.num2],'');
378        end
379    end
380    imageinput=fullfile_uvmat(RootPath,regexprep(SubDir,'.civ(_?)(\d*)$',''),RootFile,'.png',NomTypeIma,i1,[],j1);
381end
382
383%no corresponding image found, select manually with the browser
384ImaExt=ExtInput;
385if ~isempty(NomTypeNc)
386    %no corresponding image found, select manually with the browser
387    if ~exist(imageinput,'file')
388        menu={'*.png;*.jpg;*.tif;*.avi;*.AVI', '(*.png,*.jpg ,*.tif, *.avi,*.AVI)';
389            '*.png','.png image files'; ...
390            '*.jpg',' jpeg image files'; ...
391            '*.tif','.tif image files'; ...
392            '*.avi;*.AVI','.avi movie files'; ...
393            '*.*',  'All Files (*.*)'};
394        [FileName, PathName] = uigetfile( menu, 'Pick an input image file',fileparts(fileparts(fileinput)));
395        imageinput=[PathName FileName];%complete file name
396     
397    end   
398    fileinput=imageinput;
399end
400
401%% scan the image file series
402[FilePath,FileName,ImaExt]=fileparts(fileinput);
403% detect the file type, get the movie object if relevant, and look for the corresponding file series:
404% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
405[RootPath,SubdirImages,RootFile,i1_series,tild,j1_series,tild,NomTypeIma,FileType,Object,i1,i2,j1,j2]=find_file_series(FilePath,[FileName ImaExt]);
406
407switch FileType
408    case {'image','multimage','video','mmreader'}
409    otherwise
410        errormsg='invalid input file: enter an image, a movie or civ .nc file';
411        return
412end
413set(handles.RootPath,'String',RootPath)
414set(handles.SubdirImages,'String',SubdirImages)
415set(handles.RootFile,'String',RootFile)
416if strcmp(ExtInput,'.nc')
417    SubDirCiv=SubDir;
418else
419    SubDirCiv=[SubDir '.civ'];
420end
421set(handles.SubdirCiv1,'String',SubDirCiv)
422set(handles.SubdirCiv2,'String',SubDirCiv)
423browse=get(handles.RootPath,'UserData');
424browse.incr_pair=[0 0];%default
425
426%% fill reference indices from the input file indices
427num_ref_i=i1;%efaulmt ref index
428if ~isempty(i2)
429    num_ref_i=floor((num_ref_i+i2)/2);
430end
431num_ref_j=j1;
432if ~isempty(j2)
433    num_ref_j=floor((num_ref_j+j2)/2);
434end
435
436%% scan the images if a civ file has been opened
437MinIndex_i=min(i1_series(i1_series>0));
438MinIndex_j=min(j1_series(j1_series>0));
439MaxIndex_i=max(i1_series(i1_series>0));
440MaxIndex_j=max(j1_series(j1_series>0));
441
442%% look for an image documentation file
443ext_imadoc='';%default
444RootName=fullfile(RootPath,RootFile);
445if exist([RootName '.xml'],'file')
446    ext_imadoc='.xml';
447elseif exist([RootName '.civxml'],'file')
448    ext_imadoc='.civxml';
449elseif exist([RootName '.civ'],'file')
450    ext_imadoc='.civ';
451elseif exist([RootName '.avi'],'file')
452    ext_imadoc='.avi';
453elseif exist([RootName '.AVI'],'file')
454    ext_imadoc='.AVI';
455end
456set(handles.ImaDoc,'String',ext_imadoc)% display the extension name for the image documentation file used
457
458%%  read the time in the image documentation file 
459time=[];
460TimeUnit=''; %default
461CoordUnit='';%default
462pxcm_search=1;
463if ~isempty(ext_imadoc)
464    set(handles.ImaDoc,'BackgroundColor',[1 1 0]) % set edit box to yellow cloro to indicate that the file reading is beginning
465    drawnow
466    switch ext_imadoc
467        case '.civxml'%OBSOLETE
468            [tild,tild,time]=read_civxml([RootName '.civxml']);
469            mode='pair j1-j2';
470            if isempty(nom_type_ima)% dtermine types by default if not already selected by browser or uvmat
471                nom_type_ima='_i_j';
472            end
473        case '.xml'
474            [XmlData,warntext]=imadoc2struct([RootName '.xml']);
475            ext_ima_read=[];
476            nom_type_read=[];
477            if isfield(XmlData,'Heading')&&isfield(XmlData.Heading','ImageName')&&ischar(XmlData.Heading.ImageName)% get image nom type and extension from the xml file
478                %[PP,FF,fc,str2,str_a,str_b,ext_ima_read,nom_type_read]=name2display(XmlData.Heading.ImageName);
479                [tild,tild,tild,tild,tild,tild,tild,tild,nom_type_read]=fileparts_uvmat(XmlData.Heading.ImageName);
480                fullname=fullfile(fileparts(RootName),XmlData.Heading.ImageName); %full name (including path) of the first image defined by the xmle file,
481                if ~exist(fullname,'file')
482                    msgbox_uvmat('WARNING',['FirstImage ' fullname ' defined in the xml file does not exist'])
483                end
484            end
485            if isfield(XmlData,'Time')
486                time=XmlData.Time;
487                %transform .Time to a column vector if it is a line vector thenomenclature uses a single index: correct possible bug in xml
488                if isequal(MaxIndex_i,1) && ~isequal(MaxIndex_j,1)% .Time is a line vector
489                    if numel(nom_type_read)>=2 && isempty(regexp(nom_type_read(2:end),'\D','once'))
490                        time=time';
491                        MaxIndex_i=MaxIndex_j;
492                        MaxIndex_j=1;
493                    end
494                end
495            end
496            if isfield(XmlData,'TimeUnit')
497                TimeUnit=XmlData.TimeUnit;
498            end
499
500            if isfield(XmlData,'GeometryCalib')
501                tsai=XmlData.GeometryCalib;
502                if isfield(tsai,'fx_fy') 
503                    pxcm_search=max(tsai.fx_fy(1),tsai.fx_fy(2));%pixels:cm estimated for the search range
504                end
505                if isfield(tsai,'CoordUnit')
506                    CoordUnit=tsai.CoordUnit;
507                end
508            end
509        case '.civ'% OBSOLETE: case of .civ image documentation file
510            [error,time,TimeUnit,mode,npx,npy]=read_imatext([RootName '.civ']);
511            if error==2, msgbox_uvmat('WARNING',['no file ' RootName '.civ']);
512            elseif error==1, msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file');
513            end
514            nom_type_ima='001a';
515        case {'.avi','.AVI'}
516            nom_type_ima='*';
517            ImaExt=ext_imadoc;
518            set(handles.ListPairMode,'Value',1);
519            set(handles.ListPairMode,'String',{'series(Di)'})
520            dt=0.04;%default
521            if exist([RootName ext_imadoc],'file')==2
522                hhh=which('videoreader');
523                if isempty(hhh)%use old video function of matlab
524                    imainfo=aviinfo([RootName ext_imadoc]);%read infos on the avi movie
525                    dt=1/imainfo.FramesPerSecond;%time interval between successive frames
526                    MaxIndex_i=imainfo.NumFrames;%number of frames
527                    %         XmlData.Time=(0:1/imainfo.FramesPerSecond:(imainfo.NumFrames-1)/imainfo.FramesPerSecond)';
528                    %         nbfield=imainfo.NumFrames;
529                    %         set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FramesPerSecond) 'ms']);%display the elementary time interval in millisec
530                    %         ColorType=imainfo.ImageType;%='truecolor' for color images
531                else %use video function videoreader of matlab
532                    imainfo=get(videoreader([RootName ext_imadoc]));%read infos on the avi movie
533                    dt=1/imainfo.FrameRate;%time interval between successive frames
534                    MaxIndex_i=imainfo.NumberOfFrames;%number of frames
535                    %         XmlData.Time=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames-1)/imainfo.FrameRate)';
536                    %         nbfield=imainfo.NumberOfFrames;
537                    %         set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FrameRate) 'ms']);%display the elementary time interval in millisec
538                    %         ColorType='truecolor';
539                end
540               
541                time=(dt*(0:MaxIndex_i-1))';%list of image times
542                TimeUnit='s';
543            end
544            set(handles.ImaDoc,'BackgroundColor',[1 1 1])% set display box back to whiter
545    end
546end
547%% timing display
548%show the reference image edit box if relevant (not needed for movies or in the absence of time information
549if numel(time)>=2 % if there are at least two time values to define dt
550    MaxIndex_i=min(size(time,1),MaxIndex_i);
551    MaxIndex_j=min(size(time,2),MaxIndex_j);
552    time=[zeros(size(time,1),1) time]; %insert a vertical line of zeros (to deal with zero file indices)
553    time=[zeros(1,size(time,2)); time]; %insert a horizontal line of zeros
554    set(handles.ImaDoc,'UserData',time); %store the matrix of times
555    set(handles.dt_unit,'String',['dt in m' TimeUnit]);
556    set(handles.TimeUnit,'String',TimeUnit);
557else
558    set(handles.ImaDoc,'String',''); %xml file not used for timing
559    time=(i1_series(:,1)+0:size(i1_series,1)-1);% time=index i
560    time=time'*ones(1,size(i1_series,2),1); %makes a time matrix with the same time for all j indices
561    TimeUnit='frame';
562end
563set(handles.ImaDoc,'UserData',time); %store the matrix of times
564set(handles.dt_unit,'String',['dt in m' TimeUnit]);%display dt in unit 10-3 of the time (e.g ms)
565set(handles.TimeUnit,'String',TimeUnit);
566set(handles.nb_field,'String',num2str(MaxIndex_i));
567set(handles.nb_field2,'String',num2str(MaxIndex_j));
568set(handles.CoordUnit,'String',CoordUnit)
569set(handles.SearchRange,'UserData', pxcm_search);
570set(handles.ImaExt,'String',ImaExt)
571set(handles.NomType,'String',NomTypeIma)
572set(handles.ref_i,'String',num2str(num_ref_i))
573set(handles.ref_j,'String',num2str(num_ref_j))
574
575%% update i and j index range if a nc file has been opened or pb withmin max image indices:
576% then set first and last to the inputfile index by default
577first_i=str2num(get(handles.first_i,'String'));
578last_i=str2num(get(handles.last_i,'String'));
579if isempty(first_i) || isempty(last_i)||isempty(MinIndex_i)||isempty(MaxIndex_i)
580    set(handles.first_i,'String',num2str(num_ref_i));
581    set(handles.last_i,'String',num2str(num_ref_i));%
582end
583if ind_opening~=0 || isempty(first_i) || isempty(last_i)|| first_i<MinIndex_i || last_i>MaxIndex_i
584    set(handles.first_i,'String',num2str(num_ref_i));
585    set(handles.last_i,'String',num2str(num_ref_i));%
586end
587
588%j index range
589first_j=str2num(get(handles.first_j,'String'));
590last_j=str2num(get(handles.last_i,'String'));
591if isempty(first_j) || isempty(last_j)||isempty(MinIndex_j)||isempty(MaxIndex_j)
592    set(handles.first_j,'String',num2str(num_ref_j));
593    set(handles.last_j,'String',num2str(num_ref_j));%
594elseif ind_opening~=0 || first_j<MinIndex_j || last_j>MaxIndex_j
595    set(handles.first_j,'String',num2str(num_ref_j));
596set(handles.last_j,'String',num2str(num_ref_j));%
597end
598
599%% set the civ options depending on the input file content when a nc file has been opened
600ListOptions={'CheckCiv1', 'CheckFix1' 'CheckPatch1', 'CheckCiv2', 'CheckFix2', 'CheckPatch2'};
601if ind_opening~=0
602    for index = 1:ind_opening
603        set(handles.(ListOptions{index}),'value',0)
604    end
605end
606for index = ind_opening+2:6
607    set(handles.(ListOptions{index}),'value',0)
608end
609set(handles.(ListOptions{min(ind_opening+1,6)}),'value',1)
610update_CivOptions(handles,ind_opening)
611
612%%  set the menus of image pairs and default selection for civ   %%%%%%%%%%%%%%%%%%%
613%check_letter=~isempty(regexp(NomTypeIma,'[ab|AB]$'));%detect pair label by letter
614if  isequal(NomTypeNc,'_1-2')||isempty(MaxIndex_j)|| (MaxIndex_j==1)
615    set(handles.ListPairMode,'Value',1)
616    set(handles.ListPairMode,'String',{'series(Di)'})   
617elseif  MaxIndex_i==1 && MaxIndex_j>1% simple series in j
618    set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)'})
619    if  MaxIndex_j <= 10
620        set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large
621    end
622else
623    set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)';'series(Di)'})%multiple choice
624    if strcmp(NomTypeNc,'_1-2_1')
625        set(handles.ListPairMode,'Value',3)% advise 'series(Di)'
626    elseif  MaxIndex_j <= 10
627        set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large
628    end
629end
630
631%% scan files to update the subdirectory list display
632listot=dir(RootPath);%directory of RootPath
633idir=0;
634listdir={''};%default
635% get the list of existing civ subdirectories in the path of theinput root  file
636for ilist=1:length(listot)
637    if listot(ilist).isdir
638        name=listot(ilist).name;
639        if ~isequal(name,'.') && ~isequal(name,'..')
640            idir=idir+1;
641            listdir{idir,1}=listot(ilist).name;
642        end
643    end
644end
645
646%% store info
647set(handles.RootPath,'UserData',browse)% store the nomenclature type
648
649%% list the possible index pairs, depending on the option set in ListPairMode
650ListPairMode_Callback([], [], handles)
651
652%% store the root input filename for future opening
653profil_perso=fullfile(prefdir,'uvmat_perso.mat');
654if exist(profil_perso,'file')
655    save (profil_perso,'RootPath','-append'); %store the root name for future opening of uvmat
656else
657    txt=ver('MATLAB');
658    Release=txt.Release;
659    relnumb=str2double(Release(3:4));
660    if relnumb >= 14
661        save (profil_perso,'RootPath','-V6'); %store the root name for future opening of uvmat
662    else
663        save (profil_perso,'RootPath'); %store the root name for future opening of uvmat
664    end
665end
666set(handles.RootPath,'BackgroundColor',[1 1 1])
667
668%------------------------------------------------------------------------
669% --- Executes on carriage return on the subdir checkciv1 edit window
670function SubdirCiv1_Callback(hObject, eventdata, handles)
671%------------------------------------------------------------------------
672SubDir=get(handles.SubdirCiv1,'String');
673menu_str=get(handles.ListSubdirCiv1,'String');% read the list of subdirectories for update
674ichoice=find(strcmp(SubDir,menu_str),1);
675if isempty(ichoice)
676    ilist=numel(menu_str); %select 'new...' in the menu
677else
678    ilist=ichoice;
679end
680set(handles.ListSubdirCiv1,'Value',ilist)% select the selected subdir in the menu
681if get(handles.CheckCiv1,'Value')% if Civ1 is performed
682    set(handles.SubdirCiv2,'String',SubDir);% set by default civ2 directory the same as civ1
683    set(handles.ListSubdirCiv2,'Value',ilist)
684else % if Civ1 data already exist
685    errormsg=find_netcpair_civ(handles,1); %update the list of available pairs from netcdf files in the new directory
686    if ~isempty(errormsg)
687    msgbox_uvmat('ERROR',errormsg)
688    end
689end
690
691%------------------------------------------------------------------------
692% --- Executes on carriage return on the SubDir checkciv1 edit window
693function SubdirCiv2_Callback(hObject, eventdata, handles)
694%------------------------------------------------------------------------
695SubDir=get(handles.SubdirCiv1,'String');
696menu_str=get(handles.ListSubdirCiv2,'String');% read the list of subdirectories for update
697ichoice=find(strcmp(SubDir,menu_str),1);
698if isempty(ichoice)
699    ilist=numel(menu_str); %select 'new...' in the menu
700else
701    ilist=ichoice;
702end
703set(handles.ListSubdirCiv2,'Value',ilist)% select the selected subdir in the menu
704%update the list of available pairs from netcdf files in the new directory
705if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
706    errormsg=find_netcpair_civ(handles,2);
707        if ~isempty(errormsg)
708    msgbox_uvmat('ERROR',errormsg)
709    end
710end
711
712%------------------------------------------------------------------------
713% --- Executes on button press in CheckCiv1.
714function CheckCiv1_Callback(hObject, eventdata, handles)
715%------------------------------------------------------------------------
716update_CivOptions(handles,0)
717
718%------------------------------------------------------------------------
719% --- Executes on button press in CheckFix1.
720function CheckFix1_Callback(hObject, eventdata, handles)
721%------------------------------------------------------------------------
722update_CivOptions(handles,0)
723
724%------------------------------------------------------------------------
725% --- Executes on button press in CheckPatch1.
726function CheckPatch1_Callback(hObject, eventdata, handles)
727%------------------------------------------------------------------------
728update_CivOptions(handles,0)
729
730%------------------------------------------------------------------------
731% --- Executes on button press in CheckCiv2.
732function CheckCiv2_Callback(hObject, eventdata, handles)
733%------------------------------------------------------------------------
734update_CivOptions(handles,0)
735
736%------------------------------------------------------------------------
737% --- Executes on button press in CheckFix2.
738function CheckFix2_Callback(hObject, eventdata, handles)
739%------------------------------------------------------------------------
740update_CivOptions(handles,0)
741
742%------------------------------------------------------------------------
743% --- Executes on button press in CheckPatch2.
744function CheckPatch2_Callback(hObject, eventdata, handles)
745%------------------------------------------------------------------------
746update_CivOptions(handles,0)
747
748%------------------------------------------------------------------------
749% --- activated by any checkbox controling the selection of Civ1,Fix1,Patch1,Civ2,Fix2,Patch2
750function update_CivOptions(handles,opening)
751%------------------------------------------------------------------------
752checkbox=zeros(1,6);
753checkbox(1)=get(handles.CheckCiv1,'Value');
754checkbox(2)=get(handles.CheckFix1,'Value');
755checkbox(3)=get(handles.CheckPatch1,'Value');
756checkbox(4)=get(handles.CheckCiv2,'Value');
757checkbox(5)=get(handles.CheckFix2,'Value');
758checkbox(6)=get(handles.CheckPatch2,'Value');
759ind_selected=find(checkbox,1);
760if ~isempty(ind_selected)
761    RootPath=get(handles.RootPath,'String');
762    if isempty(RootPath)
763        msgbox_uvmat('ERROR','Please open an image or PIV .nc file with the upper bar menu Open/Browse...')
764        return
765    end
766end
767set(handles.PairIndices,'Visible','on')
768set(handles.SubdirCiv1,'Visible','on')
769set(handles.TitleSubdirCiv1,'Visible','on')
770if ~opening
771    errormsg=find_netcpair_civ(handles,1); % select the available netcdf files
772    if ~isempty(errormsg)
773        msgbox_uvmat('ERROR',errormsg)
774    end
775end
776if max(checkbox(4:6))% case of civ2 pair choice needed
777    set(handles.TitlePairCiv2,'Visible','on')
778    set(handles.TitleSubdirCiv2,'Visible','on')
779    set(handles.SubdirCiv2,'Visible','on')
780    %set(handles.ListSubdirCiv2,'Visible','on')
781    set(handles.ListPairCiv2,'Visible','on')
782    if ~opening
783        errormsg=find_netcpair_civ(handles,2); % select the available netcdf files
784        if ~isempty(errormsg)
785            msgbox_uvmat('ERROR',errormsg)
786        end
787    end
788else
789    set(handles.TitleSubdirCiv2,'Visible','off')
790    set(handles.SubdirCiv2,'Visible','off')
791    set(handles.ListPairCiv2,'Visible','off')
792end
793options={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'};
794for ilist=1:length(options)
795    if checkbox(ilist)
796        set(handles.(options{ilist}),'Visible','on')
797    else
798        set(handles.(options{ilist}),'Visible','off')
799    end
800end
801
802%------------------------------------------------------------------------
803% --- Executes on button press in RUN: processing on local computer
804function RUN_Callback(hObject, eventdata, handles)
805%------------------------------------------------------------------------
806set(handles.RUN, 'Enable','Off')
807set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
808batch=0;
809errormsg=launch_jobs(hObject, eventdata, handles,batch);
810set(handles.RUN, 'Enable','On')
811set(handles.RUN,'BackgroundColor',[1 0 0])
812
813% display errors or start status callback to visualise results
814if ~isempty(errormsg)
815    display(errormsg)
816    msgbox_uvmat('ERROR',errormsg)
817elseif  isfield(handles,'status') %&& ~isequal(get(handles.ListPairMode,'Value'),3)
818    set(handles.status,'Value',1);%suppress status display
819    status_Callback(hObject, eventdata, handles)
820end
821
822%------------------------------------------------------------------------
823% --- Executes on button press in BATCH: remote processing
824function BATCH_Callback(hObject, eventdata, handles)
825% -----------------------------------------------------------------------
826set(handles.BATCH, 'Enable','Off')
827set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])
828batch=1;
829errormsg=launch_jobs(hObject, eventdata, handles, batch);
830set(handles.BATCH, 'Enable','On')
831set(handles.BATCH,'BackgroundColor',[1 0 0])
832
833% display errors or start status callback to visualise results
834if ~isempty(errormsg)
835    display(errormsg)
836    msgbox_uvmat('ERROR',errormsg)
837elseif isfield(handles,'status')
838    set(handles.status,'Value',1);%suppress status display
839    status_Callback(hObject, eventdata, handles)
840end
841
842%-------------------------------------------------------------------
843% --- Executes on button press in status.
844function status_Callback(hObject, eventdata, handles)
845%-------------------------------------------------------------------
846val=get(handles.status,'Value');
847if val==0
848    set(handles.status,'BackgroundColor',[0 1 0])
849    hfig=findobj(allchild(0),'name','civ_status');
850    if ~isempty(hfig)
851        delete(hfig)
852    end
853    return
854end
855set(handles.status,'BackgroundColor',[1 1 0])
856drawnow
857listtype={'civ1','fix1','patch1','civ2','fix2','patch2'};
858Param.CheckCiv1=get(handles.CheckCiv1,'Value');
859Param.CheckFix1=get(handles.CheckFix1,'Value');
860Param.CheckPatch1=get(handles.CheckPatch1,'Value');
861Param.CheckCiv2=get(handles.CheckCiv2,'Value');
862Param.CheckFix2=get(handles.CheckFix2,'Value');
863Param.CheckPatch2=get(handles.CheckPatch2,'Value');
864box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2];
865
866option_civ=find(box_test,1,'last');%last selected option (non-zero index of box_test)
867filecell=get(handles.civ,'UserData');%retrieve the list of output files expected for PIV
868test_new=0;
869if ~isfield(filecell,'nc')
870    test_new=1;
871    [ref_i,ref_j,errormsg]=find_ref_indices(handles);
872    if ~isempty(errormsg)
873        msgbox_uvmat('ERROR',errormsg)
874        return
875    end
876    filecell=set_civ_filenames(handles,ref_i,ref_j,box_test);%determine the output file expected from the GUI status
877end
878if ~isequal(box_test(4:6),[0 0 0])
879    civ_files=filecell.nc.civ2;%case of civ2 operations
880else
881    civ_files=filecell.nc.civ1;
882end
883[root,filename,ext]=fileparts(civ_files{1});
884[rootroot,SubDir,extdir]=fileparts(root);
885hfig=findobj(allchild(0),'name','civ_status');
886if isempty(hfig)
887    hfig=figure('DeleteFcn',@stop_status);
888    set(hfig,'MenuBar','none')% suppress the menu bar
889    set(hfig,'NumberTitle','off')%suppress the fig number in the title
890    set(hfig,'name','civ_status')
891    set(hfig,'tag','civ_status')
892    set(hfig,'UserData',civ_files)
893    hlist= uicontrol('Style','listbox','Units','normalized', 'Position',[0.05 0.09 0.9 0.71], 'Callback', {'open_uvmat'},'tag','list');
894    uicontrol('Style','edit','Units','normalized', 'Position', [0.05 0.87 0.9 0.1],'tag','msgbox','Max',2,'String','checking files...');
895    uicontrol('Style','frame','Units','normalized', 'Position', [0.05 0.81 0.9 0.05]);
896    uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.7 0.01 0.2 0.07],'String','Close','FontWeight','bold','FontUnits','normalized','FontSize',0.9,'Callback',@close_GUI);
897    hrefresh=uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.1 0.01 0.2 0.07],'String','Refresh','FontWeight','bold','FontUnits','normalized','FontSize',0.9,'Callback',@refresh_GUI);
898    BarPosition=[0.05 0.81 0.01 0.05];
899    uicontrol('Style','frame','Units','normalized', 'Position',BarPosition ,'BackgroundColor',[1 0 0],'tag','waitbar');
900    drawnow
901end
902set(hrefresh,'UserData',option_civ)
903        filepath=fileparts(civ_files{1});
904set(hlist,'UserData',fileparts(filepath))
905refresh_GUI(hrefresh,[])
906
907%------------------------------------------------------------------------   
908% launched by refreshing the status figure
909function refresh_GUI(hObject, eventdata)
910%------------------------------------------------------------------------
911Tabchar={};
912BarPosition=[0.05 0.81 0.01 0.05];
913hfig=get(hObject,'parent');
914civ_files=get(hfig,'UserData');
915        [filepath,filename,ext]=fileparts(civ_files{1});
916        [tild,SubDir,extdir]=fileparts(filepath);
917        SubDir=[SubDir extdir];
918option_civ=get(hObject,'UserData');
919nbfiles=numel(civ_files);
920count=0;
921testrecent=0;
922% while count<nbfiles
923    count=0;
924    datnum=zeros(1,nbfiles);
925    for ifile=1:nbfiles
926        detect=exist(civ_files{ifile},'file'); % check the existence of the file
927        option=0;
928        if detect==0
929            option_str='not created';
930        else
931            datfile=dir(civ_files{ifile});
932            if isfield(datfile,'datenum')
933                datnum(ifile)=datfile.datenum;%only available in recent matlab versions
934                testrecent=1;
935            end
936            filefound(ifile)={datfile.name};
937            lastfield='';
938            % check the content  netcdf file
939            Data=nc2struct(civ_files{ifile},'ListGlobalAttribute','CivStage','patch2','fix2','civ2','patch','fix');
940            option_list={'civ1','fix1','patch1','civ2','fix2','patch2'};
941            if ~isempty(Data.CivStage)
942                option=Data.CivStage;%case of Matlab civ
943            else
944                if ~isempty(Data.patch2) && isequal(Data.patch2,1)
945                    option=6;
946                elseif ~isempty(Data.fix2) && isequal(Data.fix2,1)
947                    option=5;
948                elseif ~isempty(Data.civ2) && isequal(Data.civ2,1);
949                    option=4;
950                elseif ~isempty(Data.patch) && isequal(Data.patch,1);
951                    option=3;
952                elseif ~isempty(Data.fix) && isequal(Data.fix,1);
953                    option=2;
954                else
955                    option=1;
956                end
957            end
958            option_str=option_list{option};
959        end
960        if option >= option_civ
961            count=count+1;
962        end
963        [filepath,filename,ext]=fileparts(civ_files{ifile});
964        Tabchar{ifile,1}=[fullfile(SubDir,filename) ext  '...' option_str];
965    end
966    datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
967    if isempty(datnum)
968        if testrecent
969            message='no civ result created yet';
970        else
971            message='';
972        end
973    else
974        datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
975        [first,ind]=min(datnum);
976        [last,indlast]=max(datnum);
977%         if test_new
978%             message='existing file status, no processing launched yet';
979%         else
980        message={[num2str(count) ' file(s) done over ' num2str(nbfiles)] ;['oldest modification:  ' cell2mat(filefound(ind)) ' : ' datestr(first)];...
981            ['latest modification:  ' cell2mat(filefound(indlast)) ' : ' datestr(last)]};
982%         end
983    end
984    %hfig=findobj(allchild(0),'name','civ_status');
985%     if isempty(hfig)% the status list has been deleted
986%         return
987%     else
988        hlist=findobj(hfig,'tag','list');
989        hmsgbox=findobj(hfig,'tag','msgbox');
990        hwaitbar=findobj(hfig,'tag','waitbar');
991        set(hlist,'String',Tabchar)
992        set(hmsgbox,'String', message)
993        if count>0 %&& ~test_new
994            BarPosition(3)=0.9*count/nbfiles;
995            set(hwaitbar,'Position',BarPosition)
996        end
997%     end
998%     [root,filename,ext]=fileparts(civ_files{1});
999% [rootroot,SubDir,extdir]=fileparts(root);
1000%
1001%     set(hlist,'UserData',rootroot)
1002%     if count<10||(nbfiles-count)<10
1003%     pause(.5)% wait 0.5 seconds for next check
1004%     else
1005%         pause(10)% wait 10 seconds for next check
1006%     end
1007% end
1008
1009%------------------------------------------------------------------------   
1010% launched by deleting the status figure
1011function stop_status(hObject, eventdata)
1012%------------------------------------------------------------------------
1013hciv=findobj(allchild(0),'tag','civ');
1014hhciv=guidata(hciv);
1015set(hhciv.status,'value',0) %reset the status uicontrol in the GUI civ
1016set(hhciv.status,'BackgroundColor',[0 1 0])
1017
1018%------------------------------------------------------------------------   
1019% launched by pressing OK on the status figure
1020function close_GUI(hObject, eventdata)
1021%------------------------------------------------------------------------
1022    delete(gcbf)
1023
1024
1025%--------------orm----------------------------------------------------------
1026% --- Main lauch command, called by RUN and BATCH
1027function errormsg=launch_jobs(hObject, eventdata, handles, batch)
1028%-----------------------------------------------------------------------
1029errormsg='';%default
1030
1031%% read the input parameters from the  GUI civ
1032Param=read_GUI(handles.civ);
1033
1034%% check the selected list of operations:
1035operations={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'};
1036box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2];
1037index_first=find(box_test==1,1);
1038if isempty(index_first)
1039    errormsg='no selected operation';
1040    return
1041end
1042index_last=find(box_test==1,1,'last');
1043box_used=box_test(index_first : index_last);
1044[box_missing,ind_missing]=min(box_used);
1045if isequal(box_missing,0); %there is a missing step in the sequence of operations
1046    errormsg=['missing' cell2mat(operations(ind_missing))];
1047    return
1048end
1049
1050%% check mask if selecetd
1051%could be included in get_mask callback ?
1052if isequal(get(handles.CheckMask,'Value'),1)
1053    maskname=get(handles.Mask,'String');
1054    if ~exist(maskname,'file')
1055        get_mask_civ1_Callback(hObject, eventdata, handles);
1056    end
1057end
1058if isequal(get(handles.CheckMask,'Value'),1)
1059    maskname=get(handles.Mask,'String');
1060    if ~exist(maskname,'file')
1061        get_mask_fix1_Callback(hObject, eventdata, handles);
1062    end
1063end
1064if isequal(get(handles.CheckMask,'Value'),1)
1065    maskname=get(handles.Mask,'String');
1066    if ~exist(maskname,'file')
1067        get_mask_civ2_Callback(hObject, eventdata, handles);
1068    end
1069end
1070if isequal(get(handles.CheckMask,'Value'),1)
1071    maskname=get(handles.Mask,'String');
1072    if ~exist(maskname,'file')
1073        get_mask_fix2_Callback(hObject, eventdata, handles);
1074    end
1075end
1076
1077%% reinitialise status callback
1078if isfield(handles,'status')
1079    set(handles.status,'Value',0);%suppress status display
1080    status_Callback(hObject, eventdata, handles)
1081end
1082
1083%% read the PARAM.xml file to get the binaries (and batch_mode if batch)
1084path_civ=fileparts(which('civ')); %path to the source directory of uvmat
1085xmlfile='PARAM.xml';
1086if exist(xmlfile,'file')% search parameter xml file in the whole matlab path
1087    t=xmltree(xmlfile);
1088    s=convert(t);
1089else
1090    errormsg=['no file ' xmlfile];
1091    return
1092end
1093test_interp=0; %eviter les variables test_ (LG)
1094if batch
1095    if isfield(s,'BatchParam')
1096        Param.xml=s.BatchParam;
1097        if isfield(Param.xml,'BatchMode')
1098            batch_mode=Param.xml.BatchMode;
1099            if ~ismember(batch_mode,{'sge','oar'})
1100                errormsg=['batch mode ' batch_mode ' not supported by UVMAT'];
1101                return
1102            end
1103        end
1104    else
1105        errormsg='no batch civ binaries defined in PARAM.xml';
1106        return
1107    end
1108else % run
1109    if isfield(s,'RunParam')
1110        Param.xml=s.RunParam;
1111    else
1112        errormsg='no run civ binaries defined in PARAM.xml';
1113        return
1114    end
1115end
1116
1117%% check batch mode supported
1118if batch
1119    switch batch_mode
1120        case 'sge'
1121            test_command='qstat';
1122        case 'oar'
1123            test_command='oarstat';
1124    end   
1125    [s,w]=system(test_command);
1126    if ~isequal(s,0)
1127        errormsg=[batch_mode ' batch system not available'];
1128        return
1129    end
1130end
1131
1132%% check if the binaries exist
1133ListProgram=get(handles.ListProgram,'String');
1134CivMode=ListProgram{get(handles.ListProgram,'Value')};
1135binary_list={};
1136switch CivMode
1137    case 'CivX'
1138        binary_list={'Civ1Bin','Civ2Bin','PatchBin','FixBin'};
1139    case 'CivAll'% desactivated option
1140        binary_list={'Civ'};
1141    case 'Matlab'
1142        if batch
1143            binary_list={'CivmBin'};
1144            % verifier MenuMatlab installe sur le cluster
1145            % difficile a faire a priori
1146        end         
1147end
1148for bin_name=binary_list %loop on the list of binaries
1149    if isfield(Param.xml,bin_name{1})% bin_name{1} =current name in the list
1150        if exist(Param.xml.(bin_name{1}),'file')
1151            [path,name,ext]=fileparts(Param.xml.(bin_name{1}));
1152            currentdir=pwd;
1153            if exist(path,'dir')
1154                cd(path);
1155                binpath=pwd;%path of the binary
1156                Param.xml.(bin_name{1})=fullfile(binpath,[name ext]);
1157                cd(currentdir)
1158            else
1159                errormsg=['path ' path ' for binaries defined in PARAM.xml does not exist'];
1160                return
1161            end
1162        else  %look for the full path if the file name has been defined with a relative path in PARAM.xm
1163            fullname=fullfile(path_civ,Param.xml.(bin_name{1}));
1164            if exist(fullname,'file')
1165                Param.xml.(bin_name{1})=fullname;
1166            else
1167                errormsg=['Binary ' Param.xml.(bin_name{1}) ' defined in PARAM.xml does not exist'];
1168                return
1169            end
1170        end
1171    end
1172end
1173display('files OK, processing...')
1174
1175%% set the list of files and check them
1176display('checking the files...')
1177[ref_i,ref_j,errormsg]=find_ref_indices(handles);
1178if ~isempty(errormsg)
1179    return
1180end
1181[filecell,i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,tild,tild,compare,errormsg]=...
1182    set_civ_filenames(handles,ref_i,ref_j,box_test);
1183if ~isempty(errormsg)
1184    return
1185end
1186% if isempty(filecell)% (error message displayed in fct set_civ_filenames)
1187%     return
1188% end
1189Rootbat=fileparts(filecell.nc.civ1{1,1});%output netcdf file (without extention)
1190set(handles.civ,'UserData',filecell);%store for futur use of status callback
1191nbfield=numel(i1_civ1);
1192nbslice=numel(j1_civ1);
1193if ~strcmp(CivMode,'CivX')
1194    if Param.CheckCiv1
1195        [Param.Civ1.FileTypeA,FileInfo,Param.Civ1.ImageA]=get_file_type(filecell.ima1.civ1{1});
1196        [Param.Civ1.FileTypeB,FileInfo,Param.Civ1.ImageB]=get_file_type(filecell.ima2.civ1{1});
1197    end
1198    if Param.CheckCiv2
1199        [Param.Civ2.FileTypeA,FileInfo,Param.Civ2.ImageA]=get_file_type(filecell.ima1.civ2{1});
1200        [Param.Civ2.FileTypeB,FileInfo,Param.Civ2.ImageB]=get_file_type(filecell.ima2.civ2{1});
1201    end
1202end
1203
1204%% MAIN LOOP
1205time=get(handles.ImaDoc,'UserData'); %get the set of times
1206TimeUnit=get(handles.TimeUnit,'String');
1207checkframe=strcmp(TimeUnit,'frame');
1208batch_file_list=[];%should be renamed file_list, can be used for xml or bash files
1209 
1210for ifile=1:nbfield
1211    for j=1:nbslice
1212        % initiate system command
1213        switch CivMode
1214            case 'CivX'
1215                if isunix % check: necessaire aussi en RUN?
1216                    cmd=['#!/bin/bash \n '...
1217                        '#$ -cwd \n '...
1218                        'hostname && date \n '...
1219                        'umask 002 \n'];%allow writting access to created files for user group
1220                else
1221                    cmd=[];
1222                end
1223            case 'CivAll'
1224                CivAllxml=xmltree;% xml contents,  all parameters
1225                CivAllCmd='';
1226                CivAllxml=set(CivAllxml,1,'name','CivDoc');
1227        end
1228           
1229        % define output file name
1230        if Param.CheckCiv2==1 || Param.CheckFix2==1 || Param.CheckPatch2==1
1231            OutputFile=filecell.nc.civ2{ifile,j};
1232        else
1233            OutputFile=filecell.nc.civ1{ifile,j};
1234        end
1235        OutputFile=regexprep(OutputFile,'.nc','');
1236       
1237        if Param.CheckCiv1
1238            % read image-dependent parameters
1239           
1240            if ~checkframe% && size(time,1)>=i2_civ1(ifile) && size(time,2)>=j2_civ1(j)
1241                Param.Civ1.Dt=(time(i2_civ1(ifile)+1,j2_civ1(j)+1)-time(i1_civ1(ifile)+1,j1_civ1(j)+1));
1242            else
1243                Param.Civ1.Dt=1;
1244            end
1245            Param.Civ1.Time=((time(i2_civ1(ifile)+1,j2_civ1(j)+1)+time(i1_civ1(ifile)+1,j1_civ1(j)+1))/2);
1246            if strcmp(CivMode,'CivX')
1247                Param.Civ1.term_a=num2stra(j1_civ1(j),nom_type_nc);%UTILITE?
1248                Param.Civ1.term_b=num2stra(j2_civ1(j),nom_type_nc);%
1249            end
1250            if isfield(Param.Civ1,'FileTypeA')&&(strcmp(Param.Civ1.FileTypeA,'video')|| strcmp(Param.Civ1.FileTypeA,'mmreader'))
1251                %   ImageInfo=get(VideoReader(fullfile(Param.RootPath,[Param.RootFile Param.ImaExt])));
1252                ImageInfo=get(Param.Civ1.ImageA);
1253                %                 elseif strcmp(Param.Civ1.FileTypeA,'mmreader')
1254                %                     ImageInfo=get(mmreader(fullfile(Param.RootPath,[Param.RootFile Param.ImaExt])));
1255                Param.Civ1.ImageBitDepth=ImageInfo.BitsPerPixel/3;
1256                if batch
1257                    Param.Civ1.ImageA=filecell.ima1.civ1{ifile,j};%file name must be used for batch instead of video object
1258                    Param.Civ1.ImageB=filecell.ima2.civ1{ifile,j};
1259                end
1260            else
1261                Param.Civ1.ImageA=filecell.ima1.civ1{ifile,j};
1262                Param.Civ1.ImageB=filecell.ima2.civ1{ifile,j};
1263               % form=imformats(regexprep(get(handles.ImaExt,'String'),'^.',''));%look for image formats
1264                ImageInfo=imfinfo(filecell.ima1.civ1{1,1});%read the first image to get the size
1265                Param.Civ1.ImageBitDepth=ImageInfo.BitDepth;
1266            end
1267            Param.Civ1.ImageWidth=ImageInfo.Width;
1268            Param.Civ1.ImageHeight=ImageInfo.Height;
1269            Param.Civ1.FrameIndexA=i1_civ1(ifile);
1270            Param.Civ1.FrameIndexB=i2_civ1(ifile);
1271            % read mask )parameters
1272            if Param.Civ1.CheckMask % the lines below should be changed with the new gui
1273                if ~exist(Param.Civ1.Mask,'file')
1274                    maskbase=[filecell.filebase '_' Param.Civ1.Mask]; %
1275                    nbslice_mask=str2double(Param.Civ1.Mask(1:end-4)); %
1276                    i1_mask=mod(i1_civ1(ifile)-1,nbslice_mask)+1;
1277                    [RootPathMask,RootFileMask]=fileparts(maskbase);
1278                    Param.Civ1.Mask=fullfile_uvmat(RootPathMask,[],RootFileMask,'.png','_1',i1_mask);
1279                end
1280            end
1281            % read grid parameters
1282            if Param.Civ1.CheckGrid
1283                if numel(Param.Civ1.Grid)>=4 && isequal(Param.Civ1.Grid(end-3:end),'grid')
1284                    nbslice_grid=str2double(Param.Civ1.Grid(1:end-4)); %
1285                    if ~isnan(nbslice_grid)
1286                        i1_grid=mod(i1_civ1(ifile)-1,nbslice_grid)+1;
1287                        Param.Civ1.Grid=[filecell.filebase '_' fullfile_uvmat('','',Param.Civ1.Grid,'.grid','_1',i1_grid)];
1288                        %                         Param.Civ1.Grid=[filecell.filebase '_' name_generator(Param.Civ1.Grid,i1_grid,1,'.grid','_i')];
1289                        if ~exist(Param.Civ1.GridName,'file')
1290                            errormsg='grid file absent for civ1';
1291                            return
1292                        end
1293                    elseif ~exist(Param.Civ1.Grid,'file')
1294                        errormsg='grid file absent for civ1';
1295                        return
1296                    end
1297                end
1298            end
1299           
1300            % send command
1301            switch CivMode
1302                case 'CivX'
1303                    [cmd_civ,errormsg]=cmd_civ1(filecell.nc.civ1{ifile,j},Param);
1304                    cmd=[cmd cmd_civ '\n'];
1305                    if ~isempty(errormsg)
1306                        return
1307                    end
1308                case 'CivAll'
1309                    CivAllCmd=[CivAllCmd ' civ1 '];
1310                    str=CIV1_CMD_Unified(filecell.nc.civ1{ifile,j},'',Param.Civ1);
1311                    fieldnames=fields(str);
1312                    [CivAllxml,uid_civ1]=add(CivAllxml,1,'element','civ1');
1313                    for ilist=1:length(fieldnames)
1314                        val=eval(['str.' fieldnames{ilist}]);
1315                        if ischar(val)
1316                            [CivAllxml,uid_t]=add(CivAllxml,uid_civ1,'element',fieldnames{ilist});
1317                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1318                        end
1319                    end
1320            end
1321        end
1322       
1323        if Param.CheckFix1
1324            switch CivMode
1325                case 'CivX'
1326                    cmd=[cmd...
1327                        cmd_fix(filecell.nc.civ1{ifile,j},Param,'Fix1') '\n'];
1328                case 'CivAll'%to abandon
1329                    fix1.inputFileName=filecell.nc.civ1{ifile,j} ;
1330                    fix1.fi1=num2str(param.fix1.flagindex1(1));
1331                    fix1.fi2=num2str(param.fix1.flagindex1(2));
1332                    fix1.fi3=num2str(param.fix1.flagindex1(3));
1333                    fix1.threshC=num2str(param.fix1.thresh_vecC1);
1334                    fix1.threshV=num2str(param.fix1.thresh_vel1);
1335                    fieldnames=fields(fix1);
1336                    [CivAllxml,uid_fix1]=add(CivAllxml,1,'element','fix1');
1337                    for ilist=1:length(fieldnames)
1338                        val=eval(['fix1.' fieldnames{ilist}]);
1339                        if ischar(val)
1340                            [CivAllxml,uid_t]=add(CivAllxml,uid_fix1,'element',fieldnames{ilist});
1341                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1342                        end
1343                    end
1344                    CivAllCmd=[CivAllCmd ' fix1 '];
1345            end
1346        end
1347       
1348        %CheckPatch1
1349        if Param.CheckPatch1==1
1350            switch CivMode
1351                case 'CivX'
1352                    cmd=[cmd...
1353                        cmd_patch(filecell.nc.civ1{ifile,j},Param,'Patch1') '\n'];
1354                case 'CivAll'
1355                    patch1.inputFileName=filecell.nc.civ1{ifile,j} ;
1356                    patch1.nopt=subdomain_patch1;
1357                    patch1.maxdiff=thresh_patch1;
1358                    patch1.ro=rho_patch1;
1359                    test_grid=get(handles.get_gridpatch1,'Value');
1360                    if test_grid
1361                        patch1.gridflag='y';
1362                        gridname=get(handles.grid_patch1,'String');
1363                        if isequal(gridname(end-3:end),'grid')
1364                            nbslice_grid=str2double(gridname(1:end-4)); %
1365                            if ~isnan(nbslice_grid)
1366                                i1_grid=mod(i1_civ1(ifile)-1,nbslice_grid)+1;
1367                                patch1.gridPatch=[filecell.filebase '_' fullfile_uvmat('','',gridname,'.grid','_1',i1_grid)];
1368%                                 patch1.gridPatch=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')];
1369                                if ~exist(patch1.gridPatch,'file')
1370                                    errormsg='grid file absent for patch1';
1371                                    return
1372                                end
1373                            elseif exist(gridname,'file')
1374                                patch1.gridPatch=gridname;
1375                            else
1376                                errormsg='grid file absent for patch1';
1377                                return
1378                            end
1379                        end
1380                    else
1381                        patch1.gridPatch='none';
1382                        patch1.gridflag='n';
1383                        patch1.m=nx_patch1;
1384                        patch1.n=ny_patch1;
1385                    end
1386                    patch1.convectFlow='n';
1387                    fieldnames=fields(patch1);
1388                    [CivAllxml,uid_patch1]=add(CivAllxml,1,'element','patch1');
1389                    for ilist=1:length(fieldnames)
1390                        val=eval(['patch1.' fieldnames{ilist}]);
1391                        if ischar(val)
1392                            [CivAllxml,uid_t]=add(CivAllxml,uid_patch1,'element',fieldnames{ilist});
1393                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1394                        end
1395                    end
1396                    CivAllCmd=[CivAllCmd ' patch1 '];
1397            end
1398        end
1399        if Param.CheckCiv2==1
1400            if isfield(Param.Civ2,'FileTypeA') &&(strcmp(Param.Civ2.FileTypeA,'video')|| strcmp(Param.Civ2.FileTypeA,'mmreader'))
1401                %   ImageInfo=get(VideoReader(fullfile(Param.RootPath,[Param.RootFile Param.ImaExt])));
1402                ImageInfo=get(Param.Civ2.ImageA);
1403                %                 elseif strcmp(Param.Civ1.FileTypeA,'mmreader')
1404                %                     ImageInfo=get(mmreader(fullfile(Param.RootPath,[Param.RootFile Param.ImaExt])));
1405                Param.Civ2.ImageBitDepth=ImageInfo.BitsPerPixel/3;
1406                if batch
1407                    Param.Civ2.ImageA=filecell.ima1.civ2{ifile,j};%file name must be used for batch instead of video object
1408                    Param.Civ2.ImageB=filecell.ima2.civ2{ifile,j};
1409                end
1410            else
1411                Param.Civ2.ImageA=filecell.ima1.civ2{ifile,j};
1412                Param.Civ2.ImageB=filecell.ima2.civ2{ifile,j};
1413                form=imformats(regexprep(get(handles.ImaExt,'String'),'^.',''));%look for image formats
1414                ImageInfo=imfinfo(filecell.ima1.civ2{1,1});%read the first image to get the size
1415                Param.Civ2.ImageBitDepth=ImageInfo.BitDepth;
1416            end
1417           
1418            if ~checkframe %&& size(time,1)>=i2_civ2(ifile) && size(time,2)>=j2_civ2(j)
1419                Param.Civ2.Dt=time(i2_civ2(ifile)+1,j2_civ2(j)+1)-time(i1_civ2(ifile)+1,j1_civ2(j)+1);
1420            else
1421                Param.Civ2.Dt=1;
1422            end
1423            Param.Civ2.Time=(time(i2_civ2(ifile)+1,j2_civ2(j)+1)+time(i1_civ2(ifile)+1,j1_civ2(j)+1))/2;
1424            if strcmp(CivMode,'CivX')
1425            Param.Civ2.term_a=num2stra(j1_civ2(j),nom_type_nc);
1426            Param.Civ2.term_b=num2stra(j2_civ2(j),nom_type_nc);
1427            end
1428            Param.Civ2.filename_nc1=filecell.nc.civ1{ifile,j};
1429            Param.Civ2.filename_nc1(end-2:end)=[]; % remove '.nc'
1430           
1431            % mask
1432            if Param.Civ2.CheckMask
1433                if ~exist(Param.Civ2.Mask,'file')
1434                    maskbase=[filecell.filebase '_' Param.Civ2.Mask]; %
1435                    nbslice_mask=str2double(Param.Civ2.Mask(1:end-4)); %
1436                    i1_mask=mod(i1_civ2(ifile)-1,nbslice_mask)+1;
1437                    [RootPathMask,RootFileMask]=fileparts(maskbase);
1438                    Param.Civ2.Mask=fullfile_uvmat(RootPathMask,[],RootFileMask,'.png','_1',i1_mask);
1439%                     Param.Civ2.Mask=name_generator(maskbase,i1_mask,1,'.png','_i');
1440                end
1441            end
1442            %grid
1443            if Param.Civ2.CheckGrid
1444                if numel(Param.Civ2.Grid)>=4 && isequal(Param.Civ2.Grid(end-3:end),'grid')
1445                    nbslice_grid=str2double(Param.Civ2.Grid(1:end-4)); %
1446                    if ~isnan(nbslice_grid)
1447                        i1_grid=mod(i1_civ2(ifile)-1,nbslice_grid)+1;
1448                        Param.Civ2.Grid=[filecell.filebase '_' fullfile_uvmat('','',gridname,'.grid','_1',i1_grid)];
1449%                         Param.Civ2.Grid=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')];
1450                    end
1451                end
1452            end
1453            form=imformats(regexprep(get(handles.ImaExt,'String'),'^.',''));%look for image formats
1454            if isempty(form)
1455               % ImageInfo=get(VideoReader(fullfile());
1456                Param.Civ2.ImageBitDepth=ImageInfo.BitsPerPixel/3;
1457            else
1458                ImageInfo=imfinfo(filecell.ima1.civ2{1,1});%read the first image to get the size
1459                Param.Civ2.ImageBitDepth=ImageInfo.BitDepth;
1460            end
1461            Param.Civ2.ImageWidth=ImageInfo.Width;
1462            Param.Civ2.ImageHeight=ImageInfo.Height;
1463            Param.Civ2.FrameIndexA=i1_civ2(ifile);
1464             Param.Civ2.FrameIndexB=i2_civ2(ifile);
1465%             Param.Civ2.i1=i1_civ2(ifile);
1466%             Param.Civ2.i2=i2_civ2(ifile);
1467            switch CivMode
1468                case 'CivX'
1469                    cmd=[cmd...
1470                        cmd_civ2(filecell.nc.civ2{ifile,j},Param) '\n'];
1471                case 'CivAll'
1472                    CivAllCmd=[CivAllCmd ' civ2 '];
1473                    str=CIV2_CMD_Unified(filecell.nc.civ2{ifile,j},'',Param.Civ2);
1474                    fieldnames=fields(str);
1475                    [CivAllxml,uid_civ2]=add(CivAllxml,1,'element','civ2');
1476                    for ilist=1:length(fieldnames)
1477                        val=eval(['str.' fieldnames{ilist}]);
1478                        if ischar(val)
1479                            [CivAllxml,uid_t]=add(CivAllxml,uid_civ2,'element',fieldnames{ilist});
1480                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1481                        end
1482                    end
1483            end
1484        end
1485       
1486        % CheckFix2
1487        if Param.CheckFix2==1
1488            switch CivMode
1489                case 'CivX'
1490                    cmd=[cmd...
1491                        cmd_fix(filecell.nc.civ2{ifile,j},Param,'Fix2') '\n'];
1492                case 'CivAll'
1493                    fix2.inputFileName=filecell.nc.civ2{ifile,j} ;
1494                    fix2.fi1=num2str(flagindex2(1));
1495                    fix2.fi2=num2str(flagindex2(2));
1496                    fix2.fi3=num2str(flagindex2(3));
1497                    fix2.threshC=num2str(thresh_vec2C);
1498                    fix2.threshV=num2str(thresh_vel2);
1499                    fieldnames=fields(fix2);
1500                    [CivAllxml,uid_fix2]=add(CivAllxml,1,'element','fix2');
1501                    for ilist=1:length(fieldnames)
1502                        val=eval(['fix2.' fieldnames{ilist}]);
1503                        if ischar(val)
1504                            [CivAllxml,uid_t]=add(CivAllxml,uid_fix2,'element',fieldnames{ilist});
1505                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1506                        end
1507                    end
1508                    CivAllCmd=[CivAllCmd ' fix2 '];
1509            end
1510        end
1511       
1512        %CheckPatch2
1513        if Param.CheckPatch2==1
1514           
1515            switch CivMode
1516               
1517                case 'CivX'
1518                    cmd=[cmd...
1519                        cmd_patch(filecell.nc.civ1{ifile,j},Param,'Patch2') '\n'];
1520                   
1521                case 'CivAll'
1522                    patch2.inputFileName=filecell.nc.civ1{ifile,j} ;
1523                    patch2.nopt=subdomain_patch2;
1524                    patch2.maxdiff=thresh_patch2;
1525                    patch2.ro=rho_patch2;
1526                    test_grid=get(handles.get_gridpatch2,'Value');
1527                    if test_grid
1528                        patch2.gridflag='y';
1529                        gridname=get(handles.grid_patch2,'String');
1530                        if isequal(gridname(end-3:end),'grid')
1531                            nbslice_grid=str2double(gridname(1:end-4)); %
1532                            if ~isnan(nbslice_grid)
1533                                i1_grid=mod(i1_civ2(ifile)-1,nbslice_grid)+1;
1534                                patch2.gridPatch=[filecell.filebase '_' fullfile_uvmat('','',gridname,'.grid','_1',i1_grid)];
1535%                                 patch2.gridPatch=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')];
1536                                if ~exist(patch2.gridPatch,'file')
1537                                    errormsg='grid file absent for patch2';
1538                                    return
1539                                end
1540                            elseif exist(gridname,'file')
1541                                patch2.gridPatch=gridname;
1542                            else
1543                                errormsg='grid file absent for patch2';
1544                                return
1545                            end
1546                        end
1547                    else
1548                        patch2.gridPatch='none';
1549                        patch2.gridflag='n';
1550                        patch2.m=nx_patch2;
1551                        patch2.n=ny_patch2;
1552                    end
1553                    patch2.convectFlow='n';
1554                    fieldnames=fields(patch2);
1555                    [CivAllxml,uid_patch2]=add(CivAllxml,1,'element','patch2');
1556                    for ilist=1:length(fieldnames)
1557                        val=eval(['patch2.' fieldnames{ilist}]);
1558                        if ischar(val)
1559                            [CivAllxml,uid_t]=add(CivAllxml,uid_patch2,'element',fieldnames{ilist});
1560                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1561                        end
1562                    end
1563                    CivAllCmd=[CivAllCmd ' patch2 '];
1564            end
1565        end
1566       
1567        switch CivMode
1568           
1569            case {'CivX','CivAll'}
1570                if isequal(CivMode,'CivAll')
1571                    save(CivAllxml,[OutputFile '.xml']);
1572                    cmd=[cmd sparam.CivBin ' -f ' OutputFile '.xml '  CivAllCmd ' >' OutputFile '.log' '\n'];
1573                end             
1574                % create the .bat file used in run or batch
1575                filename_bat=[OutputFile '.bat'];
1576                [fid,message]=fopen(filename_bat,'w');
1577                if isequal(fid,-1)
1578                    errormsg=['creation of .bat file: ' message];
1579                    return
1580                end
1581                fprintf(fid,cmd);
1582                fclose(fid);           
1583                if isunix
1584                    system(['chmod +x ' filename_bat]);
1585                end             
1586                batch_file_list{length(batch_file_list)+1}=filename_bat;
1587               
1588            case 'Matlab'
1589                drawnow
1590                if ~strcmp(compare,'stereo PIV')
1591                    filename_xml=[OutputFile '.civ.xml'];
1592                    t=struct2xml(Param);           
1593                    save(t,filename_xml)
1594                    if batch   
1595                        path_civ=fileparts(which('civ'));
1596                        filename_bat=[OutputFile '.bat'];
1597                        [fid,message]=fopen(filename_bat,'w');
1598                        if isequal(fid,-1)
1599                            errormsg= ['creation of .bat file: ' message];
1600                            return
1601                        end
1602%                         text_matlabscript=[...
1603%                         '#!/bin/bash \n'...
1604%                         '. /etc/sysprofile \n'...
1605%                         'matlab -nodisplay -nosplash -nojvm <<END_MATLAB \n'...
1606%                         'cd(''' path_civ '''); \n'...
1607%                         'civ_matlab(''' filename_xml ''',''' OutputFile '.nc''); \n'...
1608%                         'exit \n'...
1609%                         'END_MATLAB \n'];
1610                        cmd=['#!/bin/bash \n '...
1611                        '#$ -cwd \n '...
1612                        'hostname && date \n '...
1613                        'umask 002 \n'...
1614                         Param.xml.CivmBin ' ' Param.xml.RunTime ' ' filename_xml ' ' OutputFile '.nc'];%allow writting access to created files for user group
1615                   
1616                        fprintf(fid,cmd);
1617                        fclose(fid);
1618                        if isunix
1619                            system(['chmod +x ' filename_bat]);
1620                        end
1621                        batch_file_list{length(batch_file_list)+1}=filename_bat;
1622                    else
1623                        [tild,errormsg]=civ_matlab(Param,filecell.nc.civ1{ifile,j});
1624                        if isempty(errormsg)
1625                            display([filecell.nc.civ1{ifile,j} ' written'])
1626                        end
1627                    end
1628                end
1629        end
1630    end
1631end
1632
1633if batch 
1634    switch batch_mode   
1635       
1636        case 'sge' %at the moment only psmn ENS Lyon uses it
1637            for p=1:length(batch_file_list)
1638                %cmd=['!qsub -p ' pvalue ' -q civ.q -e ' flname '.errors -o ' flname '.log' ' ' batch_file_list{p}];
1639                cmd=['!qsub -q piv1,piv2,piv3 '...
1640                    '-e ' regexprep(batch_file_list{p},'.bat','.errors') ' -o ' regexprep(batch_file_list{p},'.bat','.log ')...
1641                    ' -v ' 'LD_LIBRARY_PATH=/home/sjoubaud/matlab_sylvain/civx/lib ' batch_file_list{p}];               
1642                display(cmd);eval(cmd);
1643            end           
1644        case 'oar_old'
1645                for p=1:length(batch_file_list)
1646                    oar_command=['!oarsub -n CIVX -q nicejob '...
1647                   '-E ' regexprep(batch_file_list{p},'.bat','.errors') ' -O ' regexprep(batch_file_list{p},'.bat','.log ')...
1648                    '-l "/core=1+{type = ''smalljob''}/licence=1,walltime=00:60:00"   ' batch_file_list{p}];
1649                display(oar_command);eval(oar_command);
1650                end               
1651        case 'oar'
1652           
1653            max_walltime=3600*12; % 12h max
1654            oar_modes={'oar-parexec','oar-dispatch','mpilauncher'};
1655            text={'Batch processing on servcalcul3 LEGI';...
1656                'Please choose one of the followint modes';...
1657                '* oar-parexec : default and best choice';...
1658                '* oar-dispatch : jobs in a container of several cores';...
1659                '* mpilauncher : one single parallel mpi job using several cores';...
1660                '**********************************'...
1661                };
1662            [S,v]=listdlg('PromptString',text,'ListString',oar_modes,...
1663                'SelectionMode','single','ListSize',[400 100],'Name','LEGI job mode');
1664            switch oar_modes{S}
1665                case 'oar-parexec' %oar-dispatch.pl
1666                    answer=inputdlg({'Number of cores (max 36)','extra oar options'},'oarsub parameter',1,{'12',''});
1667                    ncores=str2double(answer{1});
1668                    extra_oar=answer{2};
1669                    walltime_onejob=600;%seconds
1670                    filename_joblist=fullfile(Rootbat,'job_list.txt');
1671                    fid=fopen(filename_joblist,'w');
1672                    for p=1:length(batch_file_list)
1673                        fprintf(fid,[batch_file_list{p} '\n']);
1674                    end
1675                    fclose(fid)
1676                    oar_command=['oarsub -n CIVX '...
1677                        '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
1678                        '-l /core=' num2str(ncores) ','...
1679                            'walltime=' datestr(min(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,max_walltime/86400),13) ' '...
1680                        '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '...
1681                        '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '...
1682                        extra_oar ' '...
1683                        '"oar-parexec -s -f ' filename_joblist ' '...
1684                            '-l ' filename_joblist '.log"'];
1685                    filename_oarcommand=fullfile(Rootbat,'oar_command');
1686                    fid=fopen(filename_oarcommand,'w');
1687                    fprintf(fid,[oar_command '\n']);
1688                    fclose(fid);
1689                    display(oar_command);
1690                    eval(['! . ' filename_oarcommand])
1691                case 'oar-dispatch' %oar-dispatch.pl
1692                    ncores=str2double(...
1693                        inputdlg('Number of cores (max 36)','oarsub parameter',1,{'6'})...
1694                        );
1695                    walltime_onejob=600;%seconds
1696                    filename_joblist=fullfile(Rootbat,'job_list.txt');
1697                    fid=fopen(filename_joblist,'w');
1698                    for p=1:length(batch_file_list)
1699                        oar_command=['oarsub -n CIVX '...
1700                            '-E ' regexprep(batch_file_list{p},'\.bat\>','.stderr') ' -O ' regexprep(batch_file_list{p},'\.bat\>','.stdout ')...
1701                            '-l "/core=1,walltime=' datestr(walltime_onejob/86400,13) '"   ' batch_file_list{p}];
1702                        fprintf(fid,[oar_command '\n']);
1703                    end
1704                    fclose(fid);
1705                    oar_command=['oarsub -t container -n civx-container '...
1706                        '-l /core=' num2str(ncores)...
1707                        ',walltime=' datestr(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,13) ' '...
1708                        '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '...
1709                        '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '...
1710                        '"oar-dispatch -f ' filename_joblist '"'];
1711                    filename_oarcommand=fullfile(Rootbat,'oar_command');
1712                    fid=fopen(filename_oarcommand,'w');
1713                    fprintf(fid,[oar_command '\n']);
1714                    fclose(fid);
1715                    display(oar_command);
1716                    eval(['! . ' filename_oarcommand])
1717                case 'mpilauncher'
1718                    filename_joblist=fullfile(Rootbat,'job_list.txt');
1719                    fid=fopen(filename_joblist,'w');
1720                   
1721                    for p=1:length(batch_file_list)
1722                        fprintf(fid,[batch_file_list{p} '\n']);
1723                    end
1724                    fclose(fid)
1725                    text_oarscript=[...
1726                        '#!/bin/bash \n'...
1727                        '#OAR -n Mylauncher \n'...
1728                        '#OAR -l node=4/core=5,walltime=0:15:00 \n'...
1729                        '#OAR -E ' fullfile(Rootbat,'stderrfile.log') ' \n'...
1730                        '#OAR -O ' fullfile(Rootbat,'stdoutfile.log') ' \n'...
1731                        '# ========================================================= \n'...
1732                        '# This simple program launch a multinode parallel OpenMPI mpilauncher \n'...
1733                        '# application for coriolis PIV post-processing. \n'...
1734                        '# OAR uses oarshmost wrapper to propagate the user environement. \n'...
1735                        '# This wrapper assert that the user has the same environment on all the \n'...
1736                        '# allocated nodes (basic behavior needed by most MPI applications).  \n'...
1737                        '# \n'...
1738                        '# REQUIREMENT: \n'...
1739                        '# the oarshmost wrapper should be installed in $HOME/bin directory. \n'...
1740                        '# If a different location is used, change the line following the comment "Bidouille" \n'...
1741                        '# ========================================================= \n'...
1742                        '#   USER should only modify these 2 lines  \n'...
1743                        'WORKDIR=' pwd ' \n'...
1744                        'COMMANDE="mpilauncher  -f ' filename_joblist '" \n'...
1745                        '# ========================================================= \n'...
1746                        '# DO NOT MODIFY the FOLOWING LINES. (or be carefull) \n'...
1747                        'echo "job starting on: "`hostname` \n'...
1748                        'MPINODES="-host `tr [\\\\\\n] [,] <$OAR_NODEFILE |sed -e "s/,$/ /"`" \n'...
1749                        'NCPUS=`cat $OAR_NODEFILE |wc -l` \n'...
1750                        '#========== Bidouille ============== \n'...
1751                        'export OMPI_MCA_plm_rsh_agent=oar-envsh \n'...%                     'cd $WORKDIR \n'...
1752                        'CMD="mpirun -np $NCPUS -wdir $WORKDIR $MPINODES $COMMANDE" \n'...
1753                        'echo "I run: $CMD"  \n'...
1754                        '$CMD \n'...
1755                        'echo "job ending" \n'...
1756                        ];
1757                    %                 oarsub -S ./oar.sub
1758                    filename_oarscript=fullfile(Rootbat,'oar_command');
1759                    fid=fopen(filename_oarscript,'w');
1760                    fprintf(fid,[text_oarscript]);
1761                    fclose(fid);
1762                    eval(['!chmod +x  ' filename_oarscript]);
1763                    eval(['!oarsub -S ' filename_oarscript]);
1764            end
1765    end
1766else
1767    if ~isequal(CivMode,'Matlab')
1768        filename_superbat=fullfile(Rootbat,'job_list.bat');
1769        fid=fopen(filename_superbat,'w');
1770        if fid==-1
1771            msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat])
1772            return
1773        end
1774        for p=1:length(batch_file_list)
1775            if isunix
1776                fprintf(fid,['sh ' batch_file_list{p} '\n']);
1777            else
1778                fprintf(fid,['@call "' regexprep(batch_file_list{p},'\\','\\\\') '"' '\n']);
1779            end
1780        end
1781        fclose(fid);
1782        if(isunix)
1783            system(['chmod +x ' filename_superbat]);
1784        end
1785        system([filename_superbat ' &']);% execute main commmand
1786    end
1787end
1788
1789
1790%% save interface state
1791if isfield(filecell,'nc')
1792    if isfield(filecell.nc,'civ2')
1793        fileresu=filecell.nc.civ2{1,1};
1794    else
1795        fileresu=filecell.nc.civ1{1,1};
1796    end
1797end
1798[RootPath,SubDir,RootFile]=fileparts_uvmat(fileresu);
1799namedoc=fullfile(RootPath,SubDir,RootFile);
1800detect=1;
1801while detect==1
1802    namefigfull=[namedoc '.fig'];
1803    hh=dir(namefigfull);
1804    if ~isempty(hh)
1805        detect=1;
1806        namedoc=[namedoc '.0'];
1807    else
1808        detect=0;
1809    end
1810end
1811Param=rmfield(Param,'status');
1812Param=rmfield(Param,'xml');
1813t=struct2xml(Param);
1814t=set(t,1,'name','Civ');% set the head label
1815save(t,[namedoc '.civ.xml']); %save GUI  parameters as xml file
1816saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER  .xml)
1817
1818%Save info in personal profile (initiate browser next time) TODO
1819MenuFile={};
1820dir_perso=prefdir;
1821profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1822if exist(profil_perso,'file')
1823    hh=load (profil_perso);
1824      if isfield(hh,'MenuFile')
1825          MenuFile=hh.MenuFile;
1826      end
1827      if isfield(filecell.nc,'civ2')
1828          MenuFile=[filecell.nc.civ2{1,1}; MenuFile];
1829      else
1830           MenuFile=[filecell.nc.civ1{1,1}; MenuFile];
1831      end
1832      save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
1833else
1834    MenuFile=filecell.ima1.civ1(1,1);
1835    save (profil_perso,'MenuFile')
1836end
1837
1838%------------------------------------------------------------------------
1839% --- determine the list of reference indices of processing file
1840function [ref_i,ref_j,errormsg]=find_ref_indices(handles)
1841%------------------------------------------------------------------------
1842errormsg=''; %default error message
1843first_i=str2double(get(handles.first_i,'String'));%first index i
1844last_i=str2double(get(handles.last_i,'String'));%last index i
1845incr_i=str2double(get(handles.incr_i,'String'));% increment
1846if isequal(get(handles.first_j,'Visible'),'on')
1847    first_j=str2double(get(handles.first_j,'String'));%first index j
1848    last_j=str2double(get(handles.last_j,'String'));%last index j
1849    incr_j=str2double(get(handles.incr_j,'String'));% increment
1850else
1851    first_j=1;
1852    last_j=1;
1853    incr_j=1;
1854end
1855ref_i=first_i:incr_i:last_i;% list of i indices (reference values for each pair)
1856ref_j=first_j:incr_j:last_j;% list of j indices (reference values for each pair)
1857if isnan(first_i)||isnan(first_j)
1858    errormsg='first field number not defined';
1859elseif isnan(last_i)||isnan(last_j)
1860    errormsg='last field number not defined';
1861elseif isnan(incr_i)||isnan(incr_j)
1862    errormsg='increment in field number not defined';
1863elseif last_i < first_i || last_j < first_j
1864    errormsg='last field number must be larger than the first one';
1865end
1866
1867%------------------------------------------------------------------------
1868% --- determine the list of filenames and indices needed for launch_job
1869%------------------------------------------------------------------------
1870% OUTPUT:
1871% filecell: structure of cell arrays {ref_i,ref_j} containing all the filenames involved in the civ process
1872%    the indices ref_i and ref_j correspond to the list of reference indices
1873%       .filebase=fullfile(RootPath,RootFile) used to construct mask names, grid names, CivDoc xml file
1874%       .ima1.civ1,.ima1.civ2: first image for civ1 and civ2 respectively (possibly different)
1875%       .ima2.civ1,.ima2.civ2: second image for civ1 and civ2 respectively (possibly different)
1876%       .nc.civ1,.nc.civ2: netcdf files containing civ1 and civ2 data respectively (possibly different)
1877% i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2: arrays of files indices, needed for timing records
1878function [filecell,i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2,NomType_nc,file_ref_fix1,file_ref_fix2,compare,errormsg]=...
1879    set_civ_filenames(handles,ref_i,ref_j,checkbox)
1880%------------------------------------------------------------------------
1881filecell=[];%default
1882errormsg='';
1883ListProgram=get(handles.ListProgram,'String');
1884CivMode=ListProgram{get(handles.ListProgram,'Value')};%Program to use , CivX or Matlab
1885
1886%% get the root name and check dir
1887RootPath=get(handles.RootPath,'String');
1888SubdirImages=get(handles.SubdirImages,'String');
1889RootFile=get(handles.RootFile,'String');
1890filecell.filebase=fullfile(RootPath,SubdirImages,RootFile);
1891if isempty(filecell.filebase)
1892    errormsg='please open an image with the upper menu option Open/Browse...';
1893    return
1894end
1895if ~exist(RootPath,'dir')
1896    errormsg=['path to images ' RootPath ' not found'];
1897    return
1898end
1899[tild,message]=fileattrib(RootPath);
1900if ~isempty(message) && ~isequal(message.UserWrite,1)
1901    errormsg=['No writting access to ' RootPath];
1902    return
1903end
1904%check result directory
1905subdir_civ1=get(handles.SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf output data
1906subdir_civ2=get(handles.SubdirCiv2,'String');
1907if isequal(subdir_civ1,''),subdir_civ1='CIV'; end% put default subdir
1908if isequal(subdir_civ2,''),subdir_civ2=subdir_civ1; end% put default subdir
1909
1910%% choose root names depending on ListCompareMode =displacement, shift, PIV or stereo PIV
1911ListCompareMode=get(handles.ListCompareMode,'String');
1912compare=ListCompareMode{get(handles.ListCompareMode,'Value')};
1913
1914% set the nomenclature type of the nc files depending on the pair mode
1915if strcmp(compare,'displacement')||strcmp(compare,'shift')
1916    mode='displacement';
1917else
1918    mode_list=get(handles.ListPairMode,'String');
1919    mode_value=get(handles.ListPairMode,'Value');
1920    mode=mode_list{mode_value};
1921end
1922NomType_ima2=get(handles.NomType,'String');
1923NomType_nc=nomtype2pair(NomType_ima2,mode);
1924
1925% set the rootfile and image indexing
1926RootFile_ima2=get(handles.RootFile,'String');%root file for the second image series
1927ext_ima=get(handles.ImaExt,'String'); % image extension (the same for all images)
1928switch compare
1929    case 'PIV'
1930       RootFile_ima1=RootFile_ima2;% root name of the two image series is the same
1931       NomType_ima1=NomType_ima2;% the index of the first image follows the index of the second one
1932       RootFile_nc=RootFile_ima2;
1933    case 'displacement'
1934       RootFile_ima1=get(handles.RootFile_1,'String');% root name of the first image series set by handles.RootFile_1
1935       NomType_ima1='';% no indexing of the first image, a fixed reference for the whole series
1936       RootFile_nc=RootFile_ima2;
1937    case 'shift'
1938       RootFile_ima1=get(handles.RootFile_1,'String');% root name of the first image series set by handles.RootFile_1
1939       NomType_ima1=NomType_ima2;% the index of the first image follows the index of the second one
1940       RootFile_nc=[RootFile_ima1 '-' RootFile_ima2];
1941end
1942
1943%determine the list of file indices involved
1944[i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2]=...
1945    find_pair_indices(handles,ref_i,ref_j,mode);
1946
1947%determine the new filebase for 'displacement' ListPairMode (comparison of two series)
1948%filebase_B=filebase;% root name of the second field series for stereo
1949% filebase_A=filebase;%default
1950% if strcmp(compare,'PIV')
1951%     filebase_AB=filebase;
1952% else
1953%     [Path2,Name2]=fileparts(filebase_B);
1954%     Name1=RootFile_ima1;
1955%     filebase_AB=fullfile(Path2,[Name2 '-' Name1]);   
1956% end
1957% [RootPath_AB,RootFile_AB]=fileparts(filebase_AB);
1958% % [RootPath_ima1,RootFile_ima1]=fileparts(filebase_B);
1959% [RootPath_ima2,RootFile_ima2]=fileparts(filebase_B);
1960% [RootPath_nc,RootFile_nc]=fileparts(filebase_B);%default
1961% if strcmp(compare,'displacement')
1962% %     [RootPath_ima1,RootFile_ima1]=fileparts(filebase_B);
1963% %     [RootPath_ima2,RootFile_ima2]=fileparts(filebase_B);
1964%     [RootPath_nc,RootFile_nc]=fileparts(filebase_B);
1965% elseif strcmp(compare,'shift')
1966%     RootPath_nc=RootPath_AB;
1967%     RootFile_nc=RootFile_AB;
1968% end
1969% else
1970%     filebase_ima1=filebase_B;
1971%     filebase_ima2=filebase_B;
1972%     filebase_nc=filebase_B;
1973% [RootPath_ima1,RootFile_ima1]=fileparts(filebase_ima1);
1974% [RootPath_ima2,RootFile_ima2]=fileparts(filebase_ima2);
1975% [RootPath_nc,RootFile_nc]=fileparts(filebase_nc);
1976% [RootPath_A,RootFile_A]=fileparts(filebase_A);
1977
1978   
1979%% determine reference files for fix:
1980file_ref_fix1={};%default
1981file_ref_fix2={};
1982nbfield=length(i1_civ1);
1983nbslice=length(j1_civ1);
1984if checkbox(2)==1% fix1 performed
1985    ref=get(handles.ref_fix1,'UserData');%read data on the ref file stored by get_ref_fix1_Callback
1986    if ~isempty(ref)
1987        first_i=str2double(get(handles.first_i,'String'));
1988        last_i=str2double(get(handles.last_i,'String'));
1989        incr_i=str2double(get(handles.incr_i,'String'));
1990        first_j=str2double(get(handles.first_j,'String'));
1991        last_j=str2double(get(handles.last_j,'String'));
1992        incr_j=str2double(get(handles.incr_j,'String'));
1993        num_i_ref=first_i:incr_i:last_i;
1994        num_j_ref=first_j:incr_j:last_j;
1995        if isequal(mode,'displacement')
1996            num_i1=num_i_ref;
1997            num_i2=num_i_ref;
1998            num_j1=num_j_ref;
1999            num_j2=num_j_ref;
2000        elseif isequal(mode,'pair j1-j2')% isequal(mode,'st_pair j1-j2')
2001            num_i1=num_i_ref;
2002            num_i2=num_i1;
2003            num_j1=ref.num_a*ones(size(num_i_ref));
2004            num_j2=ref.num_b*ones(size(num_i_ref));
2005        elseif isequal(mode,'series(Di)') % isequal(mode,'st_series(Di)')
2006            delta1=floor((ref.num2-ref.num1)/2);
2007            delta2=ceil((ref.num2-ref.num1)/2);
2008            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
2009            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
2010            if isempty(ref.num_a)
2011                ref.num_a=1;
2012            end
2013            num_j1=ref.num_a*ones(size(num_i1));
2014            num_j2=num_j1;
2015        elseif isequal(mode,'series(Dj)')%| isequal(mode,'st_series(Dj)')
2016            delta1=floor((ref.num_b-ref.num_a)/2);
2017            delta2=ceil((ref.num_b-ref.num_a)/2);
2018            num_i1=ref.num1*ones(size(num_i_ref));
2019            num_i2=num_i1;
2020            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
2021            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
2022        end
2023        for ifile=1:nbfield
2024            for j=1:nbslice
2025                [RootPathRef,RootFile]=fileparts(ref.filebase);
2026                file_ref=fullfile_uvmat(RootPathRef,ref.subdir,RootFile,'.nc',ref.NomType,num_i1(ifile),num_i2(ifile),num_j1(j),num_j2(j));
2027                file_ref_fix1(ifile,j)={file_ref};
2028                if ~exist(file_ref,'file')
2029                    errormsg=['reference file ' file_ref ' not found for fix1'];
2030                    return
2031                end
2032            end
2033        end
2034    end
2035end
2036
2037%% determine reference files for fix2:
2038if checkbox(5)==1% fix2 performed
2039    ref=get(handles.ref_fix2,'UserData');
2040    if ~isempty(ref)
2041        first_i=str2double(get(handles.first_i,'String'));
2042        last_i=str2double(get(handles.last_i,'String'));
2043        incr_i=str2double(get(handles.incr_i,'String'));
2044        first_j=str2double(get(handles.first_j,'String'));
2045        last_j=str2double(get(handles.last_j,'String'));
2046        incr_j=str2double(get(handles.incr_j,'String'));
2047        num_i_ref=first_i:incr_i:last_i;
2048        num_j_ref=first_j:incr_j:last_j;
2049        if isequal(mode,'displacement')
2050            num_i1=num_i_ref;
2051            num_i2=num_i_ref;
2052            num_j1=num_j_ref;
2053            num_j2=num_j_ref;
2054        elseif isequal(mode,'pair j1-j2')
2055            num_i1=num_i_ref;
2056            num_i2=num_i1;
2057            num_j1=ref.num_a;
2058            num_j2=ref.num_b;
2059        elseif isequal(mode,'series(Di)')
2060            delta1=floor((ref.num2-ref.num1)/2);
2061            delta2=ceil((ref.num2-ref.num1)/2);
2062            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
2063            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
2064            num_j1=ref.num_a*ones(size(num_i1));
2065            num_j2=num_j1;
2066        elseif isequal(mode,'series(Dj)')
2067            delta1=floor((ref.num_b-ref.num_a)/2);
2068            delta2=ceil((ref.num_b-ref.num_a)/2);
2069            num_i1=ref.num1*ones(size(num_i_ref));
2070            num_i2=num_i1;
2071            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
2072            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
2073        end
2074        for ifile=1:nbfield
2075            for j=1:nbslice
2076                [RootPathRef,RootFile]=fileparts(ref.filebase);
2077                file_ref=fullfile_uvmat(RootPathRef,ref.subdir,RootFile,'.nc',ref.NomType,num_i1(ifile),num_i2(ifile),num_j1(j),num_j2(j));
2078                file_ref_fix2(ifile,j)={file_ref};
2079                if ~exist(file_ref,'file')
2080                    errormsg=['reference file ' file_ref ' not found for fix2'];
2081                    return
2082                end
2083            end
2084        end
2085    end
2086end
2087
2088%% check the existence of the netcdf and image files involved
2089% %%%%%%%%%%%%  case CheckCiv1 activated   %%%%%%%%%%%%%
2090if checkbox(1)==1;
2091    detect=1;
2092    vers=0;
2093    subdir_civ1_new=subdir_civ1;
2094    while detect==1 %create a new subdir if the netcdf files already exist
2095        for ifile=1:nbfield
2096            for j=1:nbslice
2097                filename=fullfile_uvmat(RootPath,subdir_civ1_new,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
2098                detect=exist(filename,'file')==2;
2099                if detect% if a netcdf file already exists
2100                    indstr=regexp(subdir_civ1_new,'\D');
2101                    if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number
2102                        vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1;
2103                        subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)];
2104                    else
2105                        vers=vers+1;
2106                        subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) '_' num2str(vers)];       
2107                    end
2108                    subdir_civ2=subdir_civ1_new;
2109                    break
2110                end
2111                filecell.nc.civ1(ifile,j)={filename};
2112            end
2113            if detect% if a netcdf file already exists
2114                break
2115            end
2116        end
2117 
2118        %create the new SubdirCiv1
2119        if ~exist(fullfile(RootPath,subdir_civ1_new),'dir')     
2120            [xx,msg1]=mkdir(fullfile(RootPath,subdir_civ1_new));
2121            if ~strcmp(msg1,'')
2122                errormsg=['cannot create ' subdir_civ1_new ': ' msg1];%error message for directory creation
2123                return
2124            elseif isunix         
2125                [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g)
2126                if ~strcmp(msg2,'')
2127                    errormsg=['pb of permission for  ' fullfile(RootPath,subdir_civ1_new) ': ' msg2];%error message for directory creation
2128                    return
2129                end
2130            end
2131        end
2132        if strcmp(compare,'stereo PIV')&&(strcmp(mode,'pair j1-j2')||strcmp(mode,'series(Dj)')||strcmp(mode,'series(Di)'))%check second nc series
2133            for ifile=1:nbfield
2134                for j=1:nbslice
2135                     filename=fullfile_uvmat(RootPath,subdir_civ1_new,RootFile_A,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
2136                   % filename=name_generator(filebase_A,i1_civ1(ifile),j1_civ1(j),'.nc',NomType_nc,1,i2_civ1(ifile),j2_civ1(j),subdir_civ1_new);%
2137                    detect=exist(filename,'file')==2;
2138                    if detect% if a netcdf file already exists
2139                       indstr=regexp(subdir_civ1_new,'\D');
2140                       if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number
2141                           vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1;
2142                           subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)];
2143                       else
2144                           vers=vers+1;
2145                           subdir_civ1_new=[subdir_civ1_new '_' num2str(vers)];
2146                       end
2147                       subdir_civ2=subdir_civ1;
2148                       break
2149                    end
2150                    filecell.ncA.civ1(ifile,j)={filename};
2151                end
2152                if detect% if a netcdf file already exists
2153                    break
2154                end
2155            end
2156            %create the new SubdirCiv1
2157            if ~exist(fullfile(RootPath,subdir_civ1_new),'dir')       
2158                [xx,msg1]=mkdir(fullfile(RootPath,subdir_civ1_new));
2159                if ~strcmp(msg1,'')
2160                    errormsg=['cannot create ' subdir_civ1_new ': ' msg1];
2161                    return
2162                else
2163                    [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g)
2164                    if ~strcmp(msg2,'')
2165                        errormsg=['pb of permission for ' subdir_civ1_new ': ' msg2];%error message for directory creation
2166                        return
2167                    end
2168                end
2169            end
2170        end
2171    end
2172    subdir_civ1=subdir_civ1_new;
2173    % get image names
2174    for ifile=1:nbfield
2175        for j=1:nbslice
2176             filename=fullfile_uvmat(RootPath,SubdirImages,RootFile_ima1,ext_ima,NomType_ima1,i1_civ1(ifile),[],j1_civ1(j));
2177            idetect(j)=exist(filename,'file')==2;
2178            filecell.ima1.civ1(ifile,j)={filename}; %first image
2179            filename=fullfile_uvmat(RootPath,SubdirImages,RootFile_ima2,ext_ima,NomType_ima2,i2_civ1(ifile),[],j2_civ1(j));
2180            idetect_1(j)=exist(filename,'file')==2;
2181            filecell.ima2.civ1(ifile,j)={filename};%second image
2182        end
2183        [idetectmin,indexj]=min(idetect);
2184        if idetectmin==0,
2185            errormsg=[filecell.ima1.civ1{ifile,indexj} ' not found'];
2186            return
2187        end
2188        [idetectmin,indexj]=min(idetect_1);
2189        if idetectmin==0,
2190            errormsg=[filecell.ima2.civ1{ifile,indexj} ' not found'];
2191            return
2192        end
2193    end
2194    if strcmp(compare,'stereo PIV') && (strcmp(mode,'pair j1-j2') || strcmp(mode,'series(Dj)') || strcmp(mode,'series(Di)'))
2195        for ifile=1:nbfield
2196            for j=1:nbslice
2197                filename=fullfile_uvmat(RootPath,'',RootFile_A,ext_ima,NomType_ima1,i1_civ1(ifile),[],j1_civ1(j));
2198                idetect(j)=exist(filename,'file')==2;
2199                filecell.imaA1.civ1(ifile,j)={filename} ;%first image
2200                filename=fullfile_uvmat(RootPath,'',RootFile_A,ext_ima,NomType_ima2,i2_civ1(ifile),[],j2_civ1(j));
2201                idetect_1(j)=exist(filename,'file')==2;
2202                filecell.imaA2.civ1(ifile,j)={filename};%second image
2203            end
2204            [idetectmin,indexj]=min(idetect);
2205            if idetectmin==0,
2206                errormsg=[filecell.imaA1.civ1{ifile,indexj} ' not found'];
2207                return
2208            end
2209            [idetectmin,indexj]=min(idetect_1);
2210            if idetectmin==0,
2211                errormsg=[filecell.imaA2.civ1{ifile,indexj} ' not found'];
2212                return
2213            end
2214        end
2215    end
2216   
2217    %%%%%%%%%%%%%  checkfix1 or checkpatch1 activated but no checkciv1   %%%%%%%%%%%%%
2218elseif (checkbox(2)==1 || checkbox(3)==1);
2219    for ifile=1:nbfield
2220        for j=1:nbslice
2221            filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
2222            detect=exist(filename,'file')==2;
2223            if detect==0
2224                errormsg=[filename ' not found'];
2225                return
2226            end
2227            filecell.nc.civ1(ifile,j)={filename};
2228        end
2229    end
2230    if strcmp(compare,'stereo PIV')
2231        for ifile=1:nbfield
2232            for j=1:nbslice
2233                filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_A,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
2234                filecell.ncA.civ1(ifile,j)={filename};
2235                if ~exist(filename,'file')
2236                    errormsg=['input file ' filename ' not found'];
2237                    return
2238                end
2239            end
2240        end
2241    end
2242end
2243
2244%%%%%%%%%%%%%  if checkciv2 performed with pairs different than checkciv1  %%%%%%%%%%%%%
2245testdiff=0;
2246if (checkbox(4)==1)&&...
2247        ((get(handles.ListPairCiv1,'Value')~=get(handles.ListPairCiv2,'Value'))||~strcmp(subdir_civ2,subdir_civ1))
2248    testdiff=1;
2249    detect=1;
2250    vers=0;
2251    subdir_civ2_new=subdir_civ2;
2252    while detect==1 %create a new subdir if the netcdf files already exist
2253        for ifile=1:nbfield
2254            for j=1:nbslice
2255                filename=fullfile_uvmat(RootPath,subdir_civ2_new,RootFile_nc,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2256                detect=exist(filename,'file')==2;
2257                if detect% if a netcdf file already exists
2258                    indstr=regexp(subdir_civ2,'\D');
2259                    if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2260                        vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2261                        subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2262                    else
2263                        vers=vers+1;
2264                        subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2265                    end
2266                    break
2267                end
2268                filecell.nc.civ2(ifile,j)={filename};
2269            end
2270            if detect% if a netcdf file already exists
2271                break
2272            end
2273        end
2274        %create the new subdir_civ2_new
2275        if ~exist(fullfile(RootPath,subdir_civ2_new),'dir')
2276            [xx,m2]=mkdir(fullfile(RootPath,subdir_civ2_new));
2277            [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g)
2278            if ~isequal(m2,'')
2279                errormsg=['cannot create ' fullfile(RootPath,subdir_civ2_new) ': ' m2];
2280                return
2281            end
2282        end
2283        if strcmp(compare,'stereo PIV')%check second nc series
2284            for ifile=1:nbfield
2285                for j=1:nbslice
2286                    filename=fullfile_uvmat(RootPath,subdir_civ2_new,RootFile_A,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2287                    detect=exist(filename,'file')==2;
2288                    if detect% if a netcdf file already exists
2289                        indstr=regexp(subdir_civ2,'\D');
2290                        if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2291                           vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2292                           subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2293                        else
2294                           vers=vers+1;
2295                           subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2296                        end
2297                        break
2298                    end
2299                    filecell.ncA.civ2(ifile,j)={filename};
2300                end
2301                if detect% if a netcdf file already exists
2302                    break
2303                end
2304            end
2305            subdir_civ2=subdir_civ2_new;
2306            %create the new SubdirCiv1
2307            if ~exist(fullfile(RootPath,subdir_civ2_new),'dir')
2308                [xx,m2]=mkdir(subdir_civ2_new);
2309                 [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g)
2310                if ~isequal(m2,'')
2311                    errormsg= ['cannot create ' fullfile(RootPath,subdir_civ2_new) ': ' m2];%error message for directory creation
2312                    return
2313                end
2314            end
2315        end
2316    end
2317    subdir_civ2=subdir_civ2_new;
2318end
2319
2320%%%%%%%%%%%%%  if checkciv2 results are obtained or used  %%%%%%%%%%%%%
2321if checkbox(4)==1 || checkbox(5)==1 || checkbox(6)==1 %civ2
2322    %check source netcdf file of checkciv1 estimates
2323    if checkbox(1)==0; %no civ1 performed
2324        for ifile=1:nbfield
2325            for j=1:nbslice
2326                filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));%
2327                filecell.nc.civ1(ifile,j)={filename};% name of the civ1 file
2328                if ~exist(filename,'file')
2329                    errormsg=['input file ' filename ' not found'];
2330                    return
2331                end
2332                if ~testdiff % civ2 or patch2 are written in the same file as civ1
2333                    if checkbox(4)==0 ; %check the existence of civ2 if it is not calculated
2334                        Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2');
2335                        if isfield(Data,'Txt')
2336                            errormsg=Data.Txt;
2337                            return
2338                        elseif ~isempty(Data.CivStage)% case of new civ files
2339                            if Data.CivStage<4 %test for civ files
2340                            errormsg=['no civ2 data in ' filename];
2341                            return
2342                            end
2343                        elseif isempty(Data.civ2)||isequal(Data.civ2,0)
2344                            errormsg=['no civ2 data in ' filename];
2345                            return
2346                        end
2347                    elseif checkbox(3)==0; %check the existence of patch if it is not calculated
2348                        Data=nc2struct(filename,'ListGlobalAttribute','CivStage','patch');
2349                        if isfield(Data,'Txt')
2350                            errormsg=Data.Txt;
2351                            return
2352                        elseif ~isempty(Data.CivStage)
2353                            if Data.CivStage<3 %test for civ files
2354                                errormsg=['no patch data in ' filename];
2355                                return
2356                            end
2357                        elseif isempty(Data.patch)||isequal(Data.patch,0)
2358                            errormsg=['no patch data in ' filename];
2359                            return
2360                        end
2361                    end
2362                end
2363            end
2364        end
2365        if strcmp(compare,'stereo PIV')
2366            for ifile=1:nbfield
2367                for j=1:nbslice
2368                    filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_A,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2369                    filecell.ncA.civ2(ifile,j)={filename};
2370                    if ~exist(filename,'file')
2371                        errormsg=['input file ' filename ' not found'];
2372                        return
2373                    end
2374                end
2375            end
2376        end
2377    end
2378   
2379    detect=1;
2380    %     while detect==1%creates a new subdir if the netcdf files already contain checkciv2 data
2381    for ifile=1:nbfield
2382        for j=1:nbslice
2383            filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_nc,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2384            detect=exist(filename,'file')==2;
2385            filecell.nc.civ2(ifile,j)={filename};
2386        end
2387    end
2388    %get first image names for checkciv2
2389    if checkbox(1)==1 && isequal(i1_civ1,i1_civ2) && isequal(j1_civ1,j1_civ2)
2390        filecell.ima1.civ2=filecell.ima1.civ1;
2391    elseif checkbox(4)==1
2392        for ifile=1:nbfield
2393            for j=1:nbslice
2394                filename=fullfile_uvmat(RootPath,[],RootFile_ima1,ext_ima,NomType_ima1,i1_civ2(ifile),[],j1_civ2(j));
2395                idetect_2(j)=exist(filename,'file')==2;
2396                filecell.ima1.civ2(ifile,j)={filename};%first image
2397            end
2398            [idetectmin,indexj]=min(idetect_2);
2399            if idetectmin==0,
2400               errormsg=['input image ' filecell.ima1.civ2{ifile,indexj} ' not found'];
2401                return
2402            end
2403        end
2404    end
2405   
2406    %get second image names for checkciv2
2407    if checkbox(1)==1 && isequal(i2_civ1,i2_civ2) && isequal(j2_civ1,j2_civ2)
2408        filecell.ima2.civ2=filecell.ima2.civ1;
2409    elseif checkbox(4)==1
2410        for ifile=1:nbfield
2411            for j=1:nbslice
2412                filename=fullfile_uvmat(RootPath,[],RootFile_ima2,ext_ima,NomType_ima2,i2_civ2(ifile),[],j2_civ2(j));
2413                idetect_3(j)=exist(filename,'file')==2;
2414                filecell.ima2.civ2(ifile,j)={filename};%first image
2415            end
2416            [idetectmin,indexj]=min(idetect_3);
2417            if idetectmin==0,
2418                errormsg=['input image ' filecell.ima2.civ2{ifile,indexj} ' not found'];
2419                return
2420            end
2421        end
2422    end
2423end
2424if (checkbox(5) || checkbox(6)) && ~checkbox(4)  % need to read an existing netcdf civ2 file
2425    if ~testdiff
2426        filecell.nc.civ2=filecell.nc.civ1;% file already checked
2427    else     % check the civ2 files
2428        for ifile=1:nbfield
2429            for j=1:nbslice
2430                 filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_nc,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2431                filecell.nc.civ2(ifile,j)={filename};
2432                if ~exist(filename,'file')
2433                    errormsg=['input file ' filename ' not found'];
2434                    return
2435                else
2436                    Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2');
2437                    if ~isempty(Data.CivStage) && Data.CivStage<4 %test for civ files
2438                            errormsg=['no civ2 data in ' filename];
2439                            return
2440                    elseif isempty(Data.civ2)||isequal(Data.civ2,0)
2441                        errormsg=['no civ2 data in ' filename];
2442                        return
2443                    end
2444                end
2445            end
2446        end
2447    end
2448end
2449
2450%%%%%%%%%%%%%  if stereo fields are calculated by PATCH %%%%%%%%%%%%%
2451if strcmp(compare,'stereo PIV')
2452    if  checkbox(3) && isequal(get(handles.test_stereo1,'Value'),1)
2453        for ifile=1:nbfield
2454            for j=1:nbslice
2455                 filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_AB,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
2456                filecell.st(ifile,j)={filename};
2457            end
2458        end
2459    end
2460    if  checkbox(6) && isequal(get(handles.CheckStereo,'Value'),1)
2461        for ifile=1:nbfield
2462            for j=1:nbslice
2463                 filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_AB,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2464                filecell.st(ifile,j)={filename};
2465            end
2466        end
2467    end
2468end
2469set(handles.SubdirCiv1,'String',subdir_civ1);%update the edit box
2470set(handles.SubdirCiv2,'String',subdir_civ2);%update the edit box
2471
2472% For CivX COPY IMAGES TO THE FORMAT .png IF NEEDED
2473if strcmp(CivMode,'CivX')
2474    if isequal(NomType_ima1,'*')%case of movie files
2475        NomType_imanew1='_i';
2476    else
2477        NomType_imanew1=NomType_ima1;
2478    end
2479    if isequal(NomType_ima2,'*')%case of movie files
2480        NomType_imanew2='_i';
2481    else
2482        NomType_imanew2=NomType_ima2;
2483    end
2484    if ~isequal(ext_ima,'.png')
2485        %%type of image file
2486        type_ima1='none';%default
2487        movieobject1=[];%default
2488        if strcmpi(ext_ima,'.avi')
2489            if ~isempty(which('mmreader'))% if the mmreader function is found (recent version of matlab)
2490                type_ima1='movie';
2491                movieobject1=mmreader([filecell.filebase ext_ima]);
2492            else
2493                type_ima1='avi';
2494            end
2495        elseif ischar(ext_ima) && ~isempty(ext_ima(2:end))
2496            form=imformats(ext_ima(2:end));
2497            if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2498                if isequal(NomType_ima1,'*');
2499                    type_ima1='multimage';%image series in a single image file
2500                else
2501                    type_ima1='image';
2502                end
2503            end
2504        end
2505        type_ima2='none';%default
2506        movieobject2=[];
2507        if strcmpi(ext_ima,'.avi')
2508            if ~isempty(which('mmreader'))% if the mmreader function is found (recent version of matlab)
2509                type_ima2='movie';
2510                movieobject2=mmreader([filecell.filebase ext_ima]);
2511            else
2512                type_ima2='avi';
2513            end
2514        elseif ischar(ext_ima) && ~isempty(ext_ima(2:end))
2515            form=imformats(ext_ima(2:end));
2516            if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2517                if isequal(NomType_ima1,'*');
2518                    type_ima2='multimage';%image series in a single image file
2519                else
2520                    type_ima2='image';
2521                end
2522            end
2523        end
2524        if checkbox(1) %if civ1 is performed
2525            h = waitbar(0,'copy images to the .png format for civ1');% display a wait bar
2526            for ifile=1:nbfield
2527                waitbar(ifile/nbfield);
2528                for j=1:nbslice
2529                    filename=fullfile_uvmat(RootPath,[],RootFile_ima1,'.png',NomType_imanew1,i1_civ1(ifile),[],j1_civ1(j));
2530                    if ~exist(filename,'file')
2531                        A=read_image(filecell.ima1.civ1{ifile,j},type_ima1,i1_civ1(ifile),movieobject1);
2532                        imwrite(A,filename,'BitDepth',16);
2533                    end
2534                    filecell.ima1.civ1(ifile,j)={filename};
2535                    filename=fullfile_uvmat(RootPath,[],RootFile_ima2,'.png',NomType_imanew2,i2_civ1(ifile),[],j2_civ1(j));
2536                    if ~exist(filename,'file')
2537                        A=read_image(filecell.ima2.civ1{ifile,j},type_ima2,i2_civ1(ifile),movieobject2);
2538                        imwrite(A,filename,'BitDepth',16);
2539                    end
2540                    filecell.ima2.civ1(ifile,j)={filename};
2541                end
2542            end
2543            close(h)
2544        end
2545        if checkbox(4) %if civ2 is performed
2546            h = waitbar(0,'copy images to the .png format for civ2');% display a wait bar
2547            for ifile=1:nbfield
2548                waitbar(ifile/nbfield);
2549                for j=1:nbslice
2550                    filename=fullfile_uvmat(RootPath,[],RootFile_ima1,'.png',NomType_imanew1,i1_civ2(ifile),[],j1_civ2(j));
2551                    if ~exist(filename,'file')
2552                        A=read_image(cell2mat(filecell.ima1.civ2(ifile,j)),type_ima2,i1_civ2(ifile));
2553                        imwrite(A,filename,'BitDepth',16);
2554                    end
2555                    filecell.ima1.civ2(ifile,j)={filename};
2556                    filename=fullfile_uvmat(RootPath,[],RootFile_ima2,'.png',NomType_imanew2,i2_civ2(ifile),[],j2_civ2(j));
2557                    if ~exist(filename,'file')
2558                        A=read_image(cell2mat(filecell.ima2.civ2(ifile,j)),type_ima2,i2_civ2(ifile));
2559                        imwrite(A,filename,'BitDepth',16);
2560                    end
2561                    filecell.ima2.civ2(ifile,j)={filename};
2562                end
2563            end
2564            close(h);
2565        end
2566    end
2567end
2568
2569%------------------------------------------------------------------------
2570% --- determine the list of index pairs of processing file
2571function [num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=...
2572    find_pair_indices(handles,ref_i,ref_j,mode)
2573%------------------------------------------------------------------------
2574
2575list_civ1=get(handles.ListPairCiv1,'String');
2576index_civ1=get(handles.ListPairCiv1,'Value');
2577str_civ1=list_civ1{index_civ1};%string defining the image pairs for civ1
2578if isempty(str_civ1)||isequal(str_civ1,'')
2579    msgbox_uvmat('ERROR','no image pair selected for civ1')
2580    return
2581end
2582list_civ2=get(handles.ListPairCiv2,'String');
2583index_civ2=get(handles.ListPairCiv2,'Value');
2584if index_civ2>length(list_civ2)
2585    list_civ2=list_civ1;
2586    index_civ2=index_civ1;
2587end
2588str_civ2=list_civ2{index_civ2};%string defining the image pairs for civ2
2589
2590if isequal (mode,'series(Di)')
2591    lastfield=str2double(get(handles.nb_field,'String'));
2592    num1_civ1=ref_i-floor(index_civ1/2)*ones(size(ref_i));% set of first image numbers
2593    num2_civ1=ref_i+ceil(index_civ1/2)*ones(size(ref_i));
2594    num_a_civ1=ref_j;
2595    num_b_civ1=ref_j;
2596    num1_civ2=ref_i-floor(index_civ2/2)*ones(size(ref_i));
2597    num2_civ2=ref_i+ceil(index_civ2/2)*ones(size(ref_i));
2598    num_a_civ2=ref_j;
2599    num_b_civ2=ref_j;   
2600   
2601    % adjust the first and last field number
2602    lastfield=str2double(get(handles.nb_field,'String'));
2603    if isnan(lastfield)
2604        indsel=find((num1_civ1 >= 1)&(num1_civ2 >= 1));
2605    else
2606        indsel=find((num2_civ1 <= lastfield)&(num2_civ2 <= lastfield)&(num1_civ1 >= 1)&(num1_civ2 >= 1));
2607    end
2608    if length(indsel)>=1
2609        firstind=indsel(1);
2610        lastind=indsel(end);
2611        set(handles.first_i,'String',num2str(ref_i(firstind)))%update the display of first and last fields
2612        set(handles.last_i,'String',num2str(ref_i(lastind)))
2613        ref_i=ref_i(indsel);
2614        num1_civ1=num1_civ1(indsel);
2615        num1_civ2=num1_civ2(indsel);
2616        num2_civ1=num2_civ1(indsel);
2617        num2_civ2=num2_civ2(indsel);
2618    end
2619elseif isequal (mode,'series(Dj)')
2620    lastfield_j=str2double(get(handles.nb_field2,'String'));
2621    num1_civ1=ref_i;% set of first image numbers
2622    num2_civ1=ref_i;
2623    num_a_civ1=ref_j-floor(index_civ1/2)*ones(size(ref_j));
2624    num_b_civ1=ref_j+ceil(index_civ1/2)*ones(size(ref_j));
2625    num1_civ2=ref_i;
2626    num2_civ2=ref_i;
2627    num_a_civ2=ref_j-floor(index_civ2/2)*ones(size(ref_j));
2628    num_b_civ2=ref_j+ceil(index_civ2/2)*ones(size(ref_j));
2629    % adjust the first and last field number
2630    if isnan(lastfield_j)
2631        indsel=find((num_a_civ1 >= 1)&(num_a_civ2 >= 1));
2632    else
2633        indsel=find((num_b_civ1 <= lastfield_j)&(num_b_civ2 <= lastfield_j)&(num_a_civ1 >= 1)&(num_a_civ2 >= 1));
2634    end
2635    if length(indsel)>=1
2636        firstind=indsel(1);
2637        lastind=indsel(end);
2638        set(handles.first_j,'String',num2str(ref_j(firstind)))%update the display of first and last fields
2639        set(handles.last_j,'String',num2str(ref_j(lastind)))
2640        ref_j=ref_j(indsel);
2641        num_a_civ1=num_a_civ1(indsel);
2642        num_b_civ1=num_b_civ1(indsel);
2643        num_a_civ2=num_a_civ2(indsel);
2644        num_b_civ2=num_b_civ2(indsel);
2645    end
2646elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)
2647    displ_num=get(handles.ListPairCiv1,'UserData');
2648    num1_civ1=ref_i;
2649    num2_civ1=ref_i;
2650    num_a_civ1=displ_num(1,index_civ1);
2651    num_b_civ1=displ_num(2,index_civ1);
2652    num1_civ2=ref_i;
2653    num2_civ2=ref_i;
2654    num_a_civ2=displ_num(1,index_civ2);
2655    num_b_civ2=displ_num(2,index_civ2);
2656elseif isequal(mode,'displacement')
2657    num1_civ1=ref_i;
2658    num2_civ1=ref_i;
2659    num_a_civ1=ref_j;
2660    num_b_civ1=ref_j;
2661    num1_civ2=ref_i;
2662    num2_civ2=ref_i;
2663    num_a_civ2=ref_j;
2664    num_b_civ2=ref_j;
2665end
2666
2667%------------------------------------------------------------------------
2668% --- Executes on button press in ListCompareMode.
2669function ListCompareMode_Callback(hObject, eventdata, handles)
2670%------------------------------------------------------------------------
2671ListCompareMode=get(handles.ListCompareMode,'String');
2672option=ListCompareMode{get(handles.ListCompareMode,'Value')};
2673if ~strcmp(option,'PIV') % case 'displacement' or 'stereo PIV'
2674    filebase=get(handles.RootPath,'String');
2675    set(handles.sub_txt,'Visible','on')
2676    set(handles.RootFile_1,'Visible','On');%mkes the second file input window visible
2677    mode_store=get(handles.ListPairMode,'String');%get the present 'mode'
2678    set(handles.ListCompareMode,'UserData',mode_store);%store the mode display
2679    set(handles.ListPairMode,'Visible','off')
2680   
2681    %% open an image file with the browser
2682    ind_opening=1;%default
2683    browse.incr_pair=[0 0]; %default
2684    oldfile=get(handles.RootPath,'String');
2685    menu={'*.png;*.jpg;*.tif;*.avi;*.AVI;', ' (*.png,*.jpg ,.tif, *.avi,*.AVI)';
2686        '*.png','.png image files'; ...
2687        '*.jpg',' jpeg image files'; ...
2688        '*.tif','.tif image files'; ...
2689        '*.avi;*.AVI','.avi movie files'; ...
2690        '*.*',  'All Files (*.*)'};
2691    if strcmp(option,'displacement')
2692        comment='Pick the reference file for displacements';
2693    else
2694        comment='Pick a file of the second series';
2695    end
2696    [FileName, PathName] = uigetfile( menu, comment,oldfile);
2697    fileinput=[PathName FileName];%complete file name
2698    sizf=size(fileinput);
2699    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
2700    [path,name,ext]=fileparts(fileinput);
2701    [path1]=fileparts(filebase);
2702    if isunix
2703        [status,path]=system(['readlink ' path]);
2704        [status,path1]=system(['readlink ' path1]);% look for the true path in case of symbolic paths
2705    end
2706    if ~strcmp(path1,path)
2707        msgbox_uvmat('ERROR','The second image or series must be in the same directory as the first one')
2708        return
2709    end
2710    if strcmp(option,'displacement')
2711        [tild,RootFile_1]=fileparts(name);
2712    else
2713        [FilePath,FileName,Ext]=fileparts(fileinput);
2714% detect the file type, get the movie object if relevant, and look for the corresponding file series:
2715% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
2716[RootPath,SubDir,RootFile_1,i1_series,i2_series,j1_series,j2_series,nom_type_1,FileType,Object,i1,i2,j1,j2]=find_file_series(FilePath,[FileName Ext]);
2717       
2718       % [tild,tild,RootFile_1,tild,tild,tild,tild,tild,nom_type_1]=fileparts_uvmat(fileinput);
2719        %[RootFile_1,i1_series,tild,j1_series,tild,nom_type_1,FileType,Object]=find_file_series(PathName,FileName);
2720        %check image nom type
2721        if ~strcmp(nom_type_1,get(handles.NomType,'String'))
2722        msgbox_uvmat('ERROR','The second image series must have the same indexing type as the first one, or use the option displacement for a fixed image')
2723        return
2724        end
2725    end   
2726    %check image  extension
2727    if ~strcmp(ext,get(handles.ImaExt,'String'))
2728        msgbox_uvmat('ERROR','The second image series must have the same extension name as the first one')
2729        return
2730    end
2731    set(handles.RootFile_1,'String',RootFile_1);
2732else
2733    set(handles.ListPairMode,'Visible','on')
2734    set(handles.RootFile_1,'Visible','Off');
2735    set(handles.sub_txt,'Visible','off')
2736    set(handles.RootFile_1,'String',[]);
2737    mode_store=get(handles.ListCompareMode,'UserData');
2738    set(handles.ListPairMode,'Value',1)
2739    set(handles.ListPairMode,'String',mode_store)
2740    set(handles.CheckStereo,'Value',0)
2741    set(handles.ListPairMode,'Value',1) % mode 'civX' selected by default
2742end
2743% if strcmp(option,'stereo PIV') && get(handles.CheckPatch1,'Value')
2744%     set(handles.CheckStereo,'Visible','on')
2745% else
2746%     set(handles.CheckStereo,'Visible','off')
2747% end
2748% if strcmp(option,'stereo PIV') && get(handles.CheckPatch2,'Value')
2749%     set(handles.CheckStereo,'Visible','on')
2750% else
2751%     set(handles.CheckStereo,'Visible','off')
2752% end
2753ListPairMode_Callback(hObject, eventdata, handles)
2754
2755
2756%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2757% Callbacks in the uipanel Pair Indices
2758%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2759%------------------------------------------------------------------------
2760% --- Executes on button press in ListPairMode.
2761function ListPairMode_Callback(hObject, eventdata, handles)
2762%------------------------------------------------------------------------
2763compare_list=get(handles.ListCompareMode,'String');
2764val=get(handles.ListCompareMode,'Value');
2765compare=compare_list{val};
2766if strcmp(compare,'displacement')||strcmp(compare,'shift')
2767    mode='displacement';
2768else
2769    mode_list=get(handles.ListPairMode,'String');
2770    if ischar(mode_list)
2771        mode_list={mode_list};
2772    end
2773    mode_value=get(handles.ListPairMode,'Value');
2774    mode=mode_list{mode_value};
2775end
2776displ_num=[];%default
2777ref_i=str2double(get(handles.ref_i,'String'));
2778% last_i=str2num(get(handles.last_i,'String'));
2779time=get(handles.ImaDoc,'UserData'); %get the set of times
2780TimeUnit=get(handles.TimeUnit,'String');
2781checkframe=strcmp(TimeUnit,'frame');
2782siztime=size(time);
2783nbfield=siztime(1)-1;
2784nbfield2=siztime(2)-1;
2785indchosen=1;  %%first pair selected by default
2786%displ_num used to define the indices of the civ pairs
2787% in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices
2788% are relative to the reference indices ref_i and ref_j respectively.
2789if isequal(mode,'pair j1-j2')%| isequal(mode,'st_pair j1-j2')
2790    dt=1;
2791    displ='';
2792    index=0;
2793    numlist_a=[];
2794    numlist_B=[];
2795    %get all the time intervals in bursts
2796    displ_dt=1;%default
2797    nbfield2=min(nbfield2,10);%limitate the number of pairs to 10x10
2798    for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'pair j1-j2' mode
2799        for numod_b=(numod_a+1):nbfield2
2800            index=index+1;
2801            numlist_a(index)=numod_a;
2802            numlist_b(index)=numod_b;
2803            if size(time,2)>1 && ~checkframe
2804                dt(numod_a,numod_b)=time(ref_i+1,numod_b+1)-time(ref_i+1,numod_a+1);%first time interval dt
2805                displ_dt(index)=dt(numod_a,numod_b);
2806            else
2807                displ_dt(index)=1;
2808            end
2809        end
2810    end
2811    [dtsort,indsort]=sort(displ_dt);
2812    if ~isempty(numlist_a)
2813        displ_num(1,:)=numlist_a(indsort);
2814        displ_num(2,:)=numlist_b(indsort);
2815    end
2816    displ_num(3,:)=0;
2817    displ_num(4,:)=0;
2818    enable_j(handles, 'off')
2819elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)')
2820    index=1:200;
2821    displ_num(1,index)=-floor(index/2);
2822    displ_num(2,index)=ceil(index/2);
2823    displ_num(3:4,index)=zeros(2,200);
2824    enable_j(handles, 'on')
2825elseif isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)')
2826    index=1:200;
2827    displ_num(1:2,index)=zeros(2,200);
2828    displ_num(3,index)=-floor(index/2);
2829    displ_num(4,index)=ceil(index/2);
2830    enable_i(handles, 'on')
2831    if nbfield2 > 1
2832        enable_j(handles, 'on')
2833    else
2834        enable_j(handles, 'off')
2835    end
2836elseif isequal(mode,'displacement')%the pairs have the same indices
2837    displ_num(1,1)=0;
2838    displ_num(2,1)=0;
2839    displ_num(3,1)=0;
2840    displ_num(4,1)=0;
2841    if nbfield > 1 || nbfield==0
2842        enable_i(handles, 'on')
2843    else
2844        enable_j(handles, 'off')
2845    end
2846    if nbfield2 > 1
2847        enable_j(handles, 'on')
2848    else
2849        enable_j(handles, 'off')
2850    end
2851end
2852set(handles.ListPairCiv1,'UserData',displ_num);
2853errormsg=find_netcpair_civ( handles,1);
2854    if ~isempty(errormsg)
2855    msgbox_uvmat('ERROR',errormsg)
2856    end
2857% find_netcpair_civ2(handles)
2858
2859function enable_i(handles, state)
2860set(handles.itext,'Visible',state)
2861set(handles.first_i,'Visible',state)
2862set(handles.last_i,'Visible',state)
2863set(handles.incr_i,'Visible',state)
2864set(handles.nb_field,'Visible',state)
2865set(handles.ref_i,'Visible',state)
2866
2867function enable_j(handles, state)
2868set(handles.jtext,'Visible',state)
2869set(handles.first_j,'Visible',state)
2870set(handles.last_j,'Visible',state)
2871set(handles.incr_j,'Visible',state)
2872set(handles.nb_field2,'Visible',state)
2873set(handles.ref_j,'Visible',state)
2874
2875
2876%------------------------------------------------------------------------
2877% --- Executes on selection change in ListPairCiv1.
2878function ListPairCiv1_Callback(hObject, eventdata, handles)
2879%------------------------------------------------------------------------
2880%reproduce by default the chosen pair in the checkciv2 menu
2881list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
2882index_pair=get(handles.ListPairCiv1,'Value');
2883displ_num=get(handles.ListPairCiv1,'UserData');
2884% num_a=displ_num(1,index_pair);
2885% num_b=displ_num(2,index_pair);
2886list_pair2=get(handles.ListPairCiv2,'String');%get the menu of image pairs
2887if index_pair<=length(list_pair2)
2888    set(handles.ListPairCiv2,'Value',index_pair);
2889end
2890
2891%update first_i and last_i according to the chosen image pairs
2892mode_list=get(handles.ListPairMode,'String');
2893mode_value=get(handles.ListPairMode,'Value');
2894mode=mode_list{mode_value};
2895if isequal(mode,'series(Di)')
2896    first_i=str2double(get(handles.first_i,'String'));
2897    last_i=str2double(get(handles.last_i,'String'));
2898    incr_i=str2double(get(handles.incr_i,'String'));
2899    num1=first_i:incr_i:last_i;
2900    lastfield=str2double(get(handles.nb_field,'String'));
2901    if ~isnan(lastfield)
2902        test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ...
2903            (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield);
2904        num1=num1(test_find);
2905    end
2906    set(handles.first_i,'String',num2str(num1(1)));
2907    set(handles.last_i,'String',num2str(num1(end)));
2908elseif isequal(mode,'series(Dj)')
2909    first_j=str2double(get(handles.first_j,'String'));
2910    last_j=str2double(get(handles.last_j,'String'));
2911    incr_j=str2double(get(handles.incr_j,'String'));
2912    num_j=first_j:incr_j:last_j;
2913    lastfield2=str2double(get(handles.nb_field2,'String'));
2914    if ~isnan(lastfield2)
2915        test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
2916            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2);
2917        num1=num_j(test_find);
2918    end
2919    set(handles.first_j,'String',num2str(num1(1)));
2920    set(handles.last_j,'String',num2str(num1(end)));
2921end
2922
2923%------------------------------------------------------------------------
2924% --- Executes on selection change in ListPairCiv2.
2925function ListPairCiv2_Callback(hObject, eventdata, handles)
2926%------------------------------------------------------------------------
2927index_pair=get(handles.ListPairCiv2,'Value');%get the selected position index in the menu
2928
2929%update first_i and last_i according to the chosen image pairs
2930mode_list=get(handles.ListPairMode,'String');
2931mode_value=get(handles.ListPairMode,'Value');
2932mode=mode_list{mode_value};
2933if isequal(mode,'series(Di)')
2934    first_i=str2double(get(handles.first_i,'String'));
2935    last_i=str2double(get(handles.last_i,'String'));
2936    incr_i=str2double(get(handles.incr_i,'String'));
2937    num1=first_i:incr_i:last_i;
2938    lastfield=str2double(get(handles.nb_field,'String'));
2939    if ~isnan(lastfield)
2940        test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ...
2941            (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield);
2942        num1=num1(test_find);
2943    end
2944    set(handles.first_i,'String',num2str(num1(1)));
2945    set(handles.last_i,'String',num2str(num1(end)));
2946elseif isequal(mode,'series(Dj)')
2947    first_j=str2double(get(handles.first_j,'String'));
2948    last_j=str2double(get(handles.last_j,'String'));
2949    incr_j=str2double(get(handles.incr_j,'String'));
2950    num_j=first_j:incr_j:last_j;
2951    lastfield2=str2double(get(handles.nb_field2,'String'));
2952    if ~isnan(lastfield2)
2953        test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
2954            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2);
2955        num1=num_j(test_find);
2956    end
2957    set(handles.first_j,'String',num2str(num1(1)));
2958    set(handles.last_j,'String',num2str(num1(end)));
2959end
2960
2961%------------------------------------------------------------------------
2962function ref_i_Callback(hObject, eventdata, handles)
2963%------------------------------------------------------------------------
2964mode_list=get(handles.ListPairMode,'String');
2965mode_value=get(handles.ListPairMode,'Value');
2966mode=mode_list{mode_value};
2967errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files
2968if isequal(mode,'series(Di)') || ...% we do patch2 only
2969        (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
2970    errormsg=find_netcpair_civ( handles,2);
2971end
2972    if ~isempty(errormsg)
2973    msgbox_uvmat('ERROR',errormsg)
2974    end
2975
2976%------------------------------------------------------------------------
2977function ref_j_Callback(hObject, eventdata, handles)
2978%------------------------------------------------------------------------
2979mode_list=get(handles.ListPairMode,'String');
2980mode_value=get(handles.ListPairMode,'Value');
2981mode=mode_list{mode_value};
2982if isequal(get(handles.CheckCiv1,'Value'),0)|| isequal(mode,'series(Dj)')
2983    errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files
2984end
2985if isequal(mode,'series(Dj)') || ...
2986        (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
2987    errormsg=find_netcpair_civ(handles,2);
2988end
2989    if ~isempty(errormsg)
2990    msgbox_uvmat('ERROR',errormsg)
2991    end
2992
2993%------------------------------------------------------------------------
2994% determine the menu for checkciv1 pairs depending on existing netcdf file at the middle of
2995% the field series set by first_i, incr, last_i
2996% index=1: look for pairs for civ1
2997% index=2: look for pairs for civ2
2998function errormsg=find_netcpair_civ(handles,index)
2999%------------------------------------------------------------------------
3000set(gcf,'Pointer','watch')% set the mouse pointer to 'watch' (clock)
3001
3002%% initialisation
3003errormsg='';
3004browse=get(handles.RootPath,'UserData');
3005compare_list=get(handles.ListCompareMode,'String');
3006val=get(handles.ListCompareMode,'Value');
3007compare=compare_list{val};
3008if strcmp(compare,'displacement')||strcmp(compare,'shift')
3009    mode='displacement';
3010else
3011    mode_list=get(handles.ListPairMode,'String');
3012    mode_value=get(handles.ListPairMode,'Value');
3013    if isempty(mode_list)
3014        return
3015    end
3016    mode=mode_list{mode_value};
3017end
3018nom_type_ima=get(handles.NomType,'String');
3019
3020%% determine nom_type_nc, nomenclature type of the .nc files:
3021[nom_type_nc]=nomtype2pair(nom_type_ima,mode);
3022
3023%% reads .nc subdirectoy and image numbers from the interface
3024subdir_civ1=get(handles.SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf data
3025subdir_civ2=get(handles.SubdirCiv2,'String');%subdirectory subdir_civ2 for the netcdf data
3026ref_i=str2double(get(handles.ref_i,'String'));
3027if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
3028    ref_j=0;
3029else
3030    ref_j=str2double(get(handles.ref_j,'String'));
3031    if isnan(ref_j)
3032        ref_j=1;
3033    end
3034end
3035time=get(handles.ImaDoc,'UserData');%get the set of times
3036TimeUnit=get(handles.TimeUnit,'String');
3037checkframe=strcmp(TimeUnit,'frame');
3038displ_num=get(handles.ListPairCiv1,'UserData');
3039
3040%% eliminate the first pairs inconsistent with the position
3041if isempty(displ_num)
3042    nbpair=0;
3043else
3044    nbpair=length(displ_num(1,:));%nbre of displayed pairs
3045    if  isequal(mode,'series(Di)')  %| isequal(mode,'st_series(Di)')
3046        nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index
3047    elseif  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
3048        nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index
3049    end
3050end
3051nbpair=min(200,nbpair);%limit the number of displayed pairs to 200
3052
3053%% case with no Civ1 operation, netcdf files need to exist for reading
3054displ_pair={''};
3055select=ones(size(1:nbpair));%flag for displayed pairs =1 for display
3056testpair=0;
3057RootPath=get(handles.RootPath,'String');
3058RootFile=get(handles.RootFile,'String');
3059if index==1 % case civ1
3060    if ~get(handles.CheckCiv1,'Value') %
3061        if ~exist(fullfile(RootPath,subdir_civ1),'dir')
3062            errormsg=['no civ1 file available: subdirectory ' subdir_civ1 ' does not exist'];
3063            set(handles.ListPairCiv1,'String',{});
3064            return
3065        end
3066        for ipair=1:nbpair
3067            filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,...
3068                ref_i+displ_num(3,ipair),ref_i+displ_num(4,ipair),ref_j+displ_num(1,ipair),ref_j+displ_num(2,ipair));
3069            select(ipair)=exist(filename,'file')==2;% put flag to 0 if the file does not exist
3070        end
3071        % case of no displayed pair
3072        if isequal(select,zeros(size(1:nbpair)))
3073            if isfield(browse,'incr_pair') && ~isequal(browse.incr_pair,[0 0])
3074                num_i1=ref_i-floor(browse.incr_pair(1)/2);
3075                num_i2=ref_i+ceil(browse.incr_pair(1)/2);
3076                num_j1=ref_j-floor(browse.incr_pair(2)/2);
3077                num_j2=ref_j+ceil(browse.incr_pair(2)/2);
3078                filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,num_i1,num_i2,num_j1,num_j2);
3079                select(1)=exist(filename,'file')==2;
3080                testpair=1;
3081            else
3082                if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
3083                    errormsg=['no civ1 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ1];
3084                else
3085                    errormsg=['no civ1 file available for the selected reference indices (i,j)= ' num2str(ref_i) ', ' num2str(ref_j) ' and subdirectory ' subdir_civ1];
3086                end
3087                set(handles.ListPairCiv1,'String',{''});
3088                %COMPLETER CAS STEREO
3089                return
3090            end
3091        end
3092    end
3093else %case civ2 alone
3094    if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
3095        if ~exist(fullfile(RootPath,subdir_civ2),'dir')
3096            msgbox_uvmat('ERROR',['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist'])
3097            set(handles.ListPairCiv2,'Value',1);
3098            set(handles.ListPairCiv2,'String',{''});
3099            return
3100        end
3101        for ipair=1:nbpair
3102            filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,...
3103                ref_i+displ_num(3,ipair),ref_i+displ_num(4,ipair),ref_j+displ_num(1,ipair),ref_j+displ_num(2,ipair));
3104            select(ipair)=exist(filename,'file')==2;
3105        end
3106        if  isequal(select,zeros(size(1:nbpair)))
3107            if isfield(browse,'incr_pair')
3108                num_i1=ref_i-floor(browse.incr_pair(1)/2);
3109                num_i2=ref_i+floor((browse.incr_pair(1)+1)/2);
3110                num_j1=ref_j-floor(browse.incr_pair(2)/2);
3111                num_j2=ref_j+floor((browse.incr_pair(2)+1)/2);
3112                filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile,'.nc',nom_type_nc,num_i1,num_i2,num_j1,num_j2);
3113                select(1)=exist(filename,'file')==2;
3114            else
3115                if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
3116                    errormsg=['no civ2 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ2];
3117                else
3118                    errormsg=['no civ2 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ2];
3119                end
3120                set(handles.ListPairCiv2,'Value',1);
3121                set(handles.ListPairCiv2,'String',{''});
3122                return
3123            end
3124        end
3125    end
3126end
3127
3128%% determine the menu display in .ListPairCiv1
3129% the menu depends on the mode defined in ListPairMode_callback through the array displ_num:
3130% displ_num(1,:)=indices j1
3131% displ_num(2,:)=indices j2
3132% displ_num(3,:)=indices i1
3133% displ_num(4,:)=indices i2
3134% in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices
3135% are relative to the reference indices ref_i and ref_j respectively.
3136if isequal(mode,'series(Di)')
3137    if testpair
3138        displ_pair{1}=['Di= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
3139    else
3140        for ipair=1:nbpair
3141            if select(ipair)
3142                displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
3143                %if ~checkframe && size(time,1)>=ref_i+1+displ_num(4,ipair) && size(time,2)>=ref_j+1+displ_num(2,ipair)&&displ_num(2,ipair)>=1 &&displ_num(1,ipair)>=1
3144                 %   dt=time(ref_i+1+displ_num(4,ipair),ref_j+1+displ_num(2,ipair))-time(ref_i+1+displ_num(3,ipair),ref_j+1+displ_num(1,ipair));%time interval dt
3145               if ~checkframe && size(time,1)>=ref_i+1+ceil(ipair/2) && size(time,2)>=ref_j+1&& ref_i-floor(ipair/2)>=0 && ref_j>=0
3146                 dt=time(ref_i+1+ceil(ipair/2),ref_j+1)-time(ref_i+1-floor(ipair/2),ref_j+1);%time interval dtref_j+1
3147                else
3148                    dt=1;
3149                end
3150                 displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
3151            else
3152                displ_pair{ipair}='...'; %pair not displayed in the menu
3153            end
3154        end
3155    end
3156elseif isequal(mode,'series(Dj)')
3157    if testpair
3158        displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
3159    else
3160        for ipair=1:nbpair
3161            if select(ipair)
3162                displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
3163                if ~checkframe && size(time,1)>=ref_i+1+displ_num(4,ipair) && size(time,2)>=ref_j+1+displ_num(2,ipair)
3164                    dt=time(ref_i+1+displ_num(4,ipair),ref_j+1+displ_num(2,ipair))-time(ref_i+1+displ_num(3,ipair),ref_j+1+displ_num(1,ipair));%time interval dt
3165                    displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
3166                end
3167            else
3168                displ_pair{ipair}='...'; %pair not displayed in the menu
3169            end
3170        end
3171    end
3172elseif isequal(mode,'pair j1-j2')%case of pairs
3173    for ipair=1:nbpair
3174        if select(ipair)
3175            if ~checkframe && size(time,2)>1
3176            dt=time(ref_i+1+displ_num(4,ipair),displ_num(2,ipair)+1)-time(ref_i+1+displ_num(3,ipair),displ_num(1,ipair)+1);%time interval dt
3177            else % time set by default to i index
3178                dt=1;
3179            end
3180            displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ...
3181                ' :dt= ' num2str(dt*1000)];
3182        else
3183            displ_pair{ipair}='...'; %pair not displayed in the menu
3184        end
3185    end
3186elseif isequal(mode,'displacement')
3187    displ_pair={'Di=Dj=0'};
3188end
3189if index==1
3190set(handles.ListPairCiv1,'String',displ_pair');
3191end
3192
3193%% determine the default selection in the pair menu
3194ichoice=find(select,1);% index of selected pair
3195if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
3196initial=get(handles.ListPairCiv1,'Value');%initial choice of pair
3197if initial>nbpair || (numel(select)>=initial && ~isequal(select(initial),1))
3198    set(handles.ListPairCiv1,'Value',ichoice);% first valid pair proposed by default in the menu
3199end
3200initial=get(handles.ListPairCiv2,'Value');
3201if initial>length(displ_pair')%|~isequal(select(initial),1)
3202    if ichoice <= length(displ_pair')
3203        set(handles.ListPairCiv2,'Value',ichoice);% same pair proposed by default for civ2
3204    else
3205        set(handles.ListPairCiv2,'Value',1);% same pair proposed by default for civ2
3206    end
3207end
3208set(handles.ListPairCiv2,'String',displ_pair');
3209set(gcf,'Pointer','arrow')
3210
3211
3212   
3213% %------------------------------------------------------------------------   
3214% % call 'view_field.fig' to display the  field selected in the list of 'status'
3215% function open_view_field(hObject, eventdata)
3216% %------------------------------------------------------------------------
3217% list=get(hObject,'String');
3218% index=get(hObject,'Value');
3219% rootroot=get(hObject,'UserData');
3220% filename=list{index};
3221% ind_dot=strfind(filename,'...');
3222% filename=filename(1:ind_dot-1);
3223% filename=fullfile(rootroot,filename);
3224% delete(get(hObject,'parent'))%delete the display figure to stop the check process
3225% if exist(filename,'file')%visualise the vel field if it exists
3226%     uvmat(filename)
3227%     set(gcbo,'Value',1)
3228% end
3229
3230
3231%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3232% Callbacks in the uipanel Reference Indices
3233%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3234%------------------------------------------------------------------------
3235function first_i_Callback(hObject, eventdata, handles)
3236%------------------------------------------------------------------------
3237first_i=str2double(get(handles.first_i,'String'));
3238set(handles.ref_i,'String', num2str(first_i))% reference index for pair dt = first index
3239ref_i_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
3240
3241%------------------------------------------------------------------------
3242function first_j_Callback(hObject, eventdata, handles)
3243%------------------------------------------------------------------------
3244first_j=str2num(get(handles.first_j,'String'));
3245set(handles.ref_j,'String', num2str(first_j))% reference index for pair dt = first index
3246ref_j_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
3247
3248%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3249% Callbacks in the uipanel Civ1
3250%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3251%------------------------------------------------------------------------
3252% --- Executes on button press in SearchRange: determine the search range num_SearchBoxSize_1,num_SearchBoxSize_2
3253function SearchRange_Callback(hObject, eventdata, handles)
3254%------------------------------------------------------------------------
3255%determine pair numbers
3256if strcmp(get(handles.num_UMin,'Visible'),'off')
3257    set(handles.u_title,'Visible','on')
3258    set(handles.v_title,'Visible','on')
3259    set(handles.num_UMin,'Visible','on')
3260    set(handles.num_UMax,'Visible','on')
3261    set(handles.num_VMin,'Visible','on')
3262    set(handles.num_VMax,'Visible','on')
3263    set(handles.CoordUnit,'Visible','on')
3264    set(handles.TimeUnit,'Visible','on')
3265    set(handles.slash_title,'Visible','on')
3266    set(handles.min_title,'Visible','on')
3267    set(handles.max_title,'Visible','on')
3268    set(handles.unit_title,'Visible','on')
3269else
3270    get_search_range(hObject, eventdata, handles)
3271end
3272
3273%------------------------------------------------------------------------
3274% ---  determine the search range num_SearchBoxSize_1,num_SearchBoxSize_2 and shift
3275function get_search_range(hObject, eventdata, handles)
3276%------------------------------------------------------------------------
3277param_civ1=read_GUI(handles.Civ1);
3278umin=param_civ1.UMin;
3279umax=param_civ1.UMax;
3280vmin=param_civ1.VMin;
3281vmax=param_civ1.VMax;
3282%switch min_title and max_title in case of error
3283if umax<=umin
3284    umin_old=umin;
3285    umin=umax;
3286    umax=umin_old;
3287    set(handles.num_UMin,'String', num2str(umin))
3288    set(handles.num_UMax,'String', num2str(umax))
3289end
3290if vmax<=vmin
3291    vmin_old=vmin;
3292    vmin=vmax;
3293    vmax=vmin_old;
3294    set(handles.num_VMin,'String', num2str(vmin))
3295    set(handles.num_VMax,'String', num2str(vmax))
3296end   
3297if ~(isempty(umin)||isempty(umax)||isempty(vmin)||isempty(vmax))
3298    list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
3299    index=get(handles.ListPairCiv1,'Value');
3300    pair_string=list_pair{index};
3301    time=get(handles.ImaDoc,'UserData'); %get the set of times
3302    pxcm=get(handles.SearchRange,'UserData');
3303    mode_list=get(handles.ListPairMode,'String');
3304    mode_value=get(handles.ListPairMode,'Value');
3305    mode=mode_list{mode_value};     
3306    if isequal (mode, 'series(Di)' )
3307        ref_i=str2double(get(handles.ref_i,'String'));
3308        num1=ref_i-floor(index/2);%  first image numbers
3309        num2=ref_i+ceil(index/2);
3310        num_a=1;
3311        num_b=1;
3312    elseif isequal (mode, 'series(Dj)')
3313        num1=1;
3314        num2=1;
3315        ref_j=str2double(get(handles.ref_j,'String'));
3316        num_a=ref_j-floor(index/2);%  first image numbers
3317        num_b=ref_j+ceil(index/2);
3318    elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)     
3319        ref_i=str2double(get(handles.ref_i,'String'));
3320        num1=ref_i;
3321        num2=ref_i;
3322                r=regexp(pair_string,'(?<mode>(Di=)|(Dj=)) -*(?<num1>\d+)\|(?<num2>\d+)','names');
3323        if isempty(r)
3324            r=regexp(pair_string,'(?<num1>\d+)(?<mode>-)(?<num2>\d+)','names');
3325        end 
3326        num_a=str2num(r.num1);
3327        num_b=str2num(r.num2);
3328    end
3329    dt=time(num2+1,num_b+1)-time(num1+1,num_a+1);
3330    ibx=str2double(get(handles.num_CorrBoxSize_1,'String'));
3331    iby=str2double(get(handles.num_CorrBoxSize_2,'String'));
3332    umin=dt*pxcm*umin;
3333    umax=dt*pxcm*umax;
3334    vmin=dt*pxcm*vmin;
3335    vmax=dt*pxcm*vmax;
3336    shiftx=round((umin+umax)/2);
3337    shifty=round((vmin+vmax)/2);
3338    isx=(umax+2-shiftx)*2+param_civ1.Bx;
3339    isx=2*ceil(isx/2)+1;
3340    isy=(vmax+2-shifty)*2+param_civ1.Bx;
3341    isy=2*ceil(isy/2)+1;
3342    set(handles.num_SearchBoxShift_1,'String',num2str(shiftx));
3343    set(handles.num_SearchBoxShift_2,'String',num2str(shifty));
3344    set(handles.num_SearchBoxSize_1,'String',num2str(isx));
3345    set(handles.num_SearchBoxSize_2,'String',num2str(isy));
3346end
3347
3348%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3349% Callbacks in the uipanel Fix1
3350%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3351%------------------------------------------------------------------------
3352% --- Executes on button press in CheckMask.
3353function get_mask_fix1_Callback(hObject, eventdata, handles)
3354%------------------------------------------------------------------------
3355maskval=get(handles.CheckMask,'Value');
3356if isequal(maskval,0)
3357    set(handles.Mask,'String','')
3358else
3359    mask_displ='no mask'; %default
3360    filebase=get(handles.RootPath,'String');
3361    [nbslice, flag_mask]=get_mask(filebase,handles);
3362    if isequal(flag_mask,1)
3363        mask_displ=[num2str(nbslice) 'mask'];
3364    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3365        filebase_a=get(handles.RootFile_1,'String');
3366        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3367        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3368            mask_displ='no mask';
3369        end
3370    end
3371    if isequal(mask_displ,'no mask')
3372        [FileName, PathName, filterindex] = uigetfile( ...
3373            {'*.png', ' (*.png)';
3374            '*.png',  '.png files '; ...
3375            '*.*', 'All Files (*.*)'}, ...
3376            'Pick a mask file *.png',filebase);
3377        mask_displ=fullfile(PathName,FileName);
3378        if ~exist(mask_displ,'file')
3379            mask_displ='no mask';
3380        end
3381    end
3382    if isequal(mask_displ,'no mask')
3383        set(handles.CheckMask,'Value',0)
3384        set(handles.CheckMask,'Value',0)
3385        set(handles.CheckMask,'Value',0)
3386    else
3387        %set(handles.CheckMask,'Value',1)
3388        set(handles.CheckMask,'Value',1)
3389    end
3390    set(handles.Mask,'String',mask_displ)
3391    set(handles.Mask,'String',mask_displ)
3392    set(handles.Mask,'String',mask_displ)
3393end
3394
3395%------------------------------------------------------------------------
3396% --- Executes on button press in CheckMask: select box for mask option
3397function get_mask_civ2_Callback(hObject, eventdata, handles)
3398%------------------------------------------------------------------------
3399maskval=get(handles.CheckMask,'Value');
3400if isequal(maskval,0)
3401    set(handles.Mask,'String','')
3402else
3403    mask_displ='no mask'; %default
3404    filebase=get(handles.RootPath,'String');
3405    [nbslice, flag_mask]=get_mask(filebase,handles);
3406    if isequal(flag_mask,1)
3407        mask_displ=[num2str(nbslice) 'mask'];
3408    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3409        filebase_a=get(handles.RootFile_1,'String');
3410        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3411        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3412            mask_displ='no mask';
3413        end
3414    end
3415    if isequal(mask_displ,'no mask')
3416        [FileName, PathName, filterindex] = uigetfile( ...
3417            {'*.png', ' (*.png)';
3418            '*.png',  '.png files '; ...
3419            '*.*', 'All Files (*.*)'}, ...
3420            'Pick a mask file *.png',filebase);
3421        mask_displ=fullfile(PathName,FileName);
3422        if ~exist(mask_displ,'file')
3423            mask_displ='no mask';
3424        end
3425    end
3426    if isequal(mask_displ,'no mask')
3427        set(handles.CheckMask,'Value',0)
3428        set(handles.CheckMask,'Value',0)
3429    else
3430        set(handles.CheckMask,'Value',1)
3431    end
3432    set(handles.Mask,'String',mask_displ)
3433    set(handles.Mask,'String',mask_displ)
3434end
3435
3436%------------------------------------------------------------------------
3437% --- Executes on button press in CheckMask.
3438function get_mask_fix2_Callback(hObject, eventdata, handles)
3439%------------------------------------------------------------------------
3440maskval=get(handles.CheckMask,'Value');
3441if isequal(maskval,0)
3442    set(handles.Mask,'String','')
3443else
3444    mask_displ='no mask'; %default
3445    filebase=get(handles.RootPath,'String');
3446    [nbslice, flag_mask]=get_mask(filebase,handles);
3447    if isequal(flag_mask,1)
3448        mask_displ=[num2str(nbslice) 'mask'];
3449    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3450        filebase_a=get(handles.RootFile_1,'String');
3451        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3452        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3453            mask_displ='no mask';
3454        end
3455    end
3456    if isequal(mask_displ,'no mask')
3457        [FileName, PathName, filterindex] = uigetfile( ...
3458            {'*.png', ' (*.png)';
3459            '*.png',  '.png files '; ...
3460            '*.*', 'All Files (*.*)'}, ...
3461            'Pick a mask file *.png',filebase);
3462        mask_displ=fullfile(PathName,FileName);
3463        if ~exist(mask_displ,'file')
3464            mask_displ='no mask';
3465        end
3466    end
3467    if isequal(mask_displ,'no mask')
3468        set(handles.CheckMask,'Value',0)
3469    end
3470    set(handles.Mask,'String',mask_displ)
3471end
3472
3473%------------------------------------------------------------------------
3474% --- function called to look for mask files
3475function [nbslice, flag_mask]=get_mask(filebase,handles)
3476%------------------------------------------------------------------------
3477%detect mask files, images with appropriate file base
3478%[filebase '_' xx 'mask'], xx=nbslice
3479%flag_mask=1 indicates detection
3480
3481flag_mask=0;%default
3482nbslice=1;
3483
3484% subdir=get(handles.SubdirCiv1,'String');
3485[Path,Name]=fileparts(filebase);
3486if ~isdir(Path)
3487    msgbox_uvmat('ERROR','no path for input files')
3488    return
3489end
3490% currentdir=pwd;
3491% cd(Path);%move in the dir of the root name filebase
3492maskfiles=dir(fullfile(Path,[Name '_*mask_*.png']));%look for mask files
3493% cd(currentdir);%come back to the current working directory
3494if ~isempty(maskfiles)
3495    %     msgbox_uvmat('ERROR','no mask available, to create it use Tools/Make mask in the upper menu bar of uvmat')
3496    % else
3497    flag_mask=1;
3498    maskname=maskfiles(1).name;% take the first mask file in the list
3499    [Path2,Name,ext]=fileparts(maskname);
3500    Namedouble=double(Name);
3501    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3502    ind_mask=findstr('mask',Name);
3503    i=ind_mask-1;
3504    while val(i)==0 && i>0
3505        i=i-1;
3506    end
3507    nbslice=str2double(Name(i+1:ind_mask-1));
3508    if ~isnan(nbslice) && Name(i)=='_'
3509        flag_mask=1;
3510    else
3511        msgbox_uvmat('ERROR',['bad mask file ' Name ext ' found in ' Path2])
3512        return
3513        nbslice=1;
3514    end
3515end
3516
3517%------------------------------------------------------------------------
3518% --- function called to look for grid files
3519function [nbslice, flag_mask]=get_grid(filebase,handles)
3520%------------------------------------------------------------------------
3521flag_mask=0;%default
3522nbslice=1;
3523[Path,Name]=fileparts(filebase);
3524currentdir=pwd;
3525cd(Path);%move in the dir of the root name filebase
3526maskfiles=dir([Name '_*grid_*.grid']);%look for mask files
3527cd(currentdir);%come back to the current working directory
3528if ~isempty(maskfiles)
3529    flag_mask=1;
3530    maskname=maskfiles(1).name;% take the first mask file in the list
3531    [Path2,Name,ext]=fileparts(maskname);
3532    Namedouble=double(Name);
3533    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3534    ind_mask=findstr('grid',Name);
3535    i=ind_mask-1;
3536    while val(i)==0 && i>0
3537        i=i-1;
3538    end
3539    nbslice=str2double(Name(i+1:ind_mask-1));
3540    if ~isnan(nbslice) && Name(i)=='_'
3541        flag_mask=1;
3542    else
3543        msgbox_uvmat('ERROR',['bad grid file ' Name ext ' found in ' Path2])
3544        return
3545        nbslice=1;
3546    end
3547end
3548
3549%------------------------------------------------------------------------
3550% --- transform numbers to letters
3551function str=num2stra(num,nom_type)
3552%------------------------------------------------------------------------
3553if isempty(nom_type)
3554    str='';
3555elseif strcmp(nom_type(end),'a')
3556    str=char(96+num);
3557elseif strcmp(nom_type(end),'A')
3558    str=char(96+num);
3559elseif isempty(nom_type(2:end))%a single index
3560    str='';
3561else
3562    str=num2str(num);
3563end
3564
3565%------------------------------------------------------------------------
3566% --- Executes on button press in ListSubdirCiv1.
3567function ListSubdirCiv1_Callback(hObject, eventdata, handles)
3568%------------------------------------------------------------------------
3569list_subdir_civ1=get(handles.ListSubdirCiv1,'String');
3570val=get(handles.ListSubdirCiv1,'Value');
3571SubDir=list_subdir_civ1{val};
3572if strcmp(SubDir,'new...')
3573    if get(handles.CheckCiv1,'Value')
3574        SubDir='CIV'; %default subdirectory
3575    else
3576        msgbox_uvmat('ERROR','select CheckCiv1 to perform a new Civ operation')
3577        return
3578    end   
3579end
3580set(handles.SubdirCiv1,'String',SubDir);
3581errormsg=find_netcpair_civ(handles,1);
3582if ~isempty(errormsg)
3583    msgbox_uvmat('ERROR',errormsg)
3584end
3585   
3586%------------------------------------------------------------------------
3587% --- Executes on button press in ListSubdirCiv2.
3588function ListSubdirCiv2_Callback(hObject, eventdata, handles)
3589%------------------------------------------------------------------------
3590list_subdir_civ2=get(handles.ListSubdirCiv2,'String');
3591val=get(handles.ListSubdirCiv2,'Value');
3592SubDir=list_subdir_civ2{val};
3593if strcmp(SubDir,'new...')
3594    if get(handles.CheckCiv2,'Value')
3595        SubDir='CIV'; %default subdirectory
3596    else
3597        msgbox_uvmat('ERROR','select CheckCiv2 to perform a new Civ operation')
3598        return
3599    end
3600end
3601set(handles.SubdirCiv2,'String',SubDir);
3602
3603%------------------------------------------------------------------------
3604% --- Executes on button press in CheckGrid.
3605function CheckGrid_Callback(hObject, eventdata, handles)
3606%------------------------------------------------------------------------
3607value=get(hObject,'Value');
3608hparent=get(hObject,'parent');
3609hchildren=get(hparent,'children');
3610handle_txtbox=findobj(hchildren,'tag','txt_Grid');
3611handle_dx=findobj(hchildren,'tag','num_Dx');
3612handle_dy=findobj(hchildren,'tag','num_Dy');
3613handle_title_dx=findobj(hchildren,'tag','title_Dx');
3614handle_title_dy=findobj(hchildren,'tag','title_Dy');
3615testgrid=0;
3616filegrid='';
3617if value
3618    filebase=get(handles.RootPath,'String');
3619    [nbslice, flag_grid]=get_grid(filebase,handles);% look for a grid with appropriate name
3620    if isequal(flag_grid,1)
3621        filegrid=[num2str(nbslice) 'grid'];
3622        testgrid=1;
3623    else % browse for a grid
3624        filegrid=get(hObject,'UserData');%look for previous grid name stored as UserData
3625        if exist(filegrid,'file')
3626            filebase=filegrid;
3627        end
3628        [FileName, PathName, filterindex] = uigetfile( ...
3629            {'*.grid', ' (*.grid)';
3630            '*.grid',  '.grid files '; ...
3631            '*.*', 'All Files (*.*)'}, ...
3632            'Pick a file',filebase);
3633        filegrid=fullfile(PathName,FileName);
3634        set(hObject,'UserData',filegrid);%store for future use
3635        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filegrid,'file'))
3636            testgrid=1;
3637        end
3638    end
3639end
3640if testgrid
3641    set(handle_dx,'Visible','off');
3642    set(handle_dy,'Visible','off');
3643    set(handle_title_dy,'Visible','off');
3644    set(handle_title_dx,'Visible','off');
3645    set(handle_txtbox,'Visible','on')
3646    set(handle_txtbox,'String',filegrid)
3647else
3648    set(hObject,'Value',0);
3649    set(handle_dx,'Visible','on');
3650    set(handle_dy,'Visible','on');
3651    set(handle_title_dy,'Visible','on');
3652    set(handle_title_dx,'Visible','on');
3653    set(handle_txtbox,'Visible','off')
3654end
3655
3656%% if hObject is on the checkciv1 frame, duplicate action for checkciv2 frame
3657PanelName=get(hparent,'tag');
3658if strcmp(PanelName,'Civ1')
3659    hchildren=get(handles.Civ2,'children');
3660    handle_checkbox=findobj(hchildren,'tag','CheckGrid');
3661    handle_txtbox=findobj(hchildren,'tag','txt_Grid');
3662    handle_dx=findobj(hchildren,'tag','num_Dx');
3663    handle_dy=findobj(hchildren,'tag','num_Dy');
3664    handle_title_dx=findobj(hchildren,'tag','title_Dx');
3665    handle_title_dy=findobj(hchildren,'tag','title_Dy');
3666    set(handle_checkbox,'UserData',filegrid);%store for future use
3667    if testgrid
3668        set(handle_checkbox,'Value',1);
3669        set(handle_dx,'Visible','off');
3670        set(handle_dy,'Visible','off');
3671        set(handle_title_dx,'Visible','off');
3672        set(handle_title_dy,'Visible','off');
3673        set(handle_txtbox,'Visible','on')
3674        set(handle_txtbox,'String',filegrid)
3675%     else
3676%         set(handle_checkbox,'Value',0);
3677%         set(handles.CheckGrid,'Value',0);
3678%         set(handle_dx,'Visible','on');
3679%         set(handle_dy,'Visible','on');
3680%          set(handle_title_dx,'Visible','on');
3681%         set(handle_title_dy,'Visible','on');
3682%         set(handle_txtbox,'Visible','off')
3683    end
3684end
3685
3686%------------------------------------------------------------------------
3687% --- Executes on button press in CheckMask: common to all panels (civ1, Civ2..)
3688function CheckMask_Callback(hObject, eventdata, handles)
3689%------------------------------------------------------------------------
3690value=get(hObject,'Value');
3691hparent=get(hObject,'parent');
3692parent_tag=get(hparent,'Tag');
3693hchildren=get(hparent,'children');
3694handle_txtbox=findobj(hchildren,'tag','Mask');% look for the mask name box in the same panel
3695testmask=0;
3696if value
3697    filebase=get(handles.RootPath,'String');
3698    [nbslice, flag_mask]=get_mask(filebase,handles);% look for a mask with appropriate name
3699    if isequal(flag_mask,1)
3700        filemask=[num2str(nbslice) 'mask'];
3701        testmask=1;
3702    else % browse for a mask
3703        filemask=get(hObject,'UserData');%look for previous mask name stored as UserData
3704        if exist(filemask,'file')
3705            filebase=filemask;
3706        end
3707        [FileName, PathName] = uigetfile( ...
3708            {'*.png', ' (*.png)';
3709            '*.png',  '.png files '; ...
3710            '*.*', 'All Files (*.*)'}, ...
3711            'Pick a mask file *.png',filebase);
3712        filemask=fullfile(PathName,FileName);
3713        set(hObject,'UserData',filemask);%store for future use
3714        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filemask,'file'))
3715            testmask=1;
3716        end
3717    end
3718end
3719if testmask
3720    if strcmp(parent_tag,'Civ1')
3721        set(handles.Mask,'Visible','on')
3722        set(handles.Mask,'String',filemask)
3723    set(handles.CheckMask,'Value',1)
3724    end
3725%     switch parent_tag
3726% %         case 'Fix1'
3727% %             stage=2;
3728%         case 'Civ2'
3729%              stage=3;
3730% %         case 'Fix2'
3731% %             stage=4;
3732%     end
3733%     set(handles.Mask(stage:end),'Visible','on')
3734%     set(handles.Mask(stage:end),'String',filemask)
3735%     set(handles.CheckMask(stage:end),'Value',1)
3736else
3737    set(hObject,'Value',0);
3738    set(handle_txtbox,'Visible','off')
3739end
3740
3741
3742% --- Executes on button press in get_gridpatch1.
3743function get_gridpatch1_Callback(hObject, eventdata, handles)
3744filebase=get(handles.RootPath,'String');
3745[FileName, PathName, filterindex] = uigetfile( ...
3746    {'*.grid', ' (*.grid)';
3747    '*.grid',  '.grid files '; ...
3748    '*.*', 'All Files (*.*)'}, ...
3749    'Pick a file',filebase);
3750filegrid=fullfile(PathName,FileName);
3751set(handles.grid_patch1,'string',filegrid);
3752
3753
3754%------------------------------------------------------------------------
3755% --- Executes on button press in get_gridpatch2.
3756function get_gridpatch2_Callback(hObject, eventdata, handles)
3757%------------------------------------------------------------------------
3758
3759
3760%------------------------------------------------------------------------
3761% --- STEREO Interp
3762function cmd=RUN_STINTERP(stinterpBin,filename_A_nc,filename_B_nc,filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,xmlA,xmlB)
3763%------------------------------------------------------------------------
3764namelog=[filename_nc(1:end-3) '_stinterp.log'];
3765cmd=[stinterpBin ' -f1 ' filename_A_nc  ' -f2 ' filename_B_nc ' -f  ' filename_nc ...
3766    ' -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
3767
3768%------------------------------------------------------------------------
3769%--read images and convert them to the uint16 format used for PIV
3770function A=read_image(filename,type_ima,num,movieobject)
3771%------------------------------------------------------------------------
3772%num is the view number needed for an avi movie
3773switch type_ima
3774    case 'movie'
3775        A=read(movieobject,num);
3776    case 'avi'
3777        mov=aviread(filename,num);
3778        A=frame2im(mov(1));
3779    case 'multimage'
3780        A=imread(filename,num);
3781    case 'image'
3782        A=imread(filename);
3783end
3784siz=size(A);
3785if length(siz)==3;%color images
3786    A=sum(double(A),3);
3787    A=uint16(A);
3788end
3789
3790
3791%------------------------------------------------------------------------
3792% --- Executes on button press in get_ref_fix1.
3793function get_ref_fix1_Callback(hObject, eventdata, handles)
3794%------------------------------------------------------------------------
3795filebase=get(handles.RootPath,'String');
3796[FileName, PathName, filterindex] = uigetfile( ...
3797    {'*.nc', ' (*.nc)';
3798    '*.nc',  'netcdf files '; ...
3799    '*.*', 'All Files (*.*)'}, ...
3800    'Pick a file',filebase);
3801
3802fileinput=[PathName FileName];
3803sizf=size(fileinput);
3804if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
3805%[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
3806[Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput);
3807ref.filebase=fullfile(Path,File);
3808% ref.num_a=stra2num(str_a);
3809% ref.num_b=stra2num(str_b);
3810% ref.num1=str2double(field_count);
3811% ref.num2=str2double(str2);
3812browse=[];%initialisation
3813if ~isequal(ref.ext,'.nc')
3814    msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
3815    return
3816end
3817set(handles.ref_fix1,'String',[fullfile(ref.subdir,File) '....nc']);
3818set(handles.ref_fix1,'UserData',ref)
3819menu_field{1}='civ1';
3820Data=nc2struct(fileinput,[]);
3821if isfield(Data,'patch') && isequal(Data.patch,1)
3822    menu_field{2}='filter1';
3823end
3824if isfield(Data,'civ2') && isequal(Data.civ2,1)
3825    menu_field{3}='civ2';
3826end
3827if isfield(Data,'patch2') && isequal(Data.patch2,1)
3828    menu_field{4}='filter2';
3829end
3830set(handles.field_ref1,'String',menu_field);
3831set(handles.field_ref1,'Value',length(menu_field));
3832set(handles.num_MinVel,'Value',2);
3833set(handles.num_MinVel,'String','1');%default threshold
3834set(handles.ref_fix1,'Enable','on')
3835
3836%------------------------------------------------------------------------
3837% --- Executes on button press in get_ref_fix2.
3838function get_ref_fix2_Callback(hObject, eventdata, handles)
3839%------------------------------------------------------------------------
3840if isequal(get(handles.get_ref_fix2,'Value'),1)
3841    filebase=get(handles.RootPath,'String');
3842    [FileName, PathName, filterindex] = uigetfile( ...
3843        {'*.nc', ' (*.nc)';
3844        '*.nc',  'netcdf files '; ...
3845        '*.*', 'All Files (*.*)'}, ...
3846        'Pick a file',filebase);
3847    fileinput=[PathName FileName];
3848    sizf=size(fileinput);
3849    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
3850    %[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
3851    [Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput);
3852    ref.filebase=fullfile(Path,File);
3853%     ref.num_a=stra2num(str_a);
3854%     ref.num_b=stra2num(str_b);
3855%     ref.num1=str2num(field_count);
3856%     ref.num2=str2num(str2);
3857    browse=[];%initialisation
3858    if ~isequal(ref.ext,'.nc')
3859        msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
3860        return
3861    end
3862    set(handles.ref_fix2,'String',[fullfile(ref.subdir,File) '....nc']);
3863    set(handles.ref_fix2,'UserData',ref)
3864    menu_field{1}='civ1';
3865    Data=nc2struct(fileinput,[]);
3866    if isfield(Data,'patch') && isequal(Data.patch,1)
3867        menu_field{2}='filter1';
3868    end
3869    if isfield(Data,'civ2') && isequal(Data.civ2,1)
3870        menu_field{3}='civ2';
3871    end
3872    if isfield(Data,'patch2') && isequal(Data.patch2,1)
3873        menu_field{4}='filter2';
3874    end
3875    set(handles.field_ref2,'String',menu_field);
3876    set(handles.field_ref2,'Value',length(menu_field));
3877    set(handles.num_MinVel,'Value',2);
3878    set(handles.num_MinVel,'String','1');%default threshold
3879    set(handles.ref_fix2,'Enable','on')
3880    set(handles.ref_fix2,'Visible','on')
3881    set(handles.field_ref2,'Visible','on')
3882else
3883    set(handles.ref_fix2,'Visible','off')
3884    set(handles.field_ref2,'Visible','off')
3885end
3886
3887%------------------------------------------------------------------------
3888function ref_fix1_Callback(hObject, eventdata, handles)
3889%------------------------------------------------------------------------
3890set(handles.num_MinVel,'Value',1);
3891set(handles.field_ref1,'Value',1)
3892set(handles.field_ref1,'String',{' '})
3893set(handles.ref_fix1,'UserData',[]);
3894set(handles.ref_fix1,'String','');
3895set(handles.thresh_vel1,'String','0');
3896
3897%------------------------------------------------------------------------
3898function ref_fix2_Callback(hObject, eventdata, handles)
3899%------------------------------------------------------------------------
3900set(handles.num_MinVel,'Value',1);
3901set(handles.field_ref2,'Value',1)
3902set(handles.field_ref2,'String',{' '})
3903set(handles.ref_fix2,'UserData',[]);
3904set(handles.ref_fix2,'String','');
3905set(handles.num_MinVel,'String','0');
3906
3907%------------------------------------------------------------------------
3908% --- TO ABANDON Executes on button press in test_stereo1.
3909function CheckStereo_Callback(hObject, eventdata, handles)
3910%------------------------------------------------------------------------
3911hparent=get(hObject,'parent');
3912parent_tag=get(hparent,'Tag');
3913hchildren=get(hparent,'children');
3914handle_txtbox=findobj(hchildren,'tag','txt_Mask');
3915if isequal(get(hObject,'Value'),0)
3916    set(handles.num_SubdomainSize,'Visible','on')
3917    set(handles.num_FieldSmooth,'Visible','on')
3918else
3919    set(handles.num_SubdomainSize,'Visible','off')
3920    set(handles.num_FieldSmooth,'Visible','off')
3921end
3922
3923% %------------------------------------------------------------------------
3924% % --- Executes on button press in CheckStereo.
3925% function StereoCheck_Callback(hObject, eventdata, handles)
3926% %------------------------------------------------------------------------
3927% if isequal(get(handles.CheckStereo,'Value'),0)
3928%     set(handles.num_SubdomainSize,'Visible','on')
3929%     set(handles.num_FieldSmooth,'Visible','on')
3930% else
3931%     set(handles.num_SubdomainSize,'Visible','off')
3932%     set(handles.num_FieldSmooth,'Visible','off')
3933% end
3934
3935%------------------------------------------------------------------------
3936% --- Executes on button press in TestCiv1: prepare the image correlation function
3937% activated by mouse motion
3938function TestCiv1_Callback(hObject, eventdata, handles)
3939%------------------------------------------------------------------------
3940drawnow
3941if get(handles.TestCiv1,'Value')
3942    set(handles.TestCiv1,'BackgroundColor',[0.7 0.7 0.7])% paint TestCiv1 button to grey to confirm civ launch
3943    ref_i=str2double(get(handles.ref_i,'String'));% read reference i index
3944    if strcmp(get(handles.ref_j,'Visible'),'on')
3945        ref_j=str2double(get(handles.ref_j,'String'));% read reference j index if relevant
3946    else
3947        ref_j=1;%default j index
3948    end
3949    [filecell,i1,i2]=set_civ_filenames(handles,ref_i,ref_j,[1 0 0 0 0 0]);% get the corresponding file name and indices
3950    Data.ListVarName={'ny','nx','A'};
3951    Data.VarDimName= {'ny','nx',{'ny','nx'}};
3952    Data.A=imread(filecell.ima1.civ1{1}); % read the first image
3953    if ndims(Data.A)==3 %case of color image
3954        Data.VarDimName= {'ny','nx',{'ny','nx','rgb'}};
3955    end
3956    Data.ny=[size(Data.A,1) 1];
3957    Data.nx=[1 size(Data.A,2)];
3958    Data.CoordUnit='pixel';% used to set equal scaling for x and y in image dispaly
3959    par_civ1=read_GUI(handles.Civ1);
3960    par_civ1.ImageWidth=size(Data.A,2);
3961    par_civ1.ImageHeight=size(Data.A,1);
3962    par_civ1.Mask='all';% will provide only the grid set for PIV, no image correlation
3963    par_civ1.FrameIndexA=num2str(i1);
3964    par_civ1.FrameIndexB=num2str(i2);
3965    Param.Civ1=par_civ1;
3966    Grid=civ_matlab(Param);% get the grid of x, y positions set for PIV
3967    hview_field=view_field(Data); %view the image in the GUI view_field
3968    set(0,'CurrentFigure',hview_field)
3969    hhview_field=guihandles(hview_field);
3970    set(hview_field,'CurrentAxes',hhview_field.axes3)
3971    ViewData=get(hview_field,'UserData');
3972    ViewData.CivHandle=handles.civ;% indicate the handle of the civ GUI in view_field
3973    ViewData.axes3.B=imread(filecell.ima2.civ1{1});%store the second image in the UserData of the GUI view_field
3974    ViewData.axes3.X=Grid.Civ1_X; %keep the set of points in memeory
3975    ViewData.axes3.Y=Grid.Civ1_Y;
3976    set(hview_field,'UserData',ViewData)
3977    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
3978    if isempty(corrfig)
3979        corrfig=figure;
3980        set(corrfig,'tag','corrfig')
3981        set(corrfig,'name','image correlation')
3982        set(corrfig,'DeleteFcn',{@closeview_field})%
3983    end
3984    set(handles.TestCiv1,'BackgroundColor',[1 0 0])
3985else
3986    set(handles.TestCiv1,'BackgroundColor',[1 0 0])% paint button to red
3987    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
3988    if ~isempty(corrfig)
3989        delete(corrfig)
3990    end
3991    hview_field=findobj(allchild(0),'tag','view_field');% look for view_field   
3992    if ~isempty(hview_field)
3993        delete(hview_field)
3994    end
3995end
3996
3997%------------------------------------------------------------------------
3998%----function introduced for the correlation window figure, activated by deleting this window
3999function closeview_field(gcbo,eventdata)
4000%------------------------------------------------------------------------
4001hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
4002if ~isempty(hview_field)
4003    delete(hview_field)
4004end
4005
4006%------------------------------------------------------------------------
4007% --- Executes on button press in CheckThreshold.
4008function CheckThreshold_Callback(hObject, eventdata, handles)
4009%------------------------------------------------------------------------
4010huipanel=get(hObject,'parent');
4011obj(1)=findobj(huipanel,'Tag','num_MinIma');
4012obj(2)=findobj(huipanel,'Tag','num_MaxIma');
4013obj(3)=findobj(huipanel,'Tag','title_Threshold');
4014if get(hObject,'Value')
4015    set(obj,'Visible','on')
4016else
4017    set(obj,'Visible','off')
4018end
4019
4020%------------------------------------------------------------------------
4021function [cmd,errormsg]=cmd_civ1(filename,Param)
4022%------------------------------------------------------------------------
4023%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4024%changes : filename_cmx -> filename ( no extension )
4025cmd='';
4026filename=regexprep(filename,'.nc',''); %file name for the result
4027if isequal(Param.Civ1.Dt,0)
4028    Param.Civ1.Dt=1 ;%case of 'displacement' mode
4029end
4030Param.Civ1.ImageA=regexprep(Param.Civ1.ImageA,'.png','');
4031Param.Civ1.ImageB=regexprep(Param.Civ1.ImageB,'.png','');
4032[fid,errormsg]=fopen([filename '.civ1.cmx'],'w');
4033if isequal(fid,-1)
4034    errormsg=['cmd file ' filename ' cannot be created: ' errormsg];
4035    return
4036end
4037fprintf(fid,['##############   CMX file' '\n' ]);
4038fprintf(fid,   ['FirstImage ' regexprep(Param.Civ1.ImageA,'\\','\\\\') '\n' ]);% for windows compatibility
4039fprintf(fid,   ['LastImage  ' regexprep(Param.Civ1.ImageB,'\\','\\\\') '\n' ]);% for windows compatibility
4040fprintf(fid,  ['XX' '\n' ]);
4041if isfield(Param.Civ1,'Mask')
4042    fprintf(fid,  ['Mask ' 'y' '\n' ]);
4043    fprintf(fid,  ['MaskName ' regexprep(Param.Civ1.Mask,'\\','\\\\') '\n' ]);
4044else
4045    fprintf(fid,  ['Mask ' 'n' '\n' ]);
4046    fprintf(fid,  ['MaskName ' 'noFile use default' '\n' ]);
4047end
4048fprintf(fid,   ['ImageSize ' num2str(Param.Civ1.ImageWidth) ' ' num2str(Param.Civ1.ImageHeight) '\n' ]);   %VERIFIER CAS GENERAL ?
4049fprintf(fid,   ['CorrelationBoxesSize ' num2str(Param.Civ1.CorrBoxSize(1)) ' ' num2str(Param.Civ1.CorrBoxSize(2)) '\n' ]);
4050fprintf(fid,   ['SearchBoxeSize ' num2str(Param.Civ1.SearchBoxSize(1)) ' ' num2str(Param.Civ1.SearchBoxSize(2)) '\n' ]);
4051fprintf(fid,   ['RO ' num2str(Param.Civ1.CorrSmooth) '\n' ]);
4052if isfield(Param.Civ1,'Grid')
4053    fprintf(fid,   ['GridSpacing ' '25' ' ' '25' '\n' ]);
4054else
4055    fprintf(fid,   ['GridSpacing ' num2str(Param.Civ1.Dx) ' ' num2str(Param.Civ1.Dy) '\n' ]);
4056end
4057fprintf(fid,   ['XX 1.0' '\n' ]);
4058fprintf(fid,   ['Dt_TO ' num2str(Param.Civ1.Dt) ' ' num2str(Param.Civ1.Time) '\n' ]);
4059fprintf(fid,  ['PixCmXY ' '1' ' ' '1' '\n' ]);
4060fprintf(fid,  ['XX 1' '\n' ]);
4061fprintf(fid,   ['ShiftXY ' num2str(Param.Civ1.SearchBoxShift(1)) ' '  num2str(Param.Civ1.SearchBoxShift(2)) '\n' ]);
4062if isfield(Param.Civ1,'Grid')
4063    fprintf(fid,  ['Grid ' 'y' '\n' ]);
4064    fprintf(fid,   ['GridName ' regexprep(Param.Civ1.Grid,'\\','\\\\') '\n' ]);
4065else
4066    fprintf(fid,  ['Grid ' 'n' '\n' ]);
4067    fprintf(fid,   ['GridName ' 'noFile use default' '\n' ]);
4068end
4069fprintf(fid,   ['XX 85' '\n' ]);
4070fprintf(fid,   ['XX 1.0' '\n' ]);
4071fprintf(fid,   ['XX 1.0' '\n' ]);
4072fprintf(fid,   ['Hart 1' '\n' ]);
4073fprintf(fid,  [ 'DecimalShift 0' '\n' ]);
4074fprintf(fid,   ['Deformation 0' '\n' ]);
4075fprintf(fid,  ['CorrelationMin 0' '\n' ]);
4076fprintf(fid,   ['IntensityMin 0' '\n' ]);
4077if ~isfield(Param.Civ1,'MinIma')% Image threshold not activated
4078    fprintf(fid,  ['SeuilImage n' '\n' ]);
4079    fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);%not used in principle
4080else% Image threshold  activated
4081    if isempty(Param.Civ1.MaxIma)||isnan(Param.Civ1.MaxIma)
4082        Param.Civ1.MaxIma=2^Param.Civ1.ImageBitDepth;%take the max image value as upper bound by default
4083    end
4084    fprintf(fid,  ['SeuilImage y' '\n' ]);
4085    fprintf(fid,   ['SeuilImageValues ' num2str(Param.Civ1.MinIma) ' ' num2str(Param.Civ1.MaxIma) '\n' ]);
4086end
4087fprintf(fid,   ['ImageToUse ' Param.Civ1.term_a ' ' Param.Civ1.term_b '\n' ]); % VERIFIER ?
4088fprintf(fid,   ['ImageUsedBefore null null' '\n' ]);
4089fclose(fid);
4090
4091if(isunix) %unix (or Mac) system
4092    cmd=['cp -f ' filename '.civ1.cmx ' filename '.cmx \n '];% the cmx file gives the name to the nc file
4093    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
4094    cmd=[cmd 'rm ' filename '.cmx'];
4095else %Windows system
4096    filename=regexprep(filename,'\\','\\\\');
4097    cmd=['copy /Y "' filename '.civ1.cmx" "' filename '.cmx" \n '];
4098    cmd=[cmd '"' regexprep(Param.xml.Civ1Bin,'\\','\\\\')...
4099        '" -f "' filename '.cmx" >"' filename '.civ1.log" \n ' ]; % redirect standard output to the log file
4100    cmd=[cmd 'del "' filename '.cmx"'];
4101end
4102
4103
4104function cmd=cmd_fix(filename,Param,fixname)
4105%%
4106switch fixname
4107    case 'Fix1'
4108        fi2_value=num2str(Param.(fixname).CheckF2);
4109    case 'Fix2'
4110        fi2_value=num2str(Param.(fixname).CheckF4);%need to understand why...
4111end
4112filename=regexprep(filename,'.nc','');
4113MaskName_string='';%default
4114MaxVel_string='';%default
4115if ~isempty(Param.(fixname).MinVel)
4116    MaxVel_string=[' -threshV ' num2str(Param.(fixname).MinVel)];
4117end
4118if isunix
4119    cmd=[Param.xml.FixBin ' -f ' filename '.nc -fi1 ' num2str(Param.(fixname).CheckFmin2) ...
4120        ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ...
4121        ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string...
4122        ' >' filename '.' lower(fixname) '.log 2>&1'];
4123else
4124    cmd=['"' Param.xml.FixBin '" -f "' filename '.nc" -fi1 ' num2str(Param.(fixname).CheckFmin2)...
4125        ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ...
4126        ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string...
4127        ' > "' filename '.' lower(fixname) '.log"'];
4128    cmd=regexprep(cmd,'\\','\\\\');
4129end
4130
4131
4132function cmd=cmd_patch(filename,Param,patchname)
4133%% ------------------------------------------------------------------------
4134filename=regexprep(filename,'.nc','');
4135if isunix
4136    cmd=[Param.xml.PatchBin...
4137        ' -f ' filename '.nc -m ' num2str(Param.(patchname).Nx)...
4138        ' -n ' num2str(Param.(patchname).Ny) ' -ro ' num2str(Param.(patchname).FieldSmooth)...
4139        ' -nopt ' num2str(Param.(patchname).SubdomainSize) ...
4140        '  > ' filename '.' lower(patchname) '.log 2>&1']; % redirect standard output to the log file
4141else
4142    cmd=['"' Param.xml.PatchBin...
4143        '" -f "' filename '.nc" -m ' num2str(Param.(patchname).Nx)...
4144        ' -n ' num2str(Param.(patchname).Ny) ' -ro ' num2str(Param.(patchname).FieldSmooth)...
4145        ' -nopt ' num2str(Param.(patchname).SubdomainSize)...
4146        '  > "' filename '.' lower(patchname) '.log" 2>&1']; % redirect standard output to the log file
4147    cmd=regexprep(cmd,'\\','\\\\');
4148end
4149
4150%------------------------------------------------------------------------
4151% --- CheckCiv2  CheckCiv2  CheckCiv2 CheckCiv2
4152function [cmd,errormsg]=cmd_civ2(filename,Param)
4153%------------------------------------------------------------------------
4154%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4155% global civ2Bin sge%name of the executable for checkciv1 calculation
4156 cmd='';
4157filename=regexprep(filename,'.nc','');
4158if isequal(Param.Civ2.Dt,'0')
4159    Param.Civ2.Dt='1' ;%case of 'displacement' mode
4160end
4161Param.Civ2.ImageA=regexprep(Param.Civ2.ImageA,'.png','');
4162Param.Civ2.ImageB=regexprep(Param.Civ2.ImageB,'.png','');% bug : .png appears two times ?
4163[fid,errormsg]=fopen([filename '.civ2.cmx'],'w');
4164if isequal(fid,-1)
4165    return
4166end
4167fprintf(fid,['##############   CMX file' '\n' ]);
4168fprintf(fid,   ['FirstImage ' regexprep(Param.Civ2.ImageA,'\\','\\\\') '\n' ]);% for windows compatibility
4169fprintf(fid,   ['LastImage  ' regexprep(Param.Civ2.ImageB,'\\','\\\\') '\n' ]);% for windows compatibility
4170fprintf(fid,  ['XX' '\n' ]);
4171if isfield(Param.Civ2,'Mask')
4172    fprintf(fid,  ['Mask ' 'y' '\n' ]);
4173    fprintf(fid,  ['MaskName ' regexprep(Param.Civ2.Mask,'\\','\\\\') '\n' ]);
4174else
4175    fprintf(fid,  ['Mask ' 'n' '\n' ]);
4176    fprintf(fid,  ['MaskName ' 'noFile use default' '\n' ]);
4177end
4178% fprintf(fid, ['Mask ' Param.Civ2.MaskFlag '\n' ]);
4179% fprintf(fid, ['MaskName ' regexprep(Param.Civ2.MaskName,'\\','\\\\') '\n' ]);% for windows compatibility
4180fprintf(fid,   ['ImageSize ' num2str(Param.Civ2.ImageWidth) ' ' num2str(Param.Civ2.ImageHeight) '\n' ]); 
4181% fprintf(fid, ['ImageSize ' num2str(Param.Civ2.npx) ' ' num2str(Param.Civ2.npy) '\n' ]);   %VERIFIER CAS GENERAL ?
4182fprintf(fid, ['CorrelationBoxesSize ' num2str(Param.Civ2.CorrBoxSize(1)) ' ' num2str(Param.Civ2.CorrBoxSize(2)) '\n' ]);
4183fprintf(fid, ['SearchBoxeSize ' num2str(Param.Civ2.CorrBoxSize(1)) ' ' num2str(Param.Civ2.CorrBoxSize(2)) '\n']);
4184fprintf(fid, ['RO ' num2str(Param.Civ2.CorrSmooth) '\n']);
4185if isfield(Param.Civ2,'Grid')
4186    fprintf(fid,   ['GridSpacing ' '25' ' ' '25' '\n' ]);
4187else
4188    fprintf(fid,   ['GridSpacing ' num2str(Param.Civ2.Dx) ' ' num2str(Param.Civ2.Dy) '\n' ]);
4189end
4190% fprintf(fid, ['GridSpacing ' num2str(Param.Civ2.Dx) ' ' num2str(Param.Civ2.Dy) '\n']);
4191fprintf(fid, ['XX 1.0' '\n' ]);
4192fprintf(fid, ['Dt_TO ' num2str(Param.Civ2.Dt) ' ' num2str(Param.Civ2.Time) '\n' ]);
4193fprintf(fid, ['PixCmXY ' '1' ' ' '1' '\n' ]);
4194fprintf(fid, ['XX 1' '\n' ]);
4195fprintf(fid, 'ShiftXY 0 0\n');
4196if isfield(Param.Civ2,'Grid')
4197    fprintf(fid,  ['Grid ' 'y' '\n' ]);
4198    fprintf(fid,   ['GridName ' regexprep(Param.Civ2.Grid,'\\','\\\\') '\n' ]);
4199else
4200    fprintf(fid,  ['Grid ' 'n' '\n' ]);
4201    fprintf(fid,   ['GridName ' 'noFile use default' '\n' ]);
4202end
4203% fprintf(fid, ['Grid ' Param.Civ2.GridFlag '\n' ]);
4204% fprintf(fid, ['GridName ' regexprep(Param.Civ2.GridName,'\\','\\\\') '\n']);
4205fprintf(fid, ['XX 85' '\n' ]);
4206fprintf(fid, ['XX 1.0' '\n' ]);
4207fprintf(fid, ['XX 1.0' '\n' ]);
4208fprintf(fid, ['Hart 1' '\n' ]);
4209fprintf(fid, ['DecimalShift ' num2str(Param.Civ2.CheckDecimal) '\n']);
4210fprintf(fid, ['Deformation ' num2str(Param.Civ2.CheckDeformation) '\n']);
4211fprintf(fid,  ['CorrelationMin 0' '\n' ]);
4212fprintf(fid,   ['IntensityMin 0' '\n' ]);
4213
4214if ~isfield(Param.Civ2,'MinIma')% Image threshold not activated
4215    fprintf(fid,  ['SeuilImage n' '\n' ]);
4216    fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);%not used in principle
4217else% Image threshold  activated
4218    if isempty(Param.Civ2.MaxIma)||isnan(Param.Civ2.MaxIma)
4219        Param.Civ2.MaxIma=2^Param.Civ2.ImageBitDepth;%take the max image value as upper bound by default
4220    end
4221    fprintf(fid,  ['SeuilImage y' '\n' ]);
4222    fprintf(fid,   ['SeuilImageValues ' num2str(Param.Civ2.MinIma) ' ' num2str(Param.Civ2.MaxIma) '\n' ]);
4223end
4224fprintf(fid,   ['ImageToUse ' Param.Civ2.term_a ' ' Param.Civ2.term_b '\n' ]); % VERIFIER ?
4225fprintf(fid, ['ImageUsedBefore ' regexprep(Param.Civ2.filename_nc1,'\\','\\\\') '\n']);
4226fclose(fid);
4227
4228if(isunix)
4229    cmd=['cp -f ' filename '.civ2.cmx ' filename '.cmx\n'...
4230        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
4231        'rm ' filename '.cmx \n'];%rename .cmx as .checkciv2.cmx, the result file is named [filename '.nc'] by CIVx
4232else
4233    filename=regexprep(filename,'\\','\\\\');
4234    cmd=['copy /Y "' filename '.civ2.cmx" "' filename '.cmx" \n'...
4235        '"' regexprep(Param.xml.Civ2Bin,'\\','\\\\') '" -f "' filename  '.cmx" >"' filename '.civ2.log" \n'...
4236        'del "' filename '.cmx" \n'];
4237end
4238
4239%------------------------------------------------------------------------
4240% --- CheckCiv1  Unified: TO ABADON
4241function xml_civ1_parameters=CIV1_CMD_Unified(filename,namelog,par)
4242%------------------------------------------------------------------------
4243%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4244%global CivBin%name of the executable for checkciv1 calculation
4245
4246civ1.image1=par.ImageA;
4247civ1.image2=par.ImageB;
4248civ1.imageSize_X=par.npx;
4249civ1.imageSize_Y=par.npy;
4250civ1.outputFileName=[filename '.nc'];
4251civ1.correlationBoxesSize_X=par.ibx;
4252civ1.correlationBoxesSize_Y=par.iby;
4253civ1.searchBoxesSize_X=par.isx;
4254civ1.searchBoxesSize_Y=par.isy;
4255civ1.globalShift_X=par.shiftx;
4256civ1.globalShift_Y=par.shifty;
4257civ1.ro=par.rho;
4258civ1.hart='y';
4259if isequal(par.gridflag,'y')
4260    civ1.grid=par.gridname;
4261else
4262    civ1.grid='n';
4263    civ1.gridSpacing_X=par.dx;
4264    civ1.gridSpacing_Y=par.dy;
4265end
4266if isequal(par.maskflag,'y')
4267    civ1.mask=par.maskname;
4268end
4269civ1.dt=par.Dt;
4270civ1.unit='pixel';
4271civ1.absolut_time_T0=par.Time;
4272civ1.pixcmx='1';
4273civ1.pixcmy='1';
4274civ1.convectFlow='n';
4275
4276xml_civ1_parameters=civ1;
4277
4278%------------------------------------------------------------------------
4279% --- CheckCiv2  Unified: TO ABADON
4280function civ2=CIV2_CMD_Unified(filename,namelog,par)
4281%------------------------------------------------------------------------
4282%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4283%global CivBin%name of the executable for checkciv1 calculation
4284
4285filename=regexprep(filename,'.nc','');
4286
4287civ2.image1=par.ImageA;
4288civ2.image2=par.ImageB;
4289civ2.imageSize_X=par.npx;
4290civ2.imageSize_Y=par.npy;
4291civ2.inputFileName=[par.filename_nc1 '.nc'];
4292civ2.outputFileName=[filename '.nc'];
4293civ2.correlationBoxesSize_X=par.ibx;
4294civ2.correlationBoxesSize_Y=par.iby;
4295civ2.ro=par.rho;
4296%checkciv2.decimalShift=par.CheckDecimal;
4297%checkciv2.CheckDeformation=par.CheckDeformation;
4298if isequal(par.decimal,'1')
4299    civ2.decimalShift='y';
4300else
4301    civ2.decimalShift='n';
4302end
4303if isequal(par.deformation,'1')
4304    civ2.deformation='y';
4305else
4306    civ2.deformation='n';
4307end
4308if isequal(par.gridflag,'y')
4309    civ2.grid=par.gridname;
4310else
4311    civ2.grid='n';
4312    civ2.gridSpacing_X=par.dx;
4313    civ2.gridSpacing_Y=par.dy;
4314end
4315civ2.gridSpacing_X='10';
4316civ2.gridSpacing_Y='10';%NOTE: faut mettre gridSpacing pourque ca tourne, meme si c'est la grille qui est utilisee
4317if isequal(par.maskflag,'y')
4318    civ2.mask=par.maskname;
4319else
4320    civ2.mask='n';
4321end
4322civ2.dt=par.Dt;
4323civ2.unit='pixel';
4324civ2.absolut_time_T0=par.Time;
4325civ2.pixcmx='1';
4326civ2.pixcmy='1';
4327civ2.convectFlow='n';
4328
4329
4330% --- Executes on button press in TestPatch1.
4331function TestPatch1_Callback(hObject, eventdata, handles)
4332set(handles.TestPatch1,'BackgroundColor',[1 1 0])
4333drawnow
4334if get(handles.TestPatch1,'Value')
4335    ref_i=str2double(get(handles.ref_i,'String'));
4336    if strcmp(get(handles.ref_j,'Visible'),'on')
4337        ref_j=str2double(get(handles.ref_j,'String'));
4338    else
4339        ref_j=1;%default
4340    end
4341    filecell=set_civ_filenames(handles,ref_i,ref_j,[0 0 1 0 0 0]);   
4342    Data.ListVarName={'ny','nx','A'};
4343    Data.VarDimName= {'ny','nx',{'ny','nx'}};   
4344    param_patch1=read_GUI(handles.Patch1);
4345    param_patch1.CivFile=filecell.nc.civ1{1};
4346    Param.Patch1=param_patch1;
4347    for irho=1:7
4348        [Data,errormsg]=civ_matlab(Param);% get the grid of x, y positions set for PIV
4349        if ~isempty(errormsg)
4350            msgbox_uvmat('ERROR',errormsg)
4351            return
4352        end
4353        SmoothingParam(irho)=Param.Patch1.FieldSmooth;
4354        Data.Civ1_U_Diff=Data.Civ1_U_Diff(Data.Civ1_FF==0);
4355        Data.Civ1_V_Diff=Data.Civ1_V_Diff(Data.Civ1_FF==0);
4356        DiffVel(irho)=sqrt(mean(Data.Civ1_U_Diff.*Data.Civ1_U_Diff+Data.Civ1_V_Diff.*Data.Civ1_V_Diff))
4357        NbSites(irho,:)=Data.Civ1_NbSites*numel(Data.Civ1_NbSites)/numel(Data.Civ1_U_Diff);
4358        Param.Patch1.SmoothingParam=2*Param.Patch1.FieldSmooth;
4359    end
4360    figure
4361    plot(SmoothingParam,DiffVel,'b',SmoothingParam,NbSites,'r')
4362    set(handles.TestPatch1,'BackgroundColor',[1 0 0])
4363else
4364    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
4365    if ~isempty(corrfig)
4366        delete(corrfig)
4367    end
4368    hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
4369    if ~isempty(hview_field)
4370        delete(hview_field)
4371    end
4372end
4373%'nomtype2pair': creates nomencalture for index pairs knowing the image nomenclature
4374%---------------------------------------------------------------------
4375% [nom_type_pair]=nomtype2pair(nom_type,Dti,Dtj);
4376%---------------------------------------------------------------------           
4377
4378% OUTPUT:
4379%nom_type_nc
4380
4381%---------------------------------------------------------------------
4382% INPUT:
4383% 'nom_type': string defining the kind of nomenclature used:
4384     %nom_type='': constant name [filebase ext] (default output if 'nom_type' is undefined)
4385     %nom_type='*': the same  file [filebase ext] contains successive fields (ex avi movies)
4386     %nom_type='_i': series of files with a single index i preceded by '_'(e.g. 'aa_45.png').
4387     %nom_type='#' series of indexed images wich is not series_i [filebase index ext], e.g. 'aa045.jpg' or 'aa45.tif'
4388     %nom_type='_i_j' matrix of files with two indices i and j separated by '_'(e.g. 'aa_45_2.png')
4389     %nom_type='_i1-i2' from pairs from a single index (e.g. 'aa_45-47.nc')
4390     %nom_type='_i_j1-j2'pairs of j indices (e.g. 'aa_45_2-3.nc')
4391     %nom_type='_i1-i2_j' pairs of i indices (e.g. 'aa_45-46_2.nc')
4392     %nom_type='#a','#A', with a numerical index and an index letter(e.g.'aa045b.png'), OBSOLETE (replaced by 'series_i_j')
4393     %nom_type='%03d' or '%04d', series of indexed images with numbers completed with zeros to 3 or 4 digits, e.g.'aa045.tif'
4394     %nom_type='_%03d', '_%04d', or '_%05d', series of indexed images with _ and numbers completed with zeros to 3, 4 or 5 digits, e.g.'aa_045.tif'
4395     %nom_type='raw_SMD', same as '#a' but with no extension ext='', OBSOLETE
4396     %nom_type='#_ab' from pairs of '#a' images (e.g. 'aa045bc.nc'), ext='.nc', OBSOLETE (replaced by 'netc_2D')
4397     %nom_type='%3dab' from pairs of '%3da' images (e.g. 'aa045bc.nc'), ext='.nc', OBSOLETE (replaced by 'netc_2D')
4398% Dti: ~=0 if i index pairs are used
4399% Dtj: ~=0 if i index pairs are used
4400
4401function NomTypeNc=nomtype2pair(NomTypeIma,mode)
4402
4403%determine nom_type_nc:
4404NomTypeNc=NomTypeIma;%default
4405switch mode
4406    case 'pair j1-j2'     
4407    if ~isempty(regexp(NomTypeIma,'a$'))
4408        NomTypeNc=[NomTypeIma 'b'];
4409    elseif ~isempty(regexp(NomTypeIma,'A$'))
4410        NomTypeNc=[NomTypeIma 'B'];
4411    else
4412        r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
4413        if ~isempty(r)
4414            NomTypeNc='_1_1-2';
4415        end
4416    end
4417    case 'series(Dj)' 
4418        r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
4419        if ~isempty(r)
4420            NomTypeNc='_1_1-2';
4421        end
4422   case 'series(Di)'
4423        r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
4424        if ~isempty(r)
4425            NomTypeNc='_1-2_1';
4426        else
4427            NomTypeNc='_1-2';
4428        end
4429end
4430
4431function NomType_Callback(hObject, eventdata, handles)
4432set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
4433RootPath=get(handles.RootPath,'String');
4434RootFile=get(handles.RootFile,'String');
4435ref_i=str2num(get(handles.ref_i,'String'));
4436ref_j=str2num(get(handles.ref_j,'String'));
4437NomType=get(handles.NomType,'String');
4438ImaExt=get(handles.ImaExt,'String');
4439fileinput=fullfile_uvmat(RootPath,'',RootFile,ImaExt,NomType,ref_i,[],ref_j);
4440errormsg=display_file_name(handles,fileinput);
4441if ~isempty(errormsg)
4442    msgbox_uvmat('ERROR',errormsg)
4443end
4444set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
4445
4446% --- Executes on selection change in ListProgram.
4447function ListProgram_Callback(hObject, eventdata, handles)
4448ListProgram=get(handles.ListProgram,'String');
4449Program=ListProgram{get(handles.ListProgram,'value')};
4450switch Program
4451    case 'CivX'
4452        set(handles.num_MaxDiff,'Visible','off')
4453        set(handles.num_MaxVel,'Visible','off')
4454        set(handles.title_MaxVel,'Visible','off')
4455        set(handles.num_Nx,'Visible','on')
4456        set(handles.num_Ny,'Visible','on')
4457        set(handles.title_Nx,'Visible','on')
4458        set(handles.title_Ny,'Visible','on')
4459        set(handles.title_MaxDiff,'Visible','off')
4460        set(handles.num_CorrSmooth,'Style','edit')
4461        set(handles.num_CorrSmooth,'String','1')
4462        set(handles.BATCH,'Enable','on')
4463        set(handles.CheckThreshold,'Visible','off')
4464        set(handles.CheckDeformation,'Value',1)
4465        set(handles.CheckDecimal,'Value',1)
4466    case 'Matlab'
4467        set(handles.num_MaxDiff,'Visible','on')
4468        set(handles.num_MaxVel,'Visible','on')
4469        set(handles.title_MaxVel,'Visible','on')
4470        set(handles.title_MaxDiff,'Visible','on')
4471        set(handles.num_Nx,'Visible','off')
4472        set(handles.num_Ny,'Visible','off')
4473        set(handles.title_Nx,'Visible','off')
4474        set(handles.title_Ny,'Visible','off')
4475        set(handles.num_CorrSmooth,'Style','popupmenu')
4476        set(handles.num_CorrSmooth,'Value',1)
4477        set(handles.num_CorrSmooth,'String',{'1';'2'})
4478        set(handles.CheckThreshold,'Visible','on')
4479        set(handles.CheckDeformation,'Value',0)% desactivate (work in progress)
4480        set(handles.CheckDecimal,'Value',0)% desactivate (work in progress)
4481end
4482
4483
4484% --- Executes on button press in TestCiv2.
4485function TestCiv2_Callback(hObject, eventdata, handles)
4486
4487
4488
4489function RootFile_Callback(hObject, eventdata, handles)
4490
4491
4492
4493function SubdirImages_Callback(hObject, eventdata, handles)
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