source: trunk/src/civ.m @ 412

Last change on this file since 412 was 412, checked in by sommeria, 12 years ago

bug corrected in file indexing in civ
bugs corrected in calc_field for new matlab PIV

File size: 189.8 KB
Line 
1%'civ': function associated with the interface 'civ.fig' for PIV, spline interpolation and stereo PIV (patch)
2%------------------------------------------------------------------------
3%  provides an interface for the software menucivx
4% function varargout = civ(varargin)
5% provides an interface for the software menucivx
6%
7%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
8%  Copyright Joel Sommeria, 2011, LEGI / CNRS-UJF-INPG, sommeria@legi.grenoble-inp.fr
9%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
10%     This file is part of the toolbox UVMAT.
11%
12%     UVMAT is free software; you can redistribute it and/or modify
13%     it under the terms of the GNU General Public License as published by
14%     the Free Software Foundation; either version 2 of the License, or
15%     (at your option) any later version.
16%
17%     UVMAT is distributed in the hope that it will be useful,
18%     but WITHOUT ANY WARRANTY; without even the implied warranty of
19%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
20%     GNU General Public License (file UVMAT/COPYING.txt) for more details.
21%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
22function varargout = civ(varargin)
23%TODO: search range
24
25% Last Modified by GUIDE v2.5 10-Mar-2012 22:32:10
26% Begin initialization code - DO NOT EDIT
27gui_Singleton = 1;
28gui_State = struct('gui_Name',       mfilename, ...
29    'gui_Singleton',  gui_Singleton, ...
30    'gui_OpeningFcn', @civ_OpeningFcn, ...
31    'gui_OutputFcn',  @civ_OutputFcn, ...
32    'gui_LayoutFcn',  [] , ...
33    'gui_Callback',   []);
34if nargin && ischar(varargin{1}) && ~isempty(regexp(varargin{1},'_Callback$','once'))
35    gui_State.gui_Callback = str2func(varargin{1});
36end
37
38if nargout
39    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
40else
41    gui_mainfcn(gui_State, varargin{:});
42end
43% End initialization code - DO NOT EDIT
44
45%------------------------------------------------------------------------
46% --- Executes just before civ is made visible.
47function civ_OpeningFcn(hObject, eventdata, handles, fileinput)
48%------------------------------------------------------------------------
49% This function has no output args, see OutputFcn.
50
51%% General settings
52handles.output = hObject;
53guidata(hObject, handles); % Update handles structure
54set(hObject,'WindowButtonDownFcn',{'mouse_down'}) % allows mouse action with right button (zoom for uicontrol display)
55
56%% Adjust the GUI according to the binaries available in PARAM.xml
57path_civ=fileparts(which('civ')); %path to civ
58addpath (path_civ) ; %add the path to civ, (useful in case of change of working directory after civ has been s opened in the working directory)
59errormsg=[];%default error message
60xmlfile='PARAM.xml';
61if exist(xmlfile,'file')
62    try
63        t=xmltree(xmlfile);
64        sparam=convert(t);
65    catch
66        errormsg={' Unable to read the file PARAM.xml defining the civx binaries:'; lasterr};
67    end
68else
69    errormsg=[xmlfile ' not found: path to civx binaries undefined'];
70end
71if ~isempty(errormsg)
72    msgbox_uvmat('WARNING',errormsg);
73end
74test_batch=0;%default: ,no batch mode available
75if isfield(sparam,'BatchParam') && isfield(sparam.BatchParam,'BatchMode')
76    test_batch=strcmp(sparam.BatchParam.BatchMode,'sge'); %sge is currently the only implemented batch mod
77end
78if test_batch==0
79    set(handles.BATCH,'Enable','off')% put the BATCH button in grey (unactivated)
80    set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])% put the BATCH button in grey (unactivated)
81end
82if isfield(sparam.RunParam,'CivBin')
83    if ~exist(sparam.RunParam.CivBin,'file')
84        sparam.RunParam.CivBin=fullfile(path_civ,sparam.RunParam.CivBin);
85    end
86else
87    sparam.RunParam.CivBin='';
88end
89
90%% load the list of previously browsed files in the upper bar menu Open/
91dir_perso=prefdir; % path to the directory .matlab for personal data
92profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmauvmat_perso.mat' in .matlab
93if exist(profil_perso,'file')
94    h=load (profil_perso);
95    if isfield(h,'MenuFile')
96        for ifile=1:min(length(h.MenuFile),5)
97            eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',h.MenuFile{ifile});'])
98        end
99    end
100end
101
102%% prepare the GUI with parameters from the input file if opened from uvmat
103if exist('fileinput','var')% && isfield(param,'RootName') && ~isempty(param.RootName)
104    set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
105    errormsg=display_file_name(handles,fileinput);
106    if ~isempty(errormsg)
107        msgbox_uvmat('ERROR',errormsg)
108    end
109    set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
110end
111
112%------------------------------------------------------------------------
113% --- Outputs from this function are returned to the command line.
114function varargout = civ_OutputFcn(hObject, eventdata, handles)
115%------------------------------------------------------------------------
116% Get default command line output from handles structure
117varargout{1} = handles.output;
118
119%------------------------------------------------------------------------
120% --- Function activated by the Open/Browse... option in the upper menu bar.
121function MenuBrowse_Callback(hObject, eventdata, handles)
122%------------------------------------------------------------------------
123%% get the current input root file name to initiate the browser
124filebase=get(handles.RootPath,'String');
125oldfile=''; %default
126if isempty(filebase)|| isequal(filebase,'')%loads the previously stored root file name
127    dir_perso=prefdir;
128    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
129    if exist(profil_perso,'file')
130        h=load (profil_perso);
131        if isfield(h,'filebase')&& ischar(h.filebase)
132            oldfile=h.filebase;
133        end
134        if isfield(h,'RootPath') && ischar(h.RootPath)
135            oldfile=h.RootPath;
136        end
137    end
138else
139    oldfile=filebase;
140end
141
142%% get the new input file with the browser
143menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)';
144    '*.xml',  '.xml files '; ...
145    '*.civ',  '.civ files '; ...
146    '*.png','.png image files'; ...
147    '*.jpg',' jpeg image files'; ...
148    '*.tif','.tif image files'; ...
149    '*.avi;*.AVI','.avi movie files'; ...
150    '*.nc','.netcdf files'; ...
151    '*.*',  'All Files (*.*)'};
152[FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file',oldfile);
153fileinput=[PathName FileName];%complete file name
154sizf=size(fileinput);
155if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
156
157%% case of the xml file opened as input (TODO: check and see whether it is useful)
158[path,name,ext]=fileparts(fileinput);
159testeditxml=0;
160% if isequal(ext,'.xml')
161%     testeditxml=1;
162%     t_browse=xmltree(fileinput);
163%     head_element=get(t_browse,1);
164%     if isfield(head_element,'name')&& isequal(head_element.name,'ImaDoc')
165%         testeditxml=0;
166%     end
167% end
168% if testeditxml==1 || isequal(ext,'.xls')
169%     heditxml=editxml({fileinput});
170%     set(heditxml,'Tag','browser')
171%     waitfor(heditxml,'Tag','idle')
172%     if ~ishandle(heditxml)
173%         return
174%     end
175%     attr=findobj(get(heditxml,'children'),'Tag','CurrentAttributes');
176%     set(handles.browse,'UserData',fileinput)% store for future opening with browser
177%     fileinput=get(attr,'UserData');
178%     if ~exist(fileinput,'file')
179%         return
180%     end
181% end
182[tild,tild,tild,i1,i2,j1,j2,FileExt,NomType]=fileparts_uvmat(fileinput);
183
184%% prepare the GUI with parameters from the input file
185set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
186errormsg=display_file_name(handles,fileinput);
187if ~isempty(errormsg)
188    msgbox_uvmat('ERROR',erromsg)
189end
190set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
191
192%------------------------------------------------------------------------
193% --- Open again the file whose name has been recorded in MenuFile_1
194function MenuFile_1_Callback(hObject, eventdata, handles)
195%------------------------------------------------------------------------
196set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
197fileinput=get(handles.MenuFile_1,'Label');
198errormsg=display_file_name(handles,fileinput);
199if ~isempty(errormsg)
200    msgbox_uvmat('ERROR',errormsg)
201end
202set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
203
204% -----------------------------------------------------------------------
205% --- Open again the file whose name has been recorded in MenuFile_2
206function MenuFile_2_Callback(hObject, eventdata, handles)
207%------------------------------------------------------------------------
208set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
209fileinput=get(handles.MenuFile_2,'Label');
210errormsg=display_file_name(handles,fileinput);
211if ~isempty(errormsg)
212    msgbox_uvmat('ERROR',errormsg)
213end
214set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
215
216% -----------------------------------------------------------------------
217% --- Open again the file whose name has been recorded in MenuFile_3
218function MenuFile_3_Callback(hObject, eventdata, handles)
219%------------------------------------------------------------------------
220set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
221fileinput=get(handles.MenuFile_3,'Label');
222errormsg=display_file_name(handles,fileinput);
223if ~isempty(errormsg)
224    msgbox_uvmat('ERROR',errormsg)
225end
226set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
227
228% -----------------------------------------------------------------------
229% --- Open again the file whose name has been recorded in MenuFile_4
230function MenuFile_4_Callback(hObject, eventdata, handles)
231%------------------------------------------------------------------------
232set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
233fileinput=get(handles.MenuFile_4,'Label');
234errormsg=display_file_name(handles,fileinput);
235if ~isempty(errormsg)
236    msgbox_uvmat('ERROR',errormsg)
237end
238set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
239
240% -----------------------------------------------------------------------
241% --- Open again the file whose name has been recorded in MenuFile_5
242function MenuFile_5_Callback(hObject, eventdata, handles)
243%------------------------------------------------------------------------
244set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
245fileinput=get(handles.MenuFile_5,'Label');
246errormsg=display_file_name(handles,fileinput);
247if ~isempty(errormsg)
248    msgbox_uvmat('ERROR',errormsg)
249end
250set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
251
252% -----------------------------------------------------------------------
253% -----------------------------------------------------------------------
254% --- Open the help html file
255function MenuHelp_Callback(hObject, eventdata, handles)
256% -----------------------------------------------------------------------
257path_civ=fileparts(which ('civ'));
258helpfile=fullfile(path_civ,'uvmat_doc','uvmat_doc.html');
259if isempty(dir(helpfile))
260    msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
261else
262    addpath (fullfile(path_civ,'uvmat_doc'))
263    web([helpfile '#civ'])
264end
265
266%------------------------------------------------------------------------
267% --- Function activated when a new filebase (image series) is introduced
268function RootPath_Callback(hObject, eventdata, handles)
269%------------------------------------------------------------------------
270set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
271RootPath=get(handles.RootPath,'String');
272RootFile=get(handles.RootFile,'String');
273ref_i=str2num(get(handles.ref_i,'String'));
274ref_j=str2num(get(handles.ref_j,'String'));
275NomType=get(handles.NomType,'String');
276ImaExt=get(handles.ImaExt,'String');
277fileinput=fullfile_uvmat(RootPath,'',RootFile,ImaExt,NomType,ref_i,[],ref_j);
278errormsg=display_file_name(handles,fileinput);
279if ~isempty(errormsg)
280    msgbox_uvmat('ERROR',errormsg)
281end
282set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
283
284%------------------------------------------------------------------------
285% --- general function activated for an input file series
286function errormsg=display_file_name(handles,fileinput)
287%------------------------------------------------------------------------
288set(handles.ListCompareMode,'Visible','on')
289errormsg='';%default empty error message
290drawnow
291
292%% enable RUN, BATCH button and 'status' display
293set(handles.RUN, 'Enable','On')
294set(handles.RUN,'BackgroundColor',[1 0 0])%set RUN button to red color
295set(handles.BATCH,'Enable','On')
296set(handles.BATCH,'BackgroundColor',[1 0 0])%set BATCH button to red color
297if isfield(handles,'status')
298    set(handles.status,'Value',0);       %suppress the 'status' display
299    status_Callback([], [], handles)
300end
301
302%% determine nomenclature types and extension of the input files
303[RootPath,SubDir,RootFile,i1,i2,j1,j2,ExtInput,NomTypeInput]=fileparts_uvmat(fileinput);
304NomTypeNc='';%default
305
306%% case of netcdf file as input, look for a coresponding image
307ind_opening=0;%default
308if strcmp(ExtInput,'.xml')
309    Param=xml2struct(fileinput);
310    fill_GUI(Param,handles);%fill the GUI with the parameters retrieved from the xml file
311    return
312end
313if strcmp(ExtInput,'.nc')
314    NomTypeNc=NomTypeInput;
315    if isempty(regexp(NomTypeInput,'[ab|AB|-]'))
316        set(handles.ListCompareMode,'Value',2) %mode displacement advised if the nomencalture does not involve index pairs
317        [RootPath,SubDir]=fileparts(RootPath);
318    set(handles.RootFile_1,'Visible','On');
319    else
320         set(handles.ListCompareMode,'Value',1)
321         set(handles.RootFile_1,'Visible','Off');
322    end
323    Data=nc2struct(fileinput,'ListGlobalAttribute','Conventions','absolut_time_T0','CivStage','Civ2_ImageA','Civ1_ImageA','Civ2_ImageB','Civ1_ImageB','fix','patch','civ2','fix2');
324    if isfield(Data,'Txt')
325        errormsg=Data.Txt;
326        return
327    end
328    if strcmp(Data.Conventions,'uvmat/civdata')% case of new civ data,
329        set(handles.ListProgram,'Value',2) %select civ/Matlab by default
330        ListProgram_Callback([],[], handles)
331        if ~isempty(Data.CivStage)%test for civ files
332            ind_opening=Data.CivStage;
333        end
334        if  ~isempty(Data.Civ2_ImageB)%get the corresponding input image in the netcdf file
335            imageinput=Data.Civ2_ImageB;
336            [tild,ImaName,ImaExt]=fileparts(Data.Civ2_ImageA);
337            set(handles.RootFile_1,'String',[ImaName ImaExt])
338        elseif ~isempty(Data.Civ1_ImageB)
339            imageinput=Data.Civ1_ImageB;
340            [tild,ImaName,ImaExt]=fileparts(Data.Civ1_ImageA);
341            set(handles.RootFile_1,'String',[ImaName ImaExt])
342        end
343       
344    elseif ~isempty(Data.absolut_time_T0')% case of  civx data,
345        set(handles.ListProgram,'Value',1) %select Cix by default
346        ListProgram_Callback([],[], handles)
347        if ~isempty(Data.fix2)
348            ind_opening=5;
349        elseif ~isempty(Data.civ2)
350            ind_opening=4;
351        elseif ~isempty(Data.patch)
352            ind_opening=3;
353        elseif ~isempty(Data.fix)
354            ind_opening=2;
355        end
356        % look for the corresponding input images
357        check_letter=~isempty(regexp(NomTypeInput,'[ab|AB]$'));%detect pair label by letter
358        NomTypeIma=NomTypeInput;
359        if check_letter
360            NomTypeIma=NomTypeInput(1:end-1);
361        else
362            r=regexp(NomTypeIma,'.-(?<num2>\d+)$','names');
363            if ~isempty(r)
364                NomTypeIma=regexprep(NomTypeIma,['-' r.num2],'');
365            end
366            r=regexp(NomTypeIma,'.-(?<num2>\d+)','names');
367            if ~isempty(r)
368                NomTypeIma=regexprep(NomTypeIma,['-' r.num2],'');
369            end
370        end
371        imageinput=fullfile_uvmat(RootPath,'',RootFile,'.png',NomTypeIma,i1,[],j1);
372    else
373        errormsg='the input netcdf file is not civ data';
374        return
375    end
376end
377
378%no corresponding image found, select manually with the browser
379ImaExt=ExtInput;
380if ~isempty(NomTypeNc)
381    %no corresponding image found, select manually with the browser
382    if ~exist(imageinput,'file')
383        menu={'*.png;*.jpg;*.tif;*.avi;*.AVI', '(*.png,*.jpg ,*.tif, *.avi,*.AVI)';
384            '*.png','.png image files'; ...
385            '*.jpg',' jpeg image files'; ...
386            '*.tif','.tif image files'; ...
387            '*.avi;*.AVI','.avi movie files'; ...
388            '*.*',  'All Files (*.*)'};
389        [FileName, PathName] = uigetfile( menu, 'Pick an input image file',fileparts(fileparts(fileinput)));
390        imageinput=[PathName FileName];%complete file name
391     
392    end   
393    fileinput=imageinput;
394end
395
396%% scan the image file series
397[FilePath,FileName,ImaExt]=fileparts(fileinput);
398% detect the file type, get the movie object if relevant, and look for the corresponding file series:
399% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
400[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomTypeIma,FileType,Object,i1,i2,j1,j2]=find_file_series(FilePath,[FileName ImaExt]);
401
402% [RootPath,FileName,ImaExt]=fileparts(fileinput);
403% [RootFile,i1_series,tild,j1_series,tild,NomTypeIma,FileType,Object]=find_file_series(RootPath,[FileName ImaExt]);
404% if strcmp(NomTypeInput,'*')% movies will be opened at the first frame
405%     i1=1;
406%     i2=[];
407%     j1=[];
408%     j2=[];
409% end
410switch FileType
411    case {'image','multimage','video'}
412    otherwise
413        errormsg='invalid input file: enter an image, a movie or civ .nc file';
414        return
415end
416% RootName=fullfile(RootPath,RootFile);
417set(handles.RootPath,'String',RootPath)
418set(handles.RootFile,'String',RootFile)
419browse=get(handles.RootPath,'UserData');
420% browse.nom_type_nc=NomTypeNc;
421browse.incr_pair=[0 0];%default
422
423%% fill reference indices from the input file indices
424num_ref_i=i1;%efaulmt ref index
425if ~isempty(i2)
426    num_ref_i=floor((num_ref_i+i2)/2);
427end
428num_ref_j=j1;
429if ~isempty(j2)
430    num_ref_j=floor((num_ref_j+j2)/2);
431end
432
433%% scan the images if a civ file has been opened
434MinIndex_i=min(i1_series(i1_series>0));
435MinIndex_j=min(j1_series(j1_series>0));
436MaxIndex_i=max(i1_series(i1_series>0));
437MaxIndex_j=max(j1_series(j1_series>0));
438
439%% look for an image documentation file
440ext_imadoc='';%default
441RootName=fullfile(RootPath,RootFile);
442if exist([RootName '.xml'],'file')
443    ext_imadoc='.xml';
444elseif exist([RootName '.civxml'],'file')
445    ext_imadoc='.civxml';
446elseif exist([RootName '.civ'],'file')
447    ext_imadoc='.civ';
448elseif exist([RootName '.avi'],'file')
449    ext_imadoc='.avi';
450elseif exist([RootName '.AVI'],'file')
451    ext_imadoc='.AVI';
452end
453set(handles.ImaDoc,'String',ext_imadoc)% display the extension name for the image documentation file used
454
455%%  read the time in the image documentation file 
456mode=''; %default
457time=[];
458TimeUnit=''; %default
459CoordUnit='';%default
460pxcmx_search=[];%default
461pxcmy_search=[];%default
462if ~isempty(ext_imadoc)
463    set(handles.ImaDoc,'BackgroundColor',[1 1 0]) % set edit box to yellow cloro to indicate that the file reading is beginning
464    drawnow
465    switch ext_imadoc
466        case '.civxml'%OBSOLETE
467            [tild,tild,time]=read_civxml([RootName '.civxml']);
468            mode='pair j1-j2';
469            if isempty(nom_type_ima)% dtermine types by default if not already selected by browser or uvmat
470                nom_type_ima='_i_j';
471            end
472        case '.xml'
473            [XmlData,warntext]=imadoc2struct([RootName '.xml']);
474            ext_ima_read=[];
475            nom_type_read=[];
476            if isfield(XmlData,'Heading')&&isfield(XmlData.Heading','ImageName')&&ischar(XmlData.Heading.ImageName)% get image nom type and extension from the xml file
477                %[PP,FF,fc,str2,str_a,str_b,ext_ima_read,nom_type_read]=name2display(XmlData.Heading.ImageName);
478                [tild,tild,tild,tild,tild,tild,tild,tild,nom_type_read]=fileparts_uvmat(XmlData.Heading.ImageName);
479                fullname=fullfile(fileparts(RootName),XmlData.Heading.ImageName); %full name (including path) of the first image defined by the xmle file,
480                if ~exist(fullname,'file')
481                    msgbox_uvmat('WARNING',['FirstImage ' fullname ' defined in the xml file does not exist'])
482                end
483            end
484            if isfield(XmlData,'Time')
485                time=XmlData.Time;
486                %transform .Time to a column vector if it is a line vector thenomenclature uses a single index: correct possible bug in xml
487                if isequal(MaxIndex_i,1) && ~isequal(MaxIndex_j,1)% .Time is a line vector
488                    if numel(nom_type_read)>=2 && isempty(regexp(nom_type_read(2:end),'\D','once'))
489                        time=time';
490                        MaxIndex_i=MaxIndex_j;
491                        MaxIndex_j=1;
492                    end
493                end
494            end
495            if isfield(XmlData,'TimeUnit')
496                TimeUnit=XmlData.TimeUnit;
497            end
498            pxcmx_search=1;
499            pxcmy_search=1;
500            if isfield(XmlData,'GeometryCalib')
501                tsai=XmlData.GeometryCalib;
502                if isfield(tsai,'f') && isfield(tsai,'Tz') && isfield(tsai,'dpx') && isfield(tsai,'dpy')&& isfield(tsai,'R')
503                    rot2D=tsai.R(1:2,[1,2]);
504                    pxcmx_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpx);
505                    pxcmy_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpy);
506                end
507                if isfield(tsai,'CoordUnit')
508                    CoordUnit=tsai.CoordUnit;
509                end
510            end
511        case '.civ'% OBSOLETE: case of .civ image documentation file
512            [error,time,TimeUnit,mode,npx,npy]=read_imatext([RootName '.civ']);
513            if error==2, msgbox_uvmat('WARNING',['no file ' RootName '.civ']);
514            elseif error==1, msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file');
515            end
516            nom_type_ima='001a';
517        case {'.avi','.AVI'}
518            nom_type_ima='*';
519            ImaExt=ext_imadoc;
520            set(handles.ListPairMode,'Value',1);
521            set(handles.ListPairMode,'String',{'series(Di)'})
522            dt=0.04;%default
523            if exist([RootName ext_imadoc],'file')==2
524                hhh=which('videoreader');
525                if isempty(hhh)%use old video function of matlab
526                    imainfo=aviinfo([RootName ext_imadoc]);%read infos on the avi movie
527                    dt=1/imainfo.FramesPerSecond;%time interval between successive frames
528                    MaxIndex_i=imainfo.NumFrames;%number of frames
529                    %         XmlData.Time=(0:1/imainfo.FramesPerSecond:(imainfo.NumFrames-1)/imainfo.FramesPerSecond)';
530                    %         nbfield=imainfo.NumFrames;
531                    %         set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FramesPerSecond) 'ms']);%display the elementary time interval in millisec
532                    %         ColorType=imainfo.ImageType;%='truecolor' for color images
533                else %use video function videoreader of matlab
534                    imainfo=get(videoreader([RootName ext_imadoc]));%read infos on the avi movie
535                    dt=1/imainfo.FrameRate;%time interval between successive frames
536                    MaxIndex_i=imainfo.NumberOfFrames;%number of frames
537                    %         XmlData.Time=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames-1)/imainfo.FrameRate)';
538                    %         nbfield=imainfo.NumberOfFrames;
539                    %         set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FrameRate) 'ms']);%display the elementary time interval in millisec
540                    %         ColorType='truecolor';
541                end
542               
543                time=(dt*(0:MaxIndex_i-1))';%list of image times
544                TimeUnit='s';
545            end
546            set(handles.ImaDoc,'BackgroundColor',[1 1 1])% set display box back to whiter
547    end
548end
549%% timing display
550%show the reference image edit box if relevant (not needed for movies or in the absence of time information
551if numel(time)>=2 % if there are at least two time values to define dt
552    MaxIndex_i=min(size(time,1),MaxIndex_i);
553    MaxIndex_j=min(size(time,2),MaxIndex_j);
554    time=[zeros(size(time,1),1) time]; %insert a vertical line of zeros (to deal with zero file indices)
555    time=[zeros(1,size(time,2)); time]; %insert a horizontal line of zeros
556    set(handles.ImaDoc,'UserData',time); %store the matrix of times
557    set(handles.dt_unit,'String',['dt in m' TimeUnit]);
558    set(handles.TimeUnit,'String',TimeUnit);
559else
560    set(handles.ImaDoc,'String',''); %xml file not used for timing
561    time=(i1_series(:,1)+0:size(i1_series,1)-1);% time=index i
562    time=time'*ones(1,size(i1_series,2),1); %makes a time matrix with the same time for all j indices
563    TimeUnit='frame';
564end
565set(handles.ImaDoc,'UserData',time); %store the matrix of times
566set(handles.dt_unit,'String',['dt in m' TimeUnit]);%display dt in unit 10-3 of the time (e.g ms)
567set(handles.TimeUnit,'String',TimeUnit);
568set(handles.nb_field,'String',num2str(MaxIndex_i));
569set(handles.nb_field2,'String',num2str(MaxIndex_j));
570set(handles.CoordUnit,'String',CoordUnit)
571set(handles.SearchRange,'UserData',[pxcmx_search pxcmy_search]);
572set(handles.ImaExt,'String',ImaExt)
573set(handles.NomType,'String',NomTypeIma)
574set(handles.ref_i,'String',num2str(num_ref_i))
575set(handles.ref_j,'String',num2str(num_ref_j))
576
577%% update i and j index range if a nc file has been opened or pb withmin max image indices:
578% then set first and last to the inputfile index by default
579first_i=str2num(get(handles.first_i,'String'));
580last_i=str2num(get(handles.last_i,'String'));
581if isempty(first_i) || isempty(last_i)||isempty(MinIndex_i)||isempty(MaxIndex_i)
582    set(handles.first_i,'String',num2str(num_ref_i));
583    set(handles.last_i,'String',num2str(num_ref_i));%
584end
585if ind_opening~=0 || isempty(first_i) || isempty(last_i)|| first_i<MinIndex_i || last_i>MaxIndex_i
586set(handles.first_i,'String',num2str(num_ref_i));
587set(handles.last_i,'String',num2str(num_ref_i));%
588end
589
590%j index range
591first_j=str2num(get(handles.first_j,'String'));
592last_j=str2num(get(handles.last_i,'String'));
593if isempty(first_j) || isempty(last_j)||isempty(MinIndex_j)||isempty(MaxIndex_j)
594    set(handles.first_j,'String',num2str(num_ref_j));
595    set(handles.last_j,'String',num2str(num_ref_j));%
596elseif ind_opening~=0 || first_j<MinIndex_j || last_j>MaxIndex_j
597    set(handles.first_j,'String',num2str(num_ref_j));
598set(handles.last_j,'String',num2str(num_ref_j));%
599end
600
601%% set the civ options depending on the input file content when a nc file has been opened
602ListOptions={'CheckCiv1', 'CheckFix1' 'CheckPatch1', 'CheckCiv2', 'CheckFix2', 'CheckPatch2'};
603if ind_opening~=0
604    for index = 1:ind_opening
605        set(handles.(ListOptions{index}),'value',0)
606    end
607end
608for index = ind_opening+2:6
609    set(handles.(ListOptions{index}),'value',0)
610end
611set(handles.(ListOptions{min(ind_opening+1,6)}),'value',1)
612update_CivOptions(handles,1)
613
614%%  set the menus of image pairs and default selection for civ   %%%%%%%%%%%%%%%%%%%
615%check_letter=~isempty(regexp(NomTypeIma,'[ab|AB]$'));%detect pair label by letter
616if  isequal(NomTypeNc,'_1-2')||isempty(MaxIndex_j)|| (MaxIndex_j==1)
617    set(handles.ListPairMode,'Value',1)
618    set(handles.ListPairMode,'String',{'series(Di)'})   
619elseif  MaxIndex_i==1 && MaxIndex_j>1% simple series in j
620    set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)'})
621    if  MaxIndex_j <= 10
622        set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large
623    end
624else
625    set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)';'series(Di)'})%multiple choice
626    if strcmp(NomTypeNc,'_1-2_1')
627        set(handles.ListPairMode,'Value',3)% advise 'series(Di)'
628    elseif  MaxIndex_j <= 10
629        set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large
630    end
631end
632
633%% scan files to update the subdirectory list display
634listot=dir(RootPath);%directory of RootPath
635idir=0;
636listdir={''};%default
637% get the list of existing civ subdirectories in the path of theinput root  file
638for ilist=1:length(listot)
639    if listot(ilist).isdir
640        name=listot(ilist).name;
641        if ~isequal(name,'.') && ~isequal(name,'..')
642            idir=idir+1;
643            listdir{idir,1}=listot(ilist).name;
644        end
645    end
646end
647
648%% update the selection for civ1 and civ2
649if ~isempty(SubDir)% subdir for civ1 and civ2 initiated by the input
650    SubdirCiv1=SubDir;
651    SubdirCiv2=SubDir;
652    set(handles.SubdirCiv1,'String',SubDir)
653    set(handles.SubdirCiv2,'String',SubDir)
654else% currently selected subdir preserved
655    SubdirCiv1=get(handles.SubdirCiv1,'String');
656    SubdirCiv2=get(handles.SubdirCiv2,'String');
657    if isempty(SubdirCiv1)% default subdir name='CIV'
658        set(handles.SubdirCiv1,'String','CIV');
659        SubdirCiv1='CIV';
660    end
661    if isempty(SubdirCiv2)% default subdir name='CIV'
662        set(handles.SubdirCiv2,'String','CIV');
663        SubdirCiv2='CIV';
664    end
665end
666
667%% update the subdirectory menus
668ValueCiv1=find(strcmp(SubdirCiv1,listdir));%search the index of subdir in the cell listdir
669if isempty(ValueCiv1)% if the input subdir is not found
670    ValueCiv1=numel(listdir)+1;%new subdirectory requested for civ1
671end
672ValueCiv2=find(strcmp(SubdirCiv2,listdir));%search the index of subdir in the cell listdir
673if isempty(ValueCiv2)% if the input subdir is not found
674    ValueCiv2=numel(listdir)+1;%new subdirectory requested for civ2
675end
676set(handles.ListSubdirCiv1,'String',[listdir;'new...'])
677set(handles.ListSubdirCiv2,'String',[listdir;'new...'])
678set(handles.ListSubdirCiv1,'Value',ValueCiv1)
679set(handles.ListSubdirCiv2,'Value',ValueCiv2)
680if isempty(listdir)
681    set(handles.SubdirCiv1,'String','CIV')
682    set(handles.SubdirCiv2,'String','CIV')
683end
684
685%% store info
686set(handles.RootPath,'UserData',browse)% store the nomenclature type
687
688%% list the possible index pairs, depending on the option set in ListPairMode
689ListPairMode_Callback([], [], handles)
690
691%% store the root input filename for future opening
692profil_perso=fullfile(prefdir,'uvmat_perso.mat');
693if exist(profil_perso,'file')
694    save (profil_perso,'RootPath','-append'); %store the root name for future opening of uvmat
695else
696    txt=ver('MATLAB');
697    Release=txt.Release;
698    relnumb=str2double(Release(3:4));
699    if relnumb >= 14
700        save (profil_perso,'RootPath','-V6'); %store the root name for future opening of uvmat
701    else
702        save (profil_perso,'RootPath'); %store the root name for future opening of uvmat
703    end
704end
705set(handles.RootPath,'BackgroundColor',[1 1 1])
706
707%------------------------------------------------------------------------
708% --- Executes on carriage return on the subdir checkciv1 edit window
709function SubdirCiv1_Callback(hObject, eventdata, handles)
710%------------------------------------------------------------------------
711SubDir=get(handles.SubdirCiv1,'String');
712menu_str=get(handles.ListSubdirCiv1,'String');% read the list of subdirectories for update
713ichoice=find(strcmp(SubDir,menu_str),1);
714if isempty(ichoice)
715    ilist=numel(menu_str); %select 'new...' in the menu
716else
717    ilist=ichoice;
718end
719set(handles.ListSubdirCiv1,'Value',ilist)% select the selected subdir in the menu
720if get(handles.CheckCiv1,'Value')% if Civ1 is performed
721    set(handles.SubdirCiv2,'String',SubDir);% set by default civ2 directory the same as civ1
722    set(handles.ListSubdirCiv2,'Value',ilist)
723else % if Civ1 data already exist
724    errormsg=find_netcpair_civ(handles,1); %update the list of available pairs from netcdf files in the new directory
725    if ~isempty(errormsg)
726    msgbox_uvmat('ERROR',errormsg)
727    end
728end
729
730%------------------------------------------------------------------------
731% --- Executes on carriage return on the SubDir checkciv1 edit window
732function SubdirCiv2_Callback(hObject, eventdata, handles)
733%------------------------------------------------------------------------
734SubDir=get(handles.SubdirCiv1,'String');
735menu_str=get(handles.ListSubdirCiv2,'String');% read the list of subdirectories for update
736ichoice=find(strcmp(SubDir,menu_str),1);
737if isempty(ichoice)
738    ilist=numel(menu_str); %select 'new...' in the menu
739else
740    ilist=ichoice;
741end
742set(handles.ListSubdirCiv2,'Value',ilist)% select the selected subdir in the menu
743%update the list of available pairs from netcdf files in the new directory
744if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
745    errormsg=find_netcpair_civ(handles,2);
746        if ~isempty(errormsg)
747    msgbox_uvmat('ERROR',errormsg)
748    end
749end
750
751%------------------------------------------------------------------------
752% --- Executes on button press in CheckCiv1.
753function CheckCiv1_Callback(hObject, eventdata, handles)
754%------------------------------------------------------------------------
755update_CivOptions(handles,0)
756
757%------------------------------------------------------------------------
758% --- Executes on button press in CheckFix1.
759function CheckFix1_Callback(hObject, eventdata, handles)
760%------------------------------------------------------------------------
761update_CivOptions(handles,0)
762
763%------------------------------------------------------------------------
764% --- Executes on button press in CheckPatch1.
765function CheckPatch1_Callback(hObject, eventdata, handles)
766%------------------------------------------------------------------------
767update_CivOptions(handles,0)
768
769%------------------------------------------------------------------------
770% --- Executes on button press in CheckCiv2.
771function CheckCiv2_Callback(hObject, eventdata, handles)
772%------------------------------------------------------------------------
773update_CivOptions(handles,0)
774
775%------------------------------------------------------------------------
776% --- Executes on button press in CheckFix2.
777function CheckFix2_Callback(hObject, eventdata, handles)
778%------------------------------------------------------------------------
779update_CivOptions(handles,0)
780
781%------------------------------------------------------------------------
782% --- Executes on button press in CheckPatch2.
783function CheckPatch2_Callback(hObject, eventdata, handles)
784%------------------------------------------------------------------------
785update_CivOptions(handles,0)
786
787%------------------------------------------------------------------------
788% --- activated by any checkbox controling the selection of Civ1,Fix1,Patch1,Civ2,Fix2,Patch2
789function update_CivOptions(handles,opening)
790%------------------------------------------------------------------------
791checkbox=zeros(1,6);
792checkbox(1)=get(handles.CheckCiv1,'Value');
793checkbox(2)=get(handles.CheckFix1,'Value');
794checkbox(3)=get(handles.CheckPatch1,'Value');
795checkbox(4)=get(handles.CheckCiv2,'Value');
796checkbox(5)=get(handles.CheckFix2,'Value');
797checkbox(6)=get(handles.CheckPatch2,'Value');
798ind_selected=find(checkbox,1);
799if ~isempty(ind_selected)
800    RootPath=get(handles.RootPath,'String');
801    if isempty(RootPath)
802        msgbox_uvmat('ERROR','Please open an image or PIV .nc file with the upper bar menu Open/Browse...')
803        return
804    end
805end
806set(handles.PairIndices,'Visible','on')
807set(handles.SubdirCiv1,'Visible','on')
808set(handles.ListSubdirCiv1,'Visible','on')
809set(handles.TitleSubdirCiv1,'Visible','on')
810if ~opening
811    errormsg=find_netcpair_civ(handles,1); % select the available netcdf files
812    if ~isempty(errormsg)
813        msgbox_uvmat('ERROR',errormsg)
814    end
815end
816if max(checkbox(4:6))% case of civ2 pair choice needed
817    set(handles.TitlePairCiv2,'Visible','on')
818    set(handles.TitleSubdirCiv2,'Visible','on')
819    set(handles.SubdirCiv2,'Visible','on')
820    set(handles.ListSubdirCiv2,'Visible','on')
821    set(handles.ListPairCiv2,'Visible','on')
822    if ~opening
823        errormsg=find_netcpair_civ(handles,2); % select the available netcdf files
824        if ~isempty(errormsg)
825            msgbox_uvmat('ERROR',errormsg)
826        end
827    end
828else
829    set(handles.TitleSubdirCiv2,'Visible','off')
830    set(handles.SubdirCiv2,'Visible','off')
831    set(handles.ListSubdirCiv2,'Visible','off')
832    set(handles.ListPairCiv2,'Visible','off')
833end
834options={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'};
835for ilist=1:length(options)
836    if checkbox(ilist)
837        set(handles.(options{ilist}),'Visible','on')
838    else
839        set(handles.(options{ilist}),'Visible','off')
840    end
841end
842
843%------------------------------------------------------------------------
844% --- Executes on button press in RUN: processing on local computer
845function RUN_Callback(hObject, eventdata, handles)
846%------------------------------------------------------------------------
847set(handles.RUN, 'Enable','Off')
848set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
849batch=0;
850errormsg=launch_jobs(hObject, eventdata, handles,batch);
851set(handles.RUN, 'Enable','On')
852set(handles.RUN,'BackgroundColor',[1 0 0])
853
854% display errors or start status callback to visualise results
855if ~isempty(errormsg)
856    display(errormsg)
857    msgbox_uvmat('ERROR',errormsg)
858elseif  isfield(handles,'status') %&& ~isequal(get(handles.ListPairMode,'Value'),3)
859    set(handles.status,'Value',1);%suppress status display
860    status_Callback(hObject, eventdata, handles)
861end
862
863%------------------------------------------------------------------------
864% --- Executes on button press in BATCH: remote processing
865function BATCH_Callback(hObject, eventdata, handles)
866% -----------------------------------------------------------------------
867set(handles.BATCH, 'Enable','Off')
868set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])
869batch=1;
870errormsg=launch_jobs(hObject, eventdata, handles, batch);
871set(handles.BATCH, 'Enable','On')
872set(handles.BATCH,'BackgroundColor',[1 0 0])
873
874% display errors or start status callback to visualise results
875if ~isempty(errormsg)
876    display(errormsg)
877    msgbox_uvmat('ERROR',errormsg)
878elseif isfield(handles,'status')
879    set(handles.status,'Value',1);%suppress status display
880    status_Callback(hObject, eventdata, handles)
881end
882
883%-------------------------------------------------------------------
884% --- Executes on button press in status.
885function status_Callback(hObject, eventdata, handles)
886%-------------------------------------------------------------------
887val=get(handles.status,'Value');
888if val==0
889    set(handles.status,'BackgroundColor',[0 1 0])
890    hfig=findobj(allchild(0),'name','civ_status');
891    if ~isempty(hfig)
892        delete(hfig)
893    end
894    return
895end
896set(handles.status,'BackgroundColor',[1 1 0])
897drawnow
898listtype={'civ1','fix1','patch1','civ2','fix2','patch2'};
899Param.CheckCiv1=get(handles.CheckCiv1,'Value');
900Param.CheckFix1=get(handles.CheckFix1,'Value');
901Param.CheckPatch1=get(handles.CheckPatch1,'Value');
902Param.CheckCiv2=get(handles.CheckCiv2,'Value');
903Param.CheckFix2=get(handles.CheckFix2,'Value');
904Param.CheckPatch2=get(handles.CheckPatch2,'Value');
905box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2];
906
907option_civ=find(box_test,1,'last');%last selected option (non-zero index of box_test)
908filecell=get(handles.civ,'UserData');%retrieve the list of output files expected for PIV
909test_new=0;
910if ~isfield(filecell,'nc')
911    test_new=1;
912    [ref_i,ref_j,errormsg]=find_ref_indices(handles);
913    if ~isempty(errormsg)
914        msgbox_uvmat('ERROR',errormsg)
915        return
916    end
917    filecell=set_civ_filenames(handles,ref_i,ref_j,box_test);%determine the output file expected from the GUI status
918end
919if ~isequal(box_test(4:6),[0 0 0])
920    civ_files=filecell.nc.civ2;%case of civ2 operations
921else
922    civ_files=filecell.nc.civ1;
923end
924[root,filename,ext]=fileparts(civ_files{1});
925[rootroot,SubDir,extdir]=fileparts(root);
926hfig=findobj(allchild(0),'name','civ_status');
927if isempty(hfig)
928    hfig=figure('DeleteFcn',@stop_status);
929    set(hfig,'name','civ_status')
930     uicontrol('Style','listbox','Units','normalized', 'Position',[0.05 0.09 0.9 0.71], 'Callback', {'open_uvmat'},'tag','list');
931    uicontrol('Style','edit','Units','normalized', 'Position', [0.05 0.87 0.9 0.1],'tag','msgbox','Max',2,'String','checking files...');
932    uicontrol('Style','frame','Units','normalized', 'Position', [0.05 0.81 0.9 0.05]);
933    uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.7 0.01 0.2 0.07],'String','OK','FontWeight','bold','FontUnits','normalized','FontSize',0.9,'Callback',@close_GUI);
934    BarPosition=[0.05 0.81 0.01 0.05];
935    hwaitbar=uicontrol('Style','frame','Units','normalized', 'Position',BarPosition ,'BackgroundColor',[1 0 0],'tag','waitbar');
936    drawnow
937end
938Tabchar={};
939nbfiles=numel(civ_files);
940count=0;
941testrecent=0;
942while count<nbfiles
943    count=0;
944    datnum=zeros(1,nbfiles);
945    for ifile=1:nbfiles
946        detect=exist(civ_files{ifile},'file'); % check the existence of the file
947        option=0;
948        if detect==0
949            option_str='not created';
950        else
951            datfile=dir(civ_files{ifile});
952            if isfield(datfile,'datenum')
953                datnum(ifile)=datfile.datenum;%only available in recent matlab versions
954                testrecent=1;
955            end
956            filefound(ifile)={datfile.name};
957            lastfield='';
958            % check the content  netcdf file
959            Data=nc2struct(civ_files{ifile},'ListGlobalAttribute','CivStage','patch2','fix2','civ2','patch','fix');
960            option_list={'civ1','fix1','patch1','civ2','fix2','patch2'};
961            if ~isempty(Data.CivStage)
962                option=Data.CivStage;%case of Matlab civ
963            else
964                if ~isempty(Data.patch2) && isequal(Data.patch2,1)
965                    option=6;
966                elseif ~isempty(Data.fix2) && isequal(Data.fix2,1)
967                    option=5;
968                elseif ~isempty(Data.civ2) && isequal(Data.civ2,1);
969                    option=4;
970                elseif ~isempty(Data.patch) && isequal(Data.patch,1);
971                    option=3;
972                elseif ~isempty(Data.fix) && isequal(Data.fix,1);
973                    option=2;
974                else
975                    option=1;
976                end
977            end
978            option_str=option_list{option};
979        end
980        if option >= option_civ
981            count=count+1;
982        end
983        [rr,filename,ext]=fileparts(civ_files{ifile});
984        Tabchar{ifile,1}=[fullfile([SubDir extdir],filename) ext  '...' option_str];
985    end
986    datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
987    if isempty(datnum)
988        if testrecent
989            message='no civ result created yet';
990        else
991            message='';
992        end
993    else
994        datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
995        [first,ind]=min(datnum);
996        [last,indlast]=max(datnum);
997        if test_new
998            message='existing file status, no processing launched yet';
999        else
1000        message={[num2str(count) ' file(s) done over ' num2str(nbfiles)] ;['oldest modification:  ' cell2mat(filefound(ind)) ' : ' datestr(first)];...
1001            ['latest modification:  ' cell2mat(filefound(indlast)) ' : ' datestr(last)]};
1002        end
1003    end
1004    hfig=findobj(allchild(0),'name','civ_status');
1005    if isempty(hfig)% the status list has been deleted
1006        return
1007    else
1008        hlist=findobj(hfig,'tag','list');
1009        hmsgbox=findobj(hfig,'tag','msgbox');
1010        hwaitbar=findobj(hfig,'tag','waitbar');
1011        set(hlist,'String',Tabchar)
1012        set(hmsgbox,'String', message)
1013        if count>0 && ~test_new
1014            BarPosition(3)=0.9*count/nbfiles;
1015            set(hwaitbar,'Position',BarPosition)
1016        end
1017    end
1018    set(hlist,'UserData',rootroot)
1019    if count<10||(nbfiles-count)<10
1020    pause(.5)% wait 0.5 seconds for next check
1021    else
1022        pause(10)% wait 10 seconds for next check
1023    end
1024end
1025
1026%------------------------------------------------------------------------
1027% --- Main lauch command, called by RUN and BATCH
1028function errormsg=launch_jobs(hObject, eventdata, handles, batch)
1029%-----------------------------------------------------------------------
1030errormsg='';%default
1031
1032%% read the input parameters from the  GUI civ
1033Param=read_GUI(handles.civ);
1034
1035%% check the selected list of operations:
1036operations={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'};
1037box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2];
1038index_first=find(box_test==1,1);
1039if isempty(index_first)
1040    errormsg='no selected operation';
1041    return
1042end
1043index_last=find(box_test==1,1,'last');
1044box_used=box_test(index_first : index_last);
1045[box_missing,ind_missing]=min(box_used);
1046if isequal(box_missing,0); %there is a missing step in the sequence of operations
1047    errormsg=['missing' cell2mat(operations(ind_missing))];
1048    return
1049end
1050
1051%% check mask if selecetd
1052%could be included in get_mask callback ?
1053if isequal(get(handles.CheckMask,'Value'),1)
1054    maskname=get(handles.Mask,'String');
1055    if ~exist(maskname,'file')
1056        get_mask_civ1_Callback(hObject, eventdata, handles);
1057    end
1058end
1059if isequal(get(handles.CheckMask,'Value'),1)
1060    maskname=get(handles.Mask,'String');
1061    if ~exist(maskname,'file')
1062        get_mask_fix1_Callback(hObject, eventdata, handles);
1063    end
1064end
1065if isequal(get(handles.CheckMask,'Value'),1)
1066    maskname=get(handles.Mask,'String');
1067    if ~exist(maskname,'file')
1068        get_mask_civ2_Callback(hObject, eventdata, handles);
1069    end
1070end
1071if isequal(get(handles.CheckMask,'Value'),1)
1072    maskname=get(handles.Mask,'String');
1073    if ~exist(maskname,'file')
1074        get_mask_fix2_Callback(hObject, eventdata, handles);
1075    end
1076end
1077
1078%% reinitialise status callback
1079if isfield(handles,'status')
1080    set(handles.status,'Value',0);%suppress status display
1081    status_Callback(hObject, eventdata, handles)
1082end
1083
1084%% read the PARAM.xml file to get the binaries (and batch_mode if batch)
1085path_civ=fileparts(which('civ')); %path to the source directory of uvmat
1086xmlfile='PARAM.xml';
1087if exist(xmlfile,'file')% search parameter xml file in the whole matlab path
1088    t=xmltree(xmlfile);
1089    s=convert(t);
1090else
1091    errormsg=['no file ' xmlfile];
1092    return
1093end
1094test_interp=0; %eviter les variables test_ (LG)
1095if batch
1096    if isfield(s,'BatchParam')
1097        Param.xml=s.BatchParam;
1098        if isfield(Param.xml,'BatchMode')
1099            batch_mode=Param.xml.BatchMode;
1100            if ~ismember(batch_mode,{'sge','oar'})
1101                errormsg=['batch mode ' batch_mode ' not supported by UVMAT'];
1102                return
1103            end
1104        end
1105    else
1106        errormsg='no batch civ binaries defined in PARAM.xml';
1107        return
1108    end
1109else % run
1110    if isfield(s,'RunParam')
1111        Param.xml=s.RunParam;
1112    else
1113        errormsg='no run civ binaries defined in PARAM.xml';
1114        return
1115    end
1116end
1117
1118%% check batch mode supported
1119if batch
1120    switch batch_mode
1121        case 'sge'
1122            test_command='qstat';
1123        case 'oar'
1124            test_command='oarstat';
1125    end   
1126    [s,w]=system(test_command);
1127    if ~isequal(s,0)
1128        errormsg=[batch_mode ' batch system not available'];
1129        return
1130    end
1131end
1132
1133%% check if the binaries exist
1134ListProgram=get(handles.ListProgram,'String');
1135CivMode=ListProgram{get(handles.ListProgram,'Value')};
1136binary_list={};
1137switch CivMode
1138    case 'CivX'
1139        binary_list={'Civ1Bin','Civ2Bin','PatchBin','FixBin'};
1140    case 'CivAll'% desactivated option
1141        binary_list={'Civ'};
1142    case 'Matlab'
1143        if batch
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')%look for the full path if the file name has been defined with a relative path in PARAM.xml
1151            fullname=fullfile(path_civ,Param.xml.(bin_name{1}));
1152            if exist(fullname,'file')
1153                Param.xml.(bin_name{1})=fullname;
1154            else
1155                errormsg=['Binary ' Param.xml.(bin_name{1}) ' defined in PARAM.xml does not exist'];
1156                return
1157            end
1158        else
1159            [path,name,ext]=fileparts(Param.xml.(bin_name{1}));
1160            currentdir=pwd;
1161            cd(path);
1162            binpath=pwd;%path of the binary
1163            Param.xml.(bin_name{1})=fullfile(binpath,[name ext]);
1164            cd(currentdir);
1165        end
1166       
1167    end
1168end
1169display('files OK, processing...')
1170
1171%% set the list of files and check them
1172display('checking the files...')
1173[ref_i,ref_j,errormsg]=find_ref_indices(handles);
1174if ~isempty(errormsg)
1175    return
1176end
1177[filecell,i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,xx,yy,compare]=...
1178    set_civ_filenames(handles,ref_i,ref_j,box_test);
1179
1180Rootbat=fileparts(filecell.nc.civ1{1,1});%output netcdf file (without extention)
1181set(handles.civ,'UserData',filecell);%store for futur use of status callback
1182if isempty(filecell)% (error message displayed in fct set_civ_filenames)
1183    return
1184end
1185nbfield=numel(i1_civ1);
1186nbslice=numel(j1_civ1);
1187if ~strcmp(CivMode,'CivX')
1188    if Param.CheckCiv1
1189    [Param.Civ1.FileTypeA,FileInfo,Param.Civ1.ImageA]=get_file_type(filecell.ima1.civ1{1});
1190    [Param.Civ1.FileTypeB,FileInfo,Param.Civ1.ImageB]=get_file_type(filecell.ima2.civ1{1});
1191    end
1192    if Param.CheckCiv2
1193    [Param.Civ2.FileTypeA,FileInfo,Param.Civ2.ImageA]=get_file_type(filecell.ima1.civ2{1});
1194    [Param.Civ2.FileTypeB,FileInfo,Param.Civ2.ImageB]=get_file_type(filecell.ima2.civ2{1});
1195    end
1196end
1197
1198%% MAIN LOOP
1199time=get(handles.ImaDoc,'UserData'); %get the set of times
1200TimeUnit=get(handles.TimeUnit,'String');
1201checkframe=strcmp(TimeUnit,'frame');
1202batch_file_list=[];%should be renamed file_list, can be used for xml or bash files
1203 
1204for ifile=1:nbfield
1205    for j=1:nbslice
1206        % initiate system command
1207        switch CivMode
1208            case 'CivX'
1209                if isunix % check: necessaire aussi en RUN?
1210                    cmd=['#!/bin/bash \n '...
1211                        '#$ -cwd \n '...
1212                        'hostname && date \n '...
1213                        'umask 002 \n'];%allow writting access to created files for user group
1214                else
1215                    cmd=[];
1216                end
1217            case 'CivAll'
1218                CivAllxml=xmltree;% xml contents,  all parameters
1219                CivAllCmd='';
1220                CivAllxml=set(CivAllxml,1,'name','CivDoc');
1221        end
1222           
1223        % define output file name
1224        if Param.CheckCiv2==1 || Param.CheckFix2==1 || Param.CheckPatch2==1
1225            OutputFile=filecell.nc.civ2{ifile,j};
1226        else
1227            OutputFile=filecell.nc.civ1{ifile,j};
1228        end
1229        OutputFile=regexprep(OutputFile,'.nc','');
1230       
1231        if Param.CheckCiv1
1232            % read image-dependent parameters
1233            Param.Civ1.ImageA=filecell.ima1.civ1{ifile,j};
1234            Param.Civ1.ImageB=filecell.ima2.civ1{ifile,j};
1235            if ~checkframe% && size(time,1)>=i2_civ1(ifile) && size(time,2)>=j2_civ1(j)
1236                Param.Civ1.Dt=(time(i2_civ1(ifile)+1,j2_civ1(j)+1)-time(i1_civ1(ifile)+1,j1_civ1(j)+1));
1237            else
1238                Param.Civ1.Dt=1;
1239            end
1240            Param.Civ1.Time=((time(i2_civ1(ifile)+1,j2_civ1(j)+1)+time(i1_civ1(ifile)+1,j1_civ1(j)+1))/2);
1241            if strcmp(CivMode,'CivX')
1242            Param.Civ1.term_a=num2stra(j1_civ1(j),nom_type_nc);%UTILITE?
1243            Param.Civ1.term_b=num2stra(j2_civ1(j),nom_type_nc);%
1244            end
1245            form=imformats(regexprep(get(handles.ImaExt,'String'),'^.',''));%look for image formats
1246            if isempty(form)
1247                ImageInfo=get(VideoReader(filecell.ima1.civ1{1,1}));
1248                Param.Civ1.ImageBitDepth=ImageInfo.BitsPerPixel/3;
1249            else
1250                ImageInfo=imfinfo(filecell.ima1.civ1{1,1});%read the first image to get the size
1251                Param.Civ1.ImageBitDepth=ImageInfo.BitDepth;
1252            end
1253            Param.Civ1.ImageWidth=ImageInfo.Width;
1254            Param.Civ1.ImageHeight=ImageInfo.Height;
1255            Param.Civ1.i1=i1_civ1(ifile);
1256            Param.Civ1.i2=i2_civ1(ifile);
1257            % read mask parameters
1258            if Param.Civ1.CheckMask % the lines below should be changed with the new gui
1259                if ~exist(Param.Civ1.Mask,'file')
1260                    maskbase=[filecell.filebase '_' Param.Civ1.Mask]; %
1261                    nbslice_mask=str2double(Param.Civ1.Mask(1:end-4)); %
1262                    i1_mask=mod(i1_civ1(ifile)-1,nbslice_mask)+1;
1263                    [RootPathMask,RootFileMask]=fileparts(maskbase);
1264                    Param.Civ1.Mask=fullfile_uvmat(RootPathMask,[],RootFileMask,'.png','_1',i1_mask);
1265                end
1266            end
1267            % read grid parameters
1268            if Param.Civ1.CheckGrid
1269                if numel(Param.Civ1.Grid)>=4 && isequal(Param.Civ1.Grid(end-3:end),'grid')
1270                    nbslice_grid=str2double(Param.Civ1.Grid(1:end-4)); %
1271                    if ~isnan(nbslice_grid)
1272                        i1_grid=mod(i1_civ1(ifile)-1,nbslice_grid)+1;
1273                        Param.Civ1.Grid=[filecell.filebase '_' fullfile_uvmat('','',Param.Civ1.Grid,'.grid','_1',i1_grid)];
1274%                         Param.Civ1.Grid=[filecell.filebase '_' name_generator(Param.Civ1.Grid,i1_grid,1,'.grid','_i')];
1275                        if ~exist(Param.Civ1.GridName,'file')
1276                            errormsg='grid file absent for civ1';
1277                            return
1278                        end
1279                    elseif ~exist(Param.Civ1.Grid,'file')
1280                        errormsg='grid file absent for civ1';
1281                        return
1282                    end
1283                end
1284            end
1285           
1286            % send command
1287            switch CivMode
1288                case 'CivX'
1289                    [cmd_civ,errormsg]=cmd_civ1(filecell.nc.civ1{ifile,j},Param);
1290                    cmd=[cmd cmd_civ '\n'];
1291                    if ~isempty(errormsg)
1292                        return
1293                    end
1294                case 'CivAll'
1295                    CivAllCmd=[CivAllCmd ' civ1 '];
1296                    str=CIV1_CMD_Unified(filecell.nc.civ1{ifile,j},'',Param.Civ1);
1297                    fieldnames=fields(str);
1298                    [CivAllxml,uid_civ1]=add(CivAllxml,1,'element','civ1');
1299                    for ilist=1:length(fieldnames)
1300                        val=eval(['str.' fieldnames{ilist}]);
1301                        if ischar(val)
1302                            [CivAllxml,uid_t]=add(CivAllxml,uid_civ1,'element',fieldnames{ilist});
1303                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1304                        end
1305                    end
1306            end
1307        end
1308       
1309        if Param.CheckFix1
1310            switch CivMode
1311                case 'CivX'
1312                    cmd=[cmd...
1313                        cmd_fix(filecell.nc.civ1{ifile,j},Param,'Fix1') '\n'];
1314                case 'CivAll'%to abandon
1315                    fix1.inputFileName=filecell.nc.civ1{ifile,j} ;
1316                    fix1.fi1=num2str(param.fix1.flagindex1(1));
1317                    fix1.fi2=num2str(param.fix1.flagindex1(2));
1318                    fix1.fi3=num2str(param.fix1.flagindex1(3));
1319                    fix1.threshC=num2str(param.fix1.thresh_vecC1);
1320                    fix1.threshV=num2str(param.fix1.thresh_vel1);
1321                    fieldnames=fields(fix1);
1322                    [CivAllxml,uid_fix1]=add(CivAllxml,1,'element','fix1');
1323                    for ilist=1:length(fieldnames)
1324                        val=eval(['fix1.' fieldnames{ilist}]);
1325                        if ischar(val)
1326                            [CivAllxml,uid_t]=add(CivAllxml,uid_fix1,'element',fieldnames{ilist});
1327                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1328                        end
1329                    end
1330                    CivAllCmd=[CivAllCmd ' fix1 '];
1331            end
1332        end
1333       
1334        %CheckPatch1
1335        if Param.CheckPatch1==1
1336            switch CivMode
1337                case 'CivX'
1338                    cmd=[cmd...
1339                        cmd_patch(filecell.nc.civ1{ifile,j},Param,'Patch1') '\n'];
1340                case 'CivAll'
1341                    patch1.inputFileName=filecell.nc.civ1{ifile,j} ;
1342                    patch1.nopt=subdomain_patch1;
1343                    patch1.maxdiff=thresh_patch1;
1344                    patch1.ro=rho_patch1;
1345                    test_grid=get(handles.get_gridpatch1,'Value');
1346                    if test_grid
1347                        patch1.gridflag='y';
1348                        gridname=get(handles.grid_patch1,'String');
1349                        if isequal(gridname(end-3:end),'grid')
1350                            nbslice_grid=str2double(gridname(1:end-4)); %
1351                            if ~isnan(nbslice_grid)
1352                                i1_grid=mod(i1_civ1(ifile)-1,nbslice_grid)+1;
1353                                patch1.gridPatch=[filecell.filebase '_' fullfile_uvmat('','',gridname,'.grid','_1',i1_grid)];
1354%                                 patch1.gridPatch=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')];
1355                                if ~exist(patch1.gridPatch,'file')
1356                                    errormsg='grid file absent for patch1';
1357                                    return
1358                                end
1359                            elseif exist(gridname,'file')
1360                                patch1.gridPatch=gridname;
1361                            else
1362                                errormsg='grid file absent for patch1';
1363                                return
1364                            end
1365                        end
1366                    else
1367                        patch1.gridPatch='none';
1368                        patch1.gridflag='n';
1369                        patch1.m=nx_patch1;
1370                        patch1.n=ny_patch1;
1371                    end
1372                    patch1.convectFlow='n';
1373                    fieldnames=fields(patch1);
1374                    [CivAllxml,uid_patch1]=add(CivAllxml,1,'element','patch1');
1375                    for ilist=1:length(fieldnames)
1376                        val=eval(['patch1.' fieldnames{ilist}]);
1377                        if ischar(val)
1378                            [CivAllxml,uid_t]=add(CivAllxml,uid_patch1,'element',fieldnames{ilist});
1379                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1380                        end
1381                    end
1382                    CivAllCmd=[CivAllCmd ' patch1 '];
1383            end
1384        end
1385        if Param.CheckCiv2==1
1386            Param.Civ2.ImageA=filecell.ima1.civ2{ifile,j};
1387            Param.Civ2.ImageB=filecell.ima2.civ2{ifile,j};
1388            if ~checkframe %&& size(time,1)>=i2_civ2(ifile) && size(time,2)>=j2_civ2(j)
1389                Param.Civ2.Dt=time(i2_civ2(ifile)+1,j2_civ2(j)+1)-time(i1_civ2(ifile)+1,j1_civ2(j)+1);
1390            else
1391                Param.Civ2.Dt=1;
1392            end
1393            Param.Civ2.Time=(time(i2_civ2(ifile)+1,j2_civ2(j)+1)+time(i1_civ2(ifile)+1,j1_civ2(j)+1))/2;
1394            if strcmp(CivMode,'CivX')
1395            Param.Civ2.term_a=num2stra(j1_civ2(j),nom_type_nc);
1396            Param.Civ2.term_b=num2stra(j2_civ2(j),nom_type_nc);
1397            end
1398            Param.Civ2.filename_nc1=filecell.nc.civ1{ifile,j};
1399            Param.Civ2.filename_nc1(end-2:end)=[]; % remove '.nc'
1400           
1401            % mask
1402            if Param.Civ2.CheckMask
1403                if ~exist(Param.Civ2.Mask,'file')
1404                    maskbase=[filecell.filebase '_' Param.Civ2.Mask]; %
1405                    nbslice_mask=str2double(Param.Civ2.Mask(1:end-4)); %
1406                    i1_mask=mod(i1_civ2(ifile)-1,nbslice_mask)+1;
1407                    [RootPathMask,RootFileMask]=fileparts(maskbase);
1408                    Param.Civ2.Mask=fullfile_uvmat(RootPathMask,[],RootFileMask,'.png','_1',i1_mask);
1409%                     Param.Civ2.Mask=name_generator(maskbase,i1_mask,1,'.png','_i');
1410                end
1411            end
1412            %grid
1413            if Param.Civ2.CheckGrid
1414                if numel(Param.Civ2.Grid)>=4 && isequal(Param.Civ2.Grid(end-3:end),'grid')
1415                    nbslice_grid=str2double(Param.Civ2.Grid(1:end-4)); %
1416                    if ~isnan(nbslice_grid)
1417                        i1_grid=mod(i1_civ2(ifile)-1,nbslice_grid)+1;
1418                        Param.Civ2.Grid=[filecell.filebase '_' fullfile_uvmat('','',gridname,'.grid','_1',i1_grid)];
1419%                         Param.Civ2.Grid=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')];
1420                    end
1421                end
1422            end
1423            form=imformats(regexprep(get(handles.ImaExt,'String'),'^.',''));%look for image formats
1424            if isempty(form)
1425                ImageInfo=get(VideoReader(filecell.ima1.civ2{1,1}));
1426                Param.Civ2.ImageBitDepth=ImageInfo.BitsPerPixel/3;
1427            else
1428                ImageInfo=imfinfo(filecell.ima1.civ2{1,1});%read the first image to get the size
1429                Param.Civ2.ImageBitDepth=ImageInfo.BitDepth;
1430            end
1431            Param.Civ2.ImageWidth=ImageInfo.Width;
1432            Param.Civ2.ImageHeight=ImageInfo.Height;
1433            Param.Civ2.i1=i1_civ2(ifile,j);
1434            Param.Civ2.i2=i2_civ2(ifile,j);
1435            switch CivMode
1436                case 'CivX'
1437                    cmd=[cmd...
1438                        cmd_civ2(filecell.nc.civ2{ifile,j},Param) '\n'];
1439                case 'CivAll'
1440                    CivAllCmd=[CivAllCmd ' civ2 '];
1441                    str=CIV2_CMD_Unified(filecell.nc.civ2{ifile,j},'',Param.Civ2);
1442                    fieldnames=fields(str);
1443                    [CivAllxml,uid_civ2]=add(CivAllxml,1,'element','civ2');
1444                    for ilist=1:length(fieldnames)
1445                        val=eval(['str.' fieldnames{ilist}]);
1446                        if ischar(val)
1447                            [CivAllxml,uid_t]=add(CivAllxml,uid_civ2,'element',fieldnames{ilist});
1448                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1449                        end
1450                    end
1451            end
1452        end
1453       
1454        % CheckFix2
1455        if Param.CheckFix2==1
1456            switch CivMode
1457                case 'CivX'
1458                    cmd=[cmd...
1459                        cmd_fix(filecell.nc.civ2{ifile,j},Param,'Fix2') '\n'];
1460                case 'CivAll'
1461                    fix2.inputFileName=filecell.nc.civ2{ifile,j} ;
1462                    fix2.fi1=num2str(flagindex2(1));
1463                    fix2.fi2=num2str(flagindex2(2));
1464                    fix2.fi3=num2str(flagindex2(3));
1465                    fix2.threshC=num2str(thresh_vec2C);
1466                    fix2.threshV=num2str(thresh_vel2);
1467                    fieldnames=fields(fix2);
1468                    [CivAllxml,uid_fix2]=add(CivAllxml,1,'element','fix2');
1469                    for ilist=1:length(fieldnames)
1470                        val=eval(['fix2.' fieldnames{ilist}]);
1471                        if ischar(val)
1472                            [CivAllxml,uid_t]=add(CivAllxml,uid_fix2,'element',fieldnames{ilist});
1473                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1474                        end
1475                    end
1476                    CivAllCmd=[CivAllCmd ' fix2 '];
1477            end
1478        end
1479       
1480        %CheckPatch2
1481        if Param.CheckPatch2==1
1482           
1483            switch CivMode
1484               
1485                case 'CivX'
1486                    cmd=[cmd...
1487                        cmd_patch(filecell.nc.civ1{ifile,j},Param,'Patch2') '\n'];
1488                   
1489                case 'CivAll'
1490                    patch2.inputFileName=filecell.nc.civ1{ifile,j} ;
1491                    patch2.nopt=subdomain_patch2;
1492                    patch2.maxdiff=thresh_patch2;
1493                    patch2.ro=rho_patch2;
1494                    test_grid=get(handles.get_gridpatch2,'Value');
1495                    if test_grid
1496                        patch2.gridflag='y';
1497                        gridname=get(handles.grid_patch2,'String');
1498                        if isequal(gridname(end-3:end),'grid')
1499                            nbslice_grid=str2double(gridname(1:end-4)); %
1500                            if ~isnan(nbslice_grid)
1501                                i1_grid=mod(i1_civ2(ifile)-1,nbslice_grid)+1;
1502                                patch2.gridPatch=[filecell.filebase '_' fullfile_uvmat('','',gridname,'.grid','_1',i1_grid)];
1503%                                 patch2.gridPatch=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')];
1504                                if ~exist(patch2.gridPatch,'file')
1505                                    errormsg='grid file absent for patch2';
1506                                    return
1507                                end
1508                            elseif exist(gridname,'file')
1509                                patch2.gridPatch=gridname;
1510                            else
1511                                errormsg='grid file absent for patch2';
1512                                return
1513                            end
1514                        end
1515                    else
1516                        patch2.gridPatch='none';
1517                        patch2.gridflag='n';
1518                        patch2.m=nx_patch2;
1519                        patch2.n=ny_patch2;
1520                    end
1521                    patch2.convectFlow='n';
1522                    fieldnames=fields(patch2);
1523                    [CivAllxml,uid_patch2]=add(CivAllxml,1,'element','patch2');
1524                    for ilist=1:length(fieldnames)
1525                        val=eval(['patch2.' fieldnames{ilist}]);
1526                        if ischar(val)
1527                            [CivAllxml,uid_t]=add(CivAllxml,uid_patch2,'element',fieldnames{ilist});
1528                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1529                        end
1530                    end
1531                    CivAllCmd=[CivAllCmd ' patch2 '];
1532            end
1533        end
1534       
1535        switch CivMode
1536           
1537            case {'CivX','CivAll'}
1538                if isequal(CivMode,'CivAll')
1539                    save(CivAllxml,[OutputFile '.xml']);
1540                    cmd=[cmd sparam.CivBin ' -f ' OutputFile '.xml '  CivAllCmd ' >' OutputFile '.log' '\n'];
1541                end             
1542                % create the .bat file used in run or batch
1543                filename_bat=[OutputFile '.bat'];
1544                [fid,message]=fopen(filename_bat,'w');
1545                if isequal(fid,-1)
1546                    errormsg=['creation of .bat file: ' message];
1547                    return
1548                end
1549                fprintf(fid,cmd);
1550                fclose(fid);           
1551                if isunix
1552                    system(['chmod +x ' filename_bat]);
1553                end             
1554                batch_file_list{length(batch_file_list)+1}=filename_bat;
1555               
1556            case 'Matlab'
1557                drawnow
1558                if ~strcmp(compare,'stereo PIV')
1559                    filename_xml=[OutputFile '.civ.xml'];
1560                    t=struct2xml(Param);           
1561                    save(t,filename_xml)
1562                    if batch   
1563                        path_civ=fileparts(which('civ'));
1564                        filename_bat=[OutputFile '.bat'];
1565                        [fid,message]=fopen(filename_bat,'w');
1566                        if isequal(fid,-1)
1567                            errormsg= ['creation of .bat file: ' message];
1568                            return
1569                        end
1570                        text_matlabscript=[...
1571                        '#!/bin/bash \n'...
1572                        '. /etc/sysprofile \n'...
1573                        'matlab -nodisplay -nosplash -nojvm <<END_MATLAB \n'...
1574                        'cd(''' path_civ '''); \n'...
1575                        'civ_matlab(''' filename_xml ''',''' OutputFile '.nc''); \n'...
1576                        'exit \n'...
1577                        'END_MATLAB \n'];
1578                        fprintf(fid,text_matlabscript);
1579                        fclose(fid);
1580                        if isunix
1581                            system(['chmod +x ' filename_bat]);
1582                        end
1583                        batch_file_list{length(batch_file_list)+1}=filename_bat;
1584                    else
1585                        [tild,errormsg]=civ_matlab(Param,filecell.nc.civ1{ifile,j});
1586                        if isempty(errormsg)
1587                            display([filecell.nc.civ1{ifile,j} ' written'])
1588                        end
1589                    end
1590                end
1591        end
1592    end
1593end
1594
1595if batch 
1596    switch batch_mode   
1597       
1598        case 'sge' %at the moment only psmn ENS Lyon uses it
1599            for p=1:length(batch_file_list)
1600                %cmd=['!qsub -p ' pvalue ' -q civ.q -e ' flname '.errors -o ' flname '.log' ' ' batch_file_list{p}];
1601                cmd=['!qsub -q piv1,piv2,piv3 '...
1602                    '-e ' regexprep(batch_file_list{p},'.bat','.errors') ' -o ' regexprep(batch_file_list{p},'.bat','.log ')...
1603                    ' -v ' 'LD_LIBRARY_PATH=/home/sjoubaud/matlab_sylvain/civx/lib ' batch_file_list{p}];               
1604                display(cmd);eval(cmd);
1605            end           
1606        case 'oar_old'
1607                for p=1:length(batch_file_list)
1608                    oar_command=['!oarsub -n CIVX -q nicejob '...
1609                   '-E ' regexprep(batch_file_list{p},'.bat','.errors') ' -O ' regexprep(batch_file_list{p},'.bat','.log ')...
1610                    '-l "/core=1+{type = ''smalljob''}/licence=1,walltime=00:60:00"   ' batch_file_list{p}];
1611                display(oar_command);eval(oar_command);
1612                end               
1613        case 'oar'
1614           
1615            oar_modes={'oar-dispatch','mpilauncher','oar-parexec'};
1616            text={'Batch processing on servcalcul3 LEGI';...
1617                'Please choose one of the followint modes';...
1618                '* oar-dispatch : jobs in a container of several cores';...
1619                '* mpilauncher : one single parallel mpi job using several cores';...
1620                '* oar-parexec (under development) ';...
1621                '**********************************'...
1622                };
1623            [S,v]=listdlg('PromptString',text,'ListString',oar_modes,...
1624                'SelectionMode','single','ListSize',[400 100],'Name','LEGI job mode');
1625            switch oar_modes{S}
1626                case 'oar-parexec' %oar-dispatch.pl
1627                    ncores=str2double(...
1628                        inputdlg('Number of cores (max 36)','oarsub parameter',1,{'12'})...
1629                        );
1630                    walltime_onejob=600;%seconds
1631                    filename_joblist=fullfile(Rootbat,'job_list.txt');
1632                    fid=fopen(filename_joblist,'w');
1633                    for p=1:length(batch_file_list)
1634                        fprintf(fid,[batch_file_list{p} '\n']);
1635                    end
1636                    fclose(fid)
1637                    oar_command=['oarsub -n test '...
1638                         '-l /core=' num2str(ncores) ','...
1639                        'walltime=' datestr(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,13) ' '...
1640                        '-E ' regexprep(filename_joblist,'\.txt\>','.errors') ' '...
1641                        '-O ' regexprep(filename_joblist,'\.txt\>','.log') ' '...
1642                        '"oar-parexec -f ' filename_joblist ' -l ' filename_joblist '.log"'];
1643                    filename_oarcommand=fullfile(Rootbat,'oar_command');
1644                    fid=fopen(filename_oarcommand,'w');
1645                    fprintf(fid,[oar_command '\n']);
1646                    fclose(fid);
1647                    display(oar_command);
1648                    eval(['! . ' filename_oarcommand])
1649                case 'oar-dispatch' %oar-dispatch.pl
1650                    ncores=str2double(...
1651                        inputdlg('Number of cores (max 36)','oarsub parameter',1,{'6'})...
1652                        );
1653                    walltime_onejob=600;%seconds
1654                    filename_joblist=fullfile(Rootbat,'job_list.txt');
1655                    fid=fopen(filename_joblist,'w');
1656                    for p=1:length(batch_file_list)
1657                        oar_command=['oarsub -n CIVX '...
1658                            '-E ' regexprep(batch_file_list{p},'\.bat\>','.errors') ' -O ' regexprep(batch_file_list{p},'\.bat\>','.log ')...
1659                            '-l "/core=1,walltime=' datestr(walltime_onejob/86400,13) '"   ' batch_file_list{p}];
1660                        fprintf(fid,[oar_command '\n']);
1661                    end
1662                    fclose(fid);
1663                    oar_command=['oarsub -t container -n civx-container '...
1664                        '-l /core=' num2str(ncores)...
1665                        ',walltime=' datestr(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,13) ' '...
1666                        '-E ' regexprep(filename_joblist,'\.txt\>','.errors') ' '...
1667                        '-O ' regexprep(filename_joblist,'\.txt\>','.log') ' '...
1668                        '"oar-dispatch -f ' filename_joblist '"'];
1669                    filename_oarcommand=fullfile(Rootbat,'oar_command');
1670                    fid=fopen(filename_oarcommand,'w');
1671                    fprintf(fid,[oar_command '\n']);
1672                    fclose(fid);
1673                    display(oar_command);
1674                    eval(['! . ' filename_oarcommand])
1675                case 'mpilauncher'
1676                    filename_joblist=fullfile(Rootbat,'job_list.txt');
1677                    fid=fopen(filename_joblist,'w');
1678                   
1679                    for p=1:length(batch_file_list)
1680                        fprintf(fid,[batch_file_list{p} '\n']);
1681                    end
1682                    fclose(fid)
1683                    text_oarscript=[...
1684                        '#!/bin/bash \n'...
1685                        '#OAR -n Mylauncher \n'...
1686                        '#OAR -l node=4/core=5,walltime=0:15:00 \n'...
1687                        '#OAR -E ' fullfile(Rootbat,'stderrfile.log') ' \n'...
1688                        '#OAR -O ' fullfile(Rootbat,'stdoutfile.log') ' \n'...
1689                        '# ========================================================= \n'...
1690                        '# This simple program launch a multinode parallel OpenMPI mpilauncher \n'...
1691                        '# application for coriolis PIV post-processing. \n'...
1692                        '# OAR uses oarshmost wrapper to propagate the user environement. \n'...
1693                        '# This wrapper assert that the user has the same environment on all the \n'...
1694                        '# allocated nodes (basic behavior needed by most MPI applications).  \n'...
1695                        '# \n'...
1696                        '# REQUIREMENT: \n'...
1697                        '# the oarshmost wrapper should be installed in $HOME/bin directory. \n'...
1698                        '# If a different location is used, change the line following the comment "Bidouille" \n'...
1699                        '# ========================================================= \n'...
1700                        '#   USER should only modify these 2 lines  \n'...
1701                        'WORKDIR=' pwd ' \n'...
1702                        'COMMANDE="mpilauncher  -f ' filename_joblist '" \n'...
1703                        '# ========================================================= \n'...
1704                        '# DO NOT MODIFY the FOLOWING LINES. (or be carefull) \n'...
1705                        'echo "job starting on: "`hostname` \n'...
1706                        'MPINODES="-host `tr [\\\\\\n] [,] <$OAR_NODEFILE |sed -e "s/,$/ /"`" \n'...
1707                        'NCPUS=`cat $OAR_NODEFILE |wc -l` \n'...
1708                        '#========== Bidouille ============== \n'...
1709                        'export OMPI_MCA_plm_rsh_agent=oar-envsh \n'...%                     'cd $WORKDIR \n'...
1710                        'CMD="mpirun -np $NCPUS -wdir $WORKDIR $MPINODES $COMMANDE" \n'...
1711                        'echo "I run: $CMD"  \n'...
1712                        '$CMD \n'...
1713                        'echo "job ending" \n'...
1714                        ];
1715                    %                 oarsub -S ./oar.sub
1716                    filename_oarscript=fullfile(Rootbat,'oar_command');
1717                    fid=fopen(filename_oarscript,'w');
1718                    fprintf(fid,[text_oarscript]);
1719                    fclose(fid);
1720                    eval(['!chmod +x  ' filename_oarscript]);
1721                    eval(['!oarsub -S ' filename_oarscript]);
1722            end
1723    end
1724else
1725    if ~isequal(CivMode,'Matlab')
1726        filename_superbat=fullfile(Rootbat,'job_list.bat');
1727        fid=fopen(filename_superbat,'w');
1728        if fid==-1
1729            msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat])
1730            return
1731        end
1732        for p=1:length(batch_file_list)
1733            if isunix
1734                fprintf(fid,['sh ' batch_file_list{p} '\n']);
1735            else
1736                fprintf(fid,['@call "' regexprep(batch_file_list{p},'\\','\\\\') '"' '\n']);
1737            end
1738        end
1739        fclose(fid);
1740        if(isunix)
1741            system(['chmod +x ' filename_superbat]);
1742        end
1743        system([filename_superbat ' &']);% execute main commmand
1744    end
1745end
1746
1747
1748%% save interface state
1749if isfield(filecell,'nc')
1750    if isfield(filecell.nc,'civ2')
1751        fileresu=filecell.nc.civ2{1,1};
1752    else
1753        fileresu=filecell.nc.civ1{1,1};
1754    end
1755end
1756[RootPath,SubDir,RootFile]=fileparts_uvmat(fileresu);
1757namedoc=fullfile(RootPath,SubDir,RootFile);
1758detect=1;
1759while detect==1
1760    namefigfull=[namedoc '.fig'];
1761    hh=dir(namefigfull);
1762    if ~isempty(hh)
1763        detect=1;
1764        namedoc=[namedoc '.0'];
1765    else
1766        detect=0;
1767    end
1768end
1769Param=rmfield(Param,'status');
1770Param=rmfield(Param,'xml');
1771t=struct2xml(Param);
1772t=set(t,1,'Name','CivDoc');% set the head label
1773save(t,[namedoc '.CivDoc.xml']); %save GUI  parameters as xml file
1774saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER  .xml)
1775
1776%Save info in personal profile (initiate browser next time) TODO
1777MenuFile={};
1778dir_perso=prefdir;
1779profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1780if exist(profil_perso,'file')
1781    hh=load (profil_perso);
1782      if isfield(hh,'MenuFile')
1783          MenuFile=hh.MenuFile;
1784      end
1785      if isfield(filecell.nc,'civ2')
1786          MenuFile=[filecell.nc.civ2{1,1}; MenuFile];
1787      else
1788           MenuFile=[filecell.nc.civ1{1,1}; MenuFile];
1789      end
1790      save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
1791else
1792    MenuFile=filecell.ima1.civ1(1,1);
1793    save (profil_perso,'MenuFile')
1794end
1795
1796%------------------------------------------------------------------------
1797% --- determine the list of reference indices of processing file
1798function [ref_i,ref_j,errormsg]=find_ref_indices(handles)
1799%------------------------------------------------------------------------
1800errormsg=''; %default error message
1801first_i=str2double(get(handles.first_i,'String'));%first index i
1802last_i=str2double(get(handles.last_i,'String'));%last index i
1803incr_i=str2double(get(handles.incr_i,'String'));% increment
1804if isequal(get(handles.first_j,'Visible'),'on')
1805    first_j=str2double(get(handles.first_j,'String'));%first index j
1806    last_j=str2double(get(handles.last_j,'String'));%last index j
1807    incr_j=str2double(get(handles.incr_j,'String'));% increment
1808else
1809    first_j=1;
1810    last_j=1;
1811    incr_j=1;
1812end
1813ref_i=first_i:incr_i:last_i;% list of i indices (reference values for each pair)
1814ref_j=first_j:incr_j:last_j;% list of j indices (reference values for each pair)
1815if isnan(first_i)||isnan(first_j)
1816    errormsg='first field number not defined';
1817elseif isnan(last_i)||isnan(last_j)
1818    errormsg='last field number not defined';
1819elseif isnan(incr_i)||isnan(incr_j)
1820    errormsg='increment in field number not defined';
1821elseif last_i < first_i || last_j < first_j
1822    errormsg='last field number must be larger than the first one';
1823end
1824
1825%------------------------------------------------------------------------
1826% --- determine the list of filenames and indices needed for launch_job
1827%------------------------------------------------------------------------
1828% OUTPUT:
1829% filecell: structure of cell arrays {ref_i,ref_j} containing all the filenames involved in the civ process
1830%    the indices ref_i and ref_j correspond to the list of reference indices
1831%       .filebase=fullfile(RootPath,RootFile) used to construct mask names, grid names, CivDoc xml file
1832%       .ima1.civ1,.ima1.civ2: first image for civ1 and civ2 respectively (possibly different)
1833%       .ima2.civ1,.ima2.civ2: second image for civ1 and civ2 respectively (possibly different)
1834%       .nc.civ1,.nc.civ2: netcdf files containing civ1 and civ2 data respectively (possibly different)
1835% i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2: arrays of files indices, needed for timing records
1836function [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]=...
1837    set_civ_filenames(handles,ref_i,ref_j,checkbox)
1838%------------------------------------------------------------------------
1839filecell=[];%default
1840ListProgram=get(handles.ListProgram,'String');
1841CivMode=ListProgram{get(handles.ListProgram,'Value')};%Program to use , CivX or Matlab
1842
1843%% get the root name and check dir
1844RootPath=get(handles.RootPath,'String');
1845RootFile=get(handles.RootFile,'String');
1846filecell.filebase=fullfile(RootPath,RootFile);
1847if isempty(filecell.filebase)
1848    msgbox_uvmat('ERROR','please open an image with the upper menu option Open/Browse...')
1849    return
1850end
1851if ~exist(RootPath,'dir')
1852    msgbox_uvmat('ERROR',['path to images ' RootPath ' not found'])
1853    return
1854end
1855[tild,message]=fileattrib(RootPath);
1856if ~isempty(message) && ~isequal(message.UserWrite,1)
1857    msgbox_uvmat('ERROR',['No writting access to ' RootPath])
1858    return
1859end
1860%check result directory
1861subdir_civ1=get(handles.SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf output data
1862subdir_civ2=get(handles.SubdirCiv2,'String');
1863if isequal(subdir_civ1,''),subdir_civ1='CIV'; end% put default subdir
1864if isequal(subdir_civ2,''),subdir_civ2=subdir_civ1; end% put default subdir
1865
1866%% choose root names depending on ListCompareMode =displacement, shift, PIV or stereo PIV
1867ListCompareMode=get(handles.ListCompareMode,'String');
1868compare=ListCompareMode{get(handles.ListCompareMode,'Value')};
1869
1870% set the nomenclature type of the nc files depending on the pair mode
1871if strcmp(compare,'displacement')||strcmp(compare,'shift')
1872    mode='displacement';
1873else
1874    mode_list=get(handles.ListPairMode,'String');
1875    mode_value=get(handles.ListPairMode,'Value');
1876    mode=mode_list{mode_value};
1877end
1878NomType_ima2=get(handles.NomType,'String');
1879NomType_nc=nomtype2pair(NomType_ima2,mode);
1880
1881% set the rootfile and image indexing
1882RootFile_ima2=get(handles.RootFile,'String');%root file for the second image series
1883ext_ima=get(handles.ImaExt,'String'); % image extension (the same for all images)
1884switch compare
1885    case 'PIV'
1886       RootFile_ima1=RootFile_ima2;% root name of the two image series is the same
1887       NomType_ima1=NomType_ima2;% the index of the first image follows the index of the second one
1888       RootFile_nc=RootFile_ima2;
1889    case 'displacement'
1890       RootFile_ima1=get(handles.RootFile_1,'String');% root name of the first image series set by handles.RootFile_1
1891       NomType_ima1='';% no indexing of the first image, a fixed reference for the whole series
1892       RootFile_nc=RootFile_ima2;
1893    case 'shift'
1894       RootFile_ima1=get(handles.RootFile_1,'String');% root name of the first image series set by handles.RootFile_1
1895       NomType_ima1=NomType_ima2;% the index of the first image follows the index of the second one
1896       RootFile_nc=[RootFile_ima1 '-' RootFile_ima2];
1897end
1898
1899%determine the list of file indices involved
1900[i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2]=...
1901    find_pair_indices(handles,ref_i,ref_j,mode);
1902
1903%determine the new filebase for 'displacement' ListPairMode (comparison of two series)
1904%filebase_B=filebase;% root name of the second field series for stereo
1905% filebase_A=filebase;%default
1906% if strcmp(compare,'PIV')
1907%     filebase_AB=filebase;
1908% else
1909%     [Path2,Name2]=fileparts(filebase_B);
1910%     Name1=RootFile_ima1;
1911%     filebase_AB=fullfile(Path2,[Name2 '-' Name1]);   
1912% end
1913% [RootPath_AB,RootFile_AB]=fileparts(filebase_AB);
1914% % [RootPath_ima1,RootFile_ima1]=fileparts(filebase_B);
1915% [RootPath_ima2,RootFile_ima2]=fileparts(filebase_B);
1916% [RootPath_nc,RootFile_nc]=fileparts(filebase_B);%default
1917% if strcmp(compare,'displacement')
1918% %     [RootPath_ima1,RootFile_ima1]=fileparts(filebase_B);
1919% %     [RootPath_ima2,RootFile_ima2]=fileparts(filebase_B);
1920%     [RootPath_nc,RootFile_nc]=fileparts(filebase_B);
1921% elseif strcmp(compare,'shift')
1922%     RootPath_nc=RootPath_AB;
1923%     RootFile_nc=RootFile_AB;
1924% end
1925% else
1926%     filebase_ima1=filebase_B;
1927%     filebase_ima2=filebase_B;
1928%     filebase_nc=filebase_B;
1929% [RootPath_ima1,RootFile_ima1]=fileparts(filebase_ima1);
1930% [RootPath_ima2,RootFile_ima2]=fileparts(filebase_ima2);
1931% [RootPath_nc,RootFile_nc]=fileparts(filebase_nc);
1932% [RootPath_A,RootFile_A]=fileparts(filebase_A);
1933
1934   
1935%% determine reference files for fix:
1936file_ref_fix1={};%default
1937file_ref_fix2={};
1938nbfield=length(i1_civ1);
1939nbslice=length(j1_civ1);
1940if checkbox(2)==1% fix1 performed
1941    ref=get(handles.ref_fix1,'UserData');%read data on the ref file stored by get_ref_fix1_Callback
1942    if ~isempty(ref)
1943        first_i=str2double(get(handles.first_i,'String'));
1944        last_i=str2double(get(handles.last_i,'String'));
1945        incr_i=str2double(get(handles.incr_i,'String'));
1946        first_j=str2double(get(handles.first_j,'String'));
1947        last_j=str2double(get(handles.last_j,'String'));
1948        incr_j=str2double(get(handles.incr_j,'String'));
1949        num_i_ref=first_i:incr_i:last_i;
1950        num_j_ref=first_j:incr_j:last_j;
1951        if isequal(mode,'displacement')
1952            num_i1=num_i_ref;
1953            num_i2=num_i_ref;
1954            num_j1=num_j_ref;
1955            num_j2=num_j_ref;
1956        elseif isequal(mode,'pair j1-j2')% isequal(mode,'st_pair j1-j2')
1957            num_i1=num_i_ref;
1958            num_i2=num_i1;
1959            num_j1=ref.num_a*ones(size(num_i_ref));
1960            num_j2=ref.num_b*ones(size(num_i_ref));
1961        elseif isequal(mode,'series(Di)') % isequal(mode,'st_series(Di)')
1962            delta1=floor((ref.num2-ref.num1)/2);
1963            delta2=ceil((ref.num2-ref.num1)/2);
1964            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
1965            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
1966            if isempty(ref.num_a)
1967                ref.num_a=1;
1968            end
1969            num_j1=ref.num_a*ones(size(num_i1));
1970            num_j2=num_j1;
1971        elseif isequal(mode,'series(Dj)')%| isequal(mode,'st_series(Dj)')
1972            delta1=floor((ref.num_b-ref.num_a)/2);
1973            delta2=ceil((ref.num_b-ref.num_a)/2);
1974            num_i1=ref.num1*ones(size(num_i_ref));
1975            num_i2=num_i1;
1976            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
1977            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
1978        end
1979        for ifile=1:nbfield
1980            for j=1:nbslice
1981                [RootPathRef,RootFile]=fileparts(ref.filebase);
1982                file_ref=fullfile_uvmat(RootPathRef,ref.subdir,RootFile,'.nc',ref.NomType,num_i1(ifile),num_i2(ifile),num_j1(j),num_j2(j));
1983                file_ref_fix1(ifile,j)={file_ref};
1984                if ~exist(file_ref,'file')
1985                    msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix1'])
1986                    filecell=[];
1987                    return
1988                end
1989            end
1990        end
1991    end
1992end
1993
1994%% determine reference files for fix2:
1995if checkbox(5)==1% fix2 performed
1996    ref=get(handles.ref_fix2,'UserData');
1997    if ~isempty(ref)
1998        first_i=str2double(get(handles.first_i,'String'));
1999        last_i=str2double(get(handles.last_i,'String'));
2000        incr_i=str2double(get(handles.incr_i,'String'));
2001        first_j=str2double(get(handles.first_j,'String'));
2002        last_j=str2double(get(handles.last_j,'String'));
2003        incr_j=str2double(get(handles.incr_j,'String'));
2004        num_i_ref=first_i:incr_i:last_i;
2005        num_j_ref=first_j:incr_j:last_j;
2006        if isequal(mode,'displacement')
2007            num_i1=num_i_ref;
2008            num_i2=num_i_ref;
2009            num_j1=num_j_ref;
2010            num_j2=num_j_ref;
2011        elseif isequal(mode,'pair j1-j2')
2012            num_i1=num_i_ref;
2013            num_i2=num_i1;
2014            num_j1=ref.num_a;
2015            num_j2=ref.num_b;
2016        elseif isequal(mode,'series(Di)')
2017            delta1=floor((ref.num2-ref.num1)/2);
2018            delta2=ceil((ref.num2-ref.num1)/2);
2019            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
2020            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
2021            num_j1=ref.num_a*ones(size(num_i1));
2022            num_j2=num_j1;
2023        elseif isequal(mode,'series(Dj)')
2024            delta1=floor((ref.num_b-ref.num_a)/2);
2025            delta2=ceil((ref.num_b-ref.num_a)/2);
2026            num_i1=ref.num1*ones(size(num_i_ref));
2027            num_i2=num_i1;
2028            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
2029            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
2030        end
2031        for ifile=1:nbfield
2032            for j=1:nbslice
2033                [RootPathRef,RootFile]=fileparts(ref.filebase);
2034                file_ref=fullfile_uvmat(RootPathRef,ref.subdir,RootFile,'.nc',ref.NomType,num_i1(ifile),num_i2(ifile),num_j1(j),num_j2(j));
2035                file_ref_fix2(ifile,j)={file_ref};
2036                if ~exist(file_ref,'file')
2037                    msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix2'])
2038                    filecell={};
2039                    return
2040                end
2041            end
2042        end
2043    end
2044end
2045
2046%% check the existence of the netcdf and image files involved
2047% %%%%%%%%%%%%  case CheckCiv1 activated   %%%%%%%%%%%%%
2048if checkbox(1)==1;
2049    detect=1;
2050    vers=0;
2051    subdir_civ1_new=subdir_civ1;
2052    while detect==1 %create a new subdir if the netcdf files already exist
2053        for ifile=1:nbfield
2054            for j=1:nbslice
2055                filename=fullfile_uvmat(RootPath,subdir_civ1_new,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
2056                detect=exist(filename,'file')==2;
2057                if detect% if a netcdf file already exists
2058                    indstr=regexp(subdir_civ1_new,'\D');
2059                    if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number
2060                        vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1;
2061                        subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)];
2062                    else
2063                        vers=vers+1;
2064                        subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) '_' num2str(vers)];       
2065                    end
2066                    subdir_civ2=subdir_civ1_new;
2067                    break
2068                end
2069                filecell.nc.civ1(ifile,j)={filename};
2070            end
2071            if detect% if a netcdf file already exists
2072                break
2073            end
2074        end
2075 
2076        %create the new SubdirCiv1
2077        if ~exist(fullfile(RootPath,subdir_civ1_new),'dir')     
2078            [xx,msg1]=mkdir(fullfile(RootPath,subdir_civ1_new));
2079
2080            if ~strcmp(msg1,'')
2081                msgbox_uvmat('ERROR',['cannot create ' subdir_civ1_new ': ' msg1])%error message for directory creation
2082                filecell={};
2083                return
2084            elseif isunix         
2085                [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g)
2086                if ~strcmp(msg2,'')
2087                    msgbox_uvmat('ERROR',['pb of permission for  ' fullfile(RootPath,subdir_civ1_new) ': ' msg2])%error message for directory creation
2088                    filecell={};
2089                    return
2090                end
2091            end
2092        end
2093        if strcmp(compare,'stereo PIV')&&(strcmp(mode,'pair j1-j2')||strcmp(mode,'series(Dj)')||strcmp(mode,'series(Di)'))%check second nc series
2094            for ifile=1:nbfield
2095                for j=1:nbslice
2096                     filename=fullfile_uvmat(RootPath,subdir_civ1_new,RootFile_A,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
2097                   % filename=name_generator(filebase_A,i1_civ1(ifile),j1_civ1(j),'.nc',NomType_nc,1,i2_civ1(ifile),j2_civ1(j),subdir_civ1_new);%
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 '_' num2str(vers)];
2107                       end
2108                       subdir_civ2=subdir_civ1;
2109                       break
2110                    end
2111                    filecell.ncA.civ1(ifile,j)={filename};
2112                end
2113                if detect% if a netcdf file already exists
2114                    break
2115                end
2116            end
2117            %create the new SubdirCiv1
2118            if ~exist(fullfile(RootPath,subdir_civ1_new),'dir')       
2119                [xx,msg1]=mkdir(fullfile(RootPath,subdir_civ1_new));
2120                if ~strcmp(msg1,'')
2121                    msgbox_uvmat('ERROR',['cannot create ' subdir_civ1_new ': ' msg1])
2122                    filecell={};
2123                    return
2124                else
2125                    [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g)
2126                    if ~strcmp(msg2,'')
2127                        msgbox_uvmat('ERROR',['pb of permission for ' subdir_civ1_new ': ' msg2])%error message for directory creation
2128                        filecell={};
2129                        return
2130                    end
2131                end
2132            end
2133        end
2134    end
2135    subdir_civ1=subdir_civ1_new;
2136    % get image names
2137    for ifile=1:nbfield
2138        for j=1:nbslice
2139             filename=fullfile_uvmat(RootPath,'',RootFile_ima1,ext_ima,NomType_ima1,i1_civ1(ifile),[],j1_civ1(j));
2140            idetect(j)=exist(filename,'file')==2;
2141            filecell.ima1.civ1(ifile,j)={filename}; %first image
2142            filename=fullfile_uvmat(RootPath,'',RootFile_ima2,ext_ima,NomType_ima2,i2_civ1(ifile),[],j2_civ1(j));
2143            idetect_1(j)=exist(filename,'file')==2;
2144            filecell.ima2.civ1(ifile,j)={filename};%second image
2145        end
2146        [idetectmin,indexj]=min(idetect);
2147        if idetectmin==0,
2148            msgbox_uvmat('ERROR',[filecell.ima1.civ1{ifile,indexj} ' not found'])
2149            filecell={};
2150            return
2151        end
2152        [idetectmin,indexj]=min(idetect_1);
2153        if idetectmin==0,
2154            msgbox_uvmat('ERROR',[filecell.ima2.civ1{ifile,indexj} ' not found'])
2155            filecell={};
2156            return
2157        end
2158    end
2159    if strcmp(compare,'stereo PIV') && (strcmp(mode,'pair j1-j2') || strcmp(mode,'series(Dj)') || strcmp(mode,'series(Di)'))
2160        for ifile=1:nbfield
2161            for j=1:nbslice
2162                filename=fullfile_uvmat(RootPath,'',RootFile_A,ext_ima,NomType_ima1,i1_civ1(ifile),[],j1_civ1(j));
2163                idetect(j)=exist(filename,'file')==2;
2164                filecell.imaA1.civ1(ifile,j)={filename} ;%first image
2165                filename=fullfile_uvmat(RootPath,'',RootFile_A,ext_ima,NomType_ima2,i2_civ1(ifile),[],j2_civ1(j));
2166                idetect_1(j)=exist(filename,'file')==2;
2167                filecell.imaA2.civ1(ifile,j)={filename};%second image
2168            end
2169            [idetectmin,indexj]=min(idetect);
2170            if idetectmin==0,
2171                msgbox_uvmat('ERROR',[filecell.imaA1.civ1{ifile,indexj} ' not found'])
2172                filecell={};
2173               % cd(currentdir)
2174                return
2175            end
2176            [idetectmin,indexj]=min(idetect_1);
2177            if idetectmin==0,
2178                msgbox_uvmat('ERROR',[filecell.imaA2.civ1{ifile,indexj} ' not found'])
2179                filecell={};
2180               % cd(currentdir)
2181                return
2182            end
2183        end
2184    end
2185   
2186    %%%%%%%%%%%%%  checkfix1 or checkpatch1 activated but no checkciv1   %%%%%%%%%%%%%
2187elseif (checkbox(2)==1 || checkbox(3)==1);
2188    for ifile=1:nbfield
2189        for j=1:nbslice
2190            filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
2191            detect=exist(filename,'file')==2;
2192            if detect==0
2193                msgbox_uvmat('ERROR',[filename ' not found'])
2194                filecell={};
2195               % cd(currentdir)
2196                return
2197            end
2198            filecell.nc.civ1(ifile,j)={filename};
2199        end
2200    end
2201    if strcmp(compare,'stereo PIV')
2202        for ifile=1:nbfield
2203            for j=1:nbslice
2204                filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_A,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
2205                filecell.ncA.civ1(ifile,j)={filename};
2206                if ~exist(filename,'file')
2207                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2208                    set(handles.RUN, 'Enable','On')
2209                    set(handles.RUN,'BackgroundColor',[1 0 0])
2210                    filecell={};
2211                    %cd(currentdir)
2212                    return
2213                end
2214            end
2215        end
2216    end
2217end
2218
2219%%%%%%%%%%%%%  if checkciv2 performed with pairs different than checkciv1  %%%%%%%%%%%%%
2220testdiff=0;
2221if (checkbox(4)==1)&&...
2222        ((get(handles.ListPairCiv1,'Value')~=get(handles.ListPairCiv2,'Value'))||~strcmp(subdir_civ2,subdir_civ1))
2223    testdiff=1;
2224    detect=1;
2225    vers=0;
2226    subdir_civ2_new=subdir_civ2;
2227    while detect==1 %create a new subdir if the netcdf files already exist
2228        for ifile=1:nbfield
2229            for j=1:nbslice
2230                filename=fullfile_uvmat(RootPath,subdir_civ2_new,RootFile_nc,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2231                detect=exist(filename,'file')==2;
2232                if detect% if a netcdf file already exists
2233                    indstr=regexp(subdir_civ2,'\D');
2234                    if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2235                        vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2236                        subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2237                    else
2238                        vers=vers+1;
2239                        subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2240                    end
2241                    break
2242                end
2243                filecell.nc.civ2(ifile,j)={filename};
2244            end
2245            if detect% if a netcdf file already exists
2246                break
2247            end
2248        end
2249        %create the new subdir_civ2_new
2250        if ~exist(fullfile(RootPath,subdir_civ2_new),'dir')
2251            [xx,m2]=mkdir(fullfile(RootPath,subdir_civ2_new));
2252            [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g)
2253            if ~isequal(m2,'')
2254                msgbox_uvmat('ERROR',['cannot create ' fullfile(RootPath,subdir_civ2_new) ': ' m2])
2255                filecell={};
2256                return
2257            end
2258        end
2259        if strcmp(compare,'stereo PIV')%check second nc series
2260            for ifile=1:nbfield
2261                for j=1:nbslice
2262                    filename=fullfile_uvmat(RootPath,subdir_civ2_new,RootFile_A,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2263                    detect=exist(filename,'file')==2;
2264                    if detect% if a netcdf file already exists
2265                        indstr=regexp(subdir_civ2,'\D');
2266                        if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2267                           vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2268                           subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2269                        else
2270                           vers=vers+1;
2271                           subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2272                        end
2273                        break
2274                    end
2275                    filecell.ncA.civ2(ifile,j)={filename};
2276                end
2277                if detect% if a netcdf file already exists
2278                    break
2279                end
2280            end
2281            subdir_civ2=subdir_civ2_new;
2282            %create the new SubdirCiv1
2283            if ~exist(fullfile(RootPath,subdir_civ2_new),'dir')
2284                [xx,m2]=mkdir(subdir_civ2_new);
2285                 [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g)
2286                if ~isequal(m2,'')
2287                    msgbox_uvmat('ERROR', ['cannot create ' fullfile(RootPath,subdir_civ2_new) ': ' m2])%error message for directory creation
2288                  %  cd(currentdir)
2289                    filecell={};
2290                    return
2291                end
2292            end
2293        end
2294    end
2295    subdir_civ2=subdir_civ2_new;
2296end
2297%cd(currentdir);%come back to the current working directory
2298
2299%%%%%%%%%%%%%  if checkciv2 results are obtained or used  %%%%%%%%%%%%%
2300if checkbox(4)==1 || checkbox(5)==1 || checkbox(6)==1 %civ2
2301    %check source netcdf file of checkciv1 estimates
2302    if checkbox(1)==0; %no civ1 performed
2303        for ifile=1:nbfield
2304            for j=1:nbslice
2305                filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));%
2306                filecell.nc.civ1(ifile,j)={filename};% name of the civ1 file
2307                if ~exist(filename,'file')
2308                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2309                    filecell={};
2310                    return
2311                end
2312                if ~testdiff % civ2 or patch2 are written in the same file as civ1
2313                    if checkbox(4)==0 ; %check the existence of civ2 if it is not calculated
2314                        Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2');
2315                        if isfield(Data,'Txt')
2316                            msgbox_uvmat('ERROR',Data.Txt);
2317                            return
2318                        elseif ~isempty(Data.CivStage)% case of new civ files
2319                            if Data.CivStage<4 %test for civ files
2320                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2321                            filecell=[];
2322                            return
2323                            end
2324                        elseif isempty(Data.civ2)||isequal(Data.civ2,0)
2325                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2326                            filecell=[];
2327                            return
2328                        end
2329                    elseif checkbox(3)==0; %check the existence of patch if it is not calculated
2330                        Data=nc2struct(filename,'ListGlobalAttribute','CivStage','patch');
2331                        if ~isempty(Data.CivStage)
2332                            if Data.CivStage<3 %test for civ files
2333                                msgbox_uvmat('ERROR',['no patch data in ' filename])
2334                                filecell=[];
2335                                return
2336                            end
2337                        elseif isempty(Data.patch)||isequal(Data.patch,0)
2338                            msgbox_uvmat('ERROR',['no patch data in ' filename])
2339                            filecell=[];
2340                            return
2341                        end
2342                    end
2343                end
2344            end
2345        end
2346        if strcmp(compare,'stereo PIV')
2347            for ifile=1:nbfield
2348                for j=1:nbslice
2349                    filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_A,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2350                    filecell.ncA.civ2(ifile,j)={filename};
2351                    if ~exist(filename,'file')
2352                        msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2353                        set(handles.RUN, 'Enable','On')
2354                        set(handles.RUN,'BackgroundColor',[1 0 0])
2355                        return
2356                    end
2357                end
2358            end
2359        end
2360    end
2361   
2362    detect=1;
2363    %     while detect==1%creates a new subdir if the netcdf files already contain checkciv2 data
2364    for ifile=1:nbfield
2365        for j=1:nbslice
2366            filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_nc,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2367            detect=exist(filename,'file')==2;
2368            filecell.nc.civ2(ifile,j)={filename};
2369        end
2370    end
2371    %get first image names for checkciv2
2372    if checkbox(1)==1 && isequal(i1_civ1,i1_civ2) && isequal(j1_civ1,j1_civ2)
2373        filecell.ima1.civ2=filecell.ima1.civ1;
2374    elseif checkbox(4)==1
2375        for ifile=1:nbfield
2376            for j=1:nbslice
2377                filename=fullfile_uvmat(RootPath,[],RootFile_ima1,ext_ima,NomType_ima1,i1_civ2(ifile),[],j1_civ2(j));
2378                idetect_2(j)=exist(filename,'file')==2;
2379                filecell.ima1.civ2(ifile,j)={filename};%first image
2380            end
2381            [idetectmin,indexj]=min(idetect_2);
2382            if idetectmin==0,
2383                msgbox_uvmat('ERROR',['input image ' filecell.ima1.civ2{ifile,indexj} ' not found'])
2384                filecell=[];
2385                return
2386            end
2387        end
2388    end
2389   
2390    %get second image names for checkciv2
2391    if checkbox(1)==1 && isequal(i2_civ1,i2_civ2) && isequal(j2_civ1,j2_civ2)
2392        filecell.ima2.civ2=filecell.ima2.civ1;
2393    elseif checkbox(4)==1
2394        for ifile=1:nbfield
2395            for j=1:nbslice
2396                filename=fullfile_uvmat(RootPath,[],RootFile_ima2,ext_ima,NomType_ima2,i2_civ2(ifile),[],j2_civ2(j));
2397                idetect_3(j)=exist(filename,'file')==2;
2398                filecell.ima2.civ2(ifile,j)={filename};%first image
2399            end
2400            [idetectmin,indexj]=min(idetect_3);
2401            if idetectmin==0,
2402                msgbox_uvmat('ERROR',['input image ' filecell.ima2.civ2{ifile,indexj} ' not found'])
2403                filecell=[];
2404                return
2405            end
2406        end
2407    end
2408end
2409if (checkbox(5) || checkbox(6)) && ~checkbox(4)  % need to read an existing netcdf civ2 file
2410    if ~testdiff
2411        filecell.nc.civ2=filecell.nc.civ1;% file already checked
2412    else     % check the civ2 files
2413        for ifile=1:nbfield
2414            for j=1:nbslice
2415                 filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_nc,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2416                filecell.nc.civ2(ifile,j)={filename};
2417                if ~exist(filename,'file')
2418                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2419                    filecell=[];
2420                    return
2421                else
2422                    Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2');
2423                    if ~isempty(Data.CivStage) && Data.CivStage<4 %test for civ files
2424                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2425                            filecell=[];
2426                            return
2427                    elseif isempty(Data.civ2)||isequal(Data.civ2,0)
2428                        msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2429                        filecell=[];
2430                        return
2431                    end
2432                end
2433            end
2434        end
2435    end
2436end
2437
2438%%%%%%%%%%%%%  if stereo fields are calculated by PATCH %%%%%%%%%%%%%
2439if strcmp(compare,'stereo PIV')
2440    if  checkbox(3) && isequal(get(handles.test_stereo1,'Value'),1)
2441        for ifile=1:nbfield
2442            for j=1:nbslice
2443                 filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_AB,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
2444                filecell.st(ifile,j)={filename};
2445            end
2446        end
2447    end
2448    if  checkbox(6) && isequal(get(handles.CheckStereo,'Value'),1)
2449        for ifile=1:nbfield
2450            for j=1:nbslice
2451                 filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_AB,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2452                filecell.st(ifile,j)={filename};
2453            end
2454        end
2455    end
2456end
2457set(handles.SubdirCiv1,'String',subdir_civ1);%update the edit box
2458set(handles.SubdirCiv2,'String',subdir_civ2);%update the edit box
2459
2460% For CivX COPY IMAGES TO THE FORMAT .png IF NEEDED
2461if strcmp(CivMode,'CivX')
2462    if isequal(NomType_ima1,'*')%case of movie files
2463        NomType_imanew1='_i';
2464    else
2465        NomType_imanew1=NomType_ima1;
2466    end
2467    if isequal(NomType_ima2,'*')%case of movie files
2468        NomType_imanew2='_i';
2469    else
2470        NomType_imanew2=NomType_ima2;
2471    end
2472    if ~isequal(ext_ima,'.png')
2473        %%type of image file
2474        type_ima1='none';%default
2475        movieobject1=[];%default
2476        if strcmpi(ext_ima,'.avi')
2477            if ~isempty(which('mmreader'))% if the mmreader function is found (recent version of matlab)
2478                type_ima1='movie';
2479                movieobject1=mmreader([filecell.filebase ext_ima]);
2480            else
2481                type_ima1='avi';
2482            end
2483        elseif ischar(ext_ima) && ~isempty(ext_ima(2:end))
2484            form=imformats(ext_ima(2:end));
2485            if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2486                if isequal(NomType_ima1,'*');
2487                    type_ima1='multimage';%image series in a single image file
2488                else
2489                    type_ima1='image';
2490                end
2491            end
2492        end
2493        type_ima2='none';%default
2494        movieobject2=[];
2495        if strcmpi(ext_ima,'.avi')
2496            if ~isempty(which('mmreader'))% if the mmreader function is found (recent version of matlab)
2497                type_ima2='movie';
2498                movieobject2=mmreader([filecell.filebase ext_ima]);
2499            else
2500                type_ima2='avi';
2501            end
2502        elseif ischar(ext_ima) && ~isempty(ext_ima(2:end))
2503            form=imformats(ext_ima(2:end));
2504            if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2505                if isequal(NomType_ima1,'*');
2506                    type_ima2='multimage';%image series in a single image file
2507                else
2508                    type_ima2='image';
2509                end
2510            end
2511        end
2512        if checkbox(1) %if civ1 is performed
2513            h = waitbar(0,'copy images to the .png format for civ1');% display a wait bar
2514            for ifile=1:nbfield
2515                waitbar(ifile/nbfield);
2516                for j=1:nbslice
2517                    filename=fullfile_uvmat(RootPath,[],RootFile_ima1,'.png',NomType_imanew1,i1_civ1(ifile),[],j1_civ1(j));
2518                    if ~exist(filename,'file')
2519                        A=read_image(filecell.ima1.civ1{ifile,j},type_ima1,i1_civ1(ifile),movieobject1);
2520                        imwrite(A,filename,'BitDepth',16);
2521                    end
2522                    filecell.ima1.civ1(ifile,j)={filename};
2523                    filename=fullfile_uvmat(RootPath,[],RootFile_ima2,'.png',NomType_imanew2,i2_civ1(ifile),[],j2_civ1(j));
2524                    if ~exist(filename,'file')
2525                        A=read_image(filecell.ima2.civ1{ifile,j},type_ima2,i2_civ1(ifile),movieobject2);
2526                        imwrite(A,filename,'BitDepth',16);
2527                    end
2528                    filecell.ima2.civ1(ifile,j)={filename};
2529                end
2530            end
2531            close(h)
2532        end
2533        if checkbox(4) %if civ2 is performed
2534            h = waitbar(0,'copy images to the .png format for civ2');% display a wait bar
2535            for ifile=1:nbfield
2536                waitbar(ifile/nbfield);
2537                for j=1:nbslice
2538                    filename=fullfile_uvmat(RootPath,[],RootFile_ima1,'.png',NomType_imanew1,i1_civ2(ifile),[],j1_civ2(j));
2539                    if ~exist(filename,'file')
2540                        A=read_image(cell2mat(filecell.ima1.civ2(ifile,j)),type_ima2,i1_civ2(ifile));
2541                        imwrite(A,filename,'BitDepth',16);
2542                    end
2543                    filecell.ima1.civ2(ifile,j)={filename};
2544                    filename=fullfile_uvmat(RootPath,[],RootFile_ima2,'.png',NomType_imanew2,i2_civ2(ifile),[],j2_civ2(j));
2545                    if ~exist(filename,'file')
2546                        A=read_image(cell2mat(filecell.ima2.civ2(ifile,j)),type_ima2,i2_civ2(ifile));
2547                        imwrite(A,filename,'BitDepth',16);
2548                    end
2549                    filecell.ima2.civ2(ifile,j)={filename};
2550                end
2551            end
2552            close(h);
2553        end
2554    end
2555end
2556
2557%------------------------------------------------------------------------
2558% --- determine the list of index pairs of processing file
2559function [num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=...
2560    find_pair_indices(handles,ref_i,ref_j,mode)
2561%------------------------------------------------------------------------
2562
2563list_civ1=get(handles.ListPairCiv1,'String');
2564index_civ1=get(handles.ListPairCiv1,'Value');
2565str_civ1=list_civ1{index_civ1};%string defining the image pairs for civ1
2566if isempty(str_civ1)||isequal(str_civ1,'')
2567    msgbox_uvmat('ERROR','no image pair selected for civ1')
2568    return
2569end
2570list_civ2=get(handles.ListPairCiv2,'String');
2571index_civ2=get(handles.ListPairCiv2,'Value');
2572if index_civ2>length(list_civ2)
2573    list_civ2=list_civ1;
2574    index_civ2=index_civ1;
2575end
2576str_civ2=list_civ2{index_civ2};%string defining the image pairs for civ2
2577
2578if isequal (mode,'series(Di)')
2579    lastfield=str2double(get(handles.nb_field,'String'));
2580    num1_civ1=ref_i-floor(index_civ1/2)*ones(size(ref_i));% set of first image numbers
2581    num2_civ1=ref_i+ceil(index_civ1/2)*ones(size(ref_i));
2582    num_a_civ1=ref_j;
2583    num_b_civ1=ref_j;
2584    num1_civ2=ref_i-floor(index_civ2/2)*ones(size(ref_i));
2585    num2_civ2=ref_i+ceil(index_civ2/2)*ones(size(ref_i));
2586    num_a_civ2=ref_j;
2587    num_b_civ2=ref_j;   
2588   
2589    % adjust the first and last field number
2590    lastfield=str2double(get(handles.nb_field,'String'));
2591    if isnan(lastfield)
2592        indsel=find((num1_civ1 >= 1)&(num1_civ2 >= 1));
2593    else
2594        indsel=find((num2_civ1 <= lastfield)&(num2_civ2 <= lastfield)&(num1_civ1 >= 1)&(num1_civ2 >= 1));
2595    end
2596    if length(indsel)>=1
2597        firstind=indsel(1);
2598        lastind=indsel(end);
2599        set(handles.first_i,'String',num2str(ref_i(firstind)))%update the display of first and last fields
2600        set(handles.last_i,'String',num2str(ref_i(lastind)))
2601        ref_i=ref_i(indsel);
2602        num1_civ1=num1_civ1(indsel);
2603        num1_civ2=num1_civ2(indsel);
2604        num2_civ1=num2_civ1(indsel);
2605        num2_civ2=num2_civ2(indsel);
2606    end
2607elseif isequal (mode,'series(Dj)')
2608    lastfield_j=str2double(get(handles.nb_field2,'String'));
2609    num1_civ1=ref_i;% set of first image numbers
2610    num2_civ1=ref_i;
2611    num_a_civ1=ref_j-floor(index_civ1/2)*ones(size(ref_j));
2612    num_b_civ1=ref_j+ceil(index_civ1/2)*ones(size(ref_j));
2613    num1_civ2=ref_i;
2614    num2_civ2=ref_i;
2615    num_a_civ2=ref_j-floor(index_civ2/2)*ones(size(ref_j));
2616    num_b_civ2=ref_j+ceil(index_civ2/2)*ones(size(ref_j));
2617    % adjust the first and last field number
2618    if isnan(lastfield_j)
2619        indsel=find((num_a_civ1 >= 1)&(num_a_civ2 >= 1));
2620    else
2621        indsel=find((num_b_civ1 <= lastfield_j)&(num_b_civ2 <= lastfield_j)&(num_a_civ1 >= 1)&(num_a_civ2 >= 1));
2622    end
2623    if length(indsel)>=1
2624        firstind=indsel(1);
2625        lastind=indsel(end);
2626        set(handles.first_j,'String',num2str(ref_j(firstind)))%update the display of first and last fields
2627        set(handles.last_j,'String',num2str(ref_j(lastind)))
2628        ref_j=ref_j(indsel);
2629        num_a_civ1=num_a_civ1(indsel);
2630        num_b_civ1=num_b_civ1(indsel);
2631        num_a_civ2=num_a_civ2(indsel);
2632        num_b_civ2=num_b_civ2(indsel);
2633    end
2634elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)
2635    displ_num=get(handles.ListPairCiv1,'UserData');
2636    num1_civ1=ref_i;
2637    num2_civ1=ref_i;
2638    num_a_civ1=displ_num(1,index_civ1);
2639    num_b_civ1=displ_num(2,index_civ1);
2640    num1_civ2=ref_i;
2641    num2_civ2=ref_i;
2642    num_a_civ2=displ_num(1,index_civ2);
2643    num_b_civ2=displ_num(2,index_civ2);
2644elseif isequal(mode,'displacement')
2645    num1_civ1=ref_i;
2646    num2_civ1=ref_i;
2647    num_a_civ1=ref_j;
2648    num_b_civ1=ref_j;
2649    num1_civ2=ref_i;
2650    num2_civ2=ref_i;
2651    num_a_civ2=ref_j;
2652    num_b_civ2=ref_j;
2653end
2654
2655%------------------------------------------------------------------------
2656% --- Executes on button press in ListCompareMode.
2657function ListCompareMode_Callback(hObject, eventdata, handles)
2658%------------------------------------------------------------------------
2659ListCompareMode=get(handles.ListCompareMode,'String');
2660option=ListCompareMode{get(handles.ListCompareMode,'Value')};
2661if ~strcmp(option,'PIV') % case 'displacement' or 'stereo PIV'
2662    filebase=get(handles.RootPath,'String');
2663    set(handles.sub_txt,'Visible','on')
2664    set(handles.RootFile_1,'Visible','On');%mkes the second file input window visible
2665    mode_store=get(handles.ListPairMode,'String');%get the present 'mode'
2666    set(handles.ListCompareMode,'UserData',mode_store);%store the mode display
2667    set(handles.ListPairMode,'Visible','off')
2668   
2669    %% open an image file with the browser
2670    ind_opening=1;%default
2671    browse.incr_pair=[0 0]; %default
2672    oldfile=get(handles.RootPath,'String');
2673    menu={'*.png;*.jpg;*.tif;*.avi;*.AVI;', ' (*.png,*.jpg ,.tif, *.avi,*.AVI)';
2674        '*.png','.png image files'; ...
2675        '*.jpg',' jpeg image files'; ...
2676        '*.tif','.tif image files'; ...
2677        '*.avi;*.AVI','.avi movie files'; ...
2678        '*.*',  'All Files (*.*)'};
2679    if strcmp(option,'displacement')
2680        comment='Pick the reference file for displacements';
2681    else
2682        comment='Pick a file of the second series';
2683    end
2684    [FileName, PathName] = uigetfile( menu, comment,oldfile);
2685    fileinput=[PathName FileName];%complete file name
2686    sizf=size(fileinput);
2687    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
2688    [path,name,ext]=fileparts(fileinput);
2689    [path1]=fileparts(filebase);
2690    if isunix
2691        [status,path]=system(['readlink ' path]);
2692        [status,path1]=system(['readlink ' path1]);% look for the true path in case of symbolic paths
2693    end
2694    if ~strcmp(path1,path)
2695        msgbox_uvmat('ERROR','The second image or series must be in the same directory as the first one')
2696        return
2697    end
2698    if strcmp(option,'displacement')
2699        [tild,RootFile_1]=fileparts(name);
2700    else
2701        [FilePath,FileName,Ext]=fileparts(fileinput);
2702% detect the file type, get the movie object if relevant, and look for the corresponding file series:
2703% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
2704[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]);
2705       
2706       % [tild,tild,RootFile_1,tild,tild,tild,tild,tild,nom_type_1]=fileparts_uvmat(fileinput);
2707        %[RootFile_1,i1_series,tild,j1_series,tild,nom_type_1,FileType,Object]=find_file_series(PathName,FileName);
2708        %check image nom type
2709        if ~strcmp(nom_type_1,get(handles.NomType,'String'))
2710        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')
2711        return
2712        end
2713    end   
2714    %check image  extension
2715    if ~strcmp(ext,get(handles.ImaExt,'String'))
2716        msgbox_uvmat('ERROR','The second image series must have the same extension name as the first one')
2717        return
2718    end
2719    set(handles.RootFile_1,'String',RootFile_1);
2720else
2721    set(handles.ListPairMode,'Visible','on')
2722    set(handles.RootFile_1,'Visible','Off');
2723    set(handles.sub_txt,'Visible','off')
2724    set(handles.RootFile_1,'String',[]);
2725    mode_store=get(handles.ListCompareMode,'UserData');
2726    set(handles.ListPairMode,'Value',1)
2727    set(handles.ListPairMode,'String',mode_store)
2728    set(handles.CheckStereo,'Value',0)
2729    set(handles.ListPairMode,'Value',1) % mode 'civX' selected by default
2730end
2731% if strcmp(option,'stereo PIV') && get(handles.CheckPatch1,'Value')
2732%     set(handles.CheckStereo,'Visible','on')
2733% else
2734%     set(handles.CheckStereo,'Visible','off')
2735% end
2736% if strcmp(option,'stereo PIV') && get(handles.CheckPatch2,'Value')
2737%     set(handles.CheckStereo,'Visible','on')
2738% else
2739%     set(handles.CheckStereo,'Visible','off')
2740% end
2741ListPairMode_Callback(hObject, eventdata, handles)
2742
2743
2744%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2745% Callbacks in the uipanel Pair Indices
2746%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2747%------------------------------------------------------------------------
2748% --- Executes on button press in ListPairMode.
2749function ListPairMode_Callback(hObject, eventdata, handles)
2750%------------------------------------------------------------------------
2751compare_list=get(handles.ListCompareMode,'String');
2752val=get(handles.ListCompareMode,'Value');
2753compare=compare_list{val};
2754if strcmp(compare,'displacement')||strcmp(compare,'shift')
2755    mode='displacement';
2756else
2757    mode_list=get(handles.ListPairMode,'String');
2758    if ischar(mode_list)
2759        mode_list={mode_list};
2760    end
2761    mode_value=get(handles.ListPairMode,'Value');
2762    mode=mode_list{mode_value};
2763end
2764displ_num=[];%default
2765ref_i=str2double(get(handles.ref_i,'String'));
2766% last_i=str2num(get(handles.last_i,'String'));
2767time=get(handles.ImaDoc,'UserData'); %get the set of times
2768TimeUnit=get(handles.TimeUnit,'String');
2769checkframe=strcmp(TimeUnit,'frame');
2770siztime=size(time);
2771nbfield=siztime(1)-1;
2772nbfield2=siztime(2)-1;
2773indchosen=1;  %%first pair selected by default
2774%displ_num used to define the indices of the civ pairs
2775% in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices
2776% are relative to the reference indices ref_i and ref_j respectively.
2777if isequal(mode,'pair j1-j2')%| isequal(mode,'st_pair j1-j2')
2778    dt=1;
2779    displ='';
2780    index=0;
2781    numlist_a=[];
2782    numlist_B=[];
2783    %get all the time intervals in bursts
2784    displ_dt=1;%default
2785    nbfield2=min(nbfield2,10);%limitate the number of pairs to 10x10
2786    for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'pair j1-j2' mode
2787        for numod_b=(numod_a+1):nbfield2
2788            index=index+1;
2789            numlist_a(index)=numod_a;
2790            numlist_b(index)=numod_b;
2791            if size(time,2)>1 && ~checkframe
2792                dt(numod_a,numod_b)=time(ref_i+1,numod_b+1)-time(ref_i+1,numod_a+1);%first time interval dt
2793                displ_dt(index)=dt(numod_a,numod_b);
2794            else
2795                displ_dt(index)=1;
2796            end
2797        end
2798    end
2799    [dtsort,indsort]=sort(displ_dt);
2800    if ~isempty(numlist_a)
2801        displ_num(1,:)=numlist_a(indsort);
2802        displ_num(2,:)=numlist_b(indsort);
2803    end
2804    displ_num(3,:)=0;
2805    displ_num(4,:)=0;
2806    enable_j(handles, 'off')
2807elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)')
2808    index=1:200;
2809    displ_num(1,index)=-floor(index/2);
2810    displ_num(2,index)=ceil(index/2);
2811    displ_num(3:4,index)=zeros(2,200);
2812    enable_j(handles, 'on')
2813elseif isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)')
2814    index=1:200;
2815    displ_num(1:2,index)=zeros(2,200);
2816    displ_num(3,index)=-floor(index/2);
2817    displ_num(4,index)=ceil(index/2);
2818    enable_i(handles, 'on')
2819    if nbfield2 > 1
2820        enable_j(handles, 'on')
2821    else
2822        enable_j(handles, 'off')
2823    end
2824elseif isequal(mode,'displacement')%the pairs have the same indices
2825    displ_num(1,1)=0;
2826    displ_num(2,1)=0;
2827    displ_num(3,1)=0;
2828    displ_num(4,1)=0;
2829    if nbfield > 1 || nbfield==0
2830        enable_i(handles, 'on')
2831    else
2832        enable_j(handles, 'off')
2833    end
2834    if nbfield2 > 1
2835        enable_j(handles, 'on')
2836    else
2837        enable_j(handles, 'off')
2838    end
2839end
2840set(handles.ListPairCiv1,'UserData',displ_num);
2841errormsg=find_netcpair_civ( handles,1);
2842    if ~isempty(errormsg)
2843    msgbox_uvmat('ERROR',errormsg)
2844    end
2845% find_netcpair_civ2(handles)
2846
2847function enable_i(handles, state)
2848set(handles.itext,'Visible',state)
2849set(handles.first_i,'Visible',state)
2850set(handles.last_i,'Visible',state)
2851set(handles.incr_i,'Visible',state)
2852set(handles.nb_field,'Visible',state)
2853set(handles.ref_i,'Visible',state)
2854
2855function enable_j(handles, state)
2856set(handles.jtext,'Visible',state)
2857set(handles.first_j,'Visible',state)
2858set(handles.last_j,'Visible',state)
2859set(handles.incr_j,'Visible',state)
2860set(handles.nb_field2,'Visible',state)
2861set(handles.ref_j,'Visible',state)
2862
2863
2864%------------------------------------------------------------------------
2865% --- Executes on selection change in ListPairCiv1.
2866function ListPairCiv1_Callback(hObject, eventdata, handles)
2867%------------------------------------------------------------------------
2868%reproduce by default the chosen pair in the checkciv2 menu
2869list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
2870index_pair=get(handles.ListPairCiv1,'Value');
2871displ_num=get(handles.ListPairCiv1,'UserData');
2872% num_a=displ_num(1,index_pair);
2873% num_b=displ_num(2,index_pair);
2874list_pair2=get(handles.ListPairCiv2,'String');%get the menu of image pairs
2875if index_pair<=length(list_pair2)
2876    set(handles.ListPairCiv2,'Value',index_pair);
2877end
2878
2879%update first_i and last_i according to the chosen image pairs
2880mode_list=get(handles.ListPairMode,'String');
2881mode_value=get(handles.ListPairMode,'Value');
2882mode=mode_list{mode_value};
2883if isequal(mode,'series(Di)')
2884    first_i=str2double(get(handles.first_i,'String'));
2885    last_i=str2double(get(handles.last_i,'String'));
2886    incr_i=str2double(get(handles.incr_i,'String'));
2887    num1=first_i:incr_i:last_i;
2888    lastfield=str2double(get(handles.nb_field,'String'));
2889    if ~isnan(lastfield)
2890        test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ...
2891            (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield);
2892        num1=num1(test_find);
2893    end
2894    set(handles.first_i,'String',num2str(num1(1)));
2895    set(handles.last_i,'String',num2str(num1(end)));
2896elseif isequal(mode,'series(Dj)')
2897    first_j=str2double(get(handles.first_j,'String'));
2898    last_j=str2double(get(handles.last_j,'String'));
2899    incr_j=str2double(get(handles.incr_j,'String'));
2900    num_j=first_j:incr_j:last_j;
2901    lastfield2=str2double(get(handles.nb_field2,'String'));
2902    if ~isnan(lastfield2)
2903        test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
2904            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2);
2905        num1=num_j(test_find);
2906    end
2907    set(handles.first_j,'String',num2str(num1(1)));
2908    set(handles.last_j,'String',num2str(num1(end)));
2909end
2910
2911%------------------------------------------------------------------------
2912% --- Executes on selection change in ListPairCiv2.
2913function ListPairCiv2_Callback(hObject, eventdata, handles)
2914%------------------------------------------------------------------------
2915index_pair=get(handles.ListPairCiv2,'Value');%get the selected position index in the menu
2916
2917%update first_i and last_i according to the chosen image pairs
2918mode_list=get(handles.ListPairMode,'String');
2919mode_value=get(handles.ListPairMode,'Value');
2920mode=mode_list{mode_value};
2921if isequal(mode,'series(Di)')
2922    first_i=str2double(get(handles.first_i,'String'));
2923    last_i=str2double(get(handles.last_i,'String'));
2924    incr_i=str2double(get(handles.incr_i,'String'));
2925    num1=first_i:incr_i:last_i;
2926    lastfield=str2double(get(handles.nb_field,'String'));
2927    if ~isnan(lastfield)
2928        test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ...
2929            (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield);
2930        num1=num1(test_find);
2931    end
2932    set(handles.first_i,'String',num2str(num1(1)));
2933    set(handles.last_i,'String',num2str(num1(end)));
2934elseif isequal(mode,'series(Dj)')
2935    first_j=str2double(get(handles.first_j,'String'));
2936    last_j=str2double(get(handles.last_j,'String'));
2937    incr_j=str2double(get(handles.incr_j,'String'));
2938    num_j=first_j:incr_j:last_j;
2939    lastfield2=str2double(get(handles.nb_field2,'String'));
2940    if ~isnan(lastfield2)
2941        test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
2942            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2);
2943        num1=num_j(test_find);
2944    end
2945    set(handles.first_j,'String',num2str(num1(1)));
2946    set(handles.last_j,'String',num2str(num1(end)));
2947end
2948
2949%------------------------------------------------------------------------
2950function ref_i_Callback(hObject, eventdata, handles)
2951%------------------------------------------------------------------------
2952mode_list=get(handles.ListPairMode,'String');
2953mode_value=get(handles.ListPairMode,'Value');
2954mode=mode_list{mode_value};
2955errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files
2956if isequal(mode,'series(Di)') || ...% we do patch2 only
2957        (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
2958    errormsg=find_netcpair_civ( handles,2);
2959end
2960    if ~isempty(errormsg)
2961    msgbox_uvmat('ERROR',errormsg)
2962    end
2963
2964%------------------------------------------------------------------------
2965function ref_j_Callback(hObject, eventdata, handles)
2966%------------------------------------------------------------------------
2967mode_list=get(handles.ListPairMode,'String');
2968mode_value=get(handles.ListPairMode,'Value');
2969mode=mode_list{mode_value};
2970if isequal(get(handles.CheckCiv1,'Value'),0)|| isequal(mode,'series(Dj)')
2971    errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files
2972end
2973if isequal(mode,'series(Dj)') || ...
2974        (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
2975    errormsg=find_netcpair_civ(handles,2);
2976end
2977    if ~isempty(errormsg)
2978    msgbox_uvmat('ERROR',errormsg)
2979    end
2980
2981%------------------------------------------------------------------------
2982% determine the menu for checkciv1 pairs depending on existing netcdf file at the middle of
2983% the field series set by first_i, incr, last_i
2984% index=1: look for pairs for civ1
2985% index=2: look for pairs for civ2
2986function errormsg=find_netcpair_civ(handles,index)
2987%------------------------------------------------------------------------
2988set(gcf,'Pointer','watch')% set the mouse pointer to 'watch' (clock)
2989
2990%% initialisation
2991errormsg='';
2992browse=get(handles.RootPath,'UserData');
2993compare_list=get(handles.ListCompareMode,'String');
2994val=get(handles.ListCompareMode,'Value');
2995compare=compare_list{val};
2996if strcmp(compare,'displacement')||strcmp(compare,'shift')
2997    mode='displacement';
2998else
2999    mode_list=get(handles.ListPairMode,'String');
3000    mode_value=get(handles.ListPairMode,'Value');
3001    if isempty(mode_list)
3002        return
3003    end
3004    mode=mode_list{mode_value};
3005end
3006nom_type_ima=get(handles.NomType,'String');
3007
3008%% determine nom_type_nc, nomenclature type of the .nc files:
3009[nom_type_nc]=nomtype2pair(nom_type_ima,mode);
3010
3011%% reads .nc subdirectoy and image numbers from the interface
3012subdir_civ1=get(handles.SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf data
3013subdir_civ2=get(handles.SubdirCiv2,'String');%subdirectory subdir_civ2 for the netcdf data
3014ref_i=str2double(get(handles.ref_i,'String'));
3015if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
3016    ref_j=0;
3017else
3018    ref_j=str2double(get(handles.ref_j,'String'));
3019end
3020time=get(handles.ImaDoc,'UserData');%get the set of times
3021TimeUnit=get(handles.TimeUnit,'String');
3022checkframe=strcmp(TimeUnit,'frame');
3023displ_num=get(handles.ListPairCiv1,'UserData');
3024
3025%% eliminate the first pairs inconsistent with the position
3026if isempty(displ_num)
3027    nbpair=0;
3028else
3029    nbpair=length(displ_num(1,:));%nbre of displayed pairs
3030    if  isequal(mode,'series(Di)')  %| isequal(mode,'st_series(Di)')
3031        nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index
3032    elseif  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
3033        nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index
3034    end
3035end
3036nbpair=min(200,nbpair);%limit the number of displayed pairs to 200
3037
3038%% case with no Civ1 operation, netcdf files need to exist for reading
3039displ_pair={''};
3040select=ones(size(1:nbpair));%flag for displayed pairs =1 for display
3041testpair=0;
3042RootPath=get(handles.RootPath,'String');
3043RootFile=get(handles.RootFile,'String');
3044if index==1 % case civ1
3045    if ~get(handles.CheckCiv1,'Value') %
3046        if ~exist(fullfile(RootPath,subdir_civ1),'dir')
3047            errormsg=['no civ1 file available: subdirectory ' subdir_civ1 ' does not exist'];
3048            set(handles.ListPairCiv1,'String',{});
3049            return
3050        end
3051        for ipair=1:nbpair
3052            filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,...
3053                ref_i+displ_num(3,ipair),ref_i+displ_num(4,ipair),ref_j+displ_num(1,ipair),ref_j+displ_num(2,ipair));
3054            select(ipair)=exist(filename,'file')==2;% put flag to 0 if the file does not exist
3055        end
3056        % case of no displayed pair
3057        if isequal(select,zeros(size(1:nbpair)))
3058            if isfield(browse,'incr_pair') && ~isequal(browse.incr_pair,[0 0])
3059                num_i1=ref_i-floor(browse.incr_pair(1)/2);
3060                num_i2=ref_i+ceil(browse.incr_pair(1)/2);
3061                num_j1=ref_j-floor(browse.incr_pair(2)/2);
3062                num_j2=ref_j+ceil(browse.incr_pair(2)/2);
3063                filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,num_i1,num_i2,num_j1,num_j2);
3064                select(1)=exist(filename,'file')==2;
3065                testpair=1;
3066            else
3067                if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
3068                    errormsg=['no civ1 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ1];
3069                else
3070                    errormsg=['no civ1 file available for the selected reference indices (i,j)= ' num2str(ref_i) ', ' num2str(ref_j) ' and subdirectory ' subdir_civ1];
3071                end
3072                set(handles.ListPairCiv1,'String',{''});
3073                %COMPLETER CAS STEREO
3074                return
3075            end
3076        end
3077    end
3078else %case civ2 alone
3079    if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
3080        if ~exist(fullfile(RootPath,subdir_civ2,ext_dir),'dir')
3081            errordlg(['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist'])
3082            set(handles.ListPairCiv2,'Value',1);
3083            set(handles.ListPairCiv2,'String',{''});
3084            return
3085        end
3086        for ipair=1:nbpair
3087            filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,...
3088                ref_i+displ_num(3,ipair),ref_i+displ_num(4,ipair),ref_j+displ_num(1,ipair),ref_j+displ_num(2,ipair));
3089            select(ipair)=exist(filename,'file')==2;
3090        end
3091        if  isequal(select,zeros(size(1:nbpair)))
3092            if isfield(browse,'incr_pair')
3093                num_i1=ref_i-floor(browse.incr_pair(1)/2);
3094                num_i2=ref_i+floor((browse.incr_pair(1)+1)/2);
3095                num_j1=ref_j-floor(browse.incr_pair(2)/2);
3096                num_j2=ref_j+floor((browse.incr_pair(2)+1)/2);
3097                filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile,'.nc',nom_type_nc,num_i1,num_i2,num_j1,num_j2);
3098                select(1)=exist(filename,'file')==2;
3099            else
3100                if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
3101                    errormsg=['no civ2 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ2];
3102                else
3103                    errormsg=['no civ2 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ2];
3104                end
3105                set(handles.ListPairCiv2,'Value',1);
3106                set(handles.ListPairCiv2,'String',{''});
3107                return
3108            end
3109        end
3110    end
3111end
3112
3113%% determine the menu display in .ListPairCiv1
3114% the menu depends on the mode defined in ListPairMode_callback through the array displ_num:
3115% displ_num(1,:)=indices j1
3116% displ_num(2,:)=indices j2
3117% displ_num(3,:)=indices i1
3118% displ_num(4,:)=indices i2
3119% in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices
3120% are relative to the reference indices ref_i and ref_j respectively.
3121if isequal(mode,'series(Di)')
3122    if testpair
3123        displ_pair{1}=['Di= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
3124    else
3125        for ipair=1:nbpair
3126            if select(ipair)
3127                displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
3128                %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
3129                 %   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
3130               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
3131                 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
3132                else
3133                    dt=1;
3134                end
3135                 displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
3136            else
3137                displ_pair{ipair}='...'; %pair not displayed in the menu
3138            end
3139        end
3140    end
3141elseif isequal(mode,'series(Dj)')
3142    if testpair
3143        displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
3144    else
3145        for ipair=1:nbpair
3146            if select(ipair)
3147                displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
3148                if ~checkframe && size(time,1)>=ref_i+1+displ_num(4,ipair) && size(time,2)>=ref_j+1+displ_num(2,ipair)
3149                    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
3150                    displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
3151                end
3152            else
3153                displ_pair{ipair}='...'; %pair not displayed in the menu
3154            end
3155        end
3156    end
3157elseif isequal(mode,'pair j1-j2')%case of pairs
3158    for ipair=1:nbpair
3159        if select(ipair)
3160            if ~checkframe && size(time,2)>1
3161            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
3162            else % time set by default to i index
3163                dt=1;
3164            end
3165            displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ...
3166                ' :dt= ' num2str(dt*1000)];
3167        else
3168            displ_pair{ipair}='...'; %pair not displayed in the menu
3169        end
3170    end
3171elseif isequal(mode,'displacement')
3172    displ_pair={'Di=Dj=0'};
3173end
3174if index==1
3175set(handles.ListPairCiv1,'String',displ_pair');
3176end
3177
3178%% determine the default selection in the pair menu
3179ichoice=find(select,1);% index of selected pair
3180if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
3181initial=get(handles.ListPairCiv1,'Value');%initial choice of pair
3182if initial>nbpair || (numel(select)>=initial && ~isequal(select(initial),1))
3183    set(handles.ListPairCiv1,'Value',ichoice);% first valid pair proposed by default in the menu
3184end
3185initial=get(handles.ListPairCiv2,'Value');
3186if initial>length(displ_pair')%|~isequal(select(initial),1)
3187    if ichoice <= length(displ_pair')
3188        set(handles.ListPairCiv2,'Value',ichoice);% same pair proposed by default for civ2
3189    else
3190        set(handles.ListPairCiv2,'Value',1);% same pair proposed by default for civ2
3191    end
3192end
3193set(handles.ListPairCiv2,'String',displ_pair');
3194set(gcf,'Pointer','arrow')
3195
3196%-------------------------------------------------------------------
3197% ---
3198function closeview_field(gcbo,eventdata)
3199hview_field=findobj(allchild(0),'tag','view_field');% look for view_field   
3200    if ~isempty(hview_field)
3201        delete(hview_field)
3202    end
3203   
3204   
3205%------------------------------------------------------------------------   
3206% call 'view_field.fig' to display the  field selected in the list of 'status'
3207function open_view_field(hObject, eventdata)
3208%------------------------------------------------------------------------
3209list=get(hObject,'String');
3210index=get(hObject,'Value');
3211rootroot=get(hObject,'UserData');
3212filename=list{index};
3213ind_dot=strfind(filename,'...');
3214filename=filename(1:ind_dot-1);
3215filename=fullfile(rootroot,filename);
3216delete(get(hObject,'parent'))%delete the display figure to stop the check process
3217if exist(filename,'file')%visualise the vel field if it exists
3218    uvmat(filename)
3219    set(gcbo,'Value',1)
3220end
3221
3222%------------------------------------------------------------------------   
3223% launched by pressing OK on the status figure
3224function close_GUI(hObject, eventdata)
3225%------------------------------------------------------------------------
3226    delete(gcbf)
3227   
3228%------------------------------------------------------------------------   
3229% launched by deleting the status figure
3230function stop_status(hObject, eventdata)
3231%------------------------------------------------------------------------
3232hciv=findobj(allchild(0),'tag','civ');
3233hhciv=guidata(hciv);
3234set(hhciv.status,'value',0) %reset the status uicontrol in the GUI civ
3235set(hhciv.status,'BackgroundColor',[0 1 0])
3236
3237
3238%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3239% Callbacks in the uipanel Reference Indices
3240%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3241%------------------------------------------------------------------------
3242function first_i_Callback(hObject, eventdata, handles)
3243%------------------------------------------------------------------------
3244first_i=str2double(get(handles.first_i,'String'));
3245set(handles.ref_i,'String', num2str(first_i))% reference index for pair dt = first index
3246ref_i_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
3247
3248%------------------------------------------------------------------------
3249function first_j_Callback(hObject, eventdata, handles)
3250%------------------------------------------------------------------------
3251first_j=str2num(get(handles.first_j,'String'));
3252set(handles.ref_j,'String', num2str(first_j))% reference index for pair dt = first index
3253ref_j_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
3254
3255%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3256% Callbacks in the uipanel Civ1
3257%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3258%------------------------------------------------------------------------
3259% --- Executes on button press in SearchRange: determine the search range num_Searchx,num_Searchy
3260function SearchRange_Callback(hObject, eventdata, handles)
3261%------------------------------------------------------------------------
3262%determine pair numbers
3263if strcmp(get(handles.umin,'Visible'),'off')
3264    set(handles.u_title,'Visible','on')
3265    set(handles.v_title,'Visible','on')
3266    set(handles.umin,'Visible','on')
3267    set(handles.umax,'Visible','on')
3268    set(handles.vmin,'Visible','on')
3269    set(handles.vmax,'Visible','on')
3270    set(handles.CoordUnit,'Visible','on')
3271    set(handles.TimeUnit,'Visible','on')
3272    set(handles.slash_title,'Visible','on')
3273    set(handles.min_title,'Visible','on')
3274    set(handles.max_title,'Visible','on')
3275    set(handles.unit_title,'Visible','on')
3276else
3277    get_search_range(hObject, eventdata, handles)
3278end
3279
3280%------------------------------------------------------------------------
3281% ---  determine the search range num_Searchx,num_Searchy and shift
3282function get_search_range(hObject, eventdata, handles)
3283umin=str2double(get(handles.umin,'String'));
3284umax=str2double(get(handles.umax,'String'));
3285vmin=str2double(get(handles.umin,'String'));
3286vmax=str2double(get(handles.vmax,'String'));
3287%switch min_title and max_title in case of error
3288if umax<=umin
3289    umin_old=umin;
3290    umin=umax;
3291    umax=umin_old;
3292    set(handles.umin,'String', num2str(umin))
3293    set(handles.umax,'String', num2str(umax))
3294end
3295if vmax<=vmin
3296    vmin_old=vmin;
3297    vmin=vmax;
3298    vmax=vmin_old;
3299    set(handles.vmin,'String', num2str(vmin))
3300    set(handles.vmax,'String', num2str(vmax))
3301end   
3302if ~(isnan(umin)||isnan(umax)||isnan(vmin)||isnan(vmax))
3303    list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
3304    index=get(handles.ListPairCiv1,'Value');
3305    displ_num=get(handles.ListPairCiv1,'UserData');
3306    time=get(handles.ImaDoc,'UserData'); %get the set of times
3307    pxcm_xy=get(handles.SearchRange,'UserData');
3308    pxcmx=pxcm_xy(1);
3309    pxcmy=pxcm_xy(2);
3310    mode_list=get(handles.ListPairMode,'String');
3311    mode_value=get(handles.ListPairMode,'Value');
3312    mode=mode_list{mode_value};
3313    if isequal (mode, 'series(Di)' )
3314        ref_i=str2double(get(handles.ref_i,'String'));
3315        num1=ref_i-floor(index/2);%  first image numbers
3316        num2=ref_i+ceil(index/2);
3317        num_a=1;
3318        num_b=1;
3319    elseif isequal (mode, 'series(Dj)')
3320        num1=1;
3321        num2=1;
3322        ref_j=str2double(get(handles.ref_j,'String'));
3323        num_a=ref_j-floor(index/2);%  first image numbers
3324        num_b=ref_j+ceil(index/2);
3325    elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)
3326        ref_i=str2double(get(handles.ref_i,'String'));
3327        num1=ref_i;
3328        num2=ref_i;
3329        num_a=displ_num(1,index);
3330        num_b=displ_num(2,index);
3331    end
3332    dt=time(num2,num_b)-time(num1,num_a);
3333    ibx=str2double(get(handles.num_Bx,'String'));
3334    iby=str2double(get(handles.num_By,'String'));
3335    umin=dt*pxcmx*umin;
3336    umax=dt*pxcmx*umax;
3337    vmin=dt*pxcmy*vmin;
3338    vmax=dt*pxcmy*vmax;
3339    shiftx=round((umin+umax)/2);
3340    shifty=round((vmin+vmax)/2);
3341    isx=(umax+2-shiftx)*2+ibx;
3342    isx=2*ceil(isx/2)+1;
3343    isy=(vmax+2-shifty)*2+iby;
3344    isy=2*ceil(isy/2)+1;
3345    set(handles.num_Shiftx,'String',num2str(shiftx));
3346    set(handles.num_Shifty,'String',num2str(shifty));
3347    set(handles.num_Searchx,'String',num2str(isx));
3348    set(handles.num_Searchy,'String',num2str(isy));
3349end
3350
3351%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3352% Callbacks in the uipanel Fix1
3353%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3354%------------------------------------------------------------------------
3355% --- Executes on button press in CheckMask.
3356function get_mask_fix1_Callback(hObject, eventdata, handles)
3357%------------------------------------------------------------------------
3358maskval=get(handles.CheckMask,'Value');
3359if isequal(maskval,0)
3360    set(handles.Mask,'String','')
3361else
3362    mask_displ='no mask'; %default
3363    filebase=get(handles.RootPath,'String');
3364    [nbslice, flag_mask]=get_mask(filebase,handles);
3365    if isequal(flag_mask,1)
3366        mask_displ=[num2str(nbslice) 'mask'];
3367    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3368        filebase_a=get(handles.RootFile_1,'String');
3369        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3370        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3371            mask_displ='no mask';
3372        end
3373    end
3374    if isequal(mask_displ,'no mask')
3375        [FileName, PathName, filterindex] = uigetfile( ...
3376            {'*.png', ' (*.png)';
3377            '*.png',  '.png files '; ...
3378            '*.*', 'All Files (*.*)'}, ...
3379            'Pick a mask file *.png',filebase);
3380        mask_displ=fullfile(PathName,FileName);
3381        if ~exist(mask_displ,'file')
3382            mask_displ='no mask';
3383        end
3384    end
3385    if isequal(mask_displ,'no mask')
3386        set(handles.CheckMask,'Value',0)
3387        set(handles.CheckMask,'Value',0)
3388        set(handles.CheckMask,'Value',0)
3389    else
3390        %set(handles.CheckMask,'Value',1)
3391        set(handles.CheckMask,'Value',1)
3392    end
3393    set(handles.Mask,'String',mask_displ)
3394    set(handles.Mask,'String',mask_displ)
3395    set(handles.Mask,'String',mask_displ)
3396end
3397
3398%------------------------------------------------------------------------
3399% --- Executes on button press in CheckMask: select box for mask option
3400function get_mask_civ2_Callback(hObject, eventdata, handles)
3401%------------------------------------------------------------------------
3402maskval=get(handles.CheckMask,'Value');
3403if isequal(maskval,0)
3404    set(handles.Mask,'String','')
3405else
3406    mask_displ='no mask'; %default
3407    filebase=get(handles.RootPath,'String');
3408    [nbslice, flag_mask]=get_mask(filebase,handles);
3409    if isequal(flag_mask,1)
3410        mask_displ=[num2str(nbslice) 'mask'];
3411    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3412        filebase_a=get(handles.RootFile_1,'String');
3413        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3414        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3415            mask_displ='no mask';
3416        end
3417    end
3418    if isequal(mask_displ,'no mask')
3419        [FileName, PathName, filterindex] = uigetfile( ...
3420            {'*.png', ' (*.png)';
3421            '*.png',  '.png files '; ...
3422            '*.*', 'All Files (*.*)'}, ...
3423            'Pick a mask file *.png',filebase);
3424        mask_displ=fullfile(PathName,FileName);
3425        if ~exist(mask_displ,'file')
3426            mask_displ='no mask';
3427        end
3428    end
3429    if isequal(mask_displ,'no mask')
3430        set(handles.CheckMask,'Value',0)
3431        set(handles.CheckMask,'Value',0)
3432    else
3433        set(handles.CheckMask,'Value',1)
3434    end
3435    set(handles.Mask,'String',mask_displ)
3436    set(handles.Mask,'String',mask_displ)
3437end
3438
3439%------------------------------------------------------------------------
3440% --- Executes on button press in CheckMask.
3441function get_mask_fix2_Callback(hObject, eventdata, handles)
3442%------------------------------------------------------------------------
3443maskval=get(handles.CheckMask,'Value');
3444if isequal(maskval,0)
3445    set(handles.Mask,'String','')
3446else
3447    mask_displ='no mask'; %default
3448    filebase=get(handles.RootPath,'String');
3449    [nbslice, flag_mask]=get_mask(filebase,handles);
3450    if isequal(flag_mask,1)
3451        mask_displ=[num2str(nbslice) 'mask'];
3452    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3453        filebase_a=get(handles.RootFile_1,'String');
3454        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3455        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3456            mask_displ='no mask';
3457        end
3458    end
3459    if isequal(mask_displ,'no mask')
3460        [FileName, PathName, filterindex] = uigetfile( ...
3461            {'*.png', ' (*.png)';
3462            '*.png',  '.png files '; ...
3463            '*.*', 'All Files (*.*)'}, ...
3464            'Pick a mask file *.png',filebase);
3465        mask_displ=fullfile(PathName,FileName);
3466        if ~exist(mask_displ,'file')
3467            mask_displ='no mask';
3468        end
3469    end
3470    if isequal(mask_displ,'no mask')
3471        set(handles.CheckMask,'Value',0)
3472    end
3473    set(handles.Mask,'String',mask_displ)
3474end
3475
3476%------------------------------------------------------------------------
3477% --- function called to look for mask files
3478function [nbslice, flag_mask]=get_mask(filebase,handles)
3479%------------------------------------------------------------------------
3480%detect mask files, images with appropriate file base
3481%[filebase '_' xx 'mask'], xx=nbslice
3482%flag_mask=1 indicates detection
3483
3484flag_mask=0;%default
3485nbslice=1;
3486
3487% subdir=get(handles.SubdirCiv1,'String');
3488[Path,Name]=fileparts(filebase);
3489if ~isdir(Path)
3490    msgbox_uvmat('ERROR','no path for input files')
3491    return
3492end
3493% currentdir=pwd;
3494% cd(Path);%move in the dir of the root name filebase
3495maskfiles=dir(fullfile(Path,[Name '_*mask_*.png']));%look for mask files
3496% cd(currentdir);%come back to the current working directory
3497if ~isempty(maskfiles)
3498    %     msgbox_uvmat('ERROR','no mask available, to create it use Tools/Make mask in the upper menu bar of uvmat')
3499    % else
3500    flag_mask=1;
3501    maskname=maskfiles(1).name;% take the first mask file in the list
3502    [Path2,Name,ext]=fileparts(maskname);
3503    Namedouble=double(Name);
3504    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3505    ind_mask=findstr('mask',Name);
3506    i=ind_mask-1;
3507    while val(i)==0 && i>0
3508        i=i-1;
3509    end
3510    nbslice=str2double(Name(i+1:ind_mask-1));
3511    if ~isnan(nbslice) && Name(i)=='_'
3512        flag_mask=1;
3513    else
3514        msgbox_uvmat('ERROR',['bad mask file ' Name ext ' found in ' Path2])
3515        return
3516        nbslice=1;
3517    end
3518end
3519
3520%------------------------------------------------------------------------
3521% --- function called to look for grid files
3522function [nbslice, flag_mask]=get_grid(filebase,handles)
3523%------------------------------------------------------------------------
3524flag_mask=0;%default
3525nbslice=1;
3526[Path,Name]=fileparts(filebase);
3527currentdir=pwd;
3528cd(Path);%move in the dir of the root name filebase
3529maskfiles=dir([Name '_*grid_*.grid']);%look for mask files
3530cd(currentdir);%come back to the current working directory
3531if ~isempty(maskfiles)
3532    flag_mask=1;
3533    maskname=maskfiles(1).name;% take the first mask file in the list
3534    [Path2,Name,ext]=fileparts(maskname);
3535    Namedouble=double(Name);
3536    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3537    ind_mask=findstr('grid',Name);
3538    i=ind_mask-1;
3539    while val(i)==0 && i>0
3540        i=i-1;
3541    end
3542    nbslice=str2double(Name(i+1:ind_mask-1));
3543    if ~isnan(nbslice) && Name(i)=='_'
3544        flag_mask=1;
3545    else
3546        msgbox_uvmat('ERROR',['bad grid file ' Name ext ' found in ' Path2])
3547        return
3548        nbslice=1;
3549    end
3550end
3551
3552%------------------------------------------------------------------------
3553% --- transform numbers to letters
3554function str=num2stra(num,nom_type)
3555%------------------------------------------------------------------------
3556if isempty(nom_type)
3557    str='';
3558elseif strcmp(nom_type(end),'a')
3559    str=char(96+num);
3560elseif strcmp(nom_type(end),'A')
3561    str=char(96+num);
3562elseif isempty(nom_type(2:end))%a single index
3563    str='';
3564else
3565    str=num2str(num);
3566end
3567
3568%------------------------------------------------------------------------
3569% --- Executes on button press in ListSubdirCiv1.
3570function ListSubdirCiv1_Callback(hObject, eventdata, handles)
3571%------------------------------------------------------------------------
3572list_subdir_civ1=get(handles.ListSubdirCiv1,'String');
3573val=get(handles.ListSubdirCiv1,'Value');
3574SubDir=list_subdir_civ1{val};
3575if strcmp(SubDir,'new...')
3576    if get(handles.CheckCiv1,'Value')
3577        SubDir='CIV'; %default subdirectory
3578    else
3579        msgbox_uvmat('ERROR','select CheckCiv1 to perform a new Civ operation')
3580        return
3581    end   
3582end
3583set(handles.SubdirCiv1,'String',SubDir);
3584errormsg=find_netcpair_civ(handles,1);
3585if ~isempty(errormsg)
3586    msgbox_uvmat('ERROR',errormsg)
3587end
3588   
3589%------------------------------------------------------------------------
3590% --- Executes on button press in ListSubdirCiv2.
3591function ListSubdirCiv2_Callback(hObject, eventdata, handles)
3592%------------------------------------------------------------------------
3593list_subdir_civ2=get(handles.ListSubdirCiv2,'String');
3594val=get(handles.ListSubdirCiv2,'Value');
3595SubDir=list_subdir_civ2{val};
3596if strcmp(SubDir,'new...')
3597    if get(handles.CheckCiv2,'Value')
3598        SubDir='CIV'; %default subdirectory
3599    else
3600        msgbox_uvmat('ERROR','select CheckCiv2 to perform a new Civ operation')
3601        return
3602    end
3603end
3604set(handles.SubdirCiv2,'String',SubDir);
3605
3606%------------------------------------------------------------------------
3607% --- Executes on button press in CheckGrid.
3608function CheckGrid_Callback(hObject, eventdata, handles)
3609%------------------------------------------------------------------------
3610value=get(hObject,'Value');
3611hparent=get(hObject,'parent');
3612hchildren=get(hparent,'children');
3613handle_txtbox=findobj(hchildren,'tag','txt_Grid');
3614handle_dx=findobj(hchildren,'tag','num_Dx');
3615handle_dy=findobj(hchildren,'tag','num_Dy');
3616handle_title_dx=findobj(hchildren,'tag','title_Dx');
3617handle_title_dy=findobj(hchildren,'tag','title_Dy');
3618testgrid=0;
3619filegrid='';
3620if value
3621    filebase=get(handles.RootPath,'String');
3622    [nbslice, flag_grid]=get_grid(filebase,handles);% look for a grid with appropriate name
3623    if isequal(flag_grid,1)
3624        filegrid=[num2str(nbslice) 'grid'];
3625        testgrid=1;
3626    else % browse for a grid
3627        filegrid=get(hObject,'UserData');%look for previous grid name stored as UserData
3628        if exist(filegrid,'file')
3629            filebase=filegrid;
3630        end
3631        [FileName, PathName, filterindex] = uigetfile( ...
3632            {'*.grid', ' (*.grid)';
3633            '*.grid',  '.grid files '; ...
3634            '*.*', 'All Files (*.*)'}, ...
3635            'Pick a file',filebase);
3636        filegrid=fullfile(PathName,FileName);
3637        set(hObject,'UserData',filegrid);%store for future use
3638        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filegrid,'file'))
3639            testgrid=1;
3640        end
3641    end
3642end
3643if testgrid
3644    set(handle_dx,'Visible','off');
3645    set(handle_dy,'Visible','off');
3646    set(handle_title_dy,'Visible','off');
3647    set(handle_title_dx,'Visible','off');
3648    set(handle_txtbox,'Visible','on')
3649    set(handle_txtbox,'String',filegrid)
3650else
3651    set(hObject,'Value',0);
3652    set(handle_dx,'Visible','on');
3653    set(handle_dy,'Visible','on');
3654    set(handle_title_dy,'Visible','on');
3655    set(handle_title_dx,'Visible','on');
3656    set(handle_txtbox,'Visible','off')
3657end
3658
3659%% if hObject is on the checkciv1 frame, duplicate action for checkciv2 frame
3660PanelName=get(hparent,'tag');
3661if strcmp(PanelName,'Civ1')
3662    hchildren=get(handles.Civ2,'children');
3663    handle_checkbox=findobj(hchildren,'tag','CheckGrid');
3664    handle_txtbox=findobj(hchildren,'tag','txt_Grid');
3665    handle_dx=findobj(hchildren,'tag','num_Dx');
3666    handle_dy=findobj(hchildren,'tag','num_Dy');
3667    handle_title_dx=findobj(hchildren,'tag','title_Dx');
3668    handle_title_dy=findobj(hchildren,'tag','title_Dy');
3669    set(handle_checkbox,'UserData',filegrid);%store for future use
3670    if testgrid
3671        set(handle_checkbox,'Value',1);
3672        set(handle_dx,'Visible','off');
3673        set(handle_dy,'Visible','off');
3674        set(handle_title_dx,'Visible','off');
3675        set(handle_title_dy,'Visible','off');
3676        set(handle_txtbox,'Visible','on')
3677        set(handle_txtbox,'String',filegrid)
3678%     else
3679%         set(handle_checkbox,'Value',0);
3680%         set(handles.CheckGrid,'Value',0);
3681%         set(handle_dx,'Visible','on');
3682%         set(handle_dy,'Visible','on');
3683%          set(handle_title_dx,'Visible','on');
3684%         set(handle_title_dy,'Visible','on');
3685%         set(handle_txtbox,'Visible','off')
3686    end
3687end
3688
3689%------------------------------------------------------------------------
3690% --- Executes on button press in CheckMask: common to all panels (civ1, Civ2..)
3691function CheckMask_Callback(hObject, eventdata, handles)
3692%------------------------------------------------------------------------
3693value=get(hObject,'Value');
3694hparent=get(hObject,'parent');
3695parent_tag=get(hparent,'Tag');
3696hchildren=get(hparent,'children');
3697handle_txtbox=findobj(hchildren,'tag','Mask');% look for the mask name box in the same panel
3698testmask=0;
3699if value
3700    filebase=get(handles.RootPath,'String');
3701    [nbslice, flag_mask]=get_mask(filebase,handles);% look for a mask with appropriate name
3702    if isequal(flag_mask,1)
3703        filemask=[num2str(nbslice) 'mask'];
3704        testmask=1;
3705    else % browse for a mask
3706        filemask=get(hObject,'UserData');%look for previous mask name stored as UserData
3707        if exist(filemask,'file')
3708            filebase=filemask;
3709        end
3710        [FileName, PathName] = uigetfile( ...
3711            {'*.png', ' (*.png)';
3712            '*.png',  '.png files '; ...
3713            '*.*', 'All Files (*.*)'}, ...
3714            'Pick a mask file *.png',filebase);
3715        filemask=fullfile(PathName,FileName);
3716        set(hObject,'UserData',filemask);%store for future use
3717        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filemask,'file'))
3718            testmask=1;
3719        end
3720    end
3721end
3722if testmask
3723    if strcmp(parent_tag,'Civ1')
3724        set(handles.Mask,'Visible','on')
3725        set(handles.Mask,'String',filemask)
3726    set(handles.CheckMask,'Value',1)
3727    end
3728%     switch parent_tag
3729% %         case 'Fix1'
3730% %             stage=2;
3731%         case 'Civ2'
3732%              stage=3;
3733% %         case 'Fix2'
3734% %             stage=4;
3735%     end
3736%     set(handles.Mask(stage:end),'Visible','on')
3737%     set(handles.Mask(stage:end),'String',filemask)
3738%     set(handles.CheckMask(stage:end),'Value',1)
3739else
3740    set(hObject,'Value',0);
3741    set(handle_txtbox,'Visible','off')
3742end
3743
3744
3745% --- Executes on button press in get_gridpatch1.
3746function get_gridpatch1_Callback(hObject, eventdata, handles)
3747filebase=get(handles.RootPath,'String');
3748[FileName, PathName, filterindex] = uigetfile( ...
3749    {'*.grid', ' (*.grid)';
3750    '*.grid',  '.grid files '; ...
3751    '*.*', 'All Files (*.*)'}, ...
3752    'Pick a file',filebase);
3753filegrid=fullfile(PathName,FileName);
3754set(handles.grid_patch1,'string',filegrid);
3755
3756
3757%------------------------------------------------------------------------
3758% --- Executes on button press in get_gridpatch2.
3759function get_gridpatch2_Callback(hObject, eventdata, handles)
3760%------------------------------------------------------------------------
3761
3762
3763%------------------------------------------------------------------------
3764% --- STEREO Interp
3765function cmd=RUN_STINTERP(stinterpBin,filename_A_nc,filename_B_nc,filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,xmlA,xmlB)
3766%------------------------------------------------------------------------
3767namelog=[filename_nc(1:end-3) '_stinterp.log'];
3768cmd=[stinterpBin ' -f1 ' filename_A_nc  ' -f2 ' filename_B_nc ' -f  ' filename_nc ...
3769    ' -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
3770
3771%------------------------------------------------------------------------
3772%--read images and convert them to the uint16 format used for PIV
3773function A=read_image(filename,type_ima,num,movieobject)
3774%------------------------------------------------------------------------
3775%num is the view number needed for an avi movie
3776switch type_ima
3777    case 'movie'
3778        A=read(movieobject,num);
3779    case 'avi'
3780        mov=aviread(filename,num);
3781        A=frame2im(mov(1));
3782    case 'multimage'
3783        A=imread(filename,num);
3784    case 'image'
3785        A=imread(filename);
3786end
3787siz=size(A);
3788if length(siz)==3;%color images
3789    A=sum(double(A),3);
3790    A=uint16(A);
3791end
3792
3793
3794%------------------------------------------------------------------------
3795% --- Executes on button press in get_ref_fix1.
3796function get_ref_fix1_Callback(hObject, eventdata, handles)
3797%------------------------------------------------------------------------
3798filebase=get(handles.RootPath,'String');
3799[FileName, PathName, filterindex] = uigetfile( ...
3800    {'*.nc', ' (*.nc)';
3801    '*.nc',  'netcdf files '; ...
3802    '*.*', 'All Files (*.*)'}, ...
3803    'Pick a file',filebase);
3804
3805fileinput=[PathName FileName];
3806sizf=size(fileinput);
3807if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
3808%[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
3809[Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput);
3810ref.filebase=fullfile(Path,File);
3811% ref.num_a=stra2num(str_a);
3812% ref.num_b=stra2num(str_b);
3813% ref.num1=str2double(field_count);
3814% ref.num2=str2double(str2);
3815browse=[];%initialisation
3816if ~isequal(ref.ext,'.nc')
3817    msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
3818    return
3819end
3820set(handles.ref_fix1,'String',[fullfile(ref.subdir,File) '....nc']);
3821set(handles.ref_fix1,'UserData',ref)
3822menu_field{1}='civ1';
3823Data=nc2struct(fileinput,[]);
3824if isfield(Data,'patch') && isequal(Data.patch,1)
3825    menu_field{2}='filter1';
3826end
3827if isfield(Data,'civ2') && isequal(Data.civ2,1)
3828    menu_field{3}='civ2';
3829end
3830if isfield(Data,'patch2') && isequal(Data.patch2,1)
3831    menu_field{4}='filter2';
3832end
3833set(handles.field_ref1,'String',menu_field);
3834set(handles.field_ref1,'Value',length(menu_field));
3835set(handles.num_MinVel,'Value',2);
3836set(handles.num_MinVel,'String','1');%default threshold
3837set(handles.ref_fix1,'Enable','on')
3838
3839%------------------------------------------------------------------------
3840% --- Executes on button press in get_ref_fix2.
3841function get_ref_fix2_Callback(hObject, eventdata, handles)
3842%------------------------------------------------------------------------
3843if isequal(get(handles.get_ref_fix2,'Value'),1)
3844    filebase=get(handles.RootPath,'String');
3845    [FileName, PathName, filterindex] = uigetfile( ...
3846        {'*.nc', ' (*.nc)';
3847        '*.nc',  'netcdf files '; ...
3848        '*.*', 'All Files (*.*)'}, ...
3849        'Pick a file',filebase);
3850    fileinput=[PathName FileName];
3851    sizf=size(fileinput);
3852    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
3853    %[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
3854    [Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput);
3855    ref.filebase=fullfile(Path,File);
3856%     ref.num_a=stra2num(str_a);
3857%     ref.num_b=stra2num(str_b);
3858%     ref.num1=str2num(field_count);
3859%     ref.num2=str2num(str2);
3860    browse=[];%initialisation
3861    if ~isequal(ref.ext,'.nc')
3862        msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
3863        return
3864    end
3865    set(handles.ref_fix2,'String',[fullfile(ref.subdir,File) '....nc']);
3866    set(handles.ref_fix2,'UserData',ref)
3867    menu_field{1}='civ1';
3868    Data=nc2struct(fileinput,[]);
3869    if isfield(Data,'patch') && isequal(Data.patch,1)
3870        menu_field{2}='filter1';
3871    end
3872    if isfield(Data,'civ2') && isequal(Data.civ2,1)
3873        menu_field{3}='civ2';
3874    end
3875    if isfield(Data,'patch2') && isequal(Data.patch2,1)
3876        menu_field{4}='filter2';
3877    end
3878    set(handles.field_ref2,'String',menu_field);
3879    set(handles.field_ref2,'Value',length(menu_field));
3880    set(handles.num_MinVel,'Value',2);
3881    set(handles.num_MinVel,'String','1');%default threshold
3882    set(handles.ref_fix2,'Enable','on')
3883    set(handles.ref_fix2,'Visible','on')
3884    set(handles.field_ref2,'Visible','on')
3885else
3886    set(handles.ref_fix2,'Visible','off')
3887    set(handles.field_ref2,'Visible','off')
3888end
3889
3890%------------------------------------------------------------------------
3891function ref_fix1_Callback(hObject, eventdata, handles)
3892%------------------------------------------------------------------------
3893set(handles.num_MinVel,'Value',1);
3894set(handles.field_ref1,'Value',1)
3895set(handles.field_ref1,'String',{' '})
3896set(handles.ref_fix1,'UserData',[]);
3897set(handles.ref_fix1,'String','');
3898set(handles.thresh_vel1,'String','0');
3899
3900%------------------------------------------------------------------------
3901function ref_fix2_Callback(hObject, eventdata, handles)
3902%------------------------------------------------------------------------
3903set(handles.num_MinVel,'Value',1);
3904set(handles.field_ref2,'Value',1)
3905set(handles.field_ref2,'String',{' '})
3906set(handles.ref_fix2,'UserData',[]);
3907set(handles.ref_fix2,'String','');
3908set(handles.num_MinVel,'String','0');
3909
3910%------------------------------------------------------------------------
3911% --- TO ABANDON Executes on button press in test_stereo1.
3912function CheckStereo_Callback(hObject, eventdata, handles)
3913%------------------------------------------------------------------------
3914hparent=get(hObject,'parent');
3915parent_tag=get(hparent,'Tag');
3916hchildren=get(hparent,'children');
3917handle_txtbox=findobj(hchildren,'tag','txt_Mask');
3918if isequal(get(hObject,'Value'),0)
3919    set(handles.num_SubdomainSize,'Visible','on')
3920    set(handles.num_SmoothingParam,'Visible','on')
3921else
3922    set(handles.num_SubdomainSize,'Visible','off')
3923    set(handles.num_SmoothingParam,'Visible','off')
3924end
3925
3926% %------------------------------------------------------------------------
3927% % --- Executes on button press in CheckStereo.
3928% function StereoCheck_Callback(hObject, eventdata, handles)
3929% %------------------------------------------------------------------------
3930% if isequal(get(handles.CheckStereo,'Value'),0)
3931%     set(handles.num_SubdomainSize,'Visible','on')
3932%     set(handles.num_SmoothingParam,'Visible','on')
3933% else
3934%     set(handles.num_SubdomainSize,'Visible','off')
3935%     set(handles.num_SmoothingParam,'Visible','off')
3936% end
3937
3938%------------------------------------------------------------------------
3939% --- Executes on button press in TestCiv1: display image correlation function
3940function TestCiv1_Callback(hObject, eventdata, handles)
3941%------------------------------------------------------------------------
3942set(handles.TestCiv1,'BackgroundColor',[1 1 0])
3943drawnow
3944if get(handles.TestCiv1,'Value')
3945    ref_i=str2double(get(handles.ref_i,'String'));
3946    if strcmp(get(handles.ref_j,'Visible'),'on')
3947        ref_j=str2double(get(handles.ref_j,'String'));
3948    else
3949        ref_j=1;%default
3950    end
3951    [filecell,i1,i21,j1,j2,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,file_ref_fix1,file_ref_fix2]=...
3952        set_civ_filenames(handles,ref_i,ref_j,[1 0 0 0 0 0]);
3953    Data.ListVarName={'ny','nx','A'};
3954    Data.VarDimName= {'ny','nx',{'ny','nx'}};
3955    Data.A=imread(filecell.ima1.civ1{1});
3956    if ndims(Data.A)==3 %case of color image
3957        Data.VarDimName= {'ny','nx',{'ny','nx','rgb'}};
3958    end
3959    Data.ny=[size(Data.A,1) 1];
3960    Data.nx=[1 size(Data.A,2)];
3961    par_civ1=read_GUI(handles.Civ1);
3962    par_civ1.ImageWidth=size(Data.A,2);
3963    par_civ1.ImageHeight=size(Data.A,1);
3964    par_civ1.Mask='all';% will provide only the grid set for PIV, no image correlation
3965    par_civ1.i1=1;%i1_civ1;
3966    par_civ1.i2=2;%i2_civ1;
3967    Param.Civ1=par_civ1;
3968    Grid=civ_matlab(Param);% get the grid of x, y positions set for PIV
3969    hview_field=view_field(Data); %view the image in the GUI view_field
3970    set(0,'CurrentFigure',hview_field)
3971    hhview_field=guihandles(hview_field);
3972    set(hview_field,'CurrentAxes',hhview_field.axes3)
3973    ViewData=get(hview_field,'UserData');
3974    ViewData.CivHandle=handles.civ;% indicate the handle of the civ GUI in view_field
3975    ViewData.axes3.B=imread(filecell.ima2.civ1{1});%store the second image in the UserData of the GUI view_field
3976    ViewData.axes3.X=Grid.Civ1_X; %keep the set of points in memeory
3977    ViewData.axes3.Y=Grid.Civ1_Y;
3978    set(hview_field,'UserData',ViewData)
3979    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
3980    if isempty(corrfig)
3981        corrfig=figure;
3982        set(corrfig,'tag','corrfig')
3983        set(corrfig,'name','image correlation')
3984        set(corrfig,'DeleteFcn',{@closeview_field})%
3985    end
3986    set(handles.TestCiv1,'BackgroundColor',[1 0 0])
3987else
3988    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
3989    if ~isempty(corrfig)
3990        delete(corrfig)
3991    end
3992    hview_field=findobj(allchild(0),'tag','view_field');% look for view_field   
3993    if ~isempty(hview_field)
3994        delete(hview_field)
3995    end
3996end
3997
3998
3999%------------------------------------------------------------------------
4000% --- Executes on button press in CheckThreshold.
4001function CheckThreshold_Callback(hObject, eventdata, handles)
4002%------------------------------------------------------------------------
4003huipanel=get(hObject,'parent');
4004obj(1)=findobj(huipanel,'Tag','num_MinIma');
4005obj(2)=findobj(huipanel,'Tag','num_MaxIma');
4006obj(3)=findobj(huipanel,'Tag','title_Threshold');
4007if get(hObject,'Value')
4008    set(obj,'Visible','on')
4009else
4010    set(obj,'Visible','off')
4011end
4012
4013%------------------------------------------------------------------------
4014function [cmd,errormsg]=cmd_civ1(filename,Param)
4015%------------------------------------------------------------------------
4016%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4017%changes : filename_cmx -> filename ( no extension )
4018cmd='';
4019filename=regexprep(filename,'.nc',''); %file name for the result
4020if isequal(Param.Civ1.Dt,0)
4021    Param.Civ1.Dt=1 ;%case of 'displacement' mode
4022end
4023Param.Civ1.ImageA=regexprep(Param.Civ1.ImageA,'.png','');
4024Param.Civ1.ImageB=regexprep(Param.Civ1.ImageB,'.png','');
4025[fid,errormsg]=fopen([filename '.civ1.cmx'],'w');
4026if isequal(fid,-1)
4027    errormsg=['cmd file ' filename ' cannot be created: ' errormsg];
4028    return
4029end
4030fprintf(fid,['##############   CMX file' '\n' ]);
4031fprintf(fid,   ['FirstImage ' regexprep(Param.Civ1.ImageA,'\\','\\\\') '\n' ]);% for windows compatibility
4032fprintf(fid,   ['LastImage  ' regexprep(Param.Civ1.ImageB,'\\','\\\\') '\n' ]);% for windows compatibility
4033fprintf(fid,  ['XX' '\n' ]);
4034if isfield(Param.Civ1,'Mask')
4035    fprintf(fid,  ['Mask ' 'y' '\n' ]);
4036    fprintf(fid,  ['MaskName ' regexprep(Param.Civ1.Mask,'\\','\\\\') '\n' ]);
4037else
4038    fprintf(fid,  ['Mask ' 'n' '\n' ]);
4039    fprintf(fid,  ['MaskName ' 'noFile use default' '\n' ]);
4040end
4041fprintf(fid,   ['ImageSize ' num2str(Param.Civ1.ImageWidth) ' ' num2str(Param.Civ1.ImageHeight) '\n' ]);   %VERIFIER CAS GENERAL ?
4042fprintf(fid,   ['CorrelationBoxesSize ' num2str(Param.Civ1.Bx) ' ' num2str(Param.Civ1.By) '\n' ]);
4043fprintf(fid,   ['SearchBoxeSize ' num2str(Param.Civ1.Searchx) ' ' num2str(Param.Civ1.Searchy) '\n' ]);
4044fprintf(fid,   ['RO ' num2str(Param.Civ1.Rho) '\n' ]);
4045if isfield(Param.Civ1,'Grid')
4046    fprintf(fid,   ['GridSpacing ' '25' ' ' '25' '\n' ]);
4047else
4048    fprintf(fid,   ['GridSpacing ' num2str(Param.Civ1.Dx) ' ' num2str(Param.Civ1.Dy) '\n' ]);
4049end
4050fprintf(fid,   ['XX 1.0' '\n' ]);
4051fprintf(fid,   ['Dt_TO ' num2str(Param.Civ1.Dt) ' ' num2str(Param.Civ1.Time) '\n' ]);
4052fprintf(fid,  ['PixCmXY ' '1' ' ' '1' '\n' ]);
4053fprintf(fid,  ['XX 1' '\n' ]);
4054fprintf(fid,   ['ShiftXY ' num2str(Param.Civ1.Shiftx) ' '  num2str(Param.Civ1.Shifty) '\n' ]);
4055if isfield(Param.Civ1,'Grid')
4056    fprintf(fid,  ['Grid ' 'y' '\n' ]);
4057    fprintf(fid,   ['GridName ' regexprep(Param.Civ1.Grid,'\\','\\\\') '\n' ]);
4058else
4059    fprintf(fid,  ['Grid ' 'n' '\n' ]);
4060    fprintf(fid,   ['GridName ' 'noFile use default' '\n' ]);
4061end
4062fprintf(fid,   ['XX 85' '\n' ]);
4063fprintf(fid,   ['XX 1.0' '\n' ]);
4064fprintf(fid,   ['XX 1.0' '\n' ]);
4065fprintf(fid,   ['Hart 1' '\n' ]);
4066fprintf(fid,  [ 'DecimalShift 0' '\n' ]);
4067fprintf(fid,   ['Deformation 0' '\n' ]);
4068fprintf(fid,  ['CorrelationMin 0' '\n' ]);
4069fprintf(fid,   ['IntensityMin 0' '\n' ]);
4070if ~isfield(Param.Civ1,'MinIma')% Image threshold not activated
4071    fprintf(fid,  ['SeuilImage n' '\n' ]);
4072    fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);%not used in principle
4073else% Image threshold  activated
4074    if isempty(Param.Civ1.MaxIma)||isnan(Param.Civ1.MaxIma)
4075        Param.Civ1.MaxIma=2^Param.Civ1.ImageBitDepth;%take the max image value as upper bound by default
4076    end
4077    fprintf(fid,  ['SeuilImage y' '\n' ]);
4078    fprintf(fid,   ['SeuilImageValues ' num2str(Param.Civ1.MinIma) ' ' num2str(Param.Civ1.MaxIma) '\n' ]);
4079end
4080fprintf(fid,   ['ImageToUse ' Param.Civ1.term_a ' ' Param.Civ1.term_b '\n' ]); % VERIFIER ?
4081fprintf(fid,   ['ImageUsedBefore null null' '\n' ]);
4082fclose(fid);
4083
4084if(isunix) %unix (or Mac) system
4085    cmd=['cp -f ' filename '.civ1.cmx ' filename '.cmx \n '];% the cmx file gives the name to the nc file
4086    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
4087    cmd=[cmd 'rm ' filename '.cmx'];
4088else %Windows system
4089    filename=regexprep(filename,'\\','\\\\');
4090    cmd=['copy /Y "' filename '.civ1.cmx" "' filename '.cmx" \n '];
4091    cmd=[cmd '"' regexprep(Param.xml.Civ1Bin,'\\','\\\\')...
4092        '" -f "' filename '.cmx" >"' filename '.civ1.log" \n ' ]; % redirect standard output to the log file
4093    cmd=[cmd 'del "' filename '.cmx"'];
4094end
4095
4096
4097function cmd=cmd_fix(filename,Param,fixname)
4098%%
4099switch fixname
4100    case 'Fix1'
4101        fi2_value=num2str(Param.(fixname).CheckF2);
4102    case 'Fix2'
4103        fi2_value=num2str(Param.(fixname).CheckF4);%need to understand why...
4104end
4105filename=regexprep(filename,'.nc','');
4106MaskName_string='';%default
4107MaxVel_string='';%default
4108if ~isempty(Param.(fixname).MaxVel)
4109    MaxVel_string=[' -threshV ' num2str(Param.(fixname).MaxVel)];
4110end
4111if isunix
4112    cmd=[Param.xml.FixBin ' -f ' filename '.nc -fi1 ' num2str(Param.(fixname).CheckFmin2) ...
4113        ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ...
4114        ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string...
4115        ' >' filename '.' lower(fixname) '.log 2>&1'];
4116else
4117    cmd=['"' Param.xml.FixBin '" -f "' filename '.nc" -fi1 ' num2str(Param.(fixname).CheckFmin2)...
4118        ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ...
4119        ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string...
4120        ' > "' filename '.' lower(fixname) '.log"'];
4121    cmd=regexprep(cmd,'\\','\\\\');
4122end
4123
4124
4125function cmd=cmd_patch(filename,Param,patchname)
4126%% ------------------------------------------------------------------------
4127filename=regexprep(filename,'.nc','');
4128if isunix
4129    cmd=[Param.xml.PatchBin...
4130        ' -f ' filename '.nc -m ' num2str(Param.(patchname).Nx)...
4131        ' -n ' num2str(Param.(patchname).Ny) ' -ro ' num2str(Param.(patchname).SmoothingParam)...
4132        ' -nopt ' num2str(Param.(patchname).SubdomainSize) ...
4133        '  > ' filename '.' lower(patchname) '.log 2>&1']; % redirect standard output to the log file
4134else
4135    cmd=['"' Param.xml.PatchBin...
4136        '" -f "' filename '.nc" -m ' num2str(Param.(patchname).Nx)...
4137        ' -n ' num2str(Param.(patchname).Ny) ' -ro ' num2str(Param.(patchname).SmoothingParam)...
4138        ' -nopt ' num2str(Param.(patchname).SubdomainSize)...
4139        '  > "' filename '.' lower(patchname) '.log" 2>&1']; % redirect standard output to the log file
4140    cmd=regexprep(cmd,'\\','\\\\');
4141end
4142
4143%------------------------------------------------------------------------
4144% --- CheckCiv2  CheckCiv2  CheckCiv2 CheckCiv2
4145function [cmd,errormsg]=cmd_civ2(filename,Param)
4146%------------------------------------------------------------------------
4147%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4148% global civ2Bin sge%name of the executable for checkciv1 calculation
4149 cmd='';
4150filename=regexprep(filename,'.nc','');
4151if isequal(Param.Civ2.Dt,'0')
4152    Param.Civ2.Dt='1' ;%case of 'displacement' mode
4153end
4154Param.Civ2.ImageA=regexprep(Param.Civ2.ImageA,'.png','');
4155Param.Civ2.ImageB=regexprep(Param.Civ2.ImageB,'.png','');% bug : .png appears two times ?
4156[fid,errormsg]=fopen([filename '.civ2.cmx'],'w');
4157if isequal(fid,-1)
4158    return
4159end
4160fprintf(fid,['##############   CMX file' '\n' ]);
4161fprintf(fid,   ['FirstImage ' regexprep(Param.Civ2.ImageA,'\\','\\\\') '\n' ]);% for windows compatibility
4162fprintf(fid,   ['LastImage  ' regexprep(Param.Civ2.ImageB,'\\','\\\\') '\n' ]);% for windows compatibility
4163fprintf(fid,  ['XX' '\n' ]);
4164if isfield(Param.Civ2,'Mask')
4165    fprintf(fid,  ['Mask ' 'y' '\n' ]);
4166    fprintf(fid,  ['MaskName ' regexprep(Param.Civ2.Mask,'\\','\\\\') '\n' ]);
4167else
4168    fprintf(fid,  ['Mask ' 'n' '\n' ]);
4169    fprintf(fid,  ['MaskName ' 'noFile use default' '\n' ]);
4170end
4171% fprintf(fid, ['Mask ' Param.Civ2.MaskFlag '\n' ]);
4172% fprintf(fid, ['MaskName ' regexprep(Param.Civ2.MaskName,'\\','\\\\') '\n' ]);% for windows compatibility
4173fprintf(fid,   ['ImageSize ' num2str(Param.Civ2.ImageWidth) ' ' num2str(Param.Civ2.ImageHeight) '\n' ]); 
4174% fprintf(fid, ['ImageSize ' num2str(Param.Civ2.npx) ' ' num2str(Param.Civ2.npy) '\n' ]);   %VERIFIER CAS GENERAL ?
4175fprintf(fid, ['CorrelationBoxesSize ' num2str(Param.Civ2.Bx) ' ' num2str(Param.Civ2.By) '\n' ]);
4176fprintf(fid, ['SearchBoxeSize ' num2str(Param.Civ2.Bx) ' ' num2str(Param.Civ2.By) '\n']);
4177fprintf(fid, ['RO ' num2str(Param.Civ2.Rho) '\n']);
4178if isfield(Param.Civ2,'Grid')
4179    fprintf(fid,   ['GridSpacing ' '25' ' ' '25' '\n' ]);
4180else
4181    fprintf(fid,   ['GridSpacing ' num2str(Param.Civ2.Dx) ' ' num2str(Param.Civ2.Dy) '\n' ]);
4182end
4183% fprintf(fid, ['GridSpacing ' num2str(Param.Civ2.Dx) ' ' num2str(Param.Civ2.Dy) '\n']);
4184fprintf(fid, ['XX 1.0' '\n' ]);
4185fprintf(fid, ['Dt_TO ' num2str(Param.Civ2.Dt) ' ' num2str(Param.Civ2.Time) '\n' ]);
4186fprintf(fid, ['PixCmXY ' '1' ' ' '1' '\n' ]);
4187fprintf(fid, ['XX 1' '\n' ]);
4188fprintf(fid, 'ShiftXY 0 0\n');
4189if isfield(Param.Civ2,'Grid')
4190    fprintf(fid,  ['Grid ' 'y' '\n' ]);
4191    fprintf(fid,   ['GridName ' regexprep(Param.Civ2.Grid,'\\','\\\\') '\n' ]);
4192else
4193    fprintf(fid,  ['Grid ' 'n' '\n' ]);
4194    fprintf(fid,   ['GridName ' 'noFile use default' '\n' ]);
4195end
4196% fprintf(fid, ['Grid ' Param.Civ2.GridFlag '\n' ]);
4197% fprintf(fid, ['GridName ' regexprep(Param.Civ2.GridName,'\\','\\\\') '\n']);
4198fprintf(fid, ['XX 85' '\n' ]);
4199fprintf(fid, ['XX 1.0' '\n' ]);
4200fprintf(fid, ['XX 1.0' '\n' ]);
4201fprintf(fid, ['Hart 1' '\n' ]);
4202fprintf(fid, ['DecimalShift ' num2str(Param.Civ2.CheckDecimal) '\n']);
4203fprintf(fid, ['Deformation ' num2str(Param.Civ2.CheckDeformation) '\n']);
4204fprintf(fid,  ['CorrelationMin 0' '\n' ]);
4205fprintf(fid,   ['IntensityMin 0' '\n' ]);
4206
4207if ~isfield(Param.Civ2,'MinIma')% Image threshold not activated
4208    fprintf(fid,  ['SeuilImage n' '\n' ]);
4209    fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);%not used in principle
4210else% Image threshold  activated
4211    if isempty(Param.Civ2.MaxIma)||isnan(Param.Civ2.MaxIma)
4212        Param.Civ2.MaxIma=2^Param.Civ2.ImageBitDepth;%take the max image value as upper bound by default
4213    end
4214    fprintf(fid,  ['SeuilImage y' '\n' ]);
4215    fprintf(fid,   ['SeuilImageValues ' num2str(Param.Civ2.MinIma) ' ' num2str(Param.Civ2.MaxIma) '\n' ]);
4216end
4217fprintf(fid,   ['ImageToUse ' Param.Civ2.term_a ' ' Param.Civ2.term_b '\n' ]); % VERIFIER ?
4218fprintf(fid, ['ImageUsedBefore ' regexprep(Param.Civ2.filename_nc1,'\\','\\\\') '\n']);
4219fclose(fid);
4220
4221if(isunix)
4222    cmd=['cp -f ' filename '.civ2.cmx ' filename '.cmx\n'...
4223        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
4224        'rm ' filename '.cmx \n'];%rename .cmx as .checkciv2.cmx, the result file is named [filename '.nc'] by CIVx
4225else
4226    filename=regexprep(filename,'\\','\\\\');
4227    cmd=['copy /Y "' filename '.civ2.cmx" "' filename '.cmx" \n'...
4228        '"' regexprep(Param.xml.Civ2Bin,'\\','\\\\') '" -f "' filename  '.cmx" >"' filename '.civ2.log" \n'...
4229        'del "' filename '.cmx" \n'];
4230end
4231
4232%------------------------------------------------------------------------
4233% --- CheckCiv1  Unified: TO ABADON
4234function xml_civ1_parameters=CIV1_CMD_Unified(filename,namelog,par)
4235%------------------------------------------------------------------------
4236%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4237%global CivBin%name of the executable for checkciv1 calculation
4238
4239civ1.image1=par.ImageA;
4240civ1.image2=par.ImageB;
4241civ1.imageSize_X=par.npx;
4242civ1.imageSize_Y=par.npy;
4243civ1.outputFileName=[filename '.nc'];
4244civ1.correlationBoxesSize_X=par.ibx;
4245civ1.correlationBoxesSize_Y=par.iby;
4246civ1.searchBoxesSize_X=par.isx;
4247civ1.searchBoxesSize_Y=par.isy;
4248civ1.globalShift_X=par.shiftx;
4249civ1.globalShift_Y=par.shifty;
4250civ1.ro=par.rho;
4251civ1.hart='y';
4252if isequal(par.gridflag,'y')
4253    civ1.grid=par.gridname;
4254else
4255    civ1.grid='n';
4256    civ1.gridSpacing_X=par.dx;
4257    civ1.gridSpacing_Y=par.dy;
4258end
4259if isequal(par.maskflag,'y')
4260    civ1.mask=par.maskname;
4261end
4262civ1.dt=par.Dt;
4263civ1.unit='pixel';
4264civ1.absolut_time_T0=par.Time;
4265civ1.pixcmx='1';
4266civ1.pixcmy='1';
4267civ1.convectFlow='n';
4268
4269xml_civ1_parameters=civ1;
4270
4271%------------------------------------------------------------------------
4272% --- CheckCiv2  Unified: TO ABADON
4273function civ2=CIV2_CMD_Unified(filename,namelog,par)
4274%------------------------------------------------------------------------
4275%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4276%global CivBin%name of the executable for checkciv1 calculation
4277
4278filename=regexprep(filename,'.nc','');
4279
4280civ2.image1=par.ImageA;
4281civ2.image2=par.ImageB;
4282civ2.imageSize_X=par.npx;
4283civ2.imageSize_Y=par.npy;
4284civ2.inputFileName=[par.filename_nc1 '.nc'];
4285civ2.outputFileName=[filename '.nc'];
4286civ2.correlationBoxesSize_X=par.ibx;
4287civ2.correlationBoxesSize_Y=par.iby;
4288civ2.ro=par.rho;
4289%checkciv2.decimalShift=par.CheckDecimal;
4290%checkciv2.CheckDeformation=par.CheckDeformation;
4291if isequal(par.decimal,'1')
4292    civ2.decimalShift='y';
4293else
4294    civ2.decimalShift='n';
4295end
4296if isequal(par.deformation,'1')
4297    civ2.deformation='y';
4298else
4299    civ2.deformation='n';
4300end
4301if isequal(par.gridflag,'y')
4302    civ2.grid=par.gridname;
4303else
4304    civ2.grid='n';
4305    civ2.gridSpacing_X=par.dx;
4306    civ2.gridSpacing_Y=par.dy;
4307end
4308civ2.gridSpacing_X='10';
4309civ2.gridSpacing_Y='10';%NOTE: faut mettre gridSpacing pourque ca tourne, meme si c'est la grille qui est utilisee
4310if isequal(par.maskflag,'y')
4311    civ2.mask=par.maskname;
4312else
4313    civ2.mask='n';
4314end
4315civ2.dt=par.Dt;
4316civ2.unit='pixel';
4317civ2.absolut_time_T0=par.Time;
4318civ2.pixcmx='1';
4319civ2.pixcmy='1';
4320civ2.convectFlow='n';
4321
4322
4323% --- Executes on button press in TestPatch1.
4324function TestPatch1_Callback(hObject, eventdata, handles)
4325set(handles.TestPatch1,'BackgroundColor',[1 1 0])
4326drawnow
4327if get(handles.TestPatch1,'Value')
4328    ref_i=str2double(get(handles.ref_i,'String'));
4329    if strcmp(get(handles.ref_j,'Visible'),'on')
4330        ref_j=str2double(get(handles.ref_j,'String'));
4331    else
4332        ref_j=1;%default
4333    end
4334    [filecell,i1,i21,j1,j2,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,file_ref_fix1,file_ref_fix2]=...
4335        set_civ_filenames(handles,ref_i,ref_j,[0 0 1 0 0 0]);
4336   
4337    Data.ListVarName={'ny','nx','A'};
4338    Data.VarDimName= {'ny','nx',{'ny','nx'}};
4339   
4340    param_patch1=read_GUI(handles.Patch1);
4341    param_patch1.CivFile=filecell.nc.civ1{1};
4342    Param.Patch1=param_patch1;
4343    for irho=1:7
4344        [Data,errormsg]=civ_matlab(Param);% get the grid of x, y positions set for PIV
4345        if ~isempty(errormsg)
4346            msgbox_uvmat('ERROR',errormsg)
4347            return
4348        end
4349        SmoothingParam(irho)=Param.Patch1.SmoothingParam;
4350        Data.Civ1_U_Diff=Data.Civ1_U_Diff(Data.Civ1_FF==0);
4351        Data.Civ1_V_Diff=Data.Civ1_V_Diff(Data.Civ1_FF==0);
4352        DiffVel(irho)=sqrt(mean(Data.Civ1_U_Diff.*Data.Civ1_U_Diff+Data.Civ1_V_Diff.*Data.Civ1_V_Diff))
4353        NbSites(irho,:)=Data.Civ1_NbSites*numel(Data.Civ1_NbSites)/numel(Data.Civ1_U_Diff);
4354        Param.Patch1.SmoothingParam=2*Param.Patch1.SmoothingParam;
4355    end
4356    figure
4357    plot(SmoothingParam,DiffVel,'b',SmoothingParam,NbSites,'r')
4358    set(handles.TestPatch1,'BackgroundColor',[1 0 0])
4359else
4360    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
4361    if ~isempty(corrfig)
4362        delete(corrfig)
4363    end
4364    hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
4365    if ~isempty(hview_field)
4366        delete(hview_field)
4367    end
4368end
4369%'nomtype2pair': creates nomencalture for index pairs knowing the image nomenclature
4370%---------------------------------------------------------------------
4371% [nom_type_pair]=nomtype2pair(nom_type,Dti,Dtj);
4372%---------------------------------------------------------------------           
4373
4374% OUTPUT:
4375%nom_type_nc
4376
4377%---------------------------------------------------------------------
4378% INPUT:
4379% 'nom_type': string defining the kind of nomenclature used:
4380     %nom_type='': constant name [filebase ext] (default output if 'nom_type' is undefined)
4381     %nom_type='*': the same  file [filebase ext] contains successive fields (ex avi movies)
4382     %nom_type='_i': series of files with a single index i preceded by '_'(e.g. 'aa_45.png').
4383     %nom_type='#' series of indexed images wich is not series_i [filebase index ext], e.g. 'aa045.jpg' or 'aa45.tif'
4384     %nom_type='_i_j' matrix of files with two indices i and j separated by '_'(e.g. 'aa_45_2.png')
4385     %nom_type='_i1-i2' from pairs from a single index (e.g. 'aa_45-47.nc')
4386     %nom_type='_i_j1-j2'pairs of j indices (e.g. 'aa_45_2-3.nc')
4387     %nom_type='_i1-i2_j' pairs of i indices (e.g. 'aa_45-46_2.nc')
4388     %nom_type='#a','#A', with a numerical index and an index letter(e.g.'aa045b.png'), OBSOLETE (replaced by 'series_i_j')
4389     %nom_type='%03d' or '%04d', series of indexed images with numbers completed with zeros to 3 or 4 digits, e.g.'aa045.tif'
4390     %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'
4391     %nom_type='raw_SMD', same as '#a' but with no extension ext='', OBSOLETE
4392     %nom_type='#_ab' from pairs of '#a' images (e.g. 'aa045bc.nc'), ext='.nc', OBSOLETE (replaced by 'netc_2D')
4393     %nom_type='%3dab' from pairs of '%3da' images (e.g. 'aa045bc.nc'), ext='.nc', OBSOLETE (replaced by 'netc_2D')
4394% Dti: ~=0 if i index pairs are used
4395% Dtj: ~=0 if i index pairs are used
4396
4397function NomTypeNc=nomtype2pair(NomTypeIma,mode)
4398
4399%determine nom_type_nc:
4400NomTypeNc=NomTypeIma;%default
4401switch mode
4402    case 'pair j1-j2'     
4403    if ~isempty(regexp(NomTypeIma,'a$'))
4404        NomTypeNc=[NomTypeIma 'b'];
4405    elseif ~isempty(regexp(NomTypeIma,'A$'))
4406        NomTypeNc=[NomTypeIma 'B'];
4407    else
4408        r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
4409        if ~isempty(r)
4410            NomTypeNc='_1_1-2';
4411        end
4412    end
4413    case 'series(Dj)' 
4414        r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
4415        if ~isempty(r)
4416            NomTypeNc='_1_1-2';
4417        end
4418   case 'series(Di)'
4419        r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
4420        if ~isempty(r)
4421            NomTypeNc='_1-2_1';
4422        else
4423            NomTypeNc='_1-2';
4424        end
4425end
4426
4427function NomType_Callback(hObject, eventdata, handles)
4428set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
4429RootPath=get(handles.RootPath,'String');
4430RootFile=get(handles.RootFile,'String');
4431ref_i=str2num(get(handles.ref_i,'String'));
4432ref_j=str2num(get(handles.ref_j,'String'));
4433NomType=get(handles.NomType,'String');
4434ImaExt=get(handles.ImaExt,'String');
4435fileinput=fullfile_uvmat(RootPath,'',RootFile,ImaExt,NomType,ref_i,[],ref_j);
4436errormsg=display_file_name(handles,fileinput);
4437if ~isempty(errormsg)
4438    msgbox_uvmat('ERROR',errormsg)
4439end
4440set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
4441
4442% --- Executes on selection change in ListProgram.
4443function ListProgram_Callback(hObject, eventdata, handles)
4444ListProgram=get(handles.ListProgram,'String');
4445Program=ListProgram{get(handles.ListProgram,'value')};
4446switch Program
4447    case 'CivX'
4448        set(handles.num_MaxDiff,'Visible','off')
4449        set(handles.num_Nx,'Visible','on')
4450        set(handles.num_Ny,'Visible','on')
4451        set(handles.title_Nx,'Visible','on')
4452        set(handles.title_Ny,'Visible','on')
4453        set(handles.title_MaxDiff,'Visible','off')
4454        set(handles.num_Rho,'Style','edit')
4455        set(handles.num_Rho,'String','1')
4456        set(handles.BATCH,'Enable','on')
4457    case 'Matlab'
4458        set(handles.num_MaxDiff,'Visible','on')
4459        set(handles.title_MaxDiff,'Visible','on')
4460        set(handles.num_Nx,'Visible','off')
4461        set(handles.num_Ny,'Visible','off')
4462        set(handles.title_Nx,'Visible','off')
4463        set(handles.title_Ny,'Visible','off')
4464        set(handles.num_Rho,'Style','popupmenu')
4465        set(handles.num_Rho,'Value',1)
4466        set(handles.num_Rho,'String',{'1';'2'})
4467end
4468
4469
4470% --- Executes on button press in TestCiv2.
4471function TestCiv2_Callback(hObject, eventdata, handles)
4472
4473
4474
4475function RootFile_Callback(hObject, eventdata, handles)
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