source: trunk/src/civ.m @ 427

Last change on this file since 427 was 427, checked in by sommeria, 9 years ago

merge_proj corrected to project simulataneously velocity, vort, div...
Time reintroduced correctly
bug corrections for objects

File size: 192.9 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 08-May-2012 22:14:39
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 
456time=[];
457TimeUnit=''; %default
458CoordUnit='';%default
459pxcm_search=1;
460if ~isempty(ext_imadoc)
461    set(handles.ImaDoc,'BackgroundColor',[1 1 0]) % set edit box to yellow cloro to indicate that the file reading is beginning
462    drawnow
463    switch ext_imadoc
464        case '.civxml'%OBSOLETE
465            [tild,tild,time]=read_civxml([RootName '.civxml']);
466            mode='pair j1-j2';
467            if isempty(nom_type_ima)% dtermine types by default if not already selected by browser or uvmat
468                nom_type_ima='_i_j';
469            end
470        case '.xml'
471            [XmlData,warntext]=imadoc2struct([RootName '.xml']);
472            ext_ima_read=[];
473            nom_type_read=[];
474            if isfield(XmlData,'Heading')&&isfield(XmlData.Heading','ImageName')&&ischar(XmlData.Heading.ImageName)% get image nom type and extension from the xml file
475                %[PP,FF,fc,str2,str_a,str_b,ext_ima_read,nom_type_read]=name2display(XmlData.Heading.ImageName);
476                [tild,tild,tild,tild,tild,tild,tild,tild,nom_type_read]=fileparts_uvmat(XmlData.Heading.ImageName);
477                fullname=fullfile(fileparts(RootName),XmlData.Heading.ImageName); %full name (including path) of the first image defined by the xmle file,
478                if ~exist(fullname,'file')
479                    msgbox_uvmat('WARNING',['FirstImage ' fullname ' defined in the xml file does not exist'])
480                end
481            end
482            if isfield(XmlData,'Time')
483                time=XmlData.Time;
484                %transform .Time to a column vector if it is a line vector thenomenclature uses a single index: correct possible bug in xml
485                if isequal(MaxIndex_i,1) && ~isequal(MaxIndex_j,1)% .Time is a line vector
486                    if numel(nom_type_read)>=2 && isempty(regexp(nom_type_read(2:end),'\D','once'))
487                        time=time';
488                        MaxIndex_i=MaxIndex_j;
489                        MaxIndex_j=1;
490                    end
491                end
492            end
493            if isfield(XmlData,'TimeUnit')
494                TimeUnit=XmlData.TimeUnit;
495            end
496
497            if isfield(XmlData,'GeometryCalib')
498                tsai=XmlData.GeometryCalib;
499                if isfield(tsai,'fx_fy') 
500                    pxcm_search=max(tsai.fx_fy(1),tsai.fx_fy(2));%pixels:cm estimated for the search range
501                end
502                if isfield(tsai,'CoordUnit')
503                    CoordUnit=tsai.CoordUnit;
504                end
505            end
506        case '.civ'% OBSOLETE: case of .civ image documentation file
507            [error,time,TimeUnit,mode,npx,npy]=read_imatext([RootName '.civ']);
508            if error==2, msgbox_uvmat('WARNING',['no file ' RootName '.civ']);
509            elseif error==1, msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file');
510            end
511            nom_type_ima='001a';
512        case {'.avi','.AVI'}
513            nom_type_ima='*';
514            ImaExt=ext_imadoc;
515            set(handles.ListPairMode,'Value',1);
516            set(handles.ListPairMode,'String',{'series(Di)'})
517            dt=0.04;%default
518            if exist([RootName ext_imadoc],'file')==2
519                hhh=which('videoreader');
520                if isempty(hhh)%use old video function of matlab
521                    imainfo=aviinfo([RootName ext_imadoc]);%read infos on the avi movie
522                    dt=1/imainfo.FramesPerSecond;%time interval between successive frames
523                    MaxIndex_i=imainfo.NumFrames;%number of frames
524                    %         XmlData.Time=(0:1/imainfo.FramesPerSecond:(imainfo.NumFrames-1)/imainfo.FramesPerSecond)';
525                    %         nbfield=imainfo.NumFrames;
526                    %         set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FramesPerSecond) 'ms']);%display the elementary time interval in millisec
527                    %         ColorType=imainfo.ImageType;%='truecolor' for color images
528                else %use video function videoreader of matlab
529                    imainfo=get(videoreader([RootName ext_imadoc]));%read infos on the avi movie
530                    dt=1/imainfo.FrameRate;%time interval between successive frames
531                    MaxIndex_i=imainfo.NumberOfFrames;%number of frames
532                    %         XmlData.Time=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames-1)/imainfo.FrameRate)';
533                    %         nbfield=imainfo.NumberOfFrames;
534                    %         set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FrameRate) 'ms']);%display the elementary time interval in millisec
535                    %         ColorType='truecolor';
536                end
537               
538                time=(dt*(0:MaxIndex_i-1))';%list of image times
539                TimeUnit='s';
540            end
541            set(handles.ImaDoc,'BackgroundColor',[1 1 1])% set display box back to whiter
542    end
543end
544%% timing display
545%show the reference image edit box if relevant (not needed for movies or in the absence of time information
546if numel(time)>=2 % if there are at least two time values to define dt
547    MaxIndex_i=min(size(time,1),MaxIndex_i);
548    MaxIndex_j=min(size(time,2),MaxIndex_j);
549    time=[zeros(size(time,1),1) time]; %insert a vertical line of zeros (to deal with zero file indices)
550    time=[zeros(1,size(time,2)); time]; %insert a horizontal line of zeros
551    set(handles.ImaDoc,'UserData',time); %store the matrix of times
552    set(handles.dt_unit,'String',['dt in m' TimeUnit]);
553    set(handles.TimeUnit,'String',TimeUnit);
554else
555    set(handles.ImaDoc,'String',''); %xml file not used for timing
556    time=(i1_series(:,1)+0:size(i1_series,1)-1);% time=index i
557    time=time'*ones(1,size(i1_series,2),1); %makes a time matrix with the same time for all j indices
558    TimeUnit='frame';
559end
560set(handles.ImaDoc,'UserData',time); %store the matrix of times
561set(handles.dt_unit,'String',['dt in m' TimeUnit]);%display dt in unit 10-3 of the time (e.g ms)
562set(handles.TimeUnit,'String',TimeUnit);
563set(handles.nb_field,'String',num2str(MaxIndex_i));
564set(handles.nb_field2,'String',num2str(MaxIndex_j));
565set(handles.CoordUnit,'String',CoordUnit)
566set(handles.SearchRange,'UserData', pxcm_search);
567set(handles.ImaExt,'String',ImaExt)
568set(handles.NomType,'String',NomTypeIma)
569set(handles.ref_i,'String',num2str(num_ref_i))
570set(handles.ref_j,'String',num2str(num_ref_j))
571
572%% update i and j index range if a nc file has been opened or pb withmin max image indices:
573% then set first and last to the inputfile index by default
574first_i=str2num(get(handles.first_i,'String'));
575last_i=str2num(get(handles.last_i,'String'));
576if isempty(first_i) || isempty(last_i)||isempty(MinIndex_i)||isempty(MaxIndex_i)
577    set(handles.first_i,'String',num2str(num_ref_i));
578    set(handles.last_i,'String',num2str(num_ref_i));%
579end
580if ind_opening~=0 || isempty(first_i) || isempty(last_i)|| first_i<MinIndex_i || last_i>MaxIndex_i
581set(handles.first_i,'String',num2str(num_ref_i));
582set(handles.last_i,'String',num2str(num_ref_i));%
583end
584
585%j index range
586first_j=str2num(get(handles.first_j,'String'));
587last_j=str2num(get(handles.last_i,'String'));
588if isempty(first_j) || isempty(last_j)||isempty(MinIndex_j)||isempty(MaxIndex_j)
589    set(handles.first_j,'String',num2str(num_ref_j));
590    set(handles.last_j,'String',num2str(num_ref_j));%
591elseif ind_opening~=0 || first_j<MinIndex_j || last_j>MaxIndex_j
592    set(handles.first_j,'String',num2str(num_ref_j));
593set(handles.last_j,'String',num2str(num_ref_j));%
594end
595
596%% set the civ options depending on the input file content when a nc file has been opened
597ListOptions={'CheckCiv1', 'CheckFix1' 'CheckPatch1', 'CheckCiv2', 'CheckFix2', 'CheckPatch2'};
598if ind_opening~=0
599    for index = 1:ind_opening
600        set(handles.(ListOptions{index}),'value',0)
601    end
602end
603for index = ind_opening+2:6
604    set(handles.(ListOptions{index}),'value',0)
605end
606set(handles.(ListOptions{min(ind_opening+1,6)}),'value',1)
607update_CivOptions(handles,1)
608
609%%  set the menus of image pairs and default selection for civ   %%%%%%%%%%%%%%%%%%%
610%check_letter=~isempty(regexp(NomTypeIma,'[ab|AB]$'));%detect pair label by letter
611if  isequal(NomTypeNc,'_1-2')||isempty(MaxIndex_j)|| (MaxIndex_j==1)
612    set(handles.ListPairMode,'Value',1)
613    set(handles.ListPairMode,'String',{'series(Di)'})   
614elseif  MaxIndex_i==1 && MaxIndex_j>1% simple series in j
615    set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)'})
616    if  MaxIndex_j <= 10
617        set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large
618    end
619else
620    set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)';'series(Di)'})%multiple choice
621    if strcmp(NomTypeNc,'_1-2_1')
622        set(handles.ListPairMode,'Value',3)% advise 'series(Di)'
623    elseif  MaxIndex_j <= 10
624        set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large
625    end
626end
627
628%% scan files to update the subdirectory list display
629listot=dir(RootPath);%directory of RootPath
630idir=0;
631listdir={''};%default
632% get the list of existing civ subdirectories in the path of theinput root  file
633for ilist=1:length(listot)
634    if listot(ilist).isdir
635        name=listot(ilist).name;
636        if ~isequal(name,'.') && ~isequal(name,'..')
637            idir=idir+1;
638            listdir{idir,1}=listot(ilist).name;
639        end
640    end
641end
642
643%% update the selection for civ1 and civ2
644if ~isempty(SubDir)% subdir for civ1 and civ2 initiated by the input
645    SubdirCiv1=SubDir;
646    SubdirCiv2=SubDir;
647    set(handles.SubdirCiv1,'String',SubDir)
648    set(handles.SubdirCiv2,'String',SubDir)
649else% currently selected subdir preserved
650    SubdirCiv1=get(handles.SubdirCiv1,'String');
651    SubdirCiv2=get(handles.SubdirCiv2,'String');
652    if isempty(SubdirCiv1)% default subdir name='CIV'
653        set(handles.SubdirCiv1,'String','CIV');
654        SubdirCiv1='CIV';
655    end
656    if isempty(SubdirCiv2)% default subdir name='CIV'
657        set(handles.SubdirCiv2,'String','CIV');
658        SubdirCiv2='CIV';
659    end
660end
661
662%% update the subdirectory menus
663ValueCiv1=find(strcmp(SubdirCiv1,listdir));%search the index of subdir in the cell listdir
664if isempty(ValueCiv1)% if the input subdir is not found
665    ValueCiv1=numel(listdir)+1;%new subdirectory requested for civ1
666end
667ValueCiv2=find(strcmp(SubdirCiv2,listdir));%search the index of subdir in the cell listdir
668if isempty(ValueCiv2)% if the input subdir is not found
669    ValueCiv2=numel(listdir)+1;%new subdirectory requested for civ2
670end
671set(handles.ListSubdirCiv1,'String',[listdir;'new...'])
672set(handles.ListSubdirCiv2,'String',[listdir;'new...'])
673set(handles.ListSubdirCiv1,'Value',ValueCiv1)
674set(handles.ListSubdirCiv2,'Value',ValueCiv2)
675if isempty(listdir)
676    set(handles.SubdirCiv1,'String','CIV')
677    set(handles.SubdirCiv2,'String','CIV')
678end
679
680%% store info
681set(handles.RootPath,'UserData',browse)% store the nomenclature type
682
683%% list the possible index pairs, depending on the option set in ListPairMode
684ListPairMode_Callback([], [], handles)
685
686%% store the root input filename for future opening
687profil_perso=fullfile(prefdir,'uvmat_perso.mat');
688if exist(profil_perso,'file')
689    save (profil_perso,'RootPath','-append'); %store the root name for future opening of uvmat
690else
691    txt=ver('MATLAB');
692    Release=txt.Release;
693    relnumb=str2double(Release(3:4));
694    if relnumb >= 14
695        save (profil_perso,'RootPath','-V6'); %store the root name for future opening of uvmat
696    else
697        save (profil_perso,'RootPath'); %store the root name for future opening of uvmat
698    end
699end
700set(handles.RootPath,'BackgroundColor',[1 1 1])
701
702%------------------------------------------------------------------------
703% --- Executes on carriage return on the subdir checkciv1 edit window
704function SubdirCiv1_Callback(hObject, eventdata, handles)
705%------------------------------------------------------------------------
706SubDir=get(handles.SubdirCiv1,'String');
707menu_str=get(handles.ListSubdirCiv1,'String');% read the list of subdirectories for update
708ichoice=find(strcmp(SubDir,menu_str),1);
709if isempty(ichoice)
710    ilist=numel(menu_str); %select 'new...' in the menu
711else
712    ilist=ichoice;
713end
714set(handles.ListSubdirCiv1,'Value',ilist)% select the selected subdir in the menu
715if get(handles.CheckCiv1,'Value')% if Civ1 is performed
716    set(handles.SubdirCiv2,'String',SubDir);% set by default civ2 directory the same as civ1
717    set(handles.ListSubdirCiv2,'Value',ilist)
718else % if Civ1 data already exist
719    errormsg=find_netcpair_civ(handles,1); %update the list of available pairs from netcdf files in the new directory
720    if ~isempty(errormsg)
721    msgbox_uvmat('ERROR',errormsg)
722    end
723end
724
725%------------------------------------------------------------------------
726% --- Executes on carriage return on the SubDir checkciv1 edit window
727function SubdirCiv2_Callback(hObject, eventdata, handles)
728%------------------------------------------------------------------------
729SubDir=get(handles.SubdirCiv1,'String');
730menu_str=get(handles.ListSubdirCiv2,'String');% read the list of subdirectories for update
731ichoice=find(strcmp(SubDir,menu_str),1);
732if isempty(ichoice)
733    ilist=numel(menu_str); %select 'new...' in the menu
734else
735    ilist=ichoice;
736end
737set(handles.ListSubdirCiv2,'Value',ilist)% select the selected subdir in the menu
738%update the list of available pairs from netcdf files in the new directory
739if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
740    errormsg=find_netcpair_civ(handles,2);
741        if ~isempty(errormsg)
742    msgbox_uvmat('ERROR',errormsg)
743    end
744end
745
746%------------------------------------------------------------------------
747% --- Executes on button press in CheckCiv1.
748function CheckCiv1_Callback(hObject, eventdata, handles)
749%------------------------------------------------------------------------
750update_CivOptions(handles,0)
751
752%------------------------------------------------------------------------
753% --- Executes on button press in CheckFix1.
754function CheckFix1_Callback(hObject, eventdata, handles)
755%------------------------------------------------------------------------
756update_CivOptions(handles,0)
757
758%------------------------------------------------------------------------
759% --- Executes on button press in CheckPatch1.
760function CheckPatch1_Callback(hObject, eventdata, handles)
761%------------------------------------------------------------------------
762update_CivOptions(handles,0)
763
764%------------------------------------------------------------------------
765% --- Executes on button press in CheckCiv2.
766function CheckCiv2_Callback(hObject, eventdata, handles)
767%------------------------------------------------------------------------
768update_CivOptions(handles,0)
769
770%------------------------------------------------------------------------
771% --- Executes on button press in CheckFix2.
772function CheckFix2_Callback(hObject, eventdata, handles)
773%------------------------------------------------------------------------
774update_CivOptions(handles,0)
775
776%------------------------------------------------------------------------
777% --- Executes on button press in CheckPatch2.
778function CheckPatch2_Callback(hObject, eventdata, handles)
779%------------------------------------------------------------------------
780update_CivOptions(handles,0)
781
782%------------------------------------------------------------------------
783% --- activated by any checkbox controling the selection of Civ1,Fix1,Patch1,Civ2,Fix2,Patch2
784function update_CivOptions(handles,opening)
785%------------------------------------------------------------------------
786checkbox=zeros(1,6);
787checkbox(1)=get(handles.CheckCiv1,'Value');
788checkbox(2)=get(handles.CheckFix1,'Value');
789checkbox(3)=get(handles.CheckPatch1,'Value');
790checkbox(4)=get(handles.CheckCiv2,'Value');
791checkbox(5)=get(handles.CheckFix2,'Value');
792checkbox(6)=get(handles.CheckPatch2,'Value');
793ind_selected=find(checkbox,1);
794if ~isempty(ind_selected)
795    RootPath=get(handles.RootPath,'String');
796    if isempty(RootPath)
797        msgbox_uvmat('ERROR','Please open an image or PIV .nc file with the upper bar menu Open/Browse...')
798        return
799    end
800end
801set(handles.PairIndices,'Visible','on')
802set(handles.SubdirCiv1,'Visible','on')
803set(handles.ListSubdirCiv1,'Visible','on')
804set(handles.TitleSubdirCiv1,'Visible','on')
805if ~opening
806    errormsg=find_netcpair_civ(handles,1); % select the available netcdf files
807    if ~isempty(errormsg)
808        msgbox_uvmat('ERROR',errormsg)
809    end
810end
811if max(checkbox(4:6))% case of civ2 pair choice needed
812    set(handles.TitlePairCiv2,'Visible','on')
813    set(handles.TitleSubdirCiv2,'Visible','on')
814    set(handles.SubdirCiv2,'Visible','on')
815    set(handles.ListSubdirCiv2,'Visible','on')
816    set(handles.ListPairCiv2,'Visible','on')
817    if ~opening
818        errormsg=find_netcpair_civ(handles,2); % select the available netcdf files
819        if ~isempty(errormsg)
820            msgbox_uvmat('ERROR',errormsg)
821        end
822    end
823else
824    set(handles.TitleSubdirCiv2,'Visible','off')
825    set(handles.SubdirCiv2,'Visible','off')
826    set(handles.ListSubdirCiv2,'Visible','off')
827    set(handles.ListPairCiv2,'Visible','off')
828end
829options={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'};
830for ilist=1:length(options)
831    if checkbox(ilist)
832        set(handles.(options{ilist}),'Visible','on')
833    else
834        set(handles.(options{ilist}),'Visible','off')
835    end
836end
837
838%------------------------------------------------------------------------
839% --- Executes on button press in RUN: processing on local computer
840function RUN_Callback(hObject, eventdata, handles)
841%------------------------------------------------------------------------
842set(handles.RUN, 'Enable','Off')
843set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
844batch=0;
845errormsg=launch_jobs(hObject, eventdata, handles,batch);
846set(handles.RUN, 'Enable','On')
847set(handles.RUN,'BackgroundColor',[1 0 0])
848
849% display errors or start status callback to visualise results
850if ~isempty(errormsg)
851    display(errormsg)
852    msgbox_uvmat('ERROR',errormsg)
853elseif  isfield(handles,'status') %&& ~isequal(get(handles.ListPairMode,'Value'),3)
854    set(handles.status,'Value',1);%suppress status display
855    status_Callback(hObject, eventdata, handles)
856end
857
858%------------------------------------------------------------------------
859% --- Executes on button press in BATCH: remote processing
860function BATCH_Callback(hObject, eventdata, handles)
861% -----------------------------------------------------------------------
862set(handles.BATCH, 'Enable','Off')
863set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])
864batch=1;
865errormsg=launch_jobs(hObject, eventdata, handles, batch);
866set(handles.BATCH, 'Enable','On')
867set(handles.BATCH,'BackgroundColor',[1 0 0])
868
869% display errors or start status callback to visualise results
870if ~isempty(errormsg)
871    display(errormsg)
872    msgbox_uvmat('ERROR',errormsg)
873elseif isfield(handles,'status')
874    set(handles.status,'Value',1);%suppress status display
875    status_Callback(hObject, eventdata, handles)
876end
877
878%-------------------------------------------------------------------
879% --- Executes on button press in status.
880function status_Callback(hObject, eventdata, handles)
881%-------------------------------------------------------------------
882val=get(handles.status,'Value');
883if val==0
884    set(handles.status,'BackgroundColor',[0 1 0])
885    hfig=findobj(allchild(0),'name','civ_status');
886    if ~isempty(hfig)
887        delete(hfig)
888    end
889    return
890end
891set(handles.status,'BackgroundColor',[1 1 0])
892drawnow
893listtype={'civ1','fix1','patch1','civ2','fix2','patch2'};
894Param.CheckCiv1=get(handles.CheckCiv1,'Value');
895Param.CheckFix1=get(handles.CheckFix1,'Value');
896Param.CheckPatch1=get(handles.CheckPatch1,'Value');
897Param.CheckCiv2=get(handles.CheckCiv2,'Value');
898Param.CheckFix2=get(handles.CheckFix2,'Value');
899Param.CheckPatch2=get(handles.CheckPatch2,'Value');
900box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2];
901
902option_civ=find(box_test,1,'last');%last selected option (non-zero index of box_test)
903filecell=get(handles.civ,'UserData');%retrieve the list of output files expected for PIV
904test_new=0;
905if ~isfield(filecell,'nc')
906    test_new=1;
907    [ref_i,ref_j,errormsg]=find_ref_indices(handles);
908    if ~isempty(errormsg)
909        msgbox_uvmat('ERROR',errormsg)
910        return
911    end
912    filecell=set_civ_filenames(handles,ref_i,ref_j,box_test);%determine the output file expected from the GUI status
913end
914if ~isequal(box_test(4:6),[0 0 0])
915    civ_files=filecell.nc.civ2;%case of civ2 operations
916else
917    civ_files=filecell.nc.civ1;
918end
919[root,filename,ext]=fileparts(civ_files{1});
920[rootroot,SubDir,extdir]=fileparts(root);
921hfig=findobj(allchild(0),'name','civ_status');
922if isempty(hfig)
923    hfig=figure('DeleteFcn',@stop_status);
924    set(hfig,'MenuBar','none')% suppress the menu bar
925    set(hfig,'NumberTitle','off')%suppress the fig number in the title
926    set(hfig,'name','civ_status')
927    set(hfig,'tag','civ_status')
928    set(hfig,'UserData',civ_files)
929    hlist= uicontrol('Style','listbox','Units','normalized', 'Position',[0.05 0.09 0.9 0.71], 'Callback', {'open_uvmat'},'tag','list');
930    uicontrol('Style','edit','Units','normalized', 'Position', [0.05 0.87 0.9 0.1],'tag','msgbox','Max',2,'String','checking files...');
931    uicontrol('Style','frame','Units','normalized', 'Position', [0.05 0.81 0.9 0.05]);
932    uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.7 0.01 0.2 0.07],'String','Close','FontWeight','bold','FontUnits','normalized','FontSize',0.9,'Callback',@close_GUI);
933    hrefresh=uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.1 0.01 0.2 0.07],'String','Refresh','FontWeight','bold','FontUnits','normalized','FontSize',0.9,'Callback',@refresh_GUI);
934    BarPosition=[0.05 0.81 0.01 0.05];
935    uicontrol('Style','frame','Units','normalized', 'Position',BarPosition ,'BackgroundColor',[1 0 0],'tag','waitbar');
936    drawnow
937end
938set(hrefresh,'UserData',option_civ)
939        filepath=fileparts(civ_files{1});
940set(hlist,'UserData',fileparts(filepath))
941refresh_GUI(hrefresh,[])
942
943%------------------------------------------------------------------------   
944% launched by refreshing the status figure
945function refresh_GUI(hObject, eventdata)
946%------------------------------------------------------------------------
947Tabchar={};
948BarPosition=[0.05 0.81 0.01 0.05];
949hfig=get(hObject,'parent');
950civ_files=get(hfig,'UserData');
951        [filepath,filename,ext]=fileparts(civ_files{1});
952        [tild,SubDir,extdir]=fileparts(filepath);
953        SubDir=[SubDir extdir];
954option_civ=get(hObject,'UserData');
955nbfiles=numel(civ_files);
956count=0;
957testrecent=0;
958% while count<nbfiles
959    count=0;
960    datnum=zeros(1,nbfiles);
961    for ifile=1:nbfiles
962        detect=exist(civ_files{ifile},'file'); % check the existence of the file
963        option=0;
964        if detect==0
965            option_str='not created';
966        else
967            datfile=dir(civ_files{ifile});
968            if isfield(datfile,'datenum')
969                datnum(ifile)=datfile.datenum;%only available in recent matlab versions
970                testrecent=1;
971            end
972            filefound(ifile)={datfile.name};
973            lastfield='';
974            % check the content  netcdf file
975            Data=nc2struct(civ_files{ifile},'ListGlobalAttribute','CivStage','patch2','fix2','civ2','patch','fix');
976            option_list={'civ1','fix1','patch1','civ2','fix2','patch2'};
977            if ~isempty(Data.CivStage)
978                option=Data.CivStage;%case of Matlab civ
979            else
980                if ~isempty(Data.patch2) && isequal(Data.patch2,1)
981                    option=6;
982                elseif ~isempty(Data.fix2) && isequal(Data.fix2,1)
983                    option=5;
984                elseif ~isempty(Data.civ2) && isequal(Data.civ2,1);
985                    option=4;
986                elseif ~isempty(Data.patch) && isequal(Data.patch,1);
987                    option=3;
988                elseif ~isempty(Data.fix) && isequal(Data.fix,1);
989                    option=2;
990                else
991                    option=1;
992                end
993            end
994            option_str=option_list{option};
995        end
996        if option >= option_civ
997            count=count+1;
998        end
999        [filepath,filename,ext]=fileparts(civ_files{ifile});
1000        Tabchar{ifile,1}=[fullfile(SubDir,filename) ext  '...' option_str];
1001    end
1002    datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
1003    if isempty(datnum)
1004        if testrecent
1005            message='no civ result created yet';
1006        else
1007            message='';
1008        end
1009    else
1010        datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
1011        [first,ind]=min(datnum);
1012        [last,indlast]=max(datnum);
1013%         if test_new
1014%             message='existing file status, no processing launched yet';
1015%         else
1016        message={[num2str(count) ' file(s) done over ' num2str(nbfiles)] ;['oldest modification:  ' cell2mat(filefound(ind)) ' : ' datestr(first)];...
1017            ['latest modification:  ' cell2mat(filefound(indlast)) ' : ' datestr(last)]};
1018%         end
1019    end
1020    %hfig=findobj(allchild(0),'name','civ_status');
1021%     if isempty(hfig)% the status list has been deleted
1022%         return
1023%     else
1024        hlist=findobj(hfig,'tag','list');
1025        hmsgbox=findobj(hfig,'tag','msgbox');
1026        hwaitbar=findobj(hfig,'tag','waitbar');
1027        set(hlist,'String',Tabchar)
1028        set(hmsgbox,'String', message)
1029        if count>0 %&& ~test_new
1030            BarPosition(3)=0.9*count/nbfiles;
1031            set(hwaitbar,'Position',BarPosition)
1032        end
1033%     end
1034%     [root,filename,ext]=fileparts(civ_files{1});
1035% [rootroot,SubDir,extdir]=fileparts(root);
1036%
1037%     set(hlist,'UserData',rootroot)
1038%     if count<10||(nbfiles-count)<10
1039%     pause(.5)% wait 0.5 seconds for next check
1040%     else
1041%         pause(10)% wait 10 seconds for next check
1042%     end
1043% end
1044
1045%------------------------------------------------------------------------   
1046% launched by deleting the status figure
1047function stop_status(hObject, eventdata)
1048%------------------------------------------------------------------------
1049hciv=findobj(allchild(0),'tag','civ');
1050hhciv=guidata(hciv);
1051set(hhciv.status,'value',0) %reset the status uicontrol in the GUI civ
1052set(hhciv.status,'BackgroundColor',[0 1 0])
1053
1054%------------------------------------------------------------------------   
1055% launched by pressing OK on the status figure
1056function close_GUI(hObject, eventdata)
1057%------------------------------------------------------------------------
1058    delete(gcbf)
1059
1060
1061%------------------------------------------------------------------------
1062% --- Main lauch command, called by RUN and BATCH
1063function errormsg=launch_jobs(hObject, eventdata, handles, batch)
1064%-----------------------------------------------------------------------
1065errormsg='';%default
1066
1067%% read the input parameters from the  GUI civ
1068Param=read_GUI(handles.civ);
1069
1070%% check the selected list of operations:
1071operations={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'};
1072box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2];
1073index_first=find(box_test==1,1);
1074if isempty(index_first)
1075    errormsg='no selected operation';
1076    return
1077end
1078index_last=find(box_test==1,1,'last');
1079box_used=box_test(index_first : index_last);
1080[box_missing,ind_missing]=min(box_used);
1081if isequal(box_missing,0); %there is a missing step in the sequence of operations
1082    errormsg=['missing' cell2mat(operations(ind_missing))];
1083    return
1084end
1085
1086%% check mask if selecetd
1087%could be included in get_mask callback ?
1088if isequal(get(handles.CheckMask,'Value'),1)
1089    maskname=get(handles.Mask,'String');
1090    if ~exist(maskname,'file')
1091        get_mask_civ1_Callback(hObject, eventdata, handles);
1092    end
1093end
1094if isequal(get(handles.CheckMask,'Value'),1)
1095    maskname=get(handles.Mask,'String');
1096    if ~exist(maskname,'file')
1097        get_mask_fix1_Callback(hObject, eventdata, handles);
1098    end
1099end
1100if isequal(get(handles.CheckMask,'Value'),1)
1101    maskname=get(handles.Mask,'String');
1102    if ~exist(maskname,'file')
1103        get_mask_civ2_Callback(hObject, eventdata, handles);
1104    end
1105end
1106if isequal(get(handles.CheckMask,'Value'),1)
1107    maskname=get(handles.Mask,'String');
1108    if ~exist(maskname,'file')
1109        get_mask_fix2_Callback(hObject, eventdata, handles);
1110    end
1111end
1112
1113%% reinitialise status callback
1114if isfield(handles,'status')
1115    set(handles.status,'Value',0);%suppress status display
1116    status_Callback(hObject, eventdata, handles)
1117end
1118
1119%% read the PARAM.xml file to get the binaries (and batch_mode if batch)
1120path_civ=fileparts(which('civ')); %path to the source directory of uvmat
1121xmlfile='PARAM.xml';
1122if exist(xmlfile,'file')% search parameter xml file in the whole matlab path
1123    t=xmltree(xmlfile);
1124    s=convert(t);
1125else
1126    errormsg=['no file ' xmlfile];
1127    return
1128end
1129test_interp=0; %eviter les variables test_ (LG)
1130if batch
1131    if isfield(s,'BatchParam')
1132        Param.xml=s.BatchParam;
1133        if isfield(Param.xml,'BatchMode')
1134            batch_mode=Param.xml.BatchMode;
1135            if ~ismember(batch_mode,{'sge','oar'})
1136                errormsg=['batch mode ' batch_mode ' not supported by UVMAT'];
1137                return
1138            end
1139        end
1140    else
1141        errormsg='no batch civ binaries defined in PARAM.xml';
1142        return
1143    end
1144else % run
1145    if isfield(s,'RunParam')
1146        Param.xml=s.RunParam;
1147    else
1148        errormsg='no run civ binaries defined in PARAM.xml';
1149        return
1150    end
1151end
1152
1153%% check batch mode supported
1154if batch
1155    switch batch_mode
1156        case 'sge'
1157            test_command='qstat';
1158        case 'oar'
1159            test_command='oarstat';
1160    end   
1161    [s,w]=system(test_command);
1162    if ~isequal(s,0)
1163        errormsg=[batch_mode ' batch system not available'];
1164        return
1165    end
1166end
1167
1168%% check if the binaries exist
1169ListProgram=get(handles.ListProgram,'String');
1170CivMode=ListProgram{get(handles.ListProgram,'Value')};
1171binary_list={};
1172switch CivMode
1173    case 'CivX'
1174        binary_list={'Civ1Bin','Civ2Bin','PatchBin','FixBin'};
1175    case 'CivAll'% desactivated option
1176        binary_list={'Civ'};
1177    case 'Matlab'
1178        if batch
1179            binary_list={'CivmBin'};
1180            % verifier MenuMatlab installe sur le cluster
1181            % difficile a faire a priori
1182        end         
1183end
1184for bin_name=binary_list %loop on the list of binaries
1185    if isfield(Param.xml,bin_name{1})% bin_name{1} =current name in the list
1186        if exist(Param.xml.(bin_name{1}),'file')
1187            [path,name,ext]=fileparts(Param.xml.(bin_name{1}));
1188            currentdir=pwd;
1189            if exist(path,'dir')
1190                cd(path);
1191                binpath=pwd;%path of the binary
1192                Param.xml.(bin_name{1})=fullfile(binpath,[name ext]);
1193                cd(currentdir)
1194            else
1195                errormsg=['path ' path ' for binaries defined in PARAM.xml does not exist'];
1196                return
1197            end
1198        else  %look for the full path if the file name has been defined with a relative path in PARAM.xm
1199            fullname=fullfile(path_civ,Param.xml.(bin_name{1}));
1200            if exist(fullname,'file')
1201                Param.xml.(bin_name{1})=fullname;
1202            else
1203                errormsg=['Binary ' Param.xml.(bin_name{1}) ' defined in PARAM.xml does not exist'];
1204                return
1205            end
1206        end
1207    end
1208end
1209display('files OK, processing...')
1210
1211%% set the list of files and check them
1212display('checking the files...')
1213[ref_i,ref_j,errormsg]=find_ref_indices(handles);
1214if ~isempty(errormsg)
1215    return
1216end
1217[filecell,i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,xx,yy,compare]=...
1218    set_civ_filenames(handles,ref_i,ref_j,box_test);
1219
1220Rootbat=fileparts(filecell.nc.civ1{1,1});%output netcdf file (without extention)
1221set(handles.civ,'UserData',filecell);%store for futur use of status callback
1222if isempty(filecell)% (error message displayed in fct set_civ_filenames)
1223    return
1224end
1225nbfield=numel(i1_civ1);
1226nbslice=numel(j1_civ1);
1227if ~strcmp(CivMode,'CivX')
1228    if Param.CheckCiv1
1229    [Param.Civ1.FileTypeA,FileInfo,Param.Civ1.ImageA]=get_file_type(filecell.ima1.civ1{1});
1230    [Param.Civ1.FileTypeB,FileInfo,Param.Civ1.ImageB]=get_file_type(filecell.ima2.civ1{1});
1231    end
1232    if Param.CheckCiv2
1233    [Param.Civ2.FileTypeA,FileInfo,Param.Civ2.ImageA]=get_file_type(filecell.ima1.civ2{1});
1234    [Param.Civ2.FileTypeB,FileInfo,Param.Civ2.ImageB]=get_file_type(filecell.ima2.civ2{1});
1235    end
1236end
1237
1238%% MAIN LOOP
1239time=get(handles.ImaDoc,'UserData'); %get the set of times
1240TimeUnit=get(handles.TimeUnit,'String');
1241checkframe=strcmp(TimeUnit,'frame');
1242batch_file_list=[];%should be renamed file_list, can be used for xml or bash files
1243 
1244for ifile=1:nbfield
1245    for j=1:nbslice
1246        % initiate system command
1247        switch CivMode
1248            case 'CivX'
1249                if isunix % check: necessaire aussi en RUN?
1250                    cmd=['#!/bin/bash \n '...
1251                        '#$ -cwd \n '...
1252                        'hostname && date \n '...
1253                        'umask 002 \n'];%allow writting access to created files for user group
1254                else
1255                    cmd=[];
1256                end
1257            case 'CivAll'
1258                CivAllxml=xmltree;% xml contents,  all parameters
1259                CivAllCmd='';
1260                CivAllxml=set(CivAllxml,1,'name','CivDoc');
1261        end
1262           
1263        % define output file name
1264        if Param.CheckCiv2==1 || Param.CheckFix2==1 || Param.CheckPatch2==1
1265            OutputFile=filecell.nc.civ2{ifile,j};
1266        else
1267            OutputFile=filecell.nc.civ1{ifile,j};
1268        end
1269        OutputFile=regexprep(OutputFile,'.nc','');
1270       
1271        if Param.CheckCiv1
1272            % read image-dependent parameters
1273            Param.Civ1.ImageA=filecell.ima1.civ1{ifile,j};
1274            Param.Civ1.ImageB=filecell.ima2.civ1{ifile,j};
1275            if ~checkframe% && size(time,1)>=i2_civ1(ifile) && size(time,2)>=j2_civ1(j)
1276                Param.Civ1.Dt=(time(i2_civ1(ifile)+1,j2_civ1(j)+1)-time(i1_civ1(ifile)+1,j1_civ1(j)+1));
1277            else
1278                Param.Civ1.Dt=1;
1279            end
1280            Param.Civ1.Time=((time(i2_civ1(ifile)+1,j2_civ1(j)+1)+time(i1_civ1(ifile)+1,j1_civ1(j)+1))/2);
1281            if strcmp(CivMode,'CivX')
1282            Param.Civ1.term_a=num2stra(j1_civ1(j),nom_type_nc);%UTILITE?
1283            Param.Civ1.term_b=num2stra(j2_civ1(j),nom_type_nc);%
1284            end
1285            form=imformats(regexprep(get(handles.ImaExt,'String'),'^.',''));%look for image formats
1286            if isempty(form)
1287                ImageInfo=get(VideoReader(filecell.ima1.civ1{1,1}));
1288                Param.Civ1.ImageBitDepth=ImageInfo.BitsPerPixel/3;
1289            else
1290                ImageInfo=imfinfo(filecell.ima1.civ1{1,1});%read the first image to get the size
1291                Param.Civ1.ImageBitDepth=ImageInfo.BitDepth;
1292            end
1293            Param.Civ1.ImageWidth=ImageInfo.Width;
1294            Param.Civ1.ImageHeight=ImageInfo.Height;
1295            Param.Civ1.i1=i1_civ1(ifile);
1296            Param.Civ1.i2=i2_civ1(ifile);
1297            % read mask parameters
1298            if Param.Civ1.CheckMask % the lines below should be changed with the new gui
1299                if ~exist(Param.Civ1.Mask,'file')
1300                    maskbase=[filecell.filebase '_' Param.Civ1.Mask]; %
1301                    nbslice_mask=str2double(Param.Civ1.Mask(1:end-4)); %
1302                    i1_mask=mod(i1_civ1(ifile)-1,nbslice_mask)+1;
1303                    [RootPathMask,RootFileMask]=fileparts(maskbase);
1304                    Param.Civ1.Mask=fullfile_uvmat(RootPathMask,[],RootFileMask,'.png','_1',i1_mask);
1305                end
1306            end
1307            % read grid parameters
1308            if Param.Civ1.CheckGrid
1309                if numel(Param.Civ1.Grid)>=4 && isequal(Param.Civ1.Grid(end-3:end),'grid')
1310                    nbslice_grid=str2double(Param.Civ1.Grid(1:end-4)); %
1311                    if ~isnan(nbslice_grid)
1312                        i1_grid=mod(i1_civ1(ifile)-1,nbslice_grid)+1;
1313                        Param.Civ1.Grid=[filecell.filebase '_' fullfile_uvmat('','',Param.Civ1.Grid,'.grid','_1',i1_grid)];
1314%                         Param.Civ1.Grid=[filecell.filebase '_' name_generator(Param.Civ1.Grid,i1_grid,1,'.grid','_i')];
1315                        if ~exist(Param.Civ1.GridName,'file')
1316                            errormsg='grid file absent for civ1';
1317                            return
1318                        end
1319                    elseif ~exist(Param.Civ1.Grid,'file')
1320                        errormsg='grid file absent for civ1';
1321                        return
1322                    end
1323                end
1324            end
1325           
1326            % send command
1327            switch CivMode
1328                case 'CivX'
1329                    [cmd_civ,errormsg]=cmd_civ1(filecell.nc.civ1{ifile,j},Param);
1330                    cmd=[cmd cmd_civ '\n'];
1331                    if ~isempty(errormsg)
1332                        return
1333                    end
1334                case 'CivAll'
1335                    CivAllCmd=[CivAllCmd ' civ1 '];
1336                    str=CIV1_CMD_Unified(filecell.nc.civ1{ifile,j},'',Param.Civ1);
1337                    fieldnames=fields(str);
1338                    [CivAllxml,uid_civ1]=add(CivAllxml,1,'element','civ1');
1339                    for ilist=1:length(fieldnames)
1340                        val=eval(['str.' fieldnames{ilist}]);
1341                        if ischar(val)
1342                            [CivAllxml,uid_t]=add(CivAllxml,uid_civ1,'element',fieldnames{ilist});
1343                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1344                        end
1345                    end
1346            end
1347        end
1348       
1349        if Param.CheckFix1
1350            switch CivMode
1351                case 'CivX'
1352                    cmd=[cmd...
1353                        cmd_fix(filecell.nc.civ1{ifile,j},Param,'Fix1') '\n'];
1354                case 'CivAll'%to abandon
1355                    fix1.inputFileName=filecell.nc.civ1{ifile,j} ;
1356                    fix1.fi1=num2str(param.fix1.flagindex1(1));
1357                    fix1.fi2=num2str(param.fix1.flagindex1(2));
1358                    fix1.fi3=num2str(param.fix1.flagindex1(3));
1359                    fix1.threshC=num2str(param.fix1.thresh_vecC1);
1360                    fix1.threshV=num2str(param.fix1.thresh_vel1);
1361                    fieldnames=fields(fix1);
1362                    [CivAllxml,uid_fix1]=add(CivAllxml,1,'element','fix1');
1363                    for ilist=1:length(fieldnames)
1364                        val=eval(['fix1.' fieldnames{ilist}]);
1365                        if ischar(val)
1366                            [CivAllxml,uid_t]=add(CivAllxml,uid_fix1,'element',fieldnames{ilist});
1367                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1368                        end
1369                    end
1370                    CivAllCmd=[CivAllCmd ' fix1 '];
1371            end
1372        end
1373       
1374        %CheckPatch1
1375        if Param.CheckPatch1==1
1376            switch CivMode
1377                case 'CivX'
1378                    cmd=[cmd...
1379                        cmd_patch(filecell.nc.civ1{ifile,j},Param,'Patch1') '\n'];
1380                case 'CivAll'
1381                    patch1.inputFileName=filecell.nc.civ1{ifile,j} ;
1382                    patch1.nopt=subdomain_patch1;
1383                    patch1.maxdiff=thresh_patch1;
1384                    patch1.ro=rho_patch1;
1385                    test_grid=get(handles.get_gridpatch1,'Value');
1386                    if test_grid
1387                        patch1.gridflag='y';
1388                        gridname=get(handles.grid_patch1,'String');
1389                        if isequal(gridname(end-3:end),'grid')
1390                            nbslice_grid=str2double(gridname(1:end-4)); %
1391                            if ~isnan(nbslice_grid)
1392                                i1_grid=mod(i1_civ1(ifile)-1,nbslice_grid)+1;
1393                                patch1.gridPatch=[filecell.filebase '_' fullfile_uvmat('','',gridname,'.grid','_1',i1_grid)];
1394%                                 patch1.gridPatch=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')];
1395                                if ~exist(patch1.gridPatch,'file')
1396                                    errormsg='grid file absent for patch1';
1397                                    return
1398                                end
1399                            elseif exist(gridname,'file')
1400                                patch1.gridPatch=gridname;
1401                            else
1402                                errormsg='grid file absent for patch1';
1403                                return
1404                            end
1405                        end
1406                    else
1407                        patch1.gridPatch='none';
1408                        patch1.gridflag='n';
1409                        patch1.m=nx_patch1;
1410                        patch1.n=ny_patch1;
1411                    end
1412                    patch1.convectFlow='n';
1413                    fieldnames=fields(patch1);
1414                    [CivAllxml,uid_patch1]=add(CivAllxml,1,'element','patch1');
1415                    for ilist=1:length(fieldnames)
1416                        val=eval(['patch1.' fieldnames{ilist}]);
1417                        if ischar(val)
1418                            [CivAllxml,uid_t]=add(CivAllxml,uid_patch1,'element',fieldnames{ilist});
1419                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1420                        end
1421                    end
1422                    CivAllCmd=[CivAllCmd ' patch1 '];
1423            end
1424        end
1425        if Param.CheckCiv2==1
1426            Param.Civ2.ImageA=filecell.ima1.civ2{ifile,j};
1427            Param.Civ2.ImageB=filecell.ima2.civ2{ifile,j};
1428            if ~checkframe %&& size(time,1)>=i2_civ2(ifile) && size(time,2)>=j2_civ2(j)
1429                Param.Civ2.Dt=time(i2_civ2(ifile)+1,j2_civ2(j)+1)-time(i1_civ2(ifile)+1,j1_civ2(j)+1);
1430            else
1431                Param.Civ2.Dt=1;
1432            end
1433            Param.Civ2.Time=(time(i2_civ2(ifile)+1,j2_civ2(j)+1)+time(i1_civ2(ifile)+1,j1_civ2(j)+1))/2;
1434            if strcmp(CivMode,'CivX')
1435            Param.Civ2.term_a=num2stra(j1_civ2(j),nom_type_nc);
1436            Param.Civ2.term_b=num2stra(j2_civ2(j),nom_type_nc);
1437            end
1438            Param.Civ2.filename_nc1=filecell.nc.civ1{ifile,j};
1439            Param.Civ2.filename_nc1(end-2:end)=[]; % remove '.nc'
1440           
1441            % mask
1442            if Param.Civ2.CheckMask
1443                if ~exist(Param.Civ2.Mask,'file')
1444                    maskbase=[filecell.filebase '_' Param.Civ2.Mask]; %
1445                    nbslice_mask=str2double(Param.Civ2.Mask(1:end-4)); %
1446                    i1_mask=mod(i1_civ2(ifile)-1,nbslice_mask)+1;
1447                    [RootPathMask,RootFileMask]=fileparts(maskbase);
1448                    Param.Civ2.Mask=fullfile_uvmat(RootPathMask,[],RootFileMask,'.png','_1',i1_mask);
1449%                     Param.Civ2.Mask=name_generator(maskbase,i1_mask,1,'.png','_i');
1450                end
1451            end
1452            %grid
1453            if Param.Civ2.CheckGrid
1454                if numel(Param.Civ2.Grid)>=4 && isequal(Param.Civ2.Grid(end-3:end),'grid')
1455                    nbslice_grid=str2double(Param.Civ2.Grid(1:end-4)); %
1456                    if ~isnan(nbslice_grid)
1457                        i1_grid=mod(i1_civ2(ifile)-1,nbslice_grid)+1;
1458                        Param.Civ2.Grid=[filecell.filebase '_' fullfile_uvmat('','',gridname,'.grid','_1',i1_grid)];
1459%                         Param.Civ2.Grid=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')];
1460                    end
1461                end
1462            end
1463            form=imformats(regexprep(get(handles.ImaExt,'String'),'^.',''));%look for image formats
1464            if isempty(form)
1465                ImageInfo=get(VideoReader(filecell.ima1.civ2{1,1}));
1466                Param.Civ2.ImageBitDepth=ImageInfo.BitsPerPixel/3;
1467            else
1468                ImageInfo=imfinfo(filecell.ima1.civ2{1,1});%read the first image to get the size
1469                Param.Civ2.ImageBitDepth=ImageInfo.BitDepth;
1470            end
1471            Param.Civ2.ImageWidth=ImageInfo.Width;
1472            Param.Civ2.ImageHeight=ImageInfo.Height;
1473            Param.Civ2.i1=i1_civ2(ifile);
1474            Param.Civ2.i2=i2_civ2(ifile);
1475            switch CivMode
1476                case 'CivX'
1477                    cmd=[cmd...
1478                        cmd_civ2(filecell.nc.civ2{ifile,j},Param) '\n'];
1479                case 'CivAll'
1480                    CivAllCmd=[CivAllCmd ' civ2 '];
1481                    str=CIV2_CMD_Unified(filecell.nc.civ2{ifile,j},'',Param.Civ2);
1482                    fieldnames=fields(str);
1483                    [CivAllxml,uid_civ2]=add(CivAllxml,1,'element','civ2');
1484                    for ilist=1:length(fieldnames)
1485                        val=eval(['str.' fieldnames{ilist}]);
1486                        if ischar(val)
1487                            [CivAllxml,uid_t]=add(CivAllxml,uid_civ2,'element',fieldnames{ilist});
1488                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1489                        end
1490                    end
1491            end
1492        end
1493       
1494        % CheckFix2
1495        if Param.CheckFix2==1
1496            switch CivMode
1497                case 'CivX'
1498                    cmd=[cmd...
1499                        cmd_fix(filecell.nc.civ2{ifile,j},Param,'Fix2') '\n'];
1500                case 'CivAll'
1501                    fix2.inputFileName=filecell.nc.civ2{ifile,j} ;
1502                    fix2.fi1=num2str(flagindex2(1));
1503                    fix2.fi2=num2str(flagindex2(2));
1504                    fix2.fi3=num2str(flagindex2(3));
1505                    fix2.threshC=num2str(thresh_vec2C);
1506                    fix2.threshV=num2str(thresh_vel2);
1507                    fieldnames=fields(fix2);
1508                    [CivAllxml,uid_fix2]=add(CivAllxml,1,'element','fix2');
1509                    for ilist=1:length(fieldnames)
1510                        val=eval(['fix2.' fieldnames{ilist}]);
1511                        if ischar(val)
1512                            [CivAllxml,uid_t]=add(CivAllxml,uid_fix2,'element',fieldnames{ilist});
1513                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1514                        end
1515                    end
1516                    CivAllCmd=[CivAllCmd ' fix2 '];
1517            end
1518        end
1519       
1520        %CheckPatch2
1521        if Param.CheckPatch2==1
1522           
1523            switch CivMode
1524               
1525                case 'CivX'
1526                    cmd=[cmd...
1527                        cmd_patch(filecell.nc.civ1{ifile,j},Param,'Patch2') '\n'];
1528                   
1529                case 'CivAll'
1530                    patch2.inputFileName=filecell.nc.civ1{ifile,j} ;
1531                    patch2.nopt=subdomain_patch2;
1532                    patch2.maxdiff=thresh_patch2;
1533                    patch2.ro=rho_patch2;
1534                    test_grid=get(handles.get_gridpatch2,'Value');
1535                    if test_grid
1536                        patch2.gridflag='y';
1537                        gridname=get(handles.grid_patch2,'String');
1538                        if isequal(gridname(end-3:end),'grid')
1539                            nbslice_grid=str2double(gridname(1:end-4)); %
1540                            if ~isnan(nbslice_grid)
1541                                i1_grid=mod(i1_civ2(ifile)-1,nbslice_grid)+1;
1542                                patch2.gridPatch=[filecell.filebase '_' fullfile_uvmat('','',gridname,'.grid','_1',i1_grid)];
1543%                                 patch2.gridPatch=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')];
1544                                if ~exist(patch2.gridPatch,'file')
1545                                    errormsg='grid file absent for patch2';
1546                                    return
1547                                end
1548                            elseif exist(gridname,'file')
1549                                patch2.gridPatch=gridname;
1550                            else
1551                                errormsg='grid file absent for patch2';
1552                                return
1553                            end
1554                        end
1555                    else
1556                        patch2.gridPatch='none';
1557                        patch2.gridflag='n';
1558                        patch2.m=nx_patch2;
1559                        patch2.n=ny_patch2;
1560                    end
1561                    patch2.convectFlow='n';
1562                    fieldnames=fields(patch2);
1563                    [CivAllxml,uid_patch2]=add(CivAllxml,1,'element','patch2');
1564                    for ilist=1:length(fieldnames)
1565                        val=eval(['patch2.' fieldnames{ilist}]);
1566                        if ischar(val)
1567                            [CivAllxml,uid_t]=add(CivAllxml,uid_patch2,'element',fieldnames{ilist});
1568                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1569                        end
1570                    end
1571                    CivAllCmd=[CivAllCmd ' patch2 '];
1572            end
1573        end
1574       
1575        switch CivMode
1576           
1577            case {'CivX','CivAll'}
1578                if isequal(CivMode,'CivAll')
1579                    save(CivAllxml,[OutputFile '.xml']);
1580                    cmd=[cmd sparam.CivBin ' -f ' OutputFile '.xml '  CivAllCmd ' >' OutputFile '.log' '\n'];
1581                end             
1582                % create the .bat file used in run or batch
1583                filename_bat=[OutputFile '.bat'];
1584                [fid,message]=fopen(filename_bat,'w');
1585                if isequal(fid,-1)
1586                    errormsg=['creation of .bat file: ' message];
1587                    return
1588                end
1589                fprintf(fid,cmd);
1590                fclose(fid);           
1591                if isunix
1592                    system(['chmod +x ' filename_bat]);
1593                end             
1594                batch_file_list{length(batch_file_list)+1}=filename_bat;
1595               
1596            case 'Matlab'
1597                drawnow
1598                if ~strcmp(compare,'stereo PIV')
1599                    filename_xml=[OutputFile '.civ.xml'];
1600                    t=struct2xml(Param);           
1601                    save(t,filename_xml)
1602                    if batch   
1603                        path_civ=fileparts(which('civ'));
1604                        filename_bat=[OutputFile '.bat'];
1605                        [fid,message]=fopen(filename_bat,'w');
1606                        if isequal(fid,-1)
1607                            errormsg= ['creation of .bat file: ' message];
1608                            return
1609                        end
1610%                         text_matlabscript=[...
1611%                         '#!/bin/bash \n'...
1612%                         '. /etc/sysprofile \n'...
1613%                         'matlab -nodisplay -nosplash -nojvm <<END_MATLAB \n'...
1614%                         'cd(''' path_civ '''); \n'...
1615%                         'civ_matlab(''' filename_xml ''',''' OutputFile '.nc''); \n'...
1616%                         'exit \n'...
1617%                         'END_MATLAB \n'];
1618                        cmd=['#!/bin/bash \n '...
1619                        '#$ -cwd \n '...
1620                        'hostname && date \n '...
1621                        'umask 002 \n'...
1622                         Param.xml.CivmBin ' ' Param.xml.RunTime ' ' filename_xml ' ' OutputFile '.nc'];%allow writting access to created files for user group
1623                   
1624                        fprintf(fid,cmd);
1625                        fclose(fid);
1626                        if isunix
1627                            system(['chmod +x ' filename_bat]);
1628                        end
1629                        batch_file_list{length(batch_file_list)+1}=filename_bat;
1630                    else
1631                        [tild,errormsg]=civ_matlab(Param,filecell.nc.civ1{ifile,j});
1632                        if isempty(errormsg)
1633                            display([filecell.nc.civ1{ifile,j} ' written'])
1634                        end
1635                    end
1636                end
1637        end
1638    end
1639end
1640
1641if batch 
1642    switch batch_mode   
1643       
1644        case 'sge' %at the moment only psmn ENS Lyon uses it
1645            for p=1:length(batch_file_list)
1646                %cmd=['!qsub -p ' pvalue ' -q civ.q -e ' flname '.errors -o ' flname '.log' ' ' batch_file_list{p}];
1647                cmd=['!qsub -q piv1,piv2,piv3 '...
1648                    '-e ' regexprep(batch_file_list{p},'.bat','.errors') ' -o ' regexprep(batch_file_list{p},'.bat','.log ')...
1649                    ' -v ' 'LD_LIBRARY_PATH=/home/sjoubaud/matlab_sylvain/civx/lib ' batch_file_list{p}];               
1650                display(cmd);eval(cmd);
1651            end           
1652        case 'oar_old'
1653                for p=1:length(batch_file_list)
1654                    oar_command=['!oarsub -n CIVX -q nicejob '...
1655                   '-E ' regexprep(batch_file_list{p},'.bat','.errors') ' -O ' regexprep(batch_file_list{p},'.bat','.log ')...
1656                    '-l "/core=1+{type = ''smalljob''}/licence=1,walltime=00:60:00"   ' batch_file_list{p}];
1657                display(oar_command);eval(oar_command);
1658                end               
1659        case 'oar'
1660           
1661            max_walltime=3600*12; % 12h max
1662            oar_modes={'oar-parexec','oar-dispatch','mpilauncher'};
1663            text={'Batch processing on servcalcul3 LEGI';...
1664                'Please choose one of the followint modes';...
1665                '* oar-parexec : default and best choice';...
1666                '* oar-dispatch : jobs in a container of several cores';...
1667                '* mpilauncher : one single parallel mpi job using several cores';...
1668                '**********************************'...
1669                };
1670            [S,v]=listdlg('PromptString',text,'ListString',oar_modes,...
1671                'SelectionMode','single','ListSize',[400 100],'Name','LEGI job mode');
1672            switch oar_modes{S}
1673                case 'oar-parexec' %oar-dispatch.pl
1674                    answer=inputdlg({'Number of cores (max 36)','extra oar options'},'oarsub parameter',1,{'12',''});
1675                    ncores=str2double(answer{1});
1676                    extra_oar=answer{2};
1677                    walltime_onejob=600;%seconds
1678                    filename_joblist=fullfile(Rootbat,'job_list.txt');
1679                    fid=fopen(filename_joblist,'w');
1680                    for p=1:length(batch_file_list)
1681                        fprintf(fid,[batch_file_list{p} '\n']);
1682                    end
1683                    fclose(fid)
1684                    oar_command=['oarsub -n CIVX '...
1685                        '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
1686                        '-l /core=' num2str(ncores) ','...
1687                            'walltime=' datestr(min(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,max_walltime/86400),13) ' '...
1688                        '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '...
1689                        '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '...
1690                        extra_oar ' '...
1691                        '"oar-parexec -s -f ' filename_joblist ' '...
1692                            '-l ' filename_joblist '.log"'];
1693                    filename_oarcommand=fullfile(Rootbat,'oar_command');
1694                    fid=fopen(filename_oarcommand,'w');
1695                    fprintf(fid,[oar_command '\n']);
1696                    fclose(fid);
1697                    display(oar_command);
1698                    eval(['! . ' filename_oarcommand])
1699                case 'oar-dispatch' %oar-dispatch.pl
1700                    ncores=str2double(...
1701                        inputdlg('Number of cores (max 36)','oarsub parameter',1,{'6'})...
1702                        );
1703                    walltime_onejob=600;%seconds
1704                    filename_joblist=fullfile(Rootbat,'job_list.txt');
1705                    fid=fopen(filename_joblist,'w');
1706                    for p=1:length(batch_file_list)
1707                        oar_command=['oarsub -n CIVX '...
1708                            '-E ' regexprep(batch_file_list{p},'\.bat\>','.stderr') ' -O ' regexprep(batch_file_list{p},'\.bat\>','.stdout ')...
1709                            '-l "/core=1,walltime=' datestr(walltime_onejob/86400,13) '"   ' batch_file_list{p}];
1710                        fprintf(fid,[oar_command '\n']);
1711                    end
1712                    fclose(fid);
1713                    oar_command=['oarsub -t container -n civx-container '...
1714                        '-l /core=' num2str(ncores)...
1715                        ',walltime=' datestr(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,13) ' '...
1716                        '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '...
1717                        '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '...
1718                        '"oar-dispatch -f ' filename_joblist '"'];
1719                    filename_oarcommand=fullfile(Rootbat,'oar_command');
1720                    fid=fopen(filename_oarcommand,'w');
1721                    fprintf(fid,[oar_command '\n']);
1722                    fclose(fid);
1723                    display(oar_command);
1724                    eval(['! . ' filename_oarcommand])
1725                case 'mpilauncher'
1726                    filename_joblist=fullfile(Rootbat,'job_list.txt');
1727                    fid=fopen(filename_joblist,'w');
1728                   
1729                    for p=1:length(batch_file_list)
1730                        fprintf(fid,[batch_file_list{p} '\n']);
1731                    end
1732                    fclose(fid)
1733                    text_oarscript=[...
1734                        '#!/bin/bash \n'...
1735                        '#OAR -n Mylauncher \n'...
1736                        '#OAR -l node=4/core=5,walltime=0:15:00 \n'...
1737                        '#OAR -E ' fullfile(Rootbat,'stderrfile.log') ' \n'...
1738                        '#OAR -O ' fullfile(Rootbat,'stdoutfile.log') ' \n'...
1739                        '# ========================================================= \n'...
1740                        '# This simple program launch a multinode parallel OpenMPI mpilauncher \n'...
1741                        '# application for coriolis PIV post-processing. \n'...
1742                        '# OAR uses oarshmost wrapper to propagate the user environement. \n'...
1743                        '# This wrapper assert that the user has the same environment on all the \n'...
1744                        '# allocated nodes (basic behavior needed by most MPI applications).  \n'...
1745                        '# \n'...
1746                        '# REQUIREMENT: \n'...
1747                        '# the oarshmost wrapper should be installed in $HOME/bin directory. \n'...
1748                        '# If a different location is used, change the line following the comment "Bidouille" \n'...
1749                        '# ========================================================= \n'...
1750                        '#   USER should only modify these 2 lines  \n'...
1751                        'WORKDIR=' pwd ' \n'...
1752                        'COMMANDE="mpilauncher  -f ' filename_joblist '" \n'...
1753                        '# ========================================================= \n'...
1754                        '# DO NOT MODIFY the FOLOWING LINES. (or be carefull) \n'...
1755                        'echo "job starting on: "`hostname` \n'...
1756                        'MPINODES="-host `tr [\\\\\\n] [,] <$OAR_NODEFILE |sed -e "s/,$/ /"`" \n'...
1757                        'NCPUS=`cat $OAR_NODEFILE |wc -l` \n'...
1758                        '#========== Bidouille ============== \n'...
1759                        'export OMPI_MCA_plm_rsh_agent=oar-envsh \n'...%                     'cd $WORKDIR \n'...
1760                        'CMD="mpirun -np $NCPUS -wdir $WORKDIR $MPINODES $COMMANDE" \n'...
1761                        'echo "I run: $CMD"  \n'...
1762                        '$CMD \n'...
1763                        'echo "job ending" \n'...
1764                        ];
1765                    %                 oarsub -S ./oar.sub
1766                    filename_oarscript=fullfile(Rootbat,'oar_command');
1767                    fid=fopen(filename_oarscript,'w');
1768                    fprintf(fid,[text_oarscript]);
1769                    fclose(fid);
1770                    eval(['!chmod +x  ' filename_oarscript]);
1771                    eval(['!oarsub -S ' filename_oarscript]);
1772            end
1773    end
1774else
1775    if ~isequal(CivMode,'Matlab')
1776        filename_superbat=fullfile(Rootbat,'job_list.bat');
1777        fid=fopen(filename_superbat,'w');
1778        if fid==-1
1779            msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat])
1780            return
1781        end
1782        for p=1:length(batch_file_list)
1783            if isunix
1784                fprintf(fid,['sh ' batch_file_list{p} '\n']);
1785            else
1786                fprintf(fid,['@call "' regexprep(batch_file_list{p},'\\','\\\\') '"' '\n']);
1787            end
1788        end
1789        fclose(fid);
1790        if(isunix)
1791            system(['chmod +x ' filename_superbat]);
1792        end
1793        system([filename_superbat ' &']);% execute main commmand
1794    end
1795end
1796
1797
1798%% save interface state
1799if isfield(filecell,'nc')
1800    if isfield(filecell.nc,'civ2')
1801        fileresu=filecell.nc.civ2{1,1};
1802    else
1803        fileresu=filecell.nc.civ1{1,1};
1804    end
1805end
1806[RootPath,SubDir,RootFile]=fileparts_uvmat(fileresu);
1807namedoc=fullfile(RootPath,SubDir,RootFile);
1808detect=1;
1809while detect==1
1810    namefigfull=[namedoc '.fig'];
1811    hh=dir(namefigfull);
1812    if ~isempty(hh)
1813        detect=1;
1814        namedoc=[namedoc '.0'];
1815    else
1816        detect=0;
1817    end
1818end
1819Param=rmfield(Param,'status');
1820Param=rmfield(Param,'xml');
1821t=struct2xml(Param);
1822t=set(t,1,'Name','CivDoc');% set the head label
1823save(t,[namedoc '.CivDoc.xml']); %save GUI  parameters as xml file
1824saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER  .xml)
1825
1826%Save info in personal profile (initiate browser next time) TODO
1827MenuFile={};
1828dir_perso=prefdir;
1829profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1830if exist(profil_perso,'file')
1831    hh=load (profil_perso);
1832      if isfield(hh,'MenuFile')
1833          MenuFile=hh.MenuFile;
1834      end
1835      if isfield(filecell.nc,'civ2')
1836          MenuFile=[filecell.nc.civ2{1,1}; MenuFile];
1837      else
1838           MenuFile=[filecell.nc.civ1{1,1}; MenuFile];
1839      end
1840      save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
1841else
1842    MenuFile=filecell.ima1.civ1(1,1);
1843    save (profil_perso,'MenuFile')
1844end
1845
1846%------------------------------------------------------------------------
1847% --- determine the list of reference indices of processing file
1848function [ref_i,ref_j,errormsg]=find_ref_indices(handles)
1849%------------------------------------------------------------------------
1850errormsg=''; %default error message
1851first_i=str2double(get(handles.first_i,'String'));%first index i
1852last_i=str2double(get(handles.last_i,'String'));%last index i
1853incr_i=str2double(get(handles.incr_i,'String'));% increment
1854if isequal(get(handles.first_j,'Visible'),'on')
1855    first_j=str2double(get(handles.first_j,'String'));%first index j
1856    last_j=str2double(get(handles.last_j,'String'));%last index j
1857    incr_j=str2double(get(handles.incr_j,'String'));% increment
1858else
1859    first_j=1;
1860    last_j=1;
1861    incr_j=1;
1862end
1863ref_i=first_i:incr_i:last_i;% list of i indices (reference values for each pair)
1864ref_j=first_j:incr_j:last_j;% list of j indices (reference values for each pair)
1865if isnan(first_i)||isnan(first_j)
1866    errormsg='first field number not defined';
1867elseif isnan(last_i)||isnan(last_j)
1868    errormsg='last field number not defined';
1869elseif isnan(incr_i)||isnan(incr_j)
1870    errormsg='increment in field number not defined';
1871elseif last_i < first_i || last_j < first_j
1872    errormsg='last field number must be larger than the first one';
1873end
1874
1875%------------------------------------------------------------------------
1876% --- determine the list of filenames and indices needed for launch_job
1877%------------------------------------------------------------------------
1878% OUTPUT:
1879% filecell: structure of cell arrays {ref_i,ref_j} containing all the filenames involved in the civ process
1880%    the indices ref_i and ref_j correspond to the list of reference indices
1881%       .filebase=fullfile(RootPath,RootFile) used to construct mask names, grid names, CivDoc xml file
1882%       .ima1.civ1,.ima1.civ2: first image for civ1 and civ2 respectively (possibly different)
1883%       .ima2.civ1,.ima2.civ2: second image for civ1 and civ2 respectively (possibly different)
1884%       .nc.civ1,.nc.civ2: netcdf files containing civ1 and civ2 data respectively (possibly different)
1885% i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2: arrays of files indices, needed for timing records
1886function [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]=...
1887    set_civ_filenames(handles,ref_i,ref_j,checkbox)
1888%------------------------------------------------------------------------
1889filecell=[];%default
1890ListProgram=get(handles.ListProgram,'String');
1891CivMode=ListProgram{get(handles.ListProgram,'Value')};%Program to use , CivX or Matlab
1892
1893%% get the root name and check dir
1894RootPath=get(handles.RootPath,'String');
1895RootFile=get(handles.RootFile,'String');
1896filecell.filebase=fullfile(RootPath,RootFile);
1897if isempty(filecell.filebase)
1898    msgbox_uvmat('ERROR','please open an image with the upper menu option Open/Browse...')
1899    return
1900end
1901if ~exist(RootPath,'dir')
1902    msgbox_uvmat('ERROR',['path to images ' RootPath ' not found'])
1903    return
1904end
1905[tild,message]=fileattrib(RootPath);
1906if ~isempty(message) && ~isequal(message.UserWrite,1)
1907    msgbox_uvmat('ERROR',['No writting access to ' RootPath])
1908    return
1909end
1910%check result directory
1911subdir_civ1=get(handles.SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf output data
1912subdir_civ2=get(handles.SubdirCiv2,'String');
1913if isequal(subdir_civ1,''),subdir_civ1='CIV'; end% put default subdir
1914if isequal(subdir_civ2,''),subdir_civ2=subdir_civ1; end% put default subdir
1915
1916%% choose root names depending on ListCompareMode =displacement, shift, PIV or stereo PIV
1917ListCompareMode=get(handles.ListCompareMode,'String');
1918compare=ListCompareMode{get(handles.ListCompareMode,'Value')};
1919
1920% set the nomenclature type of the nc files depending on the pair mode
1921if strcmp(compare,'displacement')||strcmp(compare,'shift')
1922    mode='displacement';
1923else
1924    mode_list=get(handles.ListPairMode,'String');
1925    mode_value=get(handles.ListPairMode,'Value');
1926    mode=mode_list{mode_value};
1927end
1928NomType_ima2=get(handles.NomType,'String');
1929NomType_nc=nomtype2pair(NomType_ima2,mode);
1930
1931% set the rootfile and image indexing
1932RootFile_ima2=get(handles.RootFile,'String');%root file for the second image series
1933ext_ima=get(handles.ImaExt,'String'); % image extension (the same for all images)
1934switch compare
1935    case 'PIV'
1936       RootFile_ima1=RootFile_ima2;% root name of the two image series is the same
1937       NomType_ima1=NomType_ima2;% the index of the first image follows the index of the second one
1938       RootFile_nc=RootFile_ima2;
1939    case 'displacement'
1940       RootFile_ima1=get(handles.RootFile_1,'String');% root name of the first image series set by handles.RootFile_1
1941       NomType_ima1='';% no indexing of the first image, a fixed reference for the whole series
1942       RootFile_nc=RootFile_ima2;
1943    case 'shift'
1944       RootFile_ima1=get(handles.RootFile_1,'String');% root name of the first image series set by handles.RootFile_1
1945       NomType_ima1=NomType_ima2;% the index of the first image follows the index of the second one
1946       RootFile_nc=[RootFile_ima1 '-' RootFile_ima2];
1947end
1948
1949%determine the list of file indices involved
1950[i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2]=...
1951    find_pair_indices(handles,ref_i,ref_j,mode);
1952
1953%determine the new filebase for 'displacement' ListPairMode (comparison of two series)
1954%filebase_B=filebase;% root name of the second field series for stereo
1955% filebase_A=filebase;%default
1956% if strcmp(compare,'PIV')
1957%     filebase_AB=filebase;
1958% else
1959%     [Path2,Name2]=fileparts(filebase_B);
1960%     Name1=RootFile_ima1;
1961%     filebase_AB=fullfile(Path2,[Name2 '-' Name1]);   
1962% end
1963% [RootPath_AB,RootFile_AB]=fileparts(filebase_AB);
1964% % [RootPath_ima1,RootFile_ima1]=fileparts(filebase_B);
1965% [RootPath_ima2,RootFile_ima2]=fileparts(filebase_B);
1966% [RootPath_nc,RootFile_nc]=fileparts(filebase_B);%default
1967% if strcmp(compare,'displacement')
1968% %     [RootPath_ima1,RootFile_ima1]=fileparts(filebase_B);
1969% %     [RootPath_ima2,RootFile_ima2]=fileparts(filebase_B);
1970%     [RootPath_nc,RootFile_nc]=fileparts(filebase_B);
1971% elseif strcmp(compare,'shift')
1972%     RootPath_nc=RootPath_AB;
1973%     RootFile_nc=RootFile_AB;
1974% end
1975% else
1976%     filebase_ima1=filebase_B;
1977%     filebase_ima2=filebase_B;
1978%     filebase_nc=filebase_B;
1979% [RootPath_ima1,RootFile_ima1]=fileparts(filebase_ima1);
1980% [RootPath_ima2,RootFile_ima2]=fileparts(filebase_ima2);
1981% [RootPath_nc,RootFile_nc]=fileparts(filebase_nc);
1982% [RootPath_A,RootFile_A]=fileparts(filebase_A);
1983
1984   
1985%% determine reference files for fix:
1986file_ref_fix1={};%default
1987file_ref_fix2={};
1988nbfield=length(i1_civ1);
1989nbslice=length(j1_civ1);
1990if checkbox(2)==1% fix1 performed
1991    ref=get(handles.ref_fix1,'UserData');%read data on the ref file stored by get_ref_fix1_Callback
1992    if ~isempty(ref)
1993        first_i=str2double(get(handles.first_i,'String'));
1994        last_i=str2double(get(handles.last_i,'String'));
1995        incr_i=str2double(get(handles.incr_i,'String'));
1996        first_j=str2double(get(handles.first_j,'String'));
1997        last_j=str2double(get(handles.last_j,'String'));
1998        incr_j=str2double(get(handles.incr_j,'String'));
1999        num_i_ref=first_i:incr_i:last_i;
2000        num_j_ref=first_j:incr_j:last_j;
2001        if isequal(mode,'displacement')
2002            num_i1=num_i_ref;
2003            num_i2=num_i_ref;
2004            num_j1=num_j_ref;
2005            num_j2=num_j_ref;
2006        elseif isequal(mode,'pair j1-j2')% isequal(mode,'st_pair j1-j2')
2007            num_i1=num_i_ref;
2008            num_i2=num_i1;
2009            num_j1=ref.num_a*ones(size(num_i_ref));
2010            num_j2=ref.num_b*ones(size(num_i_ref));
2011        elseif isequal(mode,'series(Di)') % isequal(mode,'st_series(Di)')
2012            delta1=floor((ref.num2-ref.num1)/2);
2013            delta2=ceil((ref.num2-ref.num1)/2);
2014            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
2015            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
2016            if isempty(ref.num_a)
2017                ref.num_a=1;
2018            end
2019            num_j1=ref.num_a*ones(size(num_i1));
2020            num_j2=num_j1;
2021        elseif isequal(mode,'series(Dj)')%| isequal(mode,'st_series(Dj)')
2022            delta1=floor((ref.num_b-ref.num_a)/2);
2023            delta2=ceil((ref.num_b-ref.num_a)/2);
2024            num_i1=ref.num1*ones(size(num_i_ref));
2025            num_i2=num_i1;
2026            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
2027            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
2028        end
2029        for ifile=1:nbfield
2030            for j=1:nbslice
2031                [RootPathRef,RootFile]=fileparts(ref.filebase);
2032                file_ref=fullfile_uvmat(RootPathRef,ref.subdir,RootFile,'.nc',ref.NomType,num_i1(ifile),num_i2(ifile),num_j1(j),num_j2(j));
2033                file_ref_fix1(ifile,j)={file_ref};
2034                if ~exist(file_ref,'file')
2035                    msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix1'])
2036                    filecell=[];
2037                    return
2038                end
2039            end
2040        end
2041    end
2042end
2043
2044%% determine reference files for fix2:
2045if checkbox(5)==1% fix2 performed
2046    ref=get(handles.ref_fix2,'UserData');
2047    if ~isempty(ref)
2048        first_i=str2double(get(handles.first_i,'String'));
2049        last_i=str2double(get(handles.last_i,'String'));
2050        incr_i=str2double(get(handles.incr_i,'String'));
2051        first_j=str2double(get(handles.first_j,'String'));
2052        last_j=str2double(get(handles.last_j,'String'));
2053        incr_j=str2double(get(handles.incr_j,'String'));
2054        num_i_ref=first_i:incr_i:last_i;
2055        num_j_ref=first_j:incr_j:last_j;
2056        if isequal(mode,'displacement')
2057            num_i1=num_i_ref;
2058            num_i2=num_i_ref;
2059            num_j1=num_j_ref;
2060            num_j2=num_j_ref;
2061        elseif isequal(mode,'pair j1-j2')
2062            num_i1=num_i_ref;
2063            num_i2=num_i1;
2064            num_j1=ref.num_a;
2065            num_j2=ref.num_b;
2066        elseif isequal(mode,'series(Di)')
2067            delta1=floor((ref.num2-ref.num1)/2);
2068            delta2=ceil((ref.num2-ref.num1)/2);
2069            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
2070            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
2071            num_j1=ref.num_a*ones(size(num_i1));
2072            num_j2=num_j1;
2073        elseif isequal(mode,'series(Dj)')
2074            delta1=floor((ref.num_b-ref.num_a)/2);
2075            delta2=ceil((ref.num_b-ref.num_a)/2);
2076            num_i1=ref.num1*ones(size(num_i_ref));
2077            num_i2=num_i1;
2078            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
2079            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
2080        end
2081        for ifile=1:nbfield
2082            for j=1:nbslice
2083                [RootPathRef,RootFile]=fileparts(ref.filebase);
2084                file_ref=fullfile_uvmat(RootPathRef,ref.subdir,RootFile,'.nc',ref.NomType,num_i1(ifile),num_i2(ifile),num_j1(j),num_j2(j));
2085                file_ref_fix2(ifile,j)={file_ref};
2086                if ~exist(file_ref,'file')
2087                    msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix2'])
2088                    filecell={};
2089                    return
2090                end
2091            end
2092        end
2093    end
2094end
2095
2096%% check the existence of the netcdf and image files involved
2097% %%%%%%%%%%%%  case CheckCiv1 activated   %%%%%%%%%%%%%
2098if checkbox(1)==1;
2099    detect=1;
2100    vers=0;
2101    subdir_civ1_new=subdir_civ1;
2102    while detect==1 %create a new subdir if the netcdf files already exist
2103        for ifile=1:nbfield
2104            for j=1:nbslice
2105                filename=fullfile_uvmat(RootPath,subdir_civ1_new,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
2106                detect=exist(filename,'file')==2;
2107                if detect% if a netcdf file already exists
2108                    indstr=regexp(subdir_civ1_new,'\D');
2109                    if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number
2110                        vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1;
2111                        subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)];
2112                    else
2113                        vers=vers+1;
2114                        subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) '_' num2str(vers)];       
2115                    end
2116                    subdir_civ2=subdir_civ1_new;
2117                    break
2118                end
2119                filecell.nc.civ1(ifile,j)={filename};
2120            end
2121            if detect% if a netcdf file already exists
2122                break
2123            end
2124        end
2125 
2126        %create the new SubdirCiv1
2127        if ~exist(fullfile(RootPath,subdir_civ1_new),'dir')     
2128            [xx,msg1]=mkdir(fullfile(RootPath,subdir_civ1_new));
2129
2130            if ~strcmp(msg1,'')
2131                msgbox_uvmat('ERROR',['cannot create ' subdir_civ1_new ': ' msg1])%error message for directory creation
2132                filecell={};
2133                return
2134            elseif isunix         
2135                [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g)
2136                if ~strcmp(msg2,'')
2137                    msgbox_uvmat('ERROR',['pb of permission for  ' fullfile(RootPath,subdir_civ1_new) ': ' msg2])%error message for directory creation
2138                    filecell={};
2139                    return
2140                end
2141            end
2142        end
2143        if strcmp(compare,'stereo PIV')&&(strcmp(mode,'pair j1-j2')||strcmp(mode,'series(Dj)')||strcmp(mode,'series(Di)'))%check second nc series
2144            for ifile=1:nbfield
2145                for j=1:nbslice
2146                     filename=fullfile_uvmat(RootPath,subdir_civ1_new,RootFile_A,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
2147                   % filename=name_generator(filebase_A,i1_civ1(ifile),j1_civ1(j),'.nc',NomType_nc,1,i2_civ1(ifile),j2_civ1(j),subdir_civ1_new);%
2148                    detect=exist(filename,'file')==2;
2149                    if detect% if a netcdf file already exists
2150                       indstr=regexp(subdir_civ1_new,'\D');
2151                       if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number
2152                           vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1;
2153                           subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)];
2154                       else
2155                           vers=vers+1;
2156                           subdir_civ1_new=[subdir_civ1_new '_' num2str(vers)];
2157                       end
2158                       subdir_civ2=subdir_civ1;
2159                       break
2160                    end
2161                    filecell.ncA.civ1(ifile,j)={filename};
2162                end
2163                if detect% if a netcdf file already exists
2164                    break
2165                end
2166            end
2167            %create the new SubdirCiv1
2168            if ~exist(fullfile(RootPath,subdir_civ1_new),'dir')       
2169                [xx,msg1]=mkdir(fullfile(RootPath,subdir_civ1_new));
2170                if ~strcmp(msg1,'')
2171                    msgbox_uvmat('ERROR',['cannot create ' subdir_civ1_new ': ' msg1])
2172                    filecell={};
2173                    return
2174                else
2175                    [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g)
2176                    if ~strcmp(msg2,'')
2177                        msgbox_uvmat('ERROR',['pb of permission for ' subdir_civ1_new ': ' msg2])%error message for directory creation
2178                        filecell={};
2179                        return
2180                    end
2181                end
2182            end
2183        end
2184    end
2185    subdir_civ1=subdir_civ1_new;
2186    % get image names
2187    for ifile=1:nbfield
2188        for j=1:nbslice
2189             filename=fullfile_uvmat(RootPath,'',RootFile_ima1,ext_ima,NomType_ima1,i1_civ1(ifile),[],j1_civ1(j));
2190            idetect(j)=exist(filename,'file')==2;
2191            filecell.ima1.civ1(ifile,j)={filename}; %first image
2192            filename=fullfile_uvmat(RootPath,'',RootFile_ima2,ext_ima,NomType_ima2,i2_civ1(ifile),[],j2_civ1(j));
2193            idetect_1(j)=exist(filename,'file')==2;
2194            filecell.ima2.civ1(ifile,j)={filename};%second image
2195        end
2196        [idetectmin,indexj]=min(idetect);
2197        if idetectmin==0,
2198            msgbox_uvmat('ERROR',[filecell.ima1.civ1{ifile,indexj} ' not found'])
2199            filecell={};
2200            return
2201        end
2202        [idetectmin,indexj]=min(idetect_1);
2203        if idetectmin==0,
2204            msgbox_uvmat('ERROR',[filecell.ima2.civ1{ifile,indexj} ' not found'])
2205            filecell={};
2206            return
2207        end
2208    end
2209    if strcmp(compare,'stereo PIV') && (strcmp(mode,'pair j1-j2') || strcmp(mode,'series(Dj)') || strcmp(mode,'series(Di)'))
2210        for ifile=1:nbfield
2211            for j=1:nbslice
2212                filename=fullfile_uvmat(RootPath,'',RootFile_A,ext_ima,NomType_ima1,i1_civ1(ifile),[],j1_civ1(j));
2213                idetect(j)=exist(filename,'file')==2;
2214                filecell.imaA1.civ1(ifile,j)={filename} ;%first image
2215                filename=fullfile_uvmat(RootPath,'',RootFile_A,ext_ima,NomType_ima2,i2_civ1(ifile),[],j2_civ1(j));
2216                idetect_1(j)=exist(filename,'file')==2;
2217                filecell.imaA2.civ1(ifile,j)={filename};%second image
2218            end
2219            [idetectmin,indexj]=min(idetect);
2220            if idetectmin==0,
2221                msgbox_uvmat('ERROR',[filecell.imaA1.civ1{ifile,indexj} ' not found'])
2222                filecell={};
2223               % cd(currentdir)
2224                return
2225            end
2226            [idetectmin,indexj]=min(idetect_1);
2227            if idetectmin==0,
2228                msgbox_uvmat('ERROR',[filecell.imaA2.civ1{ifile,indexj} ' not found'])
2229                filecell={};
2230               % cd(currentdir)
2231                return
2232            end
2233        end
2234    end
2235   
2236    %%%%%%%%%%%%%  checkfix1 or checkpatch1 activated but no checkciv1   %%%%%%%%%%%%%
2237elseif (checkbox(2)==1 || checkbox(3)==1);
2238    for ifile=1:nbfield
2239        for j=1:nbslice
2240            filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
2241            detect=exist(filename,'file')==2;
2242            if detect==0
2243                msgbox_uvmat('ERROR',[filename ' not found'])
2244                filecell={};
2245               % cd(currentdir)
2246                return
2247            end
2248            filecell.nc.civ1(ifile,j)={filename};
2249        end
2250    end
2251    if strcmp(compare,'stereo PIV')
2252        for ifile=1:nbfield
2253            for j=1:nbslice
2254                filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_A,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
2255                filecell.ncA.civ1(ifile,j)={filename};
2256                if ~exist(filename,'file')
2257                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2258                    set(handles.RUN, 'Enable','On')
2259                    set(handles.RUN,'BackgroundColor',[1 0 0])
2260                    filecell={};
2261                    %cd(currentdir)
2262                    return
2263                end
2264            end
2265        end
2266    end
2267end
2268
2269%%%%%%%%%%%%%  if checkciv2 performed with pairs different than checkciv1  %%%%%%%%%%%%%
2270testdiff=0;
2271if (checkbox(4)==1)&&...
2272        ((get(handles.ListPairCiv1,'Value')~=get(handles.ListPairCiv2,'Value'))||~strcmp(subdir_civ2,subdir_civ1))
2273    testdiff=1;
2274    detect=1;
2275    vers=0;
2276    subdir_civ2_new=subdir_civ2;
2277    while detect==1 %create a new subdir if the netcdf files already exist
2278        for ifile=1:nbfield
2279            for j=1:nbslice
2280                filename=fullfile_uvmat(RootPath,subdir_civ2_new,RootFile_nc,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2281                detect=exist(filename,'file')==2;
2282                if detect% if a netcdf file already exists
2283                    indstr=regexp(subdir_civ2,'\D');
2284                    if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2285                        vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2286                        subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2287                    else
2288                        vers=vers+1;
2289                        subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2290                    end
2291                    break
2292                end
2293                filecell.nc.civ2(ifile,j)={filename};
2294            end
2295            if detect% if a netcdf file already exists
2296                break
2297            end
2298        end
2299        %create the new subdir_civ2_new
2300        if ~exist(fullfile(RootPath,subdir_civ2_new),'dir')
2301            [xx,m2]=mkdir(fullfile(RootPath,subdir_civ2_new));
2302            [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g)
2303            if ~isequal(m2,'')
2304                msgbox_uvmat('ERROR',['cannot create ' fullfile(RootPath,subdir_civ2_new) ': ' m2])
2305                filecell={};
2306                return
2307            end
2308        end
2309        if strcmp(compare,'stereo PIV')%check second nc series
2310            for ifile=1:nbfield
2311                for j=1:nbslice
2312                    filename=fullfile_uvmat(RootPath,subdir_civ2_new,RootFile_A,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2313                    detect=exist(filename,'file')==2;
2314                    if detect% if a netcdf file already exists
2315                        indstr=regexp(subdir_civ2,'\D');
2316                        if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2317                           vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2318                           subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2319                        else
2320                           vers=vers+1;
2321                           subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2322                        end
2323                        break
2324                    end
2325                    filecell.ncA.civ2(ifile,j)={filename};
2326                end
2327                if detect% if a netcdf file already exists
2328                    break
2329                end
2330            end
2331            subdir_civ2=subdir_civ2_new;
2332            %create the new SubdirCiv1
2333            if ~exist(fullfile(RootPath,subdir_civ2_new),'dir')
2334                [xx,m2]=mkdir(subdir_civ2_new);
2335                 [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g)
2336                if ~isequal(m2,'')
2337                    msgbox_uvmat('ERROR', ['cannot create ' fullfile(RootPath,subdir_civ2_new) ': ' m2])%error message for directory creation
2338                  %  cd(currentdir)
2339                    filecell={};
2340                    return
2341                end
2342            end
2343        end
2344    end
2345    subdir_civ2=subdir_civ2_new;
2346end
2347%cd(currentdir);%come back to the current working directory
2348
2349%%%%%%%%%%%%%  if checkciv2 results are obtained or used  %%%%%%%%%%%%%
2350if checkbox(4)==1 || checkbox(5)==1 || checkbox(6)==1 %civ2
2351    %check source netcdf file of checkciv1 estimates
2352    if checkbox(1)==0; %no civ1 performed
2353        for ifile=1:nbfield
2354            for j=1:nbslice
2355                filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));%
2356                filecell.nc.civ1(ifile,j)={filename};% name of the civ1 file
2357                if ~exist(filename,'file')
2358                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2359                    filecell={};
2360                    return
2361                end
2362                if ~testdiff % civ2 or patch2 are written in the same file as civ1
2363                    if checkbox(4)==0 ; %check the existence of civ2 if it is not calculated
2364                        Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2');
2365                        if isfield(Data,'Txt')
2366                            msgbox_uvmat('ERROR',Data.Txt);
2367                            return
2368                        elseif ~isempty(Data.CivStage)% case of new civ files
2369                            if Data.CivStage<4 %test for civ files
2370                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2371                            filecell=[];
2372                            return
2373                            end
2374                        elseif isempty(Data.civ2)||isequal(Data.civ2,0)
2375                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2376                            filecell=[];
2377                            return
2378                        end
2379                    elseif checkbox(3)==0; %check the existence of patch if it is not calculated
2380                        Data=nc2struct(filename,'ListGlobalAttribute','CivStage','patch');
2381                        if ~isempty(Data.CivStage)
2382                            if Data.CivStage<3 %test for civ files
2383                                msgbox_uvmat('ERROR',['no patch data in ' filename])
2384                                filecell=[];
2385                                return
2386                            end
2387                        elseif isempty(Data.patch)||isequal(Data.patch,0)
2388                            msgbox_uvmat('ERROR',['no patch data in ' filename])
2389                            filecell=[];
2390                            return
2391                        end
2392                    end
2393                end
2394            end
2395        end
2396        if strcmp(compare,'stereo PIV')
2397            for ifile=1:nbfield
2398                for j=1:nbslice
2399                    filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_A,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2400                    filecell.ncA.civ2(ifile,j)={filename};
2401                    if ~exist(filename,'file')
2402                        msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2403                        set(handles.RUN, 'Enable','On')
2404                        set(handles.RUN,'BackgroundColor',[1 0 0])
2405                        return
2406                    end
2407                end
2408            end
2409        end
2410    end
2411   
2412    detect=1;
2413    %     while detect==1%creates a new subdir if the netcdf files already contain checkciv2 data
2414    for ifile=1:nbfield
2415        for j=1:nbslice
2416            filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_nc,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2417            detect=exist(filename,'file')==2;
2418            filecell.nc.civ2(ifile,j)={filename};
2419        end
2420    end
2421    %get first image names for checkciv2
2422    if checkbox(1)==1 && isequal(i1_civ1,i1_civ2) && isequal(j1_civ1,j1_civ2)
2423        filecell.ima1.civ2=filecell.ima1.civ1;
2424    elseif checkbox(4)==1
2425        for ifile=1:nbfield
2426            for j=1:nbslice
2427                filename=fullfile_uvmat(RootPath,[],RootFile_ima1,ext_ima,NomType_ima1,i1_civ2(ifile),[],j1_civ2(j));
2428                idetect_2(j)=exist(filename,'file')==2;
2429                filecell.ima1.civ2(ifile,j)={filename};%first image
2430            end
2431            [idetectmin,indexj]=min(idetect_2);
2432            if idetectmin==0,
2433                msgbox_uvmat('ERROR',['input image ' filecell.ima1.civ2{ifile,indexj} ' not found'])
2434                filecell=[];
2435                return
2436            end
2437        end
2438    end
2439   
2440    %get second image names for checkciv2
2441    if checkbox(1)==1 && isequal(i2_civ1,i2_civ2) && isequal(j2_civ1,j2_civ2)
2442        filecell.ima2.civ2=filecell.ima2.civ1;
2443    elseif checkbox(4)==1
2444        for ifile=1:nbfield
2445            for j=1:nbslice
2446                filename=fullfile_uvmat(RootPath,[],RootFile_ima2,ext_ima,NomType_ima2,i2_civ2(ifile),[],j2_civ2(j));
2447                idetect_3(j)=exist(filename,'file')==2;
2448                filecell.ima2.civ2(ifile,j)={filename};%first image
2449            end
2450            [idetectmin,indexj]=min(idetect_3);
2451            if idetectmin==0,
2452                msgbox_uvmat('ERROR',['input image ' filecell.ima2.civ2{ifile,indexj} ' not found'])
2453                filecell=[];
2454                return
2455            end
2456        end
2457    end
2458end
2459if (checkbox(5) || checkbox(6)) && ~checkbox(4)  % need to read an existing netcdf civ2 file
2460    if ~testdiff
2461        filecell.nc.civ2=filecell.nc.civ1;% file already checked
2462    else     % check the civ2 files
2463        for ifile=1:nbfield
2464            for j=1:nbslice
2465                 filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_nc,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2466                filecell.nc.civ2(ifile,j)={filename};
2467                if ~exist(filename,'file')
2468                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2469                    filecell=[];
2470                    return
2471                else
2472                    Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2');
2473                    if ~isempty(Data.CivStage) && Data.CivStage<4 %test for civ files
2474                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2475                            filecell=[];
2476                            return
2477                    elseif isempty(Data.civ2)||isequal(Data.civ2,0)
2478                        msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2479                        filecell=[];
2480                        return
2481                    end
2482                end
2483            end
2484        end
2485    end
2486end
2487
2488%%%%%%%%%%%%%  if stereo fields are calculated by PATCH %%%%%%%%%%%%%
2489if strcmp(compare,'stereo PIV')
2490    if  checkbox(3) && isequal(get(handles.test_stereo1,'Value'),1)
2491        for ifile=1:nbfield
2492            for j=1:nbslice
2493                 filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_AB,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
2494                filecell.st(ifile,j)={filename};
2495            end
2496        end
2497    end
2498    if  checkbox(6) && isequal(get(handles.CheckStereo,'Value'),1)
2499        for ifile=1:nbfield
2500            for j=1:nbslice
2501                 filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_AB,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2502                filecell.st(ifile,j)={filename};
2503            end
2504        end
2505    end
2506end
2507set(handles.SubdirCiv1,'String',subdir_civ1);%update the edit box
2508set(handles.SubdirCiv2,'String',subdir_civ2);%update the edit box
2509
2510% For CivX COPY IMAGES TO THE FORMAT .png IF NEEDED
2511if strcmp(CivMode,'CivX')
2512    if isequal(NomType_ima1,'*')%case of movie files
2513        NomType_imanew1='_i';
2514    else
2515        NomType_imanew1=NomType_ima1;
2516    end
2517    if isequal(NomType_ima2,'*')%case of movie files
2518        NomType_imanew2='_i';
2519    else
2520        NomType_imanew2=NomType_ima2;
2521    end
2522    if ~isequal(ext_ima,'.png')
2523        %%type of image file
2524        type_ima1='none';%default
2525        movieobject1=[];%default
2526        if strcmpi(ext_ima,'.avi')
2527            if ~isempty(which('mmreader'))% if the mmreader function is found (recent version of matlab)
2528                type_ima1='movie';
2529                movieobject1=mmreader([filecell.filebase ext_ima]);
2530            else
2531                type_ima1='avi';
2532            end
2533        elseif ischar(ext_ima) && ~isempty(ext_ima(2:end))
2534            form=imformats(ext_ima(2:end));
2535            if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2536                if isequal(NomType_ima1,'*');
2537                    type_ima1='multimage';%image series in a single image file
2538                else
2539                    type_ima1='image';
2540                end
2541            end
2542        end
2543        type_ima2='none';%default
2544        movieobject2=[];
2545        if strcmpi(ext_ima,'.avi')
2546            if ~isempty(which('mmreader'))% if the mmreader function is found (recent version of matlab)
2547                type_ima2='movie';
2548                movieobject2=mmreader([filecell.filebase ext_ima]);
2549            else
2550                type_ima2='avi';
2551            end
2552        elseif ischar(ext_ima) && ~isempty(ext_ima(2:end))
2553            form=imformats(ext_ima(2:end));
2554            if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2555                if isequal(NomType_ima1,'*');
2556                    type_ima2='multimage';%image series in a single image file
2557                else
2558                    type_ima2='image';
2559                end
2560            end
2561        end
2562        if checkbox(1) %if civ1 is performed
2563            h = waitbar(0,'copy images to the .png format for civ1');% display a wait bar
2564            for ifile=1:nbfield
2565                waitbar(ifile/nbfield);
2566                for j=1:nbslice
2567                    filename=fullfile_uvmat(RootPath,[],RootFile_ima1,'.png',NomType_imanew1,i1_civ1(ifile),[],j1_civ1(j));
2568                    if ~exist(filename,'file')
2569                        A=read_image(filecell.ima1.civ1{ifile,j},type_ima1,i1_civ1(ifile),movieobject1);
2570                        imwrite(A,filename,'BitDepth',16);
2571                    end
2572                    filecell.ima1.civ1(ifile,j)={filename};
2573                    filename=fullfile_uvmat(RootPath,[],RootFile_ima2,'.png',NomType_imanew2,i2_civ1(ifile),[],j2_civ1(j));
2574                    if ~exist(filename,'file')
2575                        A=read_image(filecell.ima2.civ1{ifile,j},type_ima2,i2_civ1(ifile),movieobject2);
2576                        imwrite(A,filename,'BitDepth',16);
2577                    end
2578                    filecell.ima2.civ1(ifile,j)={filename};
2579                end
2580            end
2581            close(h)
2582        end
2583        if checkbox(4) %if civ2 is performed
2584            h = waitbar(0,'copy images to the .png format for civ2');% display a wait bar
2585            for ifile=1:nbfield
2586                waitbar(ifile/nbfield);
2587                for j=1:nbslice
2588                    filename=fullfile_uvmat(RootPath,[],RootFile_ima1,'.png',NomType_imanew1,i1_civ2(ifile),[],j1_civ2(j));
2589                    if ~exist(filename,'file')
2590                        A=read_image(cell2mat(filecell.ima1.civ2(ifile,j)),type_ima2,i1_civ2(ifile));
2591                        imwrite(A,filename,'BitDepth',16);
2592                    end
2593                    filecell.ima1.civ2(ifile,j)={filename};
2594                    filename=fullfile_uvmat(RootPath,[],RootFile_ima2,'.png',NomType_imanew2,i2_civ2(ifile),[],j2_civ2(j));
2595                    if ~exist(filename,'file')
2596                        A=read_image(cell2mat(filecell.ima2.civ2(ifile,j)),type_ima2,i2_civ2(ifile));
2597                        imwrite(A,filename,'BitDepth',16);
2598                    end
2599                    filecell.ima2.civ2(ifile,j)={filename};
2600                end
2601            end
2602            close(h);
2603        end
2604    end
2605end
2606
2607%------------------------------------------------------------------------
2608% --- determine the list of index pairs of processing file
2609function [num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=...
2610    find_pair_indices(handles,ref_i,ref_j,mode)
2611%------------------------------------------------------------------------
2612
2613list_civ1=get(handles.ListPairCiv1,'String');
2614index_civ1=get(handles.ListPairCiv1,'Value');
2615str_civ1=list_civ1{index_civ1};%string defining the image pairs for civ1
2616if isempty(str_civ1)||isequal(str_civ1,'')
2617    msgbox_uvmat('ERROR','no image pair selected for civ1')
2618    return
2619end
2620list_civ2=get(handles.ListPairCiv2,'String');
2621index_civ2=get(handles.ListPairCiv2,'Value');
2622if index_civ2>length(list_civ2)
2623    list_civ2=list_civ1;
2624    index_civ2=index_civ1;
2625end
2626str_civ2=list_civ2{index_civ2};%string defining the image pairs for civ2
2627
2628if isequal (mode,'series(Di)')
2629    lastfield=str2double(get(handles.nb_field,'String'));
2630    num1_civ1=ref_i-floor(index_civ1/2)*ones(size(ref_i));% set of first image numbers
2631    num2_civ1=ref_i+ceil(index_civ1/2)*ones(size(ref_i));
2632    num_a_civ1=ref_j;
2633    num_b_civ1=ref_j;
2634    num1_civ2=ref_i-floor(index_civ2/2)*ones(size(ref_i));
2635    num2_civ2=ref_i+ceil(index_civ2/2)*ones(size(ref_i));
2636    num_a_civ2=ref_j;
2637    num_b_civ2=ref_j;   
2638   
2639    % adjust the first and last field number
2640    lastfield=str2double(get(handles.nb_field,'String'));
2641    if isnan(lastfield)
2642        indsel=find((num1_civ1 >= 1)&(num1_civ2 >= 1));
2643    else
2644        indsel=find((num2_civ1 <= lastfield)&(num2_civ2 <= lastfield)&(num1_civ1 >= 1)&(num1_civ2 >= 1));
2645    end
2646    if length(indsel)>=1
2647        firstind=indsel(1);
2648        lastind=indsel(end);
2649        set(handles.first_i,'String',num2str(ref_i(firstind)))%update the display of first and last fields
2650        set(handles.last_i,'String',num2str(ref_i(lastind)))
2651        ref_i=ref_i(indsel);
2652        num1_civ1=num1_civ1(indsel);
2653        num1_civ2=num1_civ2(indsel);
2654        num2_civ1=num2_civ1(indsel);
2655        num2_civ2=num2_civ2(indsel);
2656    end
2657elseif isequal (mode,'series(Dj)')
2658    lastfield_j=str2double(get(handles.nb_field2,'String'));
2659    num1_civ1=ref_i;% set of first image numbers
2660    num2_civ1=ref_i;
2661    num_a_civ1=ref_j-floor(index_civ1/2)*ones(size(ref_j));
2662    num_b_civ1=ref_j+ceil(index_civ1/2)*ones(size(ref_j));
2663    num1_civ2=ref_i;
2664    num2_civ2=ref_i;
2665    num_a_civ2=ref_j-floor(index_civ2/2)*ones(size(ref_j));
2666    num_b_civ2=ref_j+ceil(index_civ2/2)*ones(size(ref_j));
2667    % adjust the first and last field number
2668    if isnan(lastfield_j)
2669        indsel=find((num_a_civ1 >= 1)&(num_a_civ2 >= 1));
2670    else
2671        indsel=find((num_b_civ1 <= lastfield_j)&(num_b_civ2 <= lastfield_j)&(num_a_civ1 >= 1)&(num_a_civ2 >= 1));
2672    end
2673    if length(indsel)>=1
2674        firstind=indsel(1);
2675        lastind=indsel(end);
2676        set(handles.first_j,'String',num2str(ref_j(firstind)))%update the display of first and last fields
2677        set(handles.last_j,'String',num2str(ref_j(lastind)))
2678        ref_j=ref_j(indsel);
2679        num_a_civ1=num_a_civ1(indsel);
2680        num_b_civ1=num_b_civ1(indsel);
2681        num_a_civ2=num_a_civ2(indsel);
2682        num_b_civ2=num_b_civ2(indsel);
2683    end
2684elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)
2685    displ_num=get(handles.ListPairCiv1,'UserData');
2686    num1_civ1=ref_i;
2687    num2_civ1=ref_i;
2688    num_a_civ1=displ_num(1,index_civ1);
2689    num_b_civ1=displ_num(2,index_civ1);
2690    num1_civ2=ref_i;
2691    num2_civ2=ref_i;
2692    num_a_civ2=displ_num(1,index_civ2);
2693    num_b_civ2=displ_num(2,index_civ2);
2694elseif isequal(mode,'displacement')
2695    num1_civ1=ref_i;
2696    num2_civ1=ref_i;
2697    num_a_civ1=ref_j;
2698    num_b_civ1=ref_j;
2699    num1_civ2=ref_i;
2700    num2_civ2=ref_i;
2701    num_a_civ2=ref_j;
2702    num_b_civ2=ref_j;
2703end
2704
2705%------------------------------------------------------------------------
2706% --- Executes on button press in ListCompareMode.
2707function ListCompareMode_Callback(hObject, eventdata, handles)
2708%------------------------------------------------------------------------
2709ListCompareMode=get(handles.ListCompareMode,'String');
2710option=ListCompareMode{get(handles.ListCompareMode,'Value')};
2711if ~strcmp(option,'PIV') % case 'displacement' or 'stereo PIV'
2712    filebase=get(handles.RootPath,'String');
2713    set(handles.sub_txt,'Visible','on')
2714    set(handles.RootFile_1,'Visible','On');%mkes the second file input window visible
2715    mode_store=get(handles.ListPairMode,'String');%get the present 'mode'
2716    set(handles.ListCompareMode,'UserData',mode_store);%store the mode display
2717    set(handles.ListPairMode,'Visible','off')
2718   
2719    %% open an image file with the browser
2720    ind_opening=1;%default
2721    browse.incr_pair=[0 0]; %default
2722    oldfile=get(handles.RootPath,'String');
2723    menu={'*.png;*.jpg;*.tif;*.avi;*.AVI;', ' (*.png,*.jpg ,.tif, *.avi,*.AVI)';
2724        '*.png','.png image files'; ...
2725        '*.jpg',' jpeg image files'; ...
2726        '*.tif','.tif image files'; ...
2727        '*.avi;*.AVI','.avi movie files'; ...
2728        '*.*',  'All Files (*.*)'};
2729    if strcmp(option,'displacement')
2730        comment='Pick the reference file for displacements';
2731    else
2732        comment='Pick a file of the second series';
2733    end
2734    [FileName, PathName] = uigetfile( menu, comment,oldfile);
2735    fileinput=[PathName FileName];%complete file name
2736    sizf=size(fileinput);
2737    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
2738    [path,name,ext]=fileparts(fileinput);
2739    [path1]=fileparts(filebase);
2740    if isunix
2741        [status,path]=system(['readlink ' path]);
2742        [status,path1]=system(['readlink ' path1]);% look for the true path in case of symbolic paths
2743    end
2744    if ~strcmp(path1,path)
2745        msgbox_uvmat('ERROR','The second image or series must be in the same directory as the first one')
2746        return
2747    end
2748    if strcmp(option,'displacement')
2749        [tild,RootFile_1]=fileparts(name);
2750    else
2751        [FilePath,FileName,Ext]=fileparts(fileinput);
2752% detect the file type, get the movie object if relevant, and look for the corresponding file series:
2753% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
2754[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]);
2755       
2756       % [tild,tild,RootFile_1,tild,tild,tild,tild,tild,nom_type_1]=fileparts_uvmat(fileinput);
2757        %[RootFile_1,i1_series,tild,j1_series,tild,nom_type_1,FileType,Object]=find_file_series(PathName,FileName);
2758        %check image nom type
2759        if ~strcmp(nom_type_1,get(handles.NomType,'String'))
2760        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')
2761        return
2762        end
2763    end   
2764    %check image  extension
2765    if ~strcmp(ext,get(handles.ImaExt,'String'))
2766        msgbox_uvmat('ERROR','The second image series must have the same extension name as the first one')
2767        return
2768    end
2769    set(handles.RootFile_1,'String',RootFile_1);
2770else
2771    set(handles.ListPairMode,'Visible','on')
2772    set(handles.RootFile_1,'Visible','Off');
2773    set(handles.sub_txt,'Visible','off')
2774    set(handles.RootFile_1,'String',[]);
2775    mode_store=get(handles.ListCompareMode,'UserData');
2776    set(handles.ListPairMode,'Value',1)
2777    set(handles.ListPairMode,'String',mode_store)
2778    set(handles.CheckStereo,'Value',0)
2779    set(handles.ListPairMode,'Value',1) % mode 'civX' selected by default
2780end
2781% if strcmp(option,'stereo PIV') && get(handles.CheckPatch1,'Value')
2782%     set(handles.CheckStereo,'Visible','on')
2783% else
2784%     set(handles.CheckStereo,'Visible','off')
2785% end
2786% if strcmp(option,'stereo PIV') && get(handles.CheckPatch2,'Value')
2787%     set(handles.CheckStereo,'Visible','on')
2788% else
2789%     set(handles.CheckStereo,'Visible','off')
2790% end
2791ListPairMode_Callback(hObject, eventdata, handles)
2792
2793
2794%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2795% Callbacks in the uipanel Pair Indices
2796%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2797%------------------------------------------------------------------------
2798% --- Executes on button press in ListPairMode.
2799function ListPairMode_Callback(hObject, eventdata, handles)
2800%------------------------------------------------------------------------
2801compare_list=get(handles.ListCompareMode,'String');
2802val=get(handles.ListCompareMode,'Value');
2803compare=compare_list{val};
2804if strcmp(compare,'displacement')||strcmp(compare,'shift')
2805    mode='displacement';
2806else
2807    mode_list=get(handles.ListPairMode,'String');
2808    if ischar(mode_list)
2809        mode_list={mode_list};
2810    end
2811    mode_value=get(handles.ListPairMode,'Value');
2812    mode=mode_list{mode_value};
2813end
2814displ_num=[];%default
2815ref_i=str2double(get(handles.ref_i,'String'));
2816% last_i=str2num(get(handles.last_i,'String'));
2817time=get(handles.ImaDoc,'UserData'); %get the set of times
2818TimeUnit=get(handles.TimeUnit,'String');
2819checkframe=strcmp(TimeUnit,'frame');
2820siztime=size(time);
2821nbfield=siztime(1)-1;
2822nbfield2=siztime(2)-1;
2823indchosen=1;  %%first pair selected by default
2824%displ_num used to define the indices of the civ pairs
2825% in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices
2826% are relative to the reference indices ref_i and ref_j respectively.
2827if isequal(mode,'pair j1-j2')%| isequal(mode,'st_pair j1-j2')
2828    dt=1;
2829    displ='';
2830    index=0;
2831    numlist_a=[];
2832    numlist_B=[];
2833    %get all the time intervals in bursts
2834    displ_dt=1;%default
2835    nbfield2=min(nbfield2,10);%limitate the number of pairs to 10x10
2836    for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'pair j1-j2' mode
2837        for numod_b=(numod_a+1):nbfield2
2838            index=index+1;
2839            numlist_a(index)=numod_a;
2840            numlist_b(index)=numod_b;
2841            if size(time,2)>1 && ~checkframe
2842                dt(numod_a,numod_b)=time(ref_i+1,numod_b+1)-time(ref_i+1,numod_a+1);%first time interval dt
2843                displ_dt(index)=dt(numod_a,numod_b);
2844            else
2845                displ_dt(index)=1;
2846            end
2847        end
2848    end
2849    [dtsort,indsort]=sort(displ_dt);
2850    if ~isempty(numlist_a)
2851        displ_num(1,:)=numlist_a(indsort);
2852        displ_num(2,:)=numlist_b(indsort);
2853    end
2854    displ_num(3,:)=0;
2855    displ_num(4,:)=0;
2856    enable_j(handles, 'off')
2857elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)')
2858    index=1:200;
2859    displ_num(1,index)=-floor(index/2);
2860    displ_num(2,index)=ceil(index/2);
2861    displ_num(3:4,index)=zeros(2,200);
2862    enable_j(handles, 'on')
2863elseif isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)')
2864    index=1:200;
2865    displ_num(1:2,index)=zeros(2,200);
2866    displ_num(3,index)=-floor(index/2);
2867    displ_num(4,index)=ceil(index/2);
2868    enable_i(handles, 'on')
2869    if nbfield2 > 1
2870        enable_j(handles, 'on')
2871    else
2872        enable_j(handles, 'off')
2873    end
2874elseif isequal(mode,'displacement')%the pairs have the same indices
2875    displ_num(1,1)=0;
2876    displ_num(2,1)=0;
2877    displ_num(3,1)=0;
2878    displ_num(4,1)=0;
2879    if nbfield > 1 || nbfield==0
2880        enable_i(handles, 'on')
2881    else
2882        enable_j(handles, 'off')
2883    end
2884    if nbfield2 > 1
2885        enable_j(handles, 'on')
2886    else
2887        enable_j(handles, 'off')
2888    end
2889end
2890set(handles.ListPairCiv1,'UserData',displ_num);
2891errormsg=find_netcpair_civ( handles,1);
2892    if ~isempty(errormsg)
2893    msgbox_uvmat('ERROR',errormsg)
2894    end
2895% find_netcpair_civ2(handles)
2896
2897function enable_i(handles, state)
2898set(handles.itext,'Visible',state)
2899set(handles.first_i,'Visible',state)
2900set(handles.last_i,'Visible',state)
2901set(handles.incr_i,'Visible',state)
2902set(handles.nb_field,'Visible',state)
2903set(handles.ref_i,'Visible',state)
2904
2905function enable_j(handles, state)
2906set(handles.jtext,'Visible',state)
2907set(handles.first_j,'Visible',state)
2908set(handles.last_j,'Visible',state)
2909set(handles.incr_j,'Visible',state)
2910set(handles.nb_field2,'Visible',state)
2911set(handles.ref_j,'Visible',state)
2912
2913
2914%------------------------------------------------------------------------
2915% --- Executes on selection change in ListPairCiv1.
2916function ListPairCiv1_Callback(hObject, eventdata, handles)
2917%------------------------------------------------------------------------
2918%reproduce by default the chosen pair in the checkciv2 menu
2919list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
2920index_pair=get(handles.ListPairCiv1,'Value');
2921displ_num=get(handles.ListPairCiv1,'UserData');
2922% num_a=displ_num(1,index_pair);
2923% num_b=displ_num(2,index_pair);
2924list_pair2=get(handles.ListPairCiv2,'String');%get the menu of image pairs
2925if index_pair<=length(list_pair2)
2926    set(handles.ListPairCiv2,'Value',index_pair);
2927end
2928
2929%update first_i and last_i according to the chosen image pairs
2930mode_list=get(handles.ListPairMode,'String');
2931mode_value=get(handles.ListPairMode,'Value');
2932mode=mode_list{mode_value};
2933if isequal(mode,'series(Di)')
2934    first_i=str2double(get(handles.first_i,'String'));
2935    last_i=str2double(get(handles.last_i,'String'));
2936    incr_i=str2double(get(handles.incr_i,'String'));
2937    num1=first_i:incr_i:last_i;
2938    lastfield=str2double(get(handles.nb_field,'String'));
2939    if ~isnan(lastfield)
2940        test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ...
2941            (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield);
2942        num1=num1(test_find);
2943    end
2944    set(handles.first_i,'String',num2str(num1(1)));
2945    set(handles.last_i,'String',num2str(num1(end)));
2946elseif isequal(mode,'series(Dj)')
2947    first_j=str2double(get(handles.first_j,'String'));
2948    last_j=str2double(get(handles.last_j,'String'));
2949    incr_j=str2double(get(handles.incr_j,'String'));
2950    num_j=first_j:incr_j:last_j;
2951    lastfield2=str2double(get(handles.nb_field2,'String'));
2952    if ~isnan(lastfield2)
2953        test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
2954            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2);
2955        num1=num_j(test_find);
2956    end
2957    set(handles.first_j,'String',num2str(num1(1)));
2958    set(handles.last_j,'String',num2str(num1(end)));
2959end
2960
2961%------------------------------------------------------------------------
2962% --- Executes on selection change in ListPairCiv2.
2963function ListPairCiv2_Callback(hObject, eventdata, handles)
2964%------------------------------------------------------------------------
2965index_pair=get(handles.ListPairCiv2,'Value');%get the selected position index in the menu
2966
2967%update first_i and last_i according to the chosen image pairs
2968mode_list=get(handles.ListPairMode,'String');
2969mode_value=get(handles.ListPairMode,'Value');
2970mode=mode_list{mode_value};
2971if isequal(mode,'series(Di)')
2972    first_i=str2double(get(handles.first_i,'String'));
2973    last_i=str2double(get(handles.last_i,'String'));
2974    incr_i=str2double(get(handles.incr_i,'String'));
2975    num1=first_i:incr_i:last_i;
2976    lastfield=str2double(get(handles.nb_field,'String'));
2977    if ~isnan(lastfield)
2978        test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ...
2979            (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield);
2980        num1=num1(test_find);
2981    end
2982    set(handles.first_i,'String',num2str(num1(1)));
2983    set(handles.last_i,'String',num2str(num1(end)));
2984elseif isequal(mode,'series(Dj)')
2985    first_j=str2double(get(handles.first_j,'String'));
2986    last_j=str2double(get(handles.last_j,'String'));
2987    incr_j=str2double(get(handles.incr_j,'String'));
2988    num_j=first_j:incr_j:last_j;
2989    lastfield2=str2double(get(handles.nb_field2,'String'));
2990    if ~isnan(lastfield2)
2991        test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
2992            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2);
2993        num1=num_j(test_find);
2994    end
2995    set(handles.first_j,'String',num2str(num1(1)));
2996    set(handles.last_j,'String',num2str(num1(end)));
2997end
2998
2999%------------------------------------------------------------------------
3000function ref_i_Callback(hObject, eventdata, handles)
3001%------------------------------------------------------------------------
3002mode_list=get(handles.ListPairMode,'String');
3003mode_value=get(handles.ListPairMode,'Value');
3004mode=mode_list{mode_value};
3005errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files
3006if isequal(mode,'series(Di)') || ...% we do patch2 only
3007        (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
3008    errormsg=find_netcpair_civ( handles,2);
3009end
3010    if ~isempty(errormsg)
3011    msgbox_uvmat('ERROR',errormsg)
3012    end
3013
3014%------------------------------------------------------------------------
3015function ref_j_Callback(hObject, eventdata, handles)
3016%------------------------------------------------------------------------
3017mode_list=get(handles.ListPairMode,'String');
3018mode_value=get(handles.ListPairMode,'Value');
3019mode=mode_list{mode_value};
3020if isequal(get(handles.CheckCiv1,'Value'),0)|| isequal(mode,'series(Dj)')
3021    errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files
3022end
3023if isequal(mode,'series(Dj)') || ...
3024        (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
3025    errormsg=find_netcpair_civ(handles,2);
3026end
3027    if ~isempty(errormsg)
3028    msgbox_uvmat('ERROR',errormsg)
3029    end
3030
3031%------------------------------------------------------------------------
3032% determine the menu for checkciv1 pairs depending on existing netcdf file at the middle of
3033% the field series set by first_i, incr, last_i
3034% index=1: look for pairs for civ1
3035% index=2: look for pairs for civ2
3036function errormsg=find_netcpair_civ(handles,index)
3037%------------------------------------------------------------------------
3038set(gcf,'Pointer','watch')% set the mouse pointer to 'watch' (clock)
3039
3040%% initialisation
3041errormsg='';
3042browse=get(handles.RootPath,'UserData');
3043compare_list=get(handles.ListCompareMode,'String');
3044val=get(handles.ListCompareMode,'Value');
3045compare=compare_list{val};
3046if strcmp(compare,'displacement')||strcmp(compare,'shift')
3047    mode='displacement';
3048else
3049    mode_list=get(handles.ListPairMode,'String');
3050    mode_value=get(handles.ListPairMode,'Value');
3051    if isempty(mode_list)
3052        return
3053    end
3054    mode=mode_list{mode_value};
3055end
3056nom_type_ima=get(handles.NomType,'String');
3057
3058%% determine nom_type_nc, nomenclature type of the .nc files:
3059[nom_type_nc]=nomtype2pair(nom_type_ima,mode);
3060
3061%% reads .nc subdirectoy and image numbers from the interface
3062subdir_civ1=get(handles.SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf data
3063subdir_civ2=get(handles.SubdirCiv2,'String');%subdirectory subdir_civ2 for the netcdf data
3064ref_i=str2double(get(handles.ref_i,'String'));
3065if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
3066    ref_j=0;
3067else
3068    ref_j=str2double(get(handles.ref_j,'String'));
3069    if isnan(ref_j)
3070        ref_j=1;
3071    end
3072end
3073time=get(handles.ImaDoc,'UserData');%get the set of times
3074TimeUnit=get(handles.TimeUnit,'String');
3075checkframe=strcmp(TimeUnit,'frame');
3076displ_num=get(handles.ListPairCiv1,'UserData');
3077
3078%% eliminate the first pairs inconsistent with the position
3079if isempty(displ_num)
3080    nbpair=0;
3081else
3082    nbpair=length(displ_num(1,:));%nbre of displayed pairs
3083    if  isequal(mode,'series(Di)')  %| isequal(mode,'st_series(Di)')
3084        nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index
3085    elseif  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
3086        nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index
3087    end
3088end
3089nbpair=min(200,nbpair);%limit the number of displayed pairs to 200
3090
3091%% case with no Civ1 operation, netcdf files need to exist for reading
3092displ_pair={''};
3093select=ones(size(1:nbpair));%flag for displayed pairs =1 for display
3094testpair=0;
3095RootPath=get(handles.RootPath,'String');
3096RootFile=get(handles.RootFile,'String');
3097if index==1 % case civ1
3098    if ~get(handles.CheckCiv1,'Value') %
3099        if ~exist(fullfile(RootPath,subdir_civ1),'dir')
3100            errormsg=['no civ1 file available: subdirectory ' subdir_civ1 ' does not exist'];
3101            set(handles.ListPairCiv1,'String',{});
3102            return
3103        end
3104        for ipair=1:nbpair
3105            filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,...
3106                ref_i+displ_num(3,ipair),ref_i+displ_num(4,ipair),ref_j+displ_num(1,ipair),ref_j+displ_num(2,ipair));
3107            select(ipair)=exist(filename,'file')==2;% put flag to 0 if the file does not exist
3108        end
3109        % case of no displayed pair
3110        if isequal(select,zeros(size(1:nbpair)))
3111            if isfield(browse,'incr_pair') && ~isequal(browse.incr_pair,[0 0])
3112                num_i1=ref_i-floor(browse.incr_pair(1)/2);
3113                num_i2=ref_i+ceil(browse.incr_pair(1)/2);
3114                num_j1=ref_j-floor(browse.incr_pair(2)/2);
3115                num_j2=ref_j+ceil(browse.incr_pair(2)/2);
3116                filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,num_i1,num_i2,num_j1,num_j2);
3117                select(1)=exist(filename,'file')==2;
3118                testpair=1;
3119            else
3120                if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
3121                    errormsg=['no civ1 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ1];
3122                else
3123                    errormsg=['no civ1 file available for the selected reference indices (i,j)= ' num2str(ref_i) ', ' num2str(ref_j) ' and subdirectory ' subdir_civ1];
3124                end
3125                set(handles.ListPairCiv1,'String',{''});
3126                %COMPLETER CAS STEREO
3127                return
3128            end
3129        end
3130    end
3131else %case civ2 alone
3132    if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
3133        if ~exist(fullfile(RootPath,subdir_civ2,ext_dir),'dir')
3134            errordlg(['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist'])
3135            set(handles.ListPairCiv2,'Value',1);
3136            set(handles.ListPairCiv2,'String',{''});
3137            return
3138        end
3139        for ipair=1:nbpair
3140            filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,...
3141                ref_i+displ_num(3,ipair),ref_i+displ_num(4,ipair),ref_j+displ_num(1,ipair),ref_j+displ_num(2,ipair));
3142            select(ipair)=exist(filename,'file')==2;
3143        end
3144        if  isequal(select,zeros(size(1:nbpair)))
3145            if isfield(browse,'incr_pair')
3146                num_i1=ref_i-floor(browse.incr_pair(1)/2);
3147                num_i2=ref_i+floor((browse.incr_pair(1)+1)/2);
3148                num_j1=ref_j-floor(browse.incr_pair(2)/2);
3149                num_j2=ref_j+floor((browse.incr_pair(2)+1)/2);
3150                filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile,'.nc',nom_type_nc,num_i1,num_i2,num_j1,num_j2);
3151                select(1)=exist(filename,'file')==2;
3152            else
3153                if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
3154                    errormsg=['no civ2 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ2];
3155                else
3156                    errormsg=['no civ2 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ2];
3157                end
3158                set(handles.ListPairCiv2,'Value',1);
3159                set(handles.ListPairCiv2,'String',{''});
3160                return
3161            end
3162        end
3163    end
3164end
3165
3166%% determine the menu display in .ListPairCiv1
3167% the menu depends on the mode defined in ListPairMode_callback through the array displ_num:
3168% displ_num(1,:)=indices j1
3169% displ_num(2,:)=indices j2
3170% displ_num(3,:)=indices i1
3171% displ_num(4,:)=indices i2
3172% in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices
3173% are relative to the reference indices ref_i and ref_j respectively.
3174if isequal(mode,'series(Di)')
3175    if testpair
3176        displ_pair{1}=['Di= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
3177    else
3178        for ipair=1:nbpair
3179            if select(ipair)
3180                displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
3181                %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
3182                 %   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
3183               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
3184                 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
3185                else
3186                    dt=1;
3187                end
3188                 displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
3189            else
3190                displ_pair{ipair}='...'; %pair not displayed in the menu
3191            end
3192        end
3193    end
3194elseif isequal(mode,'series(Dj)')
3195    if testpair
3196        displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
3197    else
3198        for ipair=1:nbpair
3199            if select(ipair)
3200                displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
3201                if ~checkframe && size(time,1)>=ref_i+1+displ_num(4,ipair) && size(time,2)>=ref_j+1+displ_num(2,ipair)
3202                    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
3203                    displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
3204                end
3205            else
3206                displ_pair{ipair}='...'; %pair not displayed in the menu
3207            end
3208        end
3209    end
3210elseif isequal(mode,'pair j1-j2')%case of pairs
3211    for ipair=1:nbpair
3212        if select(ipair)
3213            if ~checkframe && size(time,2)>1
3214            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
3215            else % time set by default to i index
3216                dt=1;
3217            end
3218            displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ...
3219                ' :dt= ' num2str(dt*1000)];
3220        else
3221            displ_pair{ipair}='...'; %pair not displayed in the menu
3222        end
3223    end
3224elseif isequal(mode,'displacement')
3225    displ_pair={'Di=Dj=0'};
3226end
3227if index==1
3228set(handles.ListPairCiv1,'String',displ_pair');
3229end
3230
3231%% determine the default selection in the pair menu
3232ichoice=find(select,1);% index of selected pair
3233if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
3234initial=get(handles.ListPairCiv1,'Value');%initial choice of pair
3235if initial>nbpair || (numel(select)>=initial && ~isequal(select(initial),1))
3236    set(handles.ListPairCiv1,'Value',ichoice);% first valid pair proposed by default in the menu
3237end
3238initial=get(handles.ListPairCiv2,'Value');
3239if initial>length(displ_pair')%|~isequal(select(initial),1)
3240    if ichoice <= length(displ_pair')
3241        set(handles.ListPairCiv2,'Value',ichoice);% same pair proposed by default for civ2
3242    else
3243        set(handles.ListPairCiv2,'Value',1);% same pair proposed by default for civ2
3244    end
3245end
3246set(handles.ListPairCiv2,'String',displ_pair');
3247set(gcf,'Pointer','arrow')
3248
3249
3250   
3251% %------------------------------------------------------------------------   
3252% % call 'view_field.fig' to display the  field selected in the list of 'status'
3253% function open_view_field(hObject, eventdata)
3254% %------------------------------------------------------------------------
3255% list=get(hObject,'String');
3256% index=get(hObject,'Value');
3257% rootroot=get(hObject,'UserData');
3258% filename=list{index};
3259% ind_dot=strfind(filename,'...');
3260% filename=filename(1:ind_dot-1);
3261% filename=fullfile(rootroot,filename);
3262% delete(get(hObject,'parent'))%delete the display figure to stop the check process
3263% if exist(filename,'file')%visualise the vel field if it exists
3264%     uvmat(filename)
3265%     set(gcbo,'Value',1)
3266% end
3267
3268
3269%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3270% Callbacks in the uipanel Reference Indices
3271%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3272%------------------------------------------------------------------------
3273function first_i_Callback(hObject, eventdata, handles)
3274%------------------------------------------------------------------------
3275first_i=str2double(get(handles.first_i,'String'));
3276set(handles.ref_i,'String', num2str(first_i))% reference index for pair dt = first index
3277ref_i_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
3278
3279%------------------------------------------------------------------------
3280function first_j_Callback(hObject, eventdata, handles)
3281%------------------------------------------------------------------------
3282first_j=str2num(get(handles.first_j,'String'));
3283set(handles.ref_j,'String', num2str(first_j))% reference index for pair dt = first index
3284ref_j_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
3285
3286%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3287% Callbacks in the uipanel Civ1
3288%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3289%------------------------------------------------------------------------
3290% --- Executes on button press in SearchRange: determine the search range num_Searchx,num_Searchy
3291function SearchRange_Callback(hObject, eventdata, handles)
3292%------------------------------------------------------------------------
3293%determine pair numbers
3294if strcmp(get(handles.num_UMin,'Visible'),'off')
3295    set(handles.u_title,'Visible','on')
3296    set(handles.v_title,'Visible','on')
3297    set(handles.num_UMin,'Visible','on')
3298    set(handles.num_UMax,'Visible','on')
3299    set(handles.num_VMin,'Visible','on')
3300    set(handles.num_VMax,'Visible','on')
3301    set(handles.CoordUnit,'Visible','on')
3302    set(handles.TimeUnit,'Visible','on')
3303    set(handles.slash_title,'Visible','on')
3304    set(handles.min_title,'Visible','on')
3305    set(handles.max_title,'Visible','on')
3306    set(handles.unit_title,'Visible','on')
3307else
3308    get_search_range(hObject, eventdata, handles)
3309end
3310
3311%------------------------------------------------------------------------
3312% ---  determine the search range num_Searchx,num_Searchy and shift
3313function get_search_range(hObject, eventdata, handles)
3314%------------------------------------------------------------------------
3315param_civ1=read_GUI(handles.Civ1);
3316umin=param_civ1.UMin;
3317umax=param_civ1.UMax;
3318vmin=param_civ1.VMin;
3319vmax=param_civ1.VMax;
3320%switch min_title and max_title in case of error
3321if umax<=umin
3322    umin_old=umin;
3323    umin=umax;
3324    umax=umin_old;
3325    set(handles.num_UMin,'String', num2str(umin))
3326    set(handles.num_UMax,'String', num2str(umax))
3327end
3328if vmax<=vmin
3329    vmin_old=vmin;
3330    vmin=vmax;
3331    vmax=vmin_old;
3332    set(handles.num_VMin,'String', num2str(vmin))
3333    set(handles.num_VMax,'String', num2str(vmax))
3334end   
3335if ~(isempty(umin)||isempty(umax)||isempty(vmin)||isempty(vmax))
3336    list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
3337    index=get(handles.ListPairCiv1,'Value');
3338    pair_string=list_pair{index};
3339    time=get(handles.ImaDoc,'UserData'); %get the set of times
3340    pxcm=get(handles.SearchRange,'UserData');
3341    mode_list=get(handles.ListPairMode,'String');
3342    mode_value=get(handles.ListPairMode,'Value');
3343    mode=mode_list{mode_value};     
3344    if isequal (mode, 'series(Di)' )
3345        ref_i=str2double(get(handles.ref_i,'String'));
3346        num1=ref_i-floor(index/2);%  first image numbers
3347        num2=ref_i+ceil(index/2);
3348        num_a=1;
3349        num_b=1;
3350    elseif isequal (mode, 'series(Dj)')
3351        num1=1;
3352        num2=1;
3353        ref_j=str2double(get(handles.ref_j,'String'));
3354        num_a=ref_j-floor(index/2);%  first image numbers
3355        num_b=ref_j+ceil(index/2);
3356    elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)     
3357        ref_i=str2double(get(handles.ref_i,'String'));
3358        num1=ref_i;
3359        num2=ref_i;
3360                r=regexp(pair_string,'(?<mode>(Di=)|(Dj=)) -*(?<num1>\d+)\|(?<num2>\d+)','names');
3361        if isempty(r)
3362            r=regexp(pair_string,'(?<num1>\d+)(?<mode>-)(?<num2>\d+)','names');
3363        end 
3364        num_a=str2num(r.num1);
3365        num_b=str2num(r.num2);
3366    end
3367    dt=time(num2+1,num_b+1)-time(num1+1,num_a+1);
3368    ibx=str2double(get(handles.num_Bx,'String'));
3369    iby=str2double(get(handles.num_By,'String'));
3370    umin=dt*pxcm*umin;
3371    umax=dt*pxcm*umax;
3372    vmin=dt*pxcm*vmin;
3373    vmax=dt*pxcm*vmax;
3374    shiftx=round((umin+umax)/2);
3375    shifty=round((vmin+vmax)/2);
3376    isx=(umax+2-shiftx)*2+param_civ1.Bx;
3377    isx=2*ceil(isx/2)+1;
3378    isy=(vmax+2-shifty)*2+param_civ1.Bx;
3379    isy=2*ceil(isy/2)+1;
3380    set(handles.num_Shiftx,'String',num2str(shiftx));
3381    set(handles.num_Shifty,'String',num2str(shifty));
3382    set(handles.num_Searchx,'String',num2str(isx));
3383    set(handles.num_Searchy,'String',num2str(isy));
3384end
3385
3386%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3387% Callbacks in the uipanel Fix1
3388%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3389%------------------------------------------------------------------------
3390% --- Executes on button press in CheckMask.
3391function get_mask_fix1_Callback(hObject, eventdata, handles)
3392%------------------------------------------------------------------------
3393maskval=get(handles.CheckMask,'Value');
3394if isequal(maskval,0)
3395    set(handles.Mask,'String','')
3396else
3397    mask_displ='no mask'; %default
3398    filebase=get(handles.RootPath,'String');
3399    [nbslice, flag_mask]=get_mask(filebase,handles);
3400    if isequal(flag_mask,1)
3401        mask_displ=[num2str(nbslice) 'mask'];
3402    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3403        filebase_a=get(handles.RootFile_1,'String');
3404        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3405        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3406            mask_displ='no mask';
3407        end
3408    end
3409    if isequal(mask_displ,'no mask')
3410        [FileName, PathName, filterindex] = uigetfile( ...
3411            {'*.png', ' (*.png)';
3412            '*.png',  '.png files '; ...
3413            '*.*', 'All Files (*.*)'}, ...
3414            'Pick a mask file *.png',filebase);
3415        mask_displ=fullfile(PathName,FileName);
3416        if ~exist(mask_displ,'file')
3417            mask_displ='no mask';
3418        end
3419    end
3420    if isequal(mask_displ,'no mask')
3421        set(handles.CheckMask,'Value',0)
3422        set(handles.CheckMask,'Value',0)
3423        set(handles.CheckMask,'Value',0)
3424    else
3425        %set(handles.CheckMask,'Value',1)
3426        set(handles.CheckMask,'Value',1)
3427    end
3428    set(handles.Mask,'String',mask_displ)
3429    set(handles.Mask,'String',mask_displ)
3430    set(handles.Mask,'String',mask_displ)
3431end
3432
3433%------------------------------------------------------------------------
3434% --- Executes on button press in CheckMask: select box for mask option
3435function get_mask_civ2_Callback(hObject, eventdata, handles)
3436%------------------------------------------------------------------------
3437maskval=get(handles.CheckMask,'Value');
3438if isequal(maskval,0)
3439    set(handles.Mask,'String','')
3440else
3441    mask_displ='no mask'; %default
3442    filebase=get(handles.RootPath,'String');
3443    [nbslice, flag_mask]=get_mask(filebase,handles);
3444    if isequal(flag_mask,1)
3445        mask_displ=[num2str(nbslice) 'mask'];
3446    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3447        filebase_a=get(handles.RootFile_1,'String');
3448        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3449        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3450            mask_displ='no mask';
3451        end
3452    end
3453    if isequal(mask_displ,'no mask')
3454        [FileName, PathName, filterindex] = uigetfile( ...
3455            {'*.png', ' (*.png)';
3456            '*.png',  '.png files '; ...
3457            '*.*', 'All Files (*.*)'}, ...
3458            'Pick a mask file *.png',filebase);
3459        mask_displ=fullfile(PathName,FileName);
3460        if ~exist(mask_displ,'file')
3461            mask_displ='no mask';
3462        end
3463    end
3464    if isequal(mask_displ,'no mask')
3465        set(handles.CheckMask,'Value',0)
3466        set(handles.CheckMask,'Value',0)
3467    else
3468        set(handles.CheckMask,'Value',1)
3469    end
3470    set(handles.Mask,'String',mask_displ)
3471    set(handles.Mask,'String',mask_displ)
3472end
3473
3474%------------------------------------------------------------------------
3475% --- Executes on button press in CheckMask.
3476function get_mask_fix2_Callback(hObject, eventdata, handles)
3477%------------------------------------------------------------------------
3478maskval=get(handles.CheckMask,'Value');
3479if isequal(maskval,0)
3480    set(handles.Mask,'String','')
3481else
3482    mask_displ='no mask'; %default
3483    filebase=get(handles.RootPath,'String');
3484    [nbslice, flag_mask]=get_mask(filebase,handles);
3485    if isequal(flag_mask,1)
3486        mask_displ=[num2str(nbslice) 'mask'];
3487    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3488        filebase_a=get(handles.RootFile_1,'String');
3489        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3490        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3491            mask_displ='no mask';
3492        end
3493    end
3494    if isequal(mask_displ,'no mask')
3495        [FileName, PathName, filterindex] = uigetfile( ...
3496            {'*.png', ' (*.png)';
3497            '*.png',  '.png files '; ...
3498            '*.*', 'All Files (*.*)'}, ...
3499            'Pick a mask file *.png',filebase);
3500        mask_displ=fullfile(PathName,FileName);
3501        if ~exist(mask_displ,'file')
3502            mask_displ='no mask';
3503        end
3504    end
3505    if isequal(mask_displ,'no mask')
3506        set(handles.CheckMask,'Value',0)
3507    end
3508    set(handles.Mask,'String',mask_displ)
3509end
3510
3511%------------------------------------------------------------------------
3512% --- function called to look for mask files
3513function [nbslice, flag_mask]=get_mask(filebase,handles)
3514%------------------------------------------------------------------------
3515%detect mask files, images with appropriate file base
3516%[filebase '_' xx 'mask'], xx=nbslice
3517%flag_mask=1 indicates detection
3518
3519flag_mask=0;%default
3520nbslice=1;
3521
3522% subdir=get(handles.SubdirCiv1,'String');
3523[Path,Name]=fileparts(filebase);
3524if ~isdir(Path)
3525    msgbox_uvmat('ERROR','no path for input files')
3526    return
3527end
3528% currentdir=pwd;
3529% cd(Path);%move in the dir of the root name filebase
3530maskfiles=dir(fullfile(Path,[Name '_*mask_*.png']));%look for mask files
3531% cd(currentdir);%come back to the current working directory
3532if ~isempty(maskfiles)
3533    %     msgbox_uvmat('ERROR','no mask available, to create it use Tools/Make mask in the upper menu bar of uvmat')
3534    % else
3535    flag_mask=1;
3536    maskname=maskfiles(1).name;% take the first mask file in the list
3537    [Path2,Name,ext]=fileparts(maskname);
3538    Namedouble=double(Name);
3539    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3540    ind_mask=findstr('mask',Name);
3541    i=ind_mask-1;
3542    while val(i)==0 && i>0
3543        i=i-1;
3544    end
3545    nbslice=str2double(Name(i+1:ind_mask-1));
3546    if ~isnan(nbslice) && Name(i)=='_'
3547        flag_mask=1;
3548    else
3549        msgbox_uvmat('ERROR',['bad mask file ' Name ext ' found in ' Path2])
3550        return
3551        nbslice=1;
3552    end
3553end
3554
3555%------------------------------------------------------------------------
3556% --- function called to look for grid files
3557function [nbslice, flag_mask]=get_grid(filebase,handles)
3558%------------------------------------------------------------------------
3559flag_mask=0;%default
3560nbslice=1;
3561[Path,Name]=fileparts(filebase);
3562currentdir=pwd;
3563cd(Path);%move in the dir of the root name filebase
3564maskfiles=dir([Name '_*grid_*.grid']);%look for mask files
3565cd(currentdir);%come back to the current working directory
3566if ~isempty(maskfiles)
3567    flag_mask=1;
3568    maskname=maskfiles(1).name;% take the first mask file in the list
3569    [Path2,Name,ext]=fileparts(maskname);
3570    Namedouble=double(Name);
3571    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3572    ind_mask=findstr('grid',Name);
3573    i=ind_mask-1;
3574    while val(i)==0 && i>0
3575        i=i-1;
3576    end
3577    nbslice=str2double(Name(i+1:ind_mask-1));
3578    if ~isnan(nbslice) && Name(i)=='_'
3579        flag_mask=1;
3580    else
3581        msgbox_uvmat('ERROR',['bad grid file ' Name ext ' found in ' Path2])
3582        return
3583        nbslice=1;
3584    end
3585end
3586
3587%------------------------------------------------------------------------
3588% --- transform numbers to letters
3589function str=num2stra(num,nom_type)
3590%------------------------------------------------------------------------
3591if isempty(nom_type)
3592    str='';
3593elseif strcmp(nom_type(end),'a')
3594    str=char(96+num);
3595elseif strcmp(nom_type(end),'A')
3596    str=char(96+num);
3597elseif isempty(nom_type(2:end))%a single index
3598    str='';
3599else
3600    str=num2str(num);
3601end
3602
3603%------------------------------------------------------------------------
3604% --- Executes on button press in ListSubdirCiv1.
3605function ListSubdirCiv1_Callback(hObject, eventdata, handles)
3606%------------------------------------------------------------------------
3607list_subdir_civ1=get(handles.ListSubdirCiv1,'String');
3608val=get(handles.ListSubdirCiv1,'Value');
3609SubDir=list_subdir_civ1{val};
3610if strcmp(SubDir,'new...')
3611    if get(handles.CheckCiv1,'Value')
3612        SubDir='CIV'; %default subdirectory
3613    else
3614        msgbox_uvmat('ERROR','select CheckCiv1 to perform a new Civ operation')
3615        return
3616    end   
3617end
3618set(handles.SubdirCiv1,'String',SubDir);
3619errormsg=find_netcpair_civ(handles,1);
3620if ~isempty(errormsg)
3621    msgbox_uvmat('ERROR',errormsg)
3622end
3623   
3624%------------------------------------------------------------------------
3625% --- Executes on button press in ListSubdirCiv2.
3626function ListSubdirCiv2_Callback(hObject, eventdata, handles)
3627%------------------------------------------------------------------------
3628list_subdir_civ2=get(handles.ListSubdirCiv2,'String');
3629val=get(handles.ListSubdirCiv2,'Value');
3630SubDir=list_subdir_civ2{val};
3631if strcmp(SubDir,'new...')
3632    if get(handles.CheckCiv2,'Value')
3633        SubDir='CIV'; %default subdirectory
3634    else
3635        msgbox_uvmat('ERROR','select CheckCiv2 to perform a new Civ operation')
3636        return
3637    end
3638end
3639set(handles.SubdirCiv2,'String',SubDir);
3640
3641%------------------------------------------------------------------------
3642% --- Executes on button press in CheckGrid.
3643function CheckGrid_Callback(hObject, eventdata, handles)
3644%------------------------------------------------------------------------
3645value=get(hObject,'Value');
3646hparent=get(hObject,'parent');
3647hchildren=get(hparent,'children');
3648handle_txtbox=findobj(hchildren,'tag','txt_Grid');
3649handle_dx=findobj(hchildren,'tag','num_Dx');
3650handle_dy=findobj(hchildren,'tag','num_Dy');
3651handle_title_dx=findobj(hchildren,'tag','title_Dx');
3652handle_title_dy=findobj(hchildren,'tag','title_Dy');
3653testgrid=0;
3654filegrid='';
3655if value
3656    filebase=get(handles.RootPath,'String');
3657    [nbslice, flag_grid]=get_grid(filebase,handles);% look for a grid with appropriate name
3658    if isequal(flag_grid,1)
3659        filegrid=[num2str(nbslice) 'grid'];
3660        testgrid=1;
3661    else % browse for a grid
3662        filegrid=get(hObject,'UserData');%look for previous grid name stored as UserData
3663        if exist(filegrid,'file')
3664            filebase=filegrid;
3665        end
3666        [FileName, PathName, filterindex] = uigetfile( ...
3667            {'*.grid', ' (*.grid)';
3668            '*.grid',  '.grid files '; ...
3669            '*.*', 'All Files (*.*)'}, ...
3670            'Pick a file',filebase);
3671        filegrid=fullfile(PathName,FileName);
3672        set(hObject,'UserData',filegrid);%store for future use
3673        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filegrid,'file'))
3674            testgrid=1;
3675        end
3676    end
3677end
3678if testgrid
3679    set(handle_dx,'Visible','off');
3680    set(handle_dy,'Visible','off');
3681    set(handle_title_dy,'Visible','off');
3682    set(handle_title_dx,'Visible','off');
3683    set(handle_txtbox,'Visible','on')
3684    set(handle_txtbox,'String',filegrid)
3685else
3686    set(hObject,'Value',0);
3687    set(handle_dx,'Visible','on');
3688    set(handle_dy,'Visible','on');
3689    set(handle_title_dy,'Visible','on');
3690    set(handle_title_dx,'Visible','on');
3691    set(handle_txtbox,'Visible','off')
3692end
3693
3694%% if hObject is on the checkciv1 frame, duplicate action for checkciv2 frame
3695PanelName=get(hparent,'tag');
3696if strcmp(PanelName,'Civ1')
3697    hchildren=get(handles.Civ2,'children');
3698    handle_checkbox=findobj(hchildren,'tag','CheckGrid');
3699    handle_txtbox=findobj(hchildren,'tag','txt_Grid');
3700    handle_dx=findobj(hchildren,'tag','num_Dx');
3701    handle_dy=findobj(hchildren,'tag','num_Dy');
3702    handle_title_dx=findobj(hchildren,'tag','title_Dx');
3703    handle_title_dy=findobj(hchildren,'tag','title_Dy');
3704    set(handle_checkbox,'UserData',filegrid);%store for future use
3705    if testgrid
3706        set(handle_checkbox,'Value',1);
3707        set(handle_dx,'Visible','off');
3708        set(handle_dy,'Visible','off');
3709        set(handle_title_dx,'Visible','off');
3710        set(handle_title_dy,'Visible','off');
3711        set(handle_txtbox,'Visible','on')
3712        set(handle_txtbox,'String',filegrid)
3713%     else
3714%         set(handle_checkbox,'Value',0);
3715%         set(handles.CheckGrid,'Value',0);
3716%         set(handle_dx,'Visible','on');
3717%         set(handle_dy,'Visible','on');
3718%          set(handle_title_dx,'Visible','on');
3719%         set(handle_title_dy,'Visible','on');
3720%         set(handle_txtbox,'Visible','off')
3721    end
3722end
3723
3724%------------------------------------------------------------------------
3725% --- Executes on button press in CheckMask: common to all panels (civ1, Civ2..)
3726function CheckMask_Callback(hObject, eventdata, handles)
3727%------------------------------------------------------------------------
3728value=get(hObject,'Value');
3729hparent=get(hObject,'parent');
3730parent_tag=get(hparent,'Tag');
3731hchildren=get(hparent,'children');
3732handle_txtbox=findobj(hchildren,'tag','Mask');% look for the mask name box in the same panel
3733testmask=0;
3734if value
3735    filebase=get(handles.RootPath,'String');
3736    [nbslice, flag_mask]=get_mask(filebase,handles);% look for a mask with appropriate name
3737    if isequal(flag_mask,1)
3738        filemask=[num2str(nbslice) 'mask'];
3739        testmask=1;
3740    else % browse for a mask
3741        filemask=get(hObject,'UserData');%look for previous mask name stored as UserData
3742        if exist(filemask,'file')
3743            filebase=filemask;
3744        end
3745        [FileName, PathName] = uigetfile( ...
3746            {'*.png', ' (*.png)';
3747            '*.png',  '.png files '; ...
3748            '*.*', 'All Files (*.*)'}, ...
3749            'Pick a mask file *.png',filebase);
3750        filemask=fullfile(PathName,FileName);
3751        set(hObject,'UserData',filemask);%store for future use
3752        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filemask,'file'))
3753            testmask=1;
3754        end
3755    end
3756end
3757if testmask
3758    if strcmp(parent_tag,'Civ1')
3759        set(handles.Mask,'Visible','on')
3760        set(handles.Mask,'String',filemask)
3761    set(handles.CheckMask,'Value',1)
3762    end
3763%     switch parent_tag
3764% %         case 'Fix1'
3765% %             stage=2;
3766%         case 'Civ2'
3767%              stage=3;
3768% %         case 'Fix2'
3769% %             stage=4;
3770%     end
3771%     set(handles.Mask(stage:end),'Visible','on')
3772%     set(handles.Mask(stage:end),'String',filemask)
3773%     set(handles.CheckMask(stage:end),'Value',1)
3774else
3775    set(hObject,'Value',0);
3776    set(handle_txtbox,'Visible','off')
3777end
3778
3779
3780% --- Executes on button press in get_gridpatch1.
3781function get_gridpatch1_Callback(hObject, eventdata, handles)
3782filebase=get(handles.RootPath,'String');
3783[FileName, PathName, filterindex] = uigetfile( ...
3784    {'*.grid', ' (*.grid)';
3785    '*.grid',  '.grid files '; ...
3786    '*.*', 'All Files (*.*)'}, ...
3787    'Pick a file',filebase);
3788filegrid=fullfile(PathName,FileName);
3789set(handles.grid_patch1,'string',filegrid);
3790
3791
3792%------------------------------------------------------------------------
3793% --- Executes on button press in get_gridpatch2.
3794function get_gridpatch2_Callback(hObject, eventdata, handles)
3795%------------------------------------------------------------------------
3796
3797
3798%------------------------------------------------------------------------
3799% --- STEREO Interp
3800function cmd=RUN_STINTERP(stinterpBin,filename_A_nc,filename_B_nc,filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,xmlA,xmlB)
3801%------------------------------------------------------------------------
3802namelog=[filename_nc(1:end-3) '_stinterp.log'];
3803cmd=[stinterpBin ' -f1 ' filename_A_nc  ' -f2 ' filename_B_nc ' -f  ' filename_nc ...
3804    ' -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
3805
3806%------------------------------------------------------------------------
3807%--read images and convert them to the uint16 format used for PIV
3808function A=read_image(filename,type_ima,num,movieobject)
3809%------------------------------------------------------------------------
3810%num is the view number needed for an avi movie
3811switch type_ima
3812    case 'movie'
3813        A=read(movieobject,num);
3814    case 'avi'
3815        mov=aviread(filename,num);
3816        A=frame2im(mov(1));
3817    case 'multimage'
3818        A=imread(filename,num);
3819    case 'image'
3820        A=imread(filename);
3821end
3822siz=size(A);
3823if length(siz)==3;%color images
3824    A=sum(double(A),3);
3825    A=uint16(A);
3826end
3827
3828
3829%------------------------------------------------------------------------
3830% --- Executes on button press in get_ref_fix1.
3831function get_ref_fix1_Callback(hObject, eventdata, handles)
3832%------------------------------------------------------------------------
3833filebase=get(handles.RootPath,'String');
3834[FileName, PathName, filterindex] = uigetfile( ...
3835    {'*.nc', ' (*.nc)';
3836    '*.nc',  'netcdf files '; ...
3837    '*.*', 'All Files (*.*)'}, ...
3838    'Pick a file',filebase);
3839
3840fileinput=[PathName FileName];
3841sizf=size(fileinput);
3842if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
3843%[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
3844[Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput);
3845ref.filebase=fullfile(Path,File);
3846% ref.num_a=stra2num(str_a);
3847% ref.num_b=stra2num(str_b);
3848% ref.num1=str2double(field_count);
3849% ref.num2=str2double(str2);
3850browse=[];%initialisation
3851if ~isequal(ref.ext,'.nc')
3852    msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
3853    return
3854end
3855set(handles.ref_fix1,'String',[fullfile(ref.subdir,File) '....nc']);
3856set(handles.ref_fix1,'UserData',ref)
3857menu_field{1}='civ1';
3858Data=nc2struct(fileinput,[]);
3859if isfield(Data,'patch') && isequal(Data.patch,1)
3860    menu_field{2}='filter1';
3861end
3862if isfield(Data,'civ2') && isequal(Data.civ2,1)
3863    menu_field{3}='civ2';
3864end
3865if isfield(Data,'patch2') && isequal(Data.patch2,1)
3866    menu_field{4}='filter2';
3867end
3868set(handles.field_ref1,'String',menu_field);
3869set(handles.field_ref1,'Value',length(menu_field));
3870set(handles.num_MinVel,'Value',2);
3871set(handles.num_MinVel,'String','1');%default threshold
3872set(handles.ref_fix1,'Enable','on')
3873
3874%------------------------------------------------------------------------
3875% --- Executes on button press in get_ref_fix2.
3876function get_ref_fix2_Callback(hObject, eventdata, handles)
3877%------------------------------------------------------------------------
3878if isequal(get(handles.get_ref_fix2,'Value'),1)
3879    filebase=get(handles.RootPath,'String');
3880    [FileName, PathName, filterindex] = uigetfile( ...
3881        {'*.nc', ' (*.nc)';
3882        '*.nc',  'netcdf files '; ...
3883        '*.*', 'All Files (*.*)'}, ...
3884        'Pick a file',filebase);
3885    fileinput=[PathName FileName];
3886    sizf=size(fileinput);
3887    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
3888    %[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
3889    [Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput);
3890    ref.filebase=fullfile(Path,File);
3891%     ref.num_a=stra2num(str_a);
3892%     ref.num_b=stra2num(str_b);
3893%     ref.num1=str2num(field_count);
3894%     ref.num2=str2num(str2);
3895    browse=[];%initialisation
3896    if ~isequal(ref.ext,'.nc')
3897        msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
3898        return
3899    end
3900    set(handles.ref_fix2,'String',[fullfile(ref.subdir,File) '....nc']);
3901    set(handles.ref_fix2,'UserData',ref)
3902    menu_field{1}='civ1';
3903    Data=nc2struct(fileinput,[]);
3904    if isfield(Data,'patch') && isequal(Data.patch,1)
3905        menu_field{2}='filter1';
3906    end
3907    if isfield(Data,'civ2') && isequal(Data.civ2,1)
3908        menu_field{3}='civ2';
3909    end
3910    if isfield(Data,'patch2') && isequal(Data.patch2,1)
3911        menu_field{4}='filter2';
3912    end
3913    set(handles.field_ref2,'String',menu_field);
3914    set(handles.field_ref2,'Value',length(menu_field));
3915    set(handles.num_MinVel,'Value',2);
3916    set(handles.num_MinVel,'String','1');%default threshold
3917    set(handles.ref_fix2,'Enable','on')
3918    set(handles.ref_fix2,'Visible','on')
3919    set(handles.field_ref2,'Visible','on')
3920else
3921    set(handles.ref_fix2,'Visible','off')
3922    set(handles.field_ref2,'Visible','off')
3923end
3924
3925%------------------------------------------------------------------------
3926function ref_fix1_Callback(hObject, eventdata, handles)
3927%------------------------------------------------------------------------
3928set(handles.num_MinVel,'Value',1);
3929set(handles.field_ref1,'Value',1)
3930set(handles.field_ref1,'String',{' '})
3931set(handles.ref_fix1,'UserData',[]);
3932set(handles.ref_fix1,'String','');
3933set(handles.thresh_vel1,'String','0');
3934
3935%------------------------------------------------------------------------
3936function ref_fix2_Callback(hObject, eventdata, handles)
3937%------------------------------------------------------------------------
3938set(handles.num_MinVel,'Value',1);
3939set(handles.field_ref2,'Value',1)
3940set(handles.field_ref2,'String',{' '})
3941set(handles.ref_fix2,'UserData',[]);
3942set(handles.ref_fix2,'String','');
3943set(handles.num_MinVel,'String','0');
3944
3945%------------------------------------------------------------------------
3946% --- TO ABANDON Executes on button press in test_stereo1.
3947function CheckStereo_Callback(hObject, eventdata, handles)
3948%------------------------------------------------------------------------
3949hparent=get(hObject,'parent');
3950parent_tag=get(hparent,'Tag');
3951hchildren=get(hparent,'children');
3952handle_txtbox=findobj(hchildren,'tag','txt_Mask');
3953if isequal(get(hObject,'Value'),0)
3954    set(handles.num_SubdomainSize,'Visible','on')
3955    set(handles.num_SmoothingParam,'Visible','on')
3956else
3957    set(handles.num_SubdomainSize,'Visible','off')
3958    set(handles.num_SmoothingParam,'Visible','off')
3959end
3960
3961% %------------------------------------------------------------------------
3962% % --- Executes on button press in CheckStereo.
3963% function StereoCheck_Callback(hObject, eventdata, handles)
3964% %------------------------------------------------------------------------
3965% if isequal(get(handles.CheckStereo,'Value'),0)
3966%     set(handles.num_SubdomainSize,'Visible','on')
3967%     set(handles.num_SmoothingParam,'Visible','on')
3968% else
3969%     set(handles.num_SubdomainSize,'Visible','off')
3970%     set(handles.num_SmoothingParam,'Visible','off')
3971% end
3972
3973%------------------------------------------------------------------------
3974% --- Executes on button press in TestCiv1: prepare the image correlation function
3975% activated by mouse motion
3976function TestCiv1_Callback(hObject, eventdata, handles)
3977%------------------------------------------------------------------------
3978drawnow
3979if get(handles.TestCiv1,'Value')
3980    set(handles.TestCiv1,'BackgroundColor',[0.7 0.7 0.7])% paint TestCiv1 button to grey to confirm civ launch
3981    ref_i=str2double(get(handles.ref_i,'String'));% read reference i index
3982    if strcmp(get(handles.ref_j,'Visible'),'on')
3983        ref_j=str2double(get(handles.ref_j,'String'));% read reference j index if relevant
3984    else
3985        ref_j=1;%default j index
3986    end
3987    [filecell,i1,i2,j1,j2,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,file_ref_fix1,file_ref_fix2]=...
3988        set_civ_filenames(handles,ref_i,ref_j,[1 0 0 0 0 0]);% get the corresponding file name and indices
3989    Data.ListVarName={'ny','nx','A'};
3990    Data.VarDimName= {'ny','nx',{'ny','nx'}};
3991    Data.A=imread(filecell.ima1.civ1{1}); % read the first image
3992    if ndims(Data.A)==3 %case of color image
3993        Data.VarDimName= {'ny','nx',{'ny','nx','rgb'}};
3994    end
3995    Data.ny=[size(Data.A,1) 1];
3996    Data.nx=[1 size(Data.A,2)];
3997    Data.CoordUnit='pixel';% used to set equal scaling for x and y in image dispaly
3998    par_civ1=read_GUI(handles.Civ1);
3999    par_civ1.ImageWidth=size(Data.A,2);
4000    par_civ1.ImageHeight=size(Data.A,1);
4001    par_civ1.Mask='all';% will provide only the grid set for PIV, no image correlation
4002    par_civ1.i1=i1;
4003    par_civ1.i2=i2;
4004    Param.Civ1=par_civ1;
4005    Grid=civ_matlab(Param);% get the grid of x, y positions set for PIV
4006    hview_field=view_field(Data); %view the image in the GUI view_field
4007    set(0,'CurrentFigure',hview_field)
4008    hhview_field=guihandles(hview_field);
4009    set(hview_field,'CurrentAxes',hhview_field.axes3)
4010    ViewData=get(hview_field,'UserData');
4011    ViewData.CivHandle=handles.civ;% indicate the handle of the civ GUI in view_field
4012    ViewData.axes3.B=imread(filecell.ima2.civ1{1});%store the second image in the UserData of the GUI view_field
4013    ViewData.axes3.X=Grid.Civ1_X; %keep the set of points in memeory
4014    ViewData.axes3.Y=Grid.Civ1_Y;
4015    set(hview_field,'UserData',ViewData)
4016    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
4017    if isempty(corrfig)
4018        corrfig=figure;
4019        set(corrfig,'tag','corrfig')
4020        set(corrfig,'name','image correlation')
4021        set(corrfig,'DeleteFcn',{@closeview_field})%
4022    end
4023    set(handles.TestCiv1,'BackgroundColor',[1 0 0])
4024else
4025    set(handles.TestCiv1,'BackgroundColor',[1 0 0])% paint button to red
4026    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
4027    if ~isempty(corrfig)
4028        delete(corrfig)
4029    end
4030    hview_field=findobj(allchild(0),'tag','view_field');% look for view_field   
4031    if ~isempty(hview_field)
4032        delete(hview_field)
4033    end
4034end
4035
4036%------------------------------------------------------------------------
4037%----function introduced for the correlation window figure, activated by deleting this window
4038function closeview_field(gcbo,eventdata)
4039%------------------------------------------------------------------------
4040hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
4041if ~isempty(hview_field)
4042    delete(hview_field)
4043end
4044
4045%------------------------------------------------------------------------
4046% --- Executes on button press in CheckThreshold.
4047function CheckThreshold_Callback(hObject, eventdata, handles)
4048%------------------------------------------------------------------------
4049huipanel=get(hObject,'parent');
4050obj(1)=findobj(huipanel,'Tag','num_MinIma');
4051obj(2)=findobj(huipanel,'Tag','num_MaxIma');
4052obj(3)=findobj(huipanel,'Tag','title_Threshold');
4053if get(hObject,'Value')
4054    set(obj,'Visible','on')
4055else
4056    set(obj,'Visible','off')
4057end
4058
4059%------------------------------------------------------------------------
4060function [cmd,errormsg]=cmd_civ1(filename,Param)
4061%------------------------------------------------------------------------
4062%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4063%changes : filename_cmx -> filename ( no extension )
4064cmd='';
4065filename=regexprep(filename,'.nc',''); %file name for the result
4066if isequal(Param.Civ1.Dt,0)
4067    Param.Civ1.Dt=1 ;%case of 'displacement' mode
4068end
4069Param.Civ1.ImageA=regexprep(Param.Civ1.ImageA,'.png','');
4070Param.Civ1.ImageB=regexprep(Param.Civ1.ImageB,'.png','');
4071[fid,errormsg]=fopen([filename '.civ1.cmx'],'w');
4072if isequal(fid,-1)
4073    errormsg=['cmd file ' filename ' cannot be created: ' errormsg];
4074    return
4075end
4076fprintf(fid,['##############   CMX file' '\n' ]);
4077fprintf(fid,   ['FirstImage ' regexprep(Param.Civ1.ImageA,'\\','\\\\') '\n' ]);% for windows compatibility
4078fprintf(fid,   ['LastImage  ' regexprep(Param.Civ1.ImageB,'\\','\\\\') '\n' ]);% for windows compatibility
4079fprintf(fid,  ['XX' '\n' ]);
4080if isfield(Param.Civ1,'Mask')
4081    fprintf(fid,  ['Mask ' 'y' '\n' ]);
4082    fprintf(fid,  ['MaskName ' regexprep(Param.Civ1.Mask,'\\','\\\\') '\n' ]);
4083else
4084    fprintf(fid,  ['Mask ' 'n' '\n' ]);
4085    fprintf(fid,  ['MaskName ' 'noFile use default' '\n' ]);
4086end
4087fprintf(fid,   ['ImageSize ' num2str(Param.Civ1.ImageWidth) ' ' num2str(Param.Civ1.ImageHeight) '\n' ]);   %VERIFIER CAS GENERAL ?
4088fprintf(fid,   ['CorrelationBoxesSize ' num2str(Param.Civ1.Bx) ' ' num2str(Param.Civ1.By) '\n' ]);
4089fprintf(fid,   ['SearchBoxeSize ' num2str(Param.Civ1.Searchx) ' ' num2str(Param.Civ1.Searchy) '\n' ]);
4090fprintf(fid,   ['RO ' num2str(Param.Civ1.Rho) '\n' ]);
4091if isfield(Param.Civ1,'Grid')
4092    fprintf(fid,   ['GridSpacing ' '25' ' ' '25' '\n' ]);
4093else
4094    fprintf(fid,   ['GridSpacing ' num2str(Param.Civ1.Dx) ' ' num2str(Param.Civ1.Dy) '\n' ]);
4095end
4096fprintf(fid,   ['XX 1.0' '\n' ]);
4097fprintf(fid,   ['Dt_TO ' num2str(Param.Civ1.Dt) ' ' num2str(Param.Civ1.Time) '\n' ]);
4098fprintf(fid,  ['PixCmXY ' '1' ' ' '1' '\n' ]);
4099fprintf(fid,  ['XX 1' '\n' ]);
4100fprintf(fid,   ['ShiftXY ' num2str(Param.Civ1.Shiftx) ' '  num2str(Param.Civ1.Shifty) '\n' ]);
4101if isfield(Param.Civ1,'Grid')
4102    fprintf(fid,  ['Grid ' 'y' '\n' ]);
4103    fprintf(fid,   ['GridName ' regexprep(Param.Civ1.Grid,'\\','\\\\') '\n' ]);
4104else
4105    fprintf(fid,  ['Grid ' 'n' '\n' ]);
4106    fprintf(fid,   ['GridName ' 'noFile use default' '\n' ]);
4107end
4108fprintf(fid,   ['XX 85' '\n' ]);
4109fprintf(fid,   ['XX 1.0' '\n' ]);
4110fprintf(fid,   ['XX 1.0' '\n' ]);
4111fprintf(fid,   ['Hart 1' '\n' ]);
4112fprintf(fid,  [ 'DecimalShift 0' '\n' ]);
4113fprintf(fid,   ['Deformation 0' '\n' ]);
4114fprintf(fid,  ['CorrelationMin 0' '\n' ]);
4115fprintf(fid,   ['IntensityMin 0' '\n' ]);
4116if ~isfield(Param.Civ1,'MinIma')% Image threshold not activated
4117    fprintf(fid,  ['SeuilImage n' '\n' ]);
4118    fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);%not used in principle
4119else% Image threshold  activated
4120    if isempty(Param.Civ1.MaxIma)||isnan(Param.Civ1.MaxIma)
4121        Param.Civ1.MaxIma=2^Param.Civ1.ImageBitDepth;%take the max image value as upper bound by default
4122    end
4123    fprintf(fid,  ['SeuilImage y' '\n' ]);
4124    fprintf(fid,   ['SeuilImageValues ' num2str(Param.Civ1.MinIma) ' ' num2str(Param.Civ1.MaxIma) '\n' ]);
4125end
4126fprintf(fid,   ['ImageToUse ' Param.Civ1.term_a ' ' Param.Civ1.term_b '\n' ]); % VERIFIER ?
4127fprintf(fid,   ['ImageUsedBefore null null' '\n' ]);
4128fclose(fid);
4129
4130if(isunix) %unix (or Mac) system
4131    cmd=['cp -f ' filename '.civ1.cmx ' filename '.cmx \n '];% the cmx file gives the name to the nc file
4132    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
4133    cmd=[cmd 'rm ' filename '.cmx'];
4134else %Windows system
4135    filename=regexprep(filename,'\\','\\\\');
4136    cmd=['copy /Y "' filename '.civ1.cmx" "' filename '.cmx" \n '];
4137    cmd=[cmd '"' regexprep(Param.xml.Civ1Bin,'\\','\\\\')...
4138        '" -f "' filename '.cmx" >"' filename '.civ1.log" \n ' ]; % redirect standard output to the log file
4139    cmd=[cmd 'del "' filename '.cmx"'];
4140end
4141
4142
4143function cmd=cmd_fix(filename,Param,fixname)
4144%%
4145switch fixname
4146    case 'Fix1'
4147        fi2_value=num2str(Param.(fixname).CheckF2);
4148    case 'Fix2'
4149        fi2_value=num2str(Param.(fixname).CheckF4);%need to understand why...
4150end
4151filename=regexprep(filename,'.nc','');
4152MaskName_string='';%default
4153MaxVel_string='';%default
4154if ~isempty(Param.(fixname).MinVel)
4155    MaxVel_string=[' -threshV ' num2str(Param.(fixname).MinVel)];
4156end
4157if isunix
4158    cmd=[Param.xml.FixBin ' -f ' filename '.nc -fi1 ' num2str(Param.(fixname).CheckFmin2) ...
4159        ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ...
4160        ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string...
4161        ' >' filename '.' lower(fixname) '.log 2>&1'];
4162else
4163    cmd=['"' Param.xml.FixBin '" -f "' filename '.nc" -fi1 ' num2str(Param.(fixname).CheckFmin2)...
4164        ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ...
4165        ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string...
4166        ' > "' filename '.' lower(fixname) '.log"'];
4167    cmd=regexprep(cmd,'\\','\\\\');
4168end
4169
4170
4171function cmd=cmd_patch(filename,Param,patchname)
4172%% ------------------------------------------------------------------------
4173filename=regexprep(filename,'.nc','');
4174if isunix
4175    cmd=[Param.xml.PatchBin...
4176        ' -f ' filename '.nc -m ' num2str(Param.(patchname).Nx)...
4177        ' -n ' num2str(Param.(patchname).Ny) ' -ro ' num2str(Param.(patchname).SmoothingParam)...
4178        ' -nopt ' num2str(Param.(patchname).SubdomainSize) ...
4179        '  > ' filename '.' lower(patchname) '.log 2>&1']; % redirect standard output to the log file
4180else
4181    cmd=['"' Param.xml.PatchBin...
4182        '" -f "' filename '.nc" -m ' num2str(Param.(patchname).Nx)...
4183        ' -n ' num2str(Param.(patchname).Ny) ' -ro ' num2str(Param.(patchname).SmoothingParam)...
4184        ' -nopt ' num2str(Param.(patchname).SubdomainSize)...
4185        '  > "' filename '.' lower(patchname) '.log" 2>&1']; % redirect standard output to the log file
4186    cmd=regexprep(cmd,'\\','\\\\');
4187end
4188
4189%------------------------------------------------------------------------
4190% --- CheckCiv2  CheckCiv2  CheckCiv2 CheckCiv2
4191function [cmd,errormsg]=cmd_civ2(filename,Param)
4192%------------------------------------------------------------------------
4193%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4194% global civ2Bin sge%name of the executable for checkciv1 calculation
4195 cmd='';
4196filename=regexprep(filename,'.nc','');
4197if isequal(Param.Civ2.Dt,'0')
4198    Param.Civ2.Dt='1' ;%case of 'displacement' mode
4199end
4200Param.Civ2.ImageA=regexprep(Param.Civ2.ImageA,'.png','');
4201Param.Civ2.ImageB=regexprep(Param.Civ2.ImageB,'.png','');% bug : .png appears two times ?
4202[fid,errormsg]=fopen([filename '.civ2.cmx'],'w');
4203if isequal(fid,-1)
4204    return
4205end
4206fprintf(fid,['##############   CMX file' '\n' ]);
4207fprintf(fid,   ['FirstImage ' regexprep(Param.Civ2.ImageA,'\\','\\\\') '\n' ]);% for windows compatibility
4208fprintf(fid,   ['LastImage  ' regexprep(Param.Civ2.ImageB,'\\','\\\\') '\n' ]);% for windows compatibility
4209fprintf(fid,  ['XX' '\n' ]);
4210if isfield(Param.Civ2,'Mask')
4211    fprintf(fid,  ['Mask ' 'y' '\n' ]);
4212    fprintf(fid,  ['MaskName ' regexprep(Param.Civ2.Mask,'\\','\\\\') '\n' ]);
4213else
4214    fprintf(fid,  ['Mask ' 'n' '\n' ]);
4215    fprintf(fid,  ['MaskName ' 'noFile use default' '\n' ]);
4216end
4217% fprintf(fid, ['Mask ' Param.Civ2.MaskFlag '\n' ]);
4218% fprintf(fid, ['MaskName ' regexprep(Param.Civ2.MaskName,'\\','\\\\') '\n' ]);% for windows compatibility
4219fprintf(fid,   ['ImageSize ' num2str(Param.Civ2.ImageWidth) ' ' num2str(Param.Civ2.ImageHeight) '\n' ]); 
4220% fprintf(fid, ['ImageSize ' num2str(Param.Civ2.npx) ' ' num2str(Param.Civ2.npy) '\n' ]);   %VERIFIER CAS GENERAL ?
4221fprintf(fid, ['CorrelationBoxesSize ' num2str(Param.Civ2.Bx) ' ' num2str(Param.Civ2.By) '\n' ]);
4222fprintf(fid, ['SearchBoxeSize ' num2str(Param.Civ2.Bx) ' ' num2str(Param.Civ2.By) '\n']);
4223fprintf(fid, ['RO ' num2str(Param.Civ2.Rho) '\n']);
4224if isfield(Param.Civ2,'Grid')
4225    fprintf(fid,   ['GridSpacing ' '25' ' ' '25' '\n' ]);
4226else
4227    fprintf(fid,   ['GridSpacing ' num2str(Param.Civ2.Dx) ' ' num2str(Param.Civ2.Dy) '\n' ]);
4228end
4229% fprintf(fid, ['GridSpacing ' num2str(Param.Civ2.Dx) ' ' num2str(Param.Civ2.Dy) '\n']);
4230fprintf(fid, ['XX 1.0' '\n' ]);
4231fprintf(fid, ['Dt_TO ' num2str(Param.Civ2.Dt) ' ' num2str(Param.Civ2.Time) '\n' ]);
4232fprintf(fid, ['PixCmXY ' '1' ' ' '1' '\n' ]);
4233fprintf(fid, ['XX 1' '\n' ]);
4234fprintf(fid, 'ShiftXY 0 0\n');
4235if isfield(Param.Civ2,'Grid')
4236    fprintf(fid,  ['Grid ' 'y' '\n' ]);
4237    fprintf(fid,   ['GridName ' regexprep(Param.Civ2.Grid,'\\','\\\\') '\n' ]);
4238else
4239    fprintf(fid,  ['Grid ' 'n' '\n' ]);
4240    fprintf(fid,   ['GridName ' 'noFile use default' '\n' ]);
4241end
4242% fprintf(fid, ['Grid ' Param.Civ2.GridFlag '\n' ]);
4243% fprintf(fid, ['GridName ' regexprep(Param.Civ2.GridName,'\\','\\\\') '\n']);
4244fprintf(fid, ['XX 85' '\n' ]);
4245fprintf(fid, ['XX 1.0' '\n' ]);
4246fprintf(fid, ['XX 1.0' '\n' ]);
4247fprintf(fid, ['Hart 1' '\n' ]);
4248fprintf(fid, ['DecimalShift ' num2str(Param.Civ2.CheckDecimal) '\n']);
4249fprintf(fid, ['Deformation ' num2str(Param.Civ2.CheckDeformation) '\n']);
4250fprintf(fid,  ['CorrelationMin 0' '\n' ]);
4251fprintf(fid,   ['IntensityMin 0' '\n' ]);
4252
4253if ~isfield(Param.Civ2,'MinIma')% Image threshold not activated
4254    fprintf(fid,  ['SeuilImage n' '\n' ]);
4255    fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);%not used in principle
4256else% Image threshold  activated
4257    if isempty(Param.Civ2.MaxIma)||isnan(Param.Civ2.MaxIma)
4258        Param.Civ2.MaxIma=2^Param.Civ2.ImageBitDepth;%take the max image value as upper bound by default
4259    end
4260    fprintf(fid,  ['SeuilImage y' '\n' ]);
4261    fprintf(fid,   ['SeuilImageValues ' num2str(Param.Civ2.MinIma) ' ' num2str(Param.Civ2.MaxIma) '\n' ]);
4262end
4263fprintf(fid,   ['ImageToUse ' Param.Civ2.term_a ' ' Param.Civ2.term_b '\n' ]); % VERIFIER ?
4264fprintf(fid, ['ImageUsedBefore ' regexprep(Param.Civ2.filename_nc1,'\\','\\\\') '\n']);
4265fclose(fid);
4266
4267if(isunix)
4268    cmd=['cp -f ' filename '.civ2.cmx ' filename '.cmx\n'...
4269        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
4270        'rm ' filename '.cmx \n'];%rename .cmx as .checkciv2.cmx, the result file is named [filename '.nc'] by CIVx
4271else
4272    filename=regexprep(filename,'\\','\\\\');
4273    cmd=['copy /Y "' filename '.civ2.cmx" "' filename '.cmx" \n'...
4274        '"' regexprep(Param.xml.Civ2Bin,'\\','\\\\') '" -f "' filename  '.cmx" >"' filename '.civ2.log" \n'...
4275        'del "' filename '.cmx" \n'];
4276end
4277
4278%------------------------------------------------------------------------
4279% --- CheckCiv1  Unified: TO ABADON
4280function xml_civ1_parameters=CIV1_CMD_Unified(filename,namelog,par)
4281%------------------------------------------------------------------------
4282%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4283%global CivBin%name of the executable for checkciv1 calculation
4284
4285civ1.image1=par.ImageA;
4286civ1.image2=par.ImageB;
4287civ1.imageSize_X=par.npx;
4288civ1.imageSize_Y=par.npy;
4289civ1.outputFileName=[filename '.nc'];
4290civ1.correlationBoxesSize_X=par.ibx;
4291civ1.correlationBoxesSize_Y=par.iby;
4292civ1.searchBoxesSize_X=par.isx;
4293civ1.searchBoxesSize_Y=par.isy;
4294civ1.globalShift_X=par.shiftx;
4295civ1.globalShift_Y=par.shifty;
4296civ1.ro=par.rho;
4297civ1.hart='y';
4298if isequal(par.gridflag,'y')
4299    civ1.grid=par.gridname;
4300else
4301    civ1.grid='n';
4302    civ1.gridSpacing_X=par.dx;
4303    civ1.gridSpacing_Y=par.dy;
4304end
4305if isequal(par.maskflag,'y')
4306    civ1.mask=par.maskname;
4307end
4308civ1.dt=par.Dt;
4309civ1.unit='pixel';
4310civ1.absolut_time_T0=par.Time;
4311civ1.pixcmx='1';
4312civ1.pixcmy='1';
4313civ1.convectFlow='n';
4314
4315xml_civ1_parameters=civ1;
4316
4317%------------------------------------------------------------------------
4318% --- CheckCiv2  Unified: TO ABADON
4319function civ2=CIV2_CMD_Unified(filename,namelog,par)
4320%------------------------------------------------------------------------
4321%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4322%global CivBin%name of the executable for checkciv1 calculation
4323
4324filename=regexprep(filename,'.nc','');
4325
4326civ2.image1=par.ImageA;
4327civ2.image2=par.ImageB;
4328civ2.imageSize_X=par.npx;
4329civ2.imageSize_Y=par.npy;
4330civ2.inputFileName=[par.filename_nc1 '.nc'];
4331civ2.outputFileName=[filename '.nc'];
4332civ2.correlationBoxesSize_X=par.ibx;
4333civ2.correlationBoxesSize_Y=par.iby;
4334civ2.ro=par.rho;
4335%checkciv2.decimalShift=par.CheckDecimal;
4336%checkciv2.CheckDeformation=par.CheckDeformation;
4337if isequal(par.decimal,'1')
4338    civ2.decimalShift='y';
4339else
4340    civ2.decimalShift='n';
4341end
4342if isequal(par.deformation,'1')
4343    civ2.deformation='y';
4344else
4345    civ2.deformation='n';
4346end
4347if isequal(par.gridflag,'y')
4348    civ2.grid=par.gridname;
4349else
4350    civ2.grid='n';
4351    civ2.gridSpacing_X=par.dx;
4352    civ2.gridSpacing_Y=par.dy;
4353end
4354civ2.gridSpacing_X='10';
4355civ2.gridSpacing_Y='10';%NOTE: faut mettre gridSpacing pourque ca tourne, meme si c'est la grille qui est utilisee
4356if isequal(par.maskflag,'y')
4357    civ2.mask=par.maskname;
4358else
4359    civ2.mask='n';
4360end
4361civ2.dt=par.Dt;
4362civ2.unit='pixel';
4363civ2.absolut_time_T0=par.Time;
4364civ2.pixcmx='1';
4365civ2.pixcmy='1';
4366civ2.convectFlow='n';
4367
4368
4369% --- Executes on button press in TestPatch1.
4370function TestPatch1_Callback(hObject, eventdata, handles)
4371set(handles.TestPatch1,'BackgroundColor',[1 1 0])
4372drawnow
4373if get(handles.TestPatch1,'Value')
4374    ref_i=str2double(get(handles.ref_i,'String'));
4375    if strcmp(get(handles.ref_j,'Visible'),'on')
4376        ref_j=str2double(get(handles.ref_j,'String'));
4377    else
4378        ref_j=1;%default
4379    end
4380    [filecell,i1,i21,j1,j2,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,file_ref_fix1,file_ref_fix2]=...
4381        set_civ_filenames(handles,ref_i,ref_j,[0 0 1 0 0 0]);
4382   
4383    Data.ListVarName={'ny','nx','A'};
4384    Data.VarDimName= {'ny','nx',{'ny','nx'}};
4385   
4386    param_patch1=read_GUI(handles.Patch1);
4387    param_patch1.CivFile=filecell.nc.civ1{1};
4388    Param.Patch1=param_patch1;
4389    for irho=1:7
4390        [Data,errormsg]=civ_matlab(Param);% get the grid of x, y positions set for PIV
4391        if ~isempty(errormsg)
4392            msgbox_uvmat('ERROR',errormsg)
4393            return
4394        end
4395        SmoothingParam(irho)=Param.Patch1.SmoothingParam;
4396        Data.Civ1_U_Diff=Data.Civ1_U_Diff(Data.Civ1_FF==0);
4397        Data.Civ1_V_Diff=Data.Civ1_V_Diff(Data.Civ1_FF==0);
4398        DiffVel(irho)=sqrt(mean(Data.Civ1_U_Diff.*Data.Civ1_U_Diff+Data.Civ1_V_Diff.*Data.Civ1_V_Diff))
4399        NbSites(irho,:)=Data.Civ1_NbSites*numel(Data.Civ1_NbSites)/numel(Data.Civ1_U_Diff);
4400        Param.Patch1.SmoothingParam=2*Param.Patch1.SmoothingParam;
4401    end
4402    figure
4403    plot(SmoothingParam,DiffVel,'b',SmoothingParam,NbSites,'r')
4404    set(handles.TestPatch1,'BackgroundColor',[1 0 0])
4405else
4406    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
4407    if ~isempty(corrfig)
4408        delete(corrfig)
4409    end
4410    hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
4411    if ~isempty(hview_field)
4412        delete(hview_field)
4413    end
4414end
4415%'nomtype2pair': creates nomencalture for index pairs knowing the image nomenclature
4416%---------------------------------------------------------------------
4417% [nom_type_pair]=nomtype2pair(nom_type,Dti,Dtj);
4418%---------------------------------------------------------------------           
4419
4420% OUTPUT:
4421%nom_type_nc
4422
4423%---------------------------------------------------------------------
4424% INPUT:
4425% 'nom_type': string defining the kind of nomenclature used:
4426     %nom_type='': constant name [filebase ext] (default output if 'nom_type' is undefined)
4427     %nom_type='*': the same  file [filebase ext] contains successive fields (ex avi movies)
4428     %nom_type='_i': series of files with a single index i preceded by '_'(e.g. 'aa_45.png').
4429     %nom_type='#' series of indexed images wich is not series_i [filebase index ext], e.g. 'aa045.jpg' or 'aa45.tif'
4430     %nom_type='_i_j' matrix of files with two indices i and j separated by '_'(e.g. 'aa_45_2.png')
4431     %nom_type='_i1-i2' from pairs from a single index (e.g. 'aa_45-47.nc')
4432     %nom_type='_i_j1-j2'pairs of j indices (e.g. 'aa_45_2-3.nc')
4433     %nom_type='_i1-i2_j' pairs of i indices (e.g. 'aa_45-46_2.nc')
4434     %nom_type='#a','#A', with a numerical index and an index letter(e.g.'aa045b.png'), OBSOLETE (replaced by 'series_i_j')
4435     %nom_type='%03d' or '%04d', series of indexed images with numbers completed with zeros to 3 or 4 digits, e.g.'aa045.tif'
4436     %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'
4437     %nom_type='raw_SMD', same as '#a' but with no extension ext='', OBSOLETE
4438     %nom_type='#_ab' from pairs of '#a' images (e.g. 'aa045bc.nc'), ext='.nc', OBSOLETE (replaced by 'netc_2D')
4439     %nom_type='%3dab' from pairs of '%3da' images (e.g. 'aa045bc.nc'), ext='.nc', OBSOLETE (replaced by 'netc_2D')
4440% Dti: ~=0 if i index pairs are used
4441% Dtj: ~=0 if i index pairs are used
4442
4443function NomTypeNc=nomtype2pair(NomTypeIma,mode)
4444
4445%determine nom_type_nc:
4446NomTypeNc=NomTypeIma;%default
4447switch mode
4448    case 'pair j1-j2'     
4449    if ~isempty(regexp(NomTypeIma,'a$'))
4450        NomTypeNc=[NomTypeIma 'b'];
4451    elseif ~isempty(regexp(NomTypeIma,'A$'))
4452        NomTypeNc=[NomTypeIma 'B'];
4453    else
4454        r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
4455        if ~isempty(r)
4456            NomTypeNc='_1_1-2';
4457        end
4458    end
4459    case 'series(Dj)' 
4460        r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
4461        if ~isempty(r)
4462            NomTypeNc='_1_1-2';
4463        end
4464   case 'series(Di)'
4465        r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
4466        if ~isempty(r)
4467            NomTypeNc='_1-2_1';
4468        else
4469            NomTypeNc='_1-2';
4470        end
4471end
4472
4473function NomType_Callback(hObject, eventdata, handles)
4474set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
4475RootPath=get(handles.RootPath,'String');
4476RootFile=get(handles.RootFile,'String');
4477ref_i=str2num(get(handles.ref_i,'String'));
4478ref_j=str2num(get(handles.ref_j,'String'));
4479NomType=get(handles.NomType,'String');
4480ImaExt=get(handles.ImaExt,'String');
4481fileinput=fullfile_uvmat(RootPath,'',RootFile,ImaExt,NomType,ref_i,[],ref_j);
4482errormsg=display_file_name(handles,fileinput);
4483if ~isempty(errormsg)
4484    msgbox_uvmat('ERROR',errormsg)
4485end
4486set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
4487
4488% --- Executes on selection change in ListProgram.
4489function ListProgram_Callback(hObject, eventdata, handles)
4490ListProgram=get(handles.ListProgram,'String');
4491Program=ListProgram{get(handles.ListProgram,'value')};
4492switch Program
4493    case 'CivX'
4494        set(handles.num_MaxDiff,'Visible','off')
4495        set(handles.num_MaxVel,'Visible','off')
4496        set(handles.title_MaxVel,'Visible','off')
4497        set(handles.num_Nx,'Visible','on')
4498        set(handles.num_Ny,'Visible','on')
4499        set(handles.title_Nx,'Visible','on')
4500        set(handles.title_Ny,'Visible','on')
4501        set(handles.title_MaxDiff,'Visible','off')
4502        set(handles.num_Rho,'Style','edit')
4503        set(handles.num_Rho,'String','1')
4504        set(handles.BATCH,'Enable','on')
4505        set(handles.CheckThreshold,'Visible','off')
4506        set(handles.CheckDeformation,'Value',1)
4507        set(handles.CheckDecimal,'Value',1)
4508    case 'Matlab'
4509        set(handles.num_MaxDiff,'Visible','on')
4510        set(handles.num_MaxVel,'Visible','on')
4511        set(handles.title_MaxVel,'Visible','on')
4512        set(handles.title_MaxDiff,'Visible','on')
4513        set(handles.num_Nx,'Visible','off')
4514        set(handles.num_Ny,'Visible','off')
4515        set(handles.title_Nx,'Visible','off')
4516        set(handles.title_Ny,'Visible','off')
4517        set(handles.num_Rho,'Style','popupmenu')
4518        set(handles.num_Rho,'Value',1)
4519        set(handles.num_Rho,'String',{'1';'2'})
4520        set(handles.CheckThreshold,'Visible','on')
4521        set(handles.CheckDeformation,'Value',0)% desactivate (work in progress)
4522        set(handles.CheckDecimal,'Value',0)% desactivate (work in progress)
4523end
4524
4525
4526% --- Executes on button press in TestCiv2.
4527function TestCiv2_Callback(hObject, eventdata, handles)
4528
4529
4530
4531function RootFile_Callback(hObject, eventdata, handles)
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