Description of civ

0001 %'civ_3D': function associated with the interface 'civ_3D.fig' for PIV in volume
0002 %------------------------------------------------------------------------
0003 %  provides an interface for the software CIVx
0004 % function varargout = civ_3D(varargin)
0005 % provides an interface for the software CIVx
0006 %
0007 %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
0008 %  Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org.
0009 %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
0010 %     This file is part of the toolbox UVMAT.
0011 %
0012 %     UVMAT is free software; you can redistribute it and/or modify
0013 %     it under the terms of the GNU General Public License as published by
0014 %     the Free Software Foundation; either version 2 of the License, or
0015 %     (at your option) any later version.
0016 %
0017 %     UVMAT is distributed in the hope that it will be useful,
0018 %     but WITHOUT ANY WARRANTY; without even the implied warranty of
0019 %     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
0020 %     GNU General Public License (file UVMAT/COPYING.txt) for more details.
0021 %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
0022 function varargout = civ_3D(varargin)
0023 
0024 % Last Modified by GUIDE v2.5 25-Feb-2009 23:14:16
0025 % Begin initialization code - DO NOT EDIT
0026 gui_Singleton = 1;
0027 gui_State = struct('gui_Name',       mfilename, ...
0028                    'gui_Singleton',  gui_Singleton, ...
0029                    'gui_OpeningFcn', @civ_3D_OpeningFcn, ...
0030                    'gui_OutputFcn',  @civ_3D_OutputFcn, ...
0031                    'gui_LayoutFcn',  [] , ...
0032                    'gui_Callback',   []);
0033 if nargin & isstr(varargin{1})
0034     gui_State.gui_Callback = str2func(varargin{1});
0035 end
0036 
0037 if nargout
0038     [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
0039 else
0040     gui_mainfcn(gui_State, varargin{:});
0041 end
0042 % End initialization code - DO NOT EDIT
0043 
0044 %--------------------------------------------------------------------------
0045 % --- Executes just before civ_3D is made visible.
0046 %--------------------------------------------------------------------------
0047 function civ_3D_OpeningFcn(hObject, eventdata, handles, varargin)
0048 % This function has no output args, see OutputFcn.
0049 % hObject    handle to figure
0050 % eventdata  reserved - to be defined in a future version of MATLAB
0051 % handles    structure with handles and user data (see GUIDATA)
0052 % varargin   command line arguments to civ_3D (see VARARGIN)
0053 global test_batch patch_new_exe%=1 if patch processing available
0054 %filebase: root name
0055 %nom_type: nomencalture used ('png_old','_i_j'...)
0056 %list of field numbers to process
0057 %subdir: subdirectory of the opened netcdf file
0058 %ind_opening: operation number advised for beginning (1=civ1,2=fix1,3=patch1,4=civ2,5=fix2,6=patch2),
0059 %ind_a_opening ind_b_opening chosen pair from the opened netcdf file
0060 % Choose default command line output for civ_3D
0061 handles.output = hObject;
0062 % Update handles structure
0063 guidata(hObject, handles);
0064 
0065 %default initial parameters
0066 filebase=''; % root file name ('filebase'.civ_3D)
0067 nom_type=[]; % nomenclature type
0068 ext=[];
0069 testall=0; 
0070 browse=[];
0071 
0072 %load the initial parameters if the interface is started from uvmat
0073 if ~isempty(varargin)% the interface is opened from uvmat
0074     varcell=varargin{1};
0075     filebase=varcell{1};
0076     nom_type_read=varcell{2};
0077     num1=varcell{3};
0078     num2=varcell{4};
0079     num_a=varcell{5};
0080     num_b=varcell{6};
0081     subdir=varcell{7};
0082     ind_opening=varcell{8};
0083     ind_a_opening=varcell{9};
0084     ind_b_opening=varcell{10};
0085     ext=varcell{11};
0086 else
0087     num1=1; % set of field i numbers
0088     num2=2; % set of field i numbers
0089     num_a=1; % set of field j numbers (fields a)
0090     num_b=1; % second set of field j numbers (fields b)
0091     subdir='A'; % subdir for the netcdf result files
0092     ind_opening=1; % proposed operation number (1=civ1,2=fix1,3=patch1,4=civ2,5=fix2,6=patch2)
0093     ind_a_opening=1; % proposed index in the menu of fields a
0094     ind_b_opening=2; % proposed index in the menu of fields b
0095 end
0096 
0097 if exist('ext','var') & length(ext)>1 & (~isempty(imformats(ext([2:end])))|...
0098                        isequal(ext,'.avi')|isequal(ext,'.AVI'));%if an image file has been opened by uvmat
0099         browse.ext_ima=ext; 
0100         if exist('nom_type_read','var')
0101             browse.nom_type_ima=nom_type_read; % the image nomenclature is stored
0102         end
0103 elseif isequal(ext,'.nc')
0104     if exist('nom_type_read','var')
0105         browse.nom_type_nc=nom_type_read;% the netcdf  nomenclature is stored
0106     end
0107 end
0108 set(handles.displ_filebase,'String',filebase);
0109 set(handles.ImaDoc,'UserData',testall);
0110 set(handles.browse_root,'UserData',browse)
0111 set(handles.ImaDoc,'String',ext)
0112 
0113 
0114 % set(handles.ImaDoc,'String',ext)
0115   
0116 %read names of the .exe file to adjust the interface according to
0117 %available prog
0118 %read names of the .exe file
0119 path_uvmat=which('uvmat');% check the path detected for source file uvmat
0120 path_UVMAT=fileparts(path_uvmat); %path to UVMAT
0121 if isunix
0122     syst='LINUX'
0123     %fid = fopen(fullfile(path_UVMAT,'PARAM_LINUX.txt'),'r');%open the file with civ_3D binary names
0124     xmlfile=fullfile(path_UVMAT,'PARAM_LINUX.xml')
0125     if exist(xmlfile,'file')
0126         t=xmltree(xmlfile);
0127         sparam=convert(t);
0128     end
0129 else
0130     syst='WIN'
0131     %fid = fopen(fullfile(path_UVMAT,'PARAM_WIN.txt'),'r');%open the file with civ_3D binary names
0132     xmlfile=fullfile(path_UVMAT,'PARAM_WIN.xml');
0133     if exist(xmlfile,'file')
0134         t=xmltree(xmlfile);
0135         sparam=convert(t);
0136     end
0137 end
0138    
0139 patch_new_exe='';
0140 todo_patch='';
0141 sge=0;
0142 
0143 if isfield(sparam,'PatchNew_exe')
0144     patch_new_exe=sparam.PatchNew_exe;
0145 end
0146 if isfield(sparam,'Todo_path')
0147     todo_path=sparam.Todo_path
0148 end
0149 if isfield(sparam,'SGE')
0150     sge=str2num(sparam.SGE);
0151 end   
0152 name_todo=fullfile(todo_path,'TODO.txt')
0153 test_batch=1;
0154 if ~sge
0155 if isequal(todo_path,'') |isequal(todo_path,[])
0156     ['no batch distributed processing available:file path TODO.txt not defined in UVMAT/PARAM_' syst]
0157     test_batch=0;
0158 end
0159 if exist(name_todo,'file')~=2 
0160     hwarn=warndlg(['no batch distributed processing available, queue file ' name_todo ' absent']);
0161   %  test_batch=0;  % Problems to detect file on linux/nfs filesystems
0162 end
0163 end
0164 
0165 
0166 if test_batch==0
0167     set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])% put the BATCH button in grey (unactivated)
0168 end
0169 
0170 set(handles.subdir_civ1,'String',subdir)%default subdir on which uvmat was working
0171 set(handles.subdir_civ2,'String',subdir)%default subdir on which uvmat was working
0172 
0173 %initiate advised operations
0174 if isequal(ind_opening,[])
0175     ind_opening=1; % default
0176 end
0177 % set default operation options
0178     enable_civ1(handles,'off')
0179     enable_civ2(handles,'off')
0180     desable_fix1(handles)
0181     desable_patch1(handles)
0182     desable_fix2(handles)
0183     desable_patch2(handles)
0184     set(handles.CIV1,'Value',0)
0185     set(handles.FIX1,'Value',0)
0186     set(handles.PATCH1,'Value',0)
0187     set(handles.CIV2,'Value',0)
0188     set(handles.FIX2,'Value',0)
0189     set(handles.PATCH2,'Value',0)
0190     set(handles.frame_subdirciv2,'BackgroundColor',[0.831 0.816 0.784])
0191 if isequal(ind_opening,1)
0192     set(handles.CIV1,'Value',1)
0193     enable_civ1(handles,'on')
0194 elseif isequal(ind_opening,2)
0195     set(handles.FIX1,'Value',1)
0196     enable_fix1(handles)
0197 elseif isequal(ind_opening,3)
0198     set(handles.PATCH1,'Value',1)
0199     enable_patch1(handles)
0200 elseif isequal(ind_opening,4)
0201     set(handles.CIV2,'Value',1)
0202     enable_civ2(handles,1)
0203 elseif isequal(ind_opening,5)
0204     set(handles.FIX2,'Value',1)
0205     enable_fix2(handles)
0206      set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
0207      set(handles.list_pair_civ2,'Enable','On')
0208      set(handles.list_pair_civ2,'Enable','On')
0209 elseif isequal(ind_opening,6)
0210     set(handles.PATCH2,'Value',1)
0211     enable_patch2(handles)
0212     set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
0213     set(handles.list_pair_civ2,'Enable','On')
0214 end
0215 
0216 % set the range of fields (1:1 by default) and selected pair
0217 if isempty(num2)|isequal(num2,num1)
0218     num_ref_i=num1;
0219 else
0220     num_ref_i=floor((num1+num2)/2);
0221     browse.incr_pair(1)=num2-num1;
0222     browse.incr_pair(2)=0;
0223 end
0224 if isempty(num_b)|isequal(num_a,num_b)
0225     if isempty(num_a)
0226         num_ref_j=1;
0227     else
0228         num_ref_j=num_a;
0229     end
0230 else
0231     num_ref_j=floor((num_a+num_b)/2);
0232     browse.incr_pair(2)=num_b-num_a; 
0233 end
0234 set(handles.first_i,'String',num2str(num_ref_i));
0235 set(handles.last_i,'String',num2str(num_ref_i));
0236 set(handles.first_j,'String',num2str(num_ref_j));
0237 set(handles.last_j,'String',num2str(num_ref_j));
0238 set(handles.ref_i,'String',num2str(num_ref_i));
0239 set(handles.ref_j,'String',num2str(num_ref_j));
0240 set(handles.browse_root,'UserData',browse);
0241 if ~isempty(varargin)% the interface is opened from uvmat
0242     displ_filebase_Callback(hObject, eventdata, handles); 
0243 end
0244 
0245 set(handles.waitbar_1,'Position',[0.946 0.877 0.03 0.001])
0246 set(handles.waitbar_patch1,'Position',[0.946 0.626 0.03 0.001])
0247 set(handles.waitbar_civ2,'Position',[0.946 0.406 0.03 0.001])
0248 set(handles.waitbar_patch2,'Position',[0.946 0.187 0.03 0.001])
0249 
0250 
0251 %--------------------------------------------------------------
0252 % --- Outputs from this function are returned to the command line.
0253 %-----------------------------------------------------------------
0254 function varargout = civ_3D_OutputFcn(hObject, eventdata, handles)
0255 % varargout  cell array for returning output args (see VARARGOUT);
0256 % hObject    handle to figure
0257 % eventdata  reserved - to be defined in a future version of MATLAB
0258 % handles    structure with handles and user data (see GUIDATA)
0259 % Get default command line output from handles structure
0260 varargout{1} = handles.output;
0261 
0262 %------------------------------------------------------------------
0263 % --- Executes on button press in browse_root.
0264 function browse_root_Callback(hObject, eventdata, handles)
0265 %get the input file properties
0266 filebase=get(handles.displ_filebase,'String');
0267 oldfile=''; %default
0268 if isempty(filebase)|isequal(filebase,'')%loads the previously stored file name and set it as default in the file_input box
0269      dir_perso=prefdir;
0270      profil_perso=fullfile(dir_perso,'uvmat_perso.mat')
0271      if exist(profil_perso,'file')
0272           h=load (profil_perso);
0273          if isfield(h,'filebase')&ischar(h.filebase)
0274                  oldfile=h.filebase;
0275          end
0276          if isfield(h,'RootPath')&ischar(h.RootPath)
0277 %                 oldfile=h.filebase{1}
0278                  oldfile=h.RootPath;
0279          end
0280      end
0281  else
0282      oldfile=filebase;
0283  end
0284 testall=get(handles.ImaDoc,'UserData');
0285 ind_opening=1;%default
0286 browse.incr_pair=[0 0]; %default
0287 
0288 menu={'*.*', 'All Files (*.*)'; '*.xml;*.vol; *.avi;*.AVI','(*.xml,*.civ,*.avi,*.vol)'; ...
0289         '*.xml', '.xml files';'*.civ', '.civ files';...
0290          '*.avi;*.AVI', '.avi files';'*.vol', '.vol files'};
0291 
0292 [FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file',oldfile);
0293 fileinput=[PathName FileName];%complete file name
0294 sizf=size(fileinput);
0295 if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
0296 [path,name,ext]=fileparts(fileinput);
0297 testeditxml=0;
0298 if isequal(ext,'.xml')
0299     testeditxml=1;
0300     t_browse=xmltree(fileinput);
0301     head_element=get(t_browse,1);
0302     if isfield(head_element,'name')& isequal(head_element.name,'ImaDoc')
0303         testeditxml=0;
0304     end
0305 end
0306 if testeditxml==1 | isequal(ext,'.xls')
0307    heditxml=editxml({fileinput});
0308    set(heditxml,'Tag','browser')
0309    waitfor(heditxml,'Tag','idle')
0310    if ~ishandle(heditxml)
0311        return
0312    end
0313    attr=findobj(get(heditxml,'children'),'Tag','CurrentAttributes');
0314    set(handles.browse,'UserData',fileinput)% store for future opening with browser
0315    fileinput=get(attr,'UserData');
0316    if ~exist(fileinput,'file')
0317        return
0318    end
0319 end
0320 [RootPath,RootFile,field_count,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fileinput);
0321 filebase=fullfile(RootPath,RootFile);
0322 if isequal(get(handles.compare,'Value'),1)
0323     browse=get(handles.browse_root,'UserData');
0324 else
0325     browse=[];%initialisation
0326 end
0327 if length(ext)>1 & (~isempty(imformats(ext([2:end])))||...
0328                        isequal(lower(ext),'.avi')||isequal(ext,'.vol'));%if an image file has been opened by uvmat
0329     browse.ext_ima=ext; 
0330     browse.nom_type_ima=nom_type;
0331     browse.field_count=str2num(field_count);
0332 end
0333 set(handles.ImaDoc,'String',ext);
0334 %%%%% read the state of the selected netcdf file to advise default operation
0335 if isequal(ext,'.nc')
0336     browse.nom_type_nc=nom_type;
0337     ind_opening=2;% propose 'fix' as the default option
0338     Data=nc2struct(fileinput,[]);
0339     if isfield(Data,'fix') & isequal(Data.fix,1)
0340         ind_opening=3;
0341     end
0342     if isfield(Data,'patch') & isequal(Data.patch,1)
0343         ind_opening=4;
0344     end
0345     if isfield(Data,'civ2') & isequal(Data.civ2,1)
0346         ind_opening=5;
0347     end
0348     if isfield(Data,'fix2') & isequal(Data.fix2,1)
0349         ind_opening=6;
0350     end
0351     if isfield(Data,'pixcmx') & isequal(Data,'pixcmy')
0352         browse.pxcmx=Data.pixcmx;
0353         browse.pxcmy=Data.pixcmy;
0354     end
0355     testciv=1; %TO SUPPRESS WITH NEW VERSION OF CIVX
0356     subdir='';%default
0357     if testciv
0358         [Pathbase,Namebase]=fileparts(filebase)
0359         [Pathprev,subdir,extdir]=fileparts(Pathbase)
0360         subdir=[subdir extdir]
0361 %         if isequal (subdir,subdir_obs)
0362         filebase=fullfile(Pathprev,Namebase)% move upward to get the base name (corresponding to the .civ_3D file and images)
0363 %         end
0364     end
0365     set(handles.subdir_civ1,'String',subdir);%set the default subdir directories for installing the .nc results
0366     set(handles.subdir_civ2,'String',subdir);
0367     browse.testciv=testciv;
0368     browse.ind_opening=ind_opening;
0369 end
0370 set(handles.displ_filebase,'String',filebase);
0371 set(handles.ImaDoc,'String',ext);
0372 if ~isempty(str2num(field_count))
0373     ref_i=str2num(field_count);
0374     if ~isempty(str2num(str2))
0375         ref_i=floor((ref_i+str2num(str2))/2);% reference image number corresponding to the file
0376         browse.incr_pair(1)=str2num(str2)-str2num(field_count);
0377         browse.incr_pair(2)=0;
0378     end
0379     set(handles.first_i,'String',num2str(ref_i));
0380     set(handles.last_i,'String',num2str(ref_i));
0381     set(handles.ref_i,'String',num2str(ref_i)); 
0382 end
0383 if isempty(str2num(str_a))
0384     set(handles.ref_j,'String','1');
0385 else
0386     ref_j=str2num(str_a);
0387     if ~isempty(str2num(str_b))
0388         ref_j=floor((str2num(str_a)+str2num(str_b))/2);
0389         browse.incr_pair(2)=str2num(str_b)-str2num(str_a); 
0390     end
0391     set(handles.first_j,'String',num2str(ref_j));
0392     set(handles.last_j,'String',num2str(ref_j));
0393     set(handles.ref_j,'String',num2str(ref_j)); 
0394 end;
0395 if isequal(ind_opening,1)
0396     set(handles.CIV1,'Value',1)
0397     enable_civ1(handles,'on')
0398 elseif isequal(ind_opening,2)
0399     set(handles.FIX1,'Value',1)
0400     enable_fix1(handles)
0401 elseif isequal(ind_opening,3)
0402     set(handles.PATCH1,'Value',1)
0403     enable_patch1(handles)
0404 elseif isequal(ind_opening,4)
0405     set(handles.CIV2,'Value',1)
0406     enable_civ2(handles,1)
0407 elseif isequal(ind_opening,5)
0408     set(handles.FIX2,'Value',1)
0409     enable_fix2(handles)
0410      set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
0411      set(handles.list_pair_civ2,'Enable','On')
0412      set(handles.list_pair_civ2,'Enable','On')
0413 elseif isequal(ind_opening,6)
0414     set(handles.PATCH2,'Value',1)
0415     enable_patch2(handles)
0416     set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
0417     set(handles.list_pair_civ2,'Enable','On')
0418 end
0419 set(handles.browse_root,'UserData',browse);% store information from browser
0420 testall=isequal(menu(filtindex,1),{'*.*'});
0421 set(handles.ImaDoc,'UserData',testall);
0422 
0423 displ_filebase_Callback(hObject, eventdata, handles);
0424 
0425 %------------------------------------------------
0426 
0427 function ImaDoc_Callback(hObject, eventdata, handles)
0428 displ_filebase_Callback(hObject, eventdata, handles)
0429 
0430 %--------------------------------------------------------------
0431 %function activated when a new filebase (image series) is introduced
0432 %------------------------------------------------------------
0433 function displ_filebase_Callback(hObject, eventdata, handles)
0434 
0435 global test_batch
0436 set(gcf,'Pointer','watch')
0437 ext_ima=[]; %default
0438 nom_type_ima=[];%default
0439 field_count=1;%default
0440 nom_type_nc=[];
0441 npx=[];%default
0442 npy=[];
0443 TimeUnit='s'; %default
0444 CoordUnit='cm';%default
0445 pxcmx_search=[];%default
0446 pxcmy_search=[];%default
0447 filebase=get(handles.displ_filebase,'String');
0448 
0449 ext=get(handles.ImaDoc,'String');
0450 browse=get(handles.browse_root,'UserData');%default
0451 if ~isempty(browse) 
0452     if isfield(browse,'ext_ima')
0453         ext_ima=browse.ext_ima;
0454     end
0455     if isfield(browse,'nom_type_ima')
0456         nom_type_ima=browse.nom_type_ima;
0457     end
0458     if isfield(browse,'field_count')
0459         field_count=browse.field_count;
0460     end
0461 end
0462 
0463 %default first_i and j and increments
0464 first_i=str2num(get(handles.first_i,'String'));%value possibly set by uvmat_Opening
0465 if isempty(first_i)| first_i < 1
0466     first_i=1; %default first_i
0467 end
0468 last_i=str2num(get(handles.last_i,'String'));
0469 if isempty(last_i)| last_i < first_i
0470     last_i=first_i;  %default last_i
0471 end
0472 first_j=str2num(get(handles.first_j,'String'));
0473 if isempty(first_j)| first_j < 1
0474     first_j=1; %default first_j
0475 end
0476 last_j=str2num(get(handles.last_j,'String'));
0477 if isempty(last_j)| last_j < first_j
0478     last_j=first_j; %default last_j
0479 end
0480 incr_i=str2num(get(handles.incr_i,'String'));
0481 if isempty(incr_i) | incr_i < 1;
0482     set(handles.incr_i,'String','1') %default incr_i
0483 end
0484 incr_j=str2num(get(handles.incr_j,'String'));
0485 if isempty(incr_j) | incr_j < 1;
0486     set(handles.incr_j,'String','1') %default incr_j
0487 end
0488 dt=[];%default
0489 testmode=0;%default
0490 nbfield=1; %default
0491 if isfield(browse,'pxcmx') & isfield(browse,'pxcmy')
0492     pxcmx=num2str(browse.pxcmx);
0493     pxcmy=num2str(browse.pxcmy); 
0494 else
0495     pxcmx=1;%default
0496     pxcmy=1; 
0497 end
0498  %look for an image documentation file
0499 if ~isequal(ext,'.xml') & ~ isequal(ext,'.avi')& ~ isequal(ext,'.AVI')
0500     if exist([filebase '.xml'],'file')
0501          ext='.xml';
0502          set(handles.ImaDoc,'String','.xml')
0503     elseif exist([filebase '.civ_3D'],'file')
0504          ext='.civ_3D';
0505          set(handles.ImaDoc,'String','.civ_3D')
0506     elseif exist([filebase '.avi'],'file') 
0507          ext='.avi';
0508          set(handles.ImaDoc,'String','.avi')
0509     elseif exist([filebase '.AVI'],'file')
0510          ext='.AVI';
0511          set(handles.ImaDoc,'String','.AVI')
0512     end
0513 end
0514 %%%%%%%%   read image documentation file  %%%%%%%%%%%%%%%%%%%%%%%%%%%
0515     mode=''; %default
0516     %read the image documentation file if found
0517 if  isequal(ext,'.xml')
0518     set(handles.ref_i,'Visible','On')%use a reference index
0519     set(handles.ref_j,'Visible','On')
0520     set(handles.dt,'Visible','Off')
0521     set(handles.dt_text,'String','ref. ind.')
0522 elseif isequal(ext,'.avi') | isequal(ext,'.AVI')
0523     set(handles.ref_j,'Visible','Off')
0524     set(handles.dt,'Visible','Off')
0525     set(handles.dt_text,'String','ref. ind.')
0526 else
0527     set(handles.ref_i,'Visible','Off')
0528     set(handles.ref_j,'Visible','Off')
0529     set(handles.dt,'Visible','On')
0530     set(handles.dt_text,'String','dt(ms)=')
0531 end
0532 
0533 if isequal(ext,'.xml')
0534     [XmlData,warntext]=imadoc2struct([filebase '.xml']);
0535         if isfield(XmlData,'Heading')&&isfield(XmlData.Heading','ImageName')
0536             [PP,FF,fc,str2,str_a,str_b,ext_ima_read,nom_type_read]=name2display(XmlData.Heading.ImageName);
0537         end
0538         if isfield(XmlData,'Camera')
0539             if isfield(XmlData.Camera,'TimeUnit')
0540                 TimeUnit=XmlData.Camera.TimeUnit;
0541             end
0542             if isfield(XmlData.Camera,'ImageSize')
0543                ImageSize=XmlData.Camera.ImageSize;
0544                if ~isempty(ImageSize)&& ~isempty(ImageSize)
0545                    xindex=findstr(ImageSize,'x');
0546                    if length(xindex)>=2
0547                         npx=str2num(ImageSize(1:xindex(1)-1));
0548                         npy=str2num(ImageSize(xindex(1)+1:xindex(2)-1));
0549                    end
0550                end
0551            end
0552         end
0553         pxcmx_search=1;
0554         pxcmy_search=1;
0555         if isfield(XmlData,'GeometryCalib')
0556             tsai=XmlData.GeometryCalib;
0557             if isfield(tsai,'f') & isfield(tsai,'Tz') & isfield(tsai,'dpx') & isfield(tsai,'dpy')& isfield(tsai,'R') 
0558                  rot2D=tsai.R([1:2],[1,2]);
0559                  pxcmx_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpx);
0560                  pxcmy_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpy);           
0561             end
0562             if isfield(tsai,'CoordUnit') 
0563                  CoordUnit=tsai.CoordUnit;
0564             end
0565         end               
0566         if isempty(ext_ima_read)
0567               ext_ima='.png';%default
0568         else
0569               ext_ima=ext_ima_read;
0570         end
0571         if isempty(nom_type_read)
0572                 nom_type_ima='_i_j';
0573                 warndlg_uvmat('no ImageName defined in ImaDoc/Heading, take _i_j indexing by default','WARNING')
0574         else
0575                 nom_type_ima=nom_type_read;
0576         end
0577         
0578 elseif isequal(ext,'.avi')|isequal(ext,'.AVI') 
0579         nom_type_ima='avi';
0580         ext_ima=ext;
0581         set(handles.mode,'String',{'series(Di)'})
0582         dt=0.04;%default
0583         if exist([filebase ext],'file')==2
0584             info=aviinfo([filebase ext]);%read infos on the avi movie
0585             dt=1/info.FramesPerSecond;%time interval between successive frames
0586             nbfield=info.NumFrames;%number of frames
0587         end
0588         time=(dt*[0:nbfield-1])';%list of image times
0589         set(handles.dt,'String',num2str(dt*1000));%store the time interval between successive images
0590         
0591      % no image documentation file found: look for a series of existing images or .nc files
0592 elseif ~isequal(ext,'.nc') 
0593         subdir=get(handles.subdir_civ1,'String');
0594         incr_pair=[0 0];%default
0595         if isfield(browse,'incr_pair')
0596                 incr_pair=browse.incr_pair;
0597         end
0598         nbdetect=0;%test of detected images
0599         field_i=field_count;
0600         idetect=1;
0601 %         imagename='';%default
0602         while idetect==1 %look for the maximum file number in the series
0603                 field_i=field_i+1;
0604 %                 imagename_last=imagename;
0605                 [imagename,idetect]=name_generator(filebase,field_i,1,ext_ima,nom_type_ima);
0606                 if isequal(nom_type_ima,'none')
0607                    idetect=0; %stop if the same image is repeated (if nom_type='none')
0608                    nbdetect=1;
0609                 end
0610                 %SEE CASE OF NETCDF FILES
0611                 nbdetect=nbdetect+idetect;
0612         end
0613 %         nb_field=field_i-1;% last detected field number
0614         nb_field=field_i;% last detected field number
0615         field_i=field_count;%look for the minimum file number in the series
0616         idetect=1;
0617         while idetect==1 
0618                     field_i=field_i-1;
0619                     [imagename,idetect]=name_generator(filebase,field_i,1,ext_ima,nom_type_ima);
0620                     if isequal(nom_type_ima,'none')
0621                         idetect=0; %stop if the same image is repeted (if nom_type='none')
0622                         nbdetect=1;
0623                     end
0624                     nbdetect=nbdetect+idetect;
0625         end
0626         first_i=max(field_i+1,1);
0627             %determine the set of times and possible intervals for CIV_3D
0628         dt=(1/1000)*str2num(get(handles.dt,'String'));
0629         time=(dt*[0:nb_field-1])';
0630 %             set(handles.incr_i,'UserData',dt);%store the time interval
0631 %             between successive images
0632             %displ_num:list  of possible time intervals for civ_3D calculations
0633         set(handles.mode,'String',{'series(Di)'})
0634 end
0635 if isequal(nom_type_ima,'none')% no file numbering used
0636   first_i=1; 
0637   last_i=1;
0638    first_j=1;
0639   last_j=1;
0640 end
0641 if exist('time','var')
0642     siztime=size(time);
0643     nbfield=siztime(1);
0644     nbfield2=siztime(2);
0645     set(handles.displ_filebase,'UserData',time); %store the set of times
0646     set(handles.dt_unit,'String',['m' TimeUnit]);
0647     set(handles.TimeUnit,'String',TimeUnit);
0648     set(handles.nb_field,'String',num2str(nbfield));
0649     set(handles.nb_field2,'String',num2str(nbfield2));
0650 end
0651 set(handles.CoordUnit,'String',[CoordUnit '/'])
0652 set(handles.pxcmx,'String',num2str(pxcmx));
0653 set(handles.pxcmy,'String',num2str(pxcmy));
0654 if isempty(pxcmx_search)
0655    set(handles.calcul_search,'UserData',[pxcmx pxcmy]);
0656 else
0657    set(handles.calcul_search,'UserData',[pxcmx_search pxcmy_search]);
0658 end
0659 set(handles.pxcmx,'UserData',npx);
0660 set(handles.pxcmy,'UserData',npy);
0661 set(handles.first_i,'String',num2str(first_i));
0662 set(handles.last_i,'String',num2str(last_i));%
0663 set(handles.first_j,'String',num2str(first_j));
0664 set(handles.last_j,'String',num2str(last_j));%
0665 browse.ext_ima=ext_ima;
0666 browse.nom_type_ima=nom_type_ima;
0667 set(handles.browse_root,'UserData',browse)% store the nomenclature type
0668 
0669         %%%%%%%%%%%  set the menus of image pairs and default selection for civ_3D   %%%%%%%%%%%%%%%%%%%
0670 if isequal(get(handles.compare,'Value'),1)
0671     if isequal(nom_type_ima,'_i')| isequal(nom_type_nc,'_i1-i2')|~exist('nbfield2','var')|(nbfield2==1)
0672         set(handles.mode,'String',{'st_series(Di)';'displacement'})
0673         set(handles.mode,'Value',1)
0674     elseif (nbfield==1)% simple series in j
0675         set(handles.mode,'String',{'st_series(Dj)';'displacement'})
0676         set(handles.mode,'Value',1)
0677     else
0678         set(handles.mode,'String',{'st_pair j1-j2';'st_series(Dj)';'st_series(Di)';'displacement'})%multiple choice
0679         if isequal(mode,'volume')
0680             set(handles.mode,'Value',3)
0681         elseif nbfield2 <= 5
0682             set(handles.mode,'Value',1)% advice 'pair j1-j2' for small bursts
0683         end
0684     end
0685 else
0686     if isequal(nom_type_ima,'_i')| isequal(nom_type_nc,'_i1-i2')|~exist('nbfield2','var')|(nbfield2==1)
0687         set(handles.mode,'String',{'series(Di)'})
0688         set(handles.mode,'Value',1)
0689     elseif isequal(nom_type_ima,'png_old')|isequal(nom_type_nc,'netc_old')
0690         set(handles.mode,'String',{'pair j1-j2'})
0691         set(handles.mode,'Value',1)
0692     elseif (nbfield==1)% simple series in j
0693         set(handles.mode,'String',{'series(Dj)'})
0694         set(handles.mode,'Value',1)
0695     else
0696         set(handles.mode,'String',{'pair j1-j2';'series(Dj)';'series(Di)'})%multiple choice
0697         if isequal(mode,'volume')
0698             set(handles.mode,'Value',3)
0699         elseif nbfield2 <= 5
0700             set(handles.mode,'Value',1)% advice 'pair j1-j2' for small bursts
0701         else
0702             set(handles.mode,'Value',2)% advice series Dj for long bursts, not volume
0703         end
0704     end
0705 end
0706 mode_Callback(hObject, eventdata, handles)  
0707 
0708 %%%%%% initialize waitbars and RUN button
0709 set(handles.waitbar_1,'Position',[0.946 0.876 0.03 0.001])
0710 set(handles.waitbar_patch1,'Position',[0.946 0.439 0.03 0.001])
0711 set(handles.waitbar_civ2,'Position',[0.946 0.219 0.03 0.001])
0712 set(handles.waitbar_patch2,'Position',[0.946 0.0 0.03 0.001])
0713 set(handles.RUN, 'Enable','On')
0714 set(handles.RUN,'BackgroundColor',[1 0 0])
0715 if isequal(test_batch,1)%if batch installation is available
0716     set(handles.BATCH, 'Enable','On')
0717     set(handles.BATCH,'BackgroundColor',[1 0 0])
0718 end
0719     
0720 %%%%% store the root input filename for future opening
0721 dir_perso=prefdir;
0722 profil_perso=fullfile(prefdir,'uvmat_perso.mat');
0723 RootPath=fileparts(filebase);
0724 if exist(profil_perso,'file')
0725     save (profil_perso,'RootPath','-append'); %store the root name for future opening of uvmat
0726 else
0727     txt=ver;
0728     Release=txt(1).Release;
0729     relnumb=str2num(Release(3:4));
0730     if relnumb >= 14
0731         save (profil_perso,'RootPath','-V6'); %store the root name for future opening of uvmat
0732     else
0733         save (profil_perso,'RootPath'); %store the root name for future opening of uvmat
0734     end
0735 end
0736 % save(profil_perso, 'filebase'); %store the root name for future opening of uvmat
0737 set(gcf,'Pointer','arrow')
0738 
0739 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%????????????
0740 % --- Executes on button press in mode.
0741 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0742 function mode_Callback(hObject, eventdata, handles)
0743 browse=get(handles.browse_root,'UserData');
0744 mode_list=get(handles.mode,'String');
0745 mode_value=get(handles.mode,'Value');
0746 mode=mode_list{mode_value};
0747 displ_num=[];%default
0748 first_i=str2num(get(handles.first_i,'String'));
0749 % last_i=str2num(get(handles.last_i,'String'));
0750 time=get(handles.displ_filebase,'UserData'); %get the set of times
0751 siztime=size(time);
0752 nbfield=siztime(1);
0753 nbfield2=siztime(2);
0754 indchosen=1;  %%first pair selected by default
0755 if isequal(mode,'pair j1-j2')| isequal(mode,'st_pair j1-j2')
0756     dt=1;
0757     displ='';
0758     index=0;
0759     %get all the time intervals in bursts
0760     displ_dt=1;%default
0761     nbfield2=min(nbfield2,10),%limitate the number of pairs to 10x10
0762 %     if nbfield2<2
0763 %         nbfield2=2,
0764 %     end
0765     for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'pair j1-j2' mode
0766         for numod_b=(numod_a+1):nbfield2
0767              index=index+1;
0768              numlist_a(index)=numod_a;
0769              numlist_b(index)=numod_b;
0770              if ~isempty(time)
0771                 dt(numod_a,numod_b)=time(first_i,numod_b)-time(first_i,numod_a);%first time interval dt
0772                 displ_dt(index)=dt(numod_a,numod_b);
0773              else
0774                  displ_dt(index)=1
0775              end
0776          end
0777      end
0778      [dtsort,indsort]=sort(displ_dt);
0779      displ_num(1,:)=numlist_a(indsort);
0780      displ_num(2,:)=numlist_b(indsort);
0781      displ_num(3,:)=0;
0782      displ_num(4,:)=0;
0783      set(handles.jtext,'Visible','Off')
0784     set(handles.first_j,'Visible','Off')
0785     set(handles.last_j,'Visible','Off')
0786     set(handles.incr_j,'Visible','Off')
0787     set(handles.nb_field2,'Visible','Off')
0788     set(handles.ref_j,'Visible','Off')
0789 elseif isequal(mode,'series(Dj)') | isequal(mode,'st_series(Dj)')
0790      for index=1:min(nbfield2-1,200)
0791          displ_num(1,index)=-floor(index/2);
0792          displ_num(2,index)=ceil(index/2);
0793          displ_num(3,index)=0;
0794          displ_num(4,index)=0;
0795      end       
0796      set(handles.jtext,'Visible','On')
0797      set(handles.first_j,'Visible','On')
0798      set(handles.last_j,'Visible','On')
0799      set(handles.incr_j,'Visible','On')
0800      set(handles.nb_field2,'Visible','On')
0801      set(handles.ref_j,'Visible','On')
0802      if nbfield > 1
0803         set(handles.itext,'Visible','On')
0804         set(handles.first_i,'Visible','On')
0805         set(handles.last_i,'Visible','On')
0806         set(handles.incr_i,'Visible','On')
0807         set(handles.nb_field,'Visible','On')
0808         set(handles.ref_i,'Visible','On')
0809     else
0810         set(handles.itext,'Visible','Off')
0811         set(handles.first_i,'Visible','Off')
0812         set(handles.last_i,'Visible','Off')
0813         set(handles.incr_i,'Visible','Off')
0814         set(handles.nb_field,'Visible','Off')
0815         set(handles.ref_i,'Visible','Off')
0816     end
0817 elseif isequal(mode,'series(Di)') | isequal(mode,'st_series(Di)') 
0818      for index=1:min(nbfield-1,200)
0819          displ_num(1,index)=0;
0820          displ_num(2,index)=0;
0821          displ_num(3,index)=-floor(index/2);
0822          displ_num(4,index)=ceil(index/2);
0823      end
0824      set(handles.itext,'Visible','On')
0825      set(handles.first_i,'Visible','On')
0826      set(handles.last_i,'Visible','On')
0827      set(handles.incr_i,'Visible','On')
0828      set(handles.nb_field,'Visible','On')
0829      set(handles.ref_i,'Visible','On')
0830      if nbfield2 > 1
0831         set(handles.jtext,'Visible','On')
0832         set(handles.first_j,'Visible','On')
0833         set(handles.last_j,'Visible','On')
0834         set(handles.incr_j,'Visible','On')
0835         set(handles.nb_field2,'Visible','On')
0836         set(handles.ref_j,'Visible','On')
0837      else
0838         set(handles.jtext,'Visible','Off')
0839         set(handles.first_j,'Visible','Off')
0840         set(handles.last_j,'Visible','Off')
0841         set(handles.incr_j,'Visible','Off')
0842         set(handles.nb_field2,'Visible','Off')
0843         set(handles.ref_j,'Visible','Off')
0844     end
0845 elseif isequal(mode,'displacement')%the pairs have the same indices
0846      displ_num(1,1)=0; 
0847      displ_num(2,1)=0;
0848      displ_num(3,1)=0;
0849      displ_num(4,1)=0;
0850      if nbfield > 1
0851         set(handles.itext,'Visible','On')
0852         set(handles.first_i,'Visible','On')
0853         set(handles.last_i,'Visible','On')
0854         set(handles.incr_i,'Visible','On')
0855         set(handles.nb_field,'Visible','On')
0856         set(handles.ref_i,'Visible','On')
0857     else
0858         set(handles.itext,'Visible','Off')
0859         set(handles.first_i,'Visible','Off')
0860         set(handles.last_i,'Visible','Off')
0861         set(handles.incr_i,'Visible','Off')
0862         set(handles.nb_field,'Visible','Off')
0863         set(handles.ref_i,'Visible','Off')
0864     end
0865     if nbfield2 > 1
0866       set(handles.jtext,'Visible','On')
0867      set(handles.first_j,'Visible','On')
0868      set(handles.last_j,'Visible','On')
0869      set(handles.incr_j,'Visible','On')
0870      set(handles.nb_field2,'Visible','On')
0871      set(handles.ref_j,'Visible','On')
0872     else
0873         set(handles.jtext,'Visible','Off')
0874         set(handles.first_j,'Visible','Off')
0875         set(handles.last_j,'Visible','Off')
0876         set(handles.incr_j,'Visible','Off')
0877         set(handles.nb_field2,'Visible','Off')
0878         set(handles.ref_j,'Visible','Off')
0879     end
0880 end  
0881 set(handles.list_pair_civ1,'UserData',displ_num);
0882 find_netcpair_civ1(hObject, eventdata, handles)
0883 find_netcpair_civ2(hObject, eventdata, handles)
0884 
0885 %--------------------------------------------------------------
0886 % determine the menu for civ1 pairs depending on existing netcdf file at the middle of
0887 % the field series set by first_i, incr, last_i
0888 %----------------------------------------------------------------
0889 function find_netcpair_civ1(hObject, eventdata, handles)
0890 set(gcf,'Pointer','watch')
0891 %nomenclature types
0892 filebase=get(handles.displ_filebase,'String');
0893 [filepath,Nme,ext_dir]=fileparts(filebase);
0894 browse=get(handles.browse_root,'UserData');
0895 mode_list=get(handles.mode,'String');
0896 mode_value=get(handles.mode,'Value');
0897 mode=mode_list{mode_value};
0898 % nomenclature type of the .nc files
0899 nom_type_ima=[];%default
0900 if isfield(browse,'nom_type_ima')
0901     nom_type_ima=browse.nom_type_ima;
0902 end
0903 
0904 %determine nom_type_nc:
0905 nom_type_nc=[];%default
0906 if isfield(browse,'nom_type_nc')
0907     nom_type_nc=browse.nom_type_nc;
0908 end
0909 if isequal(nom_type_ima,'png_old') | isequal(nom_type_nc,'netc_old')| isequal(nom_type_ima,'raw_SMD')
0910     nom_type_nc='netc_old';%nom_type for the netcdf files
0911 elseif isequal(nom_type_ima,'none')|isequal(nom_type_nc,'none')
0912     nom_type_nc='none';
0913 elseif isequal(nom_type_ima,'avi')|isequal(nom_type_ima,'_i')|isequal(nom_type_ima,'ima_num')|...
0914         isequal(nom_type_nc,'_i1-i2')
0915      nom_type_nc='_i1-i2';
0916 elseif isequal(nom_type_ima,'_i_j1-j2')||isequal(nom_type_nc,'_i1-i2_j1-j2')
0917      nom_type_nc='_i1-i2_j1-j2';
0918 else
0919     if  isequal(mode,'series(Di)')|isequal(mode,'st_series(Di)')
0920         nom_type_nc='_i1-i2_j'; % PIV in volume
0921     else
0922         nom_type_nc='_i_j1-j2';
0923     end    
0924 end
0925 browse.nom_type_nc=nom_type_nc;
0926 set(handles.browse_root,'UserData',browse)
0927 
0928 %reads .nc subdirectoy and image numbers from the interface
0929 subdir_civ1=get(handles.subdir_civ1,'String');%subdirectory subdir_civ1 for the netcdf data
0930 first_i=str2num(get(handles.first_i,'String'));
0931 last_i=str2num(get(handles.last_i,'String'));
0932 incr=str2num(get(handles.incr_i,'String'));
0933 num1=first_i:incr:last_i;
0934 if isempty(num1)
0935     set(handles.list_pair_civ1,'String',{''});
0936     return
0937 end
0938 ref_i=str2num(get(handles.ref_i,'String'));
0939 if isequal(mode,'pair j1-j2')|isequal(mode,'st_pair j1-j2')
0940     ref_j=0;
0941 else
0942     ref_j=str2num(get(handles.ref_j,'String'));
0943 end
0944 if isequal(get(handles.dt_text,'String'),'dt(ms)=')%simple series(Di) with equal interval
0945     ref_i=floor((first_i+last_i)/2);
0946     ref_j=1;
0947 end
0948 time=get(handles.displ_filebase,'UserData');%get the set of times
0949 if isempty(time)
0950     time=[0 1];
0951 end 
0952 dt_unit=str2num(get(handles.dt,'String'));% used when there is no image documentation file
0953 displ_num=get(handles.list_pair_civ1,'UserData');
0954 
0955 %eliminate the first pairs inconsistent with the position
0956 if isempty(displ_num)
0957     nbpair=0;
0958 else
0959     nbpair=length(displ_num(1,:));%nbre of displayed pairs
0960     if  isequal(mode,'series(Di)')  | isequal(mode,'st_series(Di)')
0961         nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index
0962     elseif  isequal(mode,'series(Dj)') | isequal(mode,'st_series(Dj)')
0963         nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index
0964     end
0965 end
0966 nbpair=min(200,nbpair);%limit the number of displayed pairs to 200
0967 
0968 %look for existing processed pairs involving the field at the middle of the series if civ1 will not
0969 % be performed, while the result is needed for next steps.
0970 displ_pair={''};
0971 select=ones(size(1:nbpair));%default =1 for numbers of displayed pairs
0972 testpair=0;
0973 if get(handles.CIV1,'Value')==0 %
0974     dirname=fullfile(filepath,subdir_civ1,ext_dir);
0975     if ~exist(fullfile(filepath,subdir_civ1,ext_dir),'dir') 
0976          hwarn=warndlg_uvmat(['no civ1 file available: subdirectory ' subdir_civ1 ' does not exist'],'ERROR');
0977          set(handles.list_pair_civ1,'String',{});
0978          return
0979     end
0980     for ipair=1:nbpair   
0981         [filename,select(ipair)]=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,...
0982         ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1);
0983     end
0984     if ~exist('select','var') | isequal(select,zeros(size(1:nbpair)))
0985         if isfield(browse,'incr_pair') 
0986             num_i1=ref_i-floor(browse.incr_pair(1)/2);
0987             num_i2=ref_i+ceil(browse.incr_pair(1)/2);
0988             num_j1=ref_j-floor(browse.incr_pair(2)/2);
0989             num_j2=ref_j+ceil(browse.incr_pair(2)/2);
0990             [filename,select(1)]=name_generator(filebase,num_i1,num_j1,'.nc',nom_type_nc,1,num_i2,num_j2,subdir_civ1);
0991             testpair=1;
0992         else
0993             if  isequal(mode,'series(Dj)') | isequal(mode,'st_series(Dj)') 
0994                 hwarn=warndlg_uvmat(['no civ1 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ1],'ERROR');
0995                 set(hwarn,'WindowStyle','modal');
0996             else
0997                 hwarn=warndlg_uvmat(['no civ1 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ1],'ERROR');
0998                 set(hwarn,'WindowStyle','modal');
0999             end
1000              set(handles.list_pair_civ1,'String',{''});
1001              %COMPLETER CAS STEREO
1002             return
1003         end
1004     end
1005 end
1006 if isequal(mode,'series(Di)') | isequal(mode,'st_series(Di)')
1007     if testpair
1008               displ_pair{1}=['Di= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];        
1009     elseif ~isequal(get(handles.dt_text,'String'),'dt(ms)=') 
1010        for ipair=1:nbpair
1011           if select(ipair)          
1012               dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt
1013               displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
1014           else 
1015              displ_pair{ipair}='...'; %pair not displayed in the menu
1016           end
1017        end
1018     else
1019        for ipair=1:nbpair
1020          if select(ipair)
1021             displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt_unit*ipair)];
1022          else 
1023             displ_pair{ipair}='...'; %pair not displayed in the menu
1024          end
1025        end
1026     end
1027 elseif isequal(mode,'series(Dj)')|isequal(mode,'st_series(Dj)')% series on the j index
1028     if testpair
1029          displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))]; 
1030     else
1031        for ipair=1:nbpair
1032           if select(ipair)
1033               dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt
1034               displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
1035            elseif testpair
1036               displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(2)/2)) '|' num2str(ceil(browse.incr_pair(2)/2))];
1037           else 
1038              displ_pair{ipair}='...'; %pair not displayed in the menu
1039           end
1040        end
1041    end
1042 elseif isequal(mode,'pair j1-j2')|isequal(mode,'st_pair j1-j2')%case of pairs
1043     for ipair=1:nbpair
1044         if select(ipair)
1045            dt=time(ref_i+displ_num(4,ipair),displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),displ_num(1,ipair));%time interval dt
1046            displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ...
1047                         ' :dt= ' num2str(dt*1000)];
1048        else 
1049           displ_pair{ipair}='...'; %pair not displayed in the menu
1050         end   
1051    end
1052 elseif isequal(mode,'displacement')
1053     displ_pair={'Di=Dj=0'};  
1054 end   
1055 set(handles.list_pair_civ1,'String',displ_pair');
1056 ichoice=min(find(select));
1057 if (isempty(ichoice) | ichoice < 1); ichoice=1; end;
1058 initial=get(handles.list_pair_civ1,'Value');
1059 if initial>nbpair |~isequal(select(initial),1)
1060     set(handles.list_pair_civ1,'Value',ichoice);% first valid pair proposed by default in the menu
1061 end
1062 set(handles.list_pair_civ2,'String',displ_pair');
1063 initial=get(handles.list_pair_civ2,'Value');
1064 if initial>nbpair |~isequal(select(initial),1)
1065     set(handles.list_pair_civ2,'Value',ichoice);% same pair proposed by default for civ2
1066 end
1067 set(gcf,'Pointer','arrow')
1068 %--------------------------------------------------------------
1069 % determine the menu for civ2 pairs depending on the existing netcdf file at the
1070 %middle of the series set by first_i, incr, last_i
1071 %--------------------------------------------------------------
1072 function find_netcpair_civ2(hObject, eventdata, handles)
1073 set(gcf,'Pointer','watch')
1074 %nomenclature types
1075 filebase=get(handles.displ_filebase,'String');
1076 [filepath,Nme,ext_dir]=fileparts(filebase);
1077 browse=get(handles.browse_root,'UserData');
1078 mode_list=get(handles.mode,'String');
1079 mode_value=get(handles.mode,'Value');
1080 mode=mode_list{mode_value};
1081 
1082 % nomenclature type of the .nc files
1083 nom_type_ima='ima_num';%default
1084 if isfield(browse,'nom_type_ima')
1085     nom_type_ima=browse.nom_type_ima;
1086 end
1087 nom_type_nc='_i1-i2';%default
1088 if isfield(browse,'nom_type_nc')
1089     nom_type_nc=browse.nom_type_nc;
1090 end
1091 if isequal(nom_type_ima,'png_old') | isequal(nom_type_ima,'netc_old')| isequal(nom_type_ima,'raw_SMD')| isequal(nom_type_nc,'netc_old')
1092     nom_type_nc='netc_old';%nom_type for the netcdf files
1093 elseif isequal(nom_type_ima,'none')|isequal(nom_type_nc,'none')
1094     nom_type_nc='none';
1095 elseif isequal(nom_type_ima,'avi')|isequal(nom_type_ima,'_i')|isequal(nom_type_ima,'ima_num')|isequal(nom_type_nc,'_i1-i2')
1096      nom_type_nc='_i1-i2';
1097 else
1098     if  isequal(mode,'series(Di)')|isequal(mode,'st_series(Di)')
1099         nom_type_nc='_i1-i2_j'; % PIV in volume
1100     else
1101         nom_type_nc='_i_j1-j2';
1102     end    
1103 end
1104 browse.nom_type_nc=nom_type_nc;
1105 set(handles.browse_root,'UserData',browse)
1106 
1107 %reads .nc subdirectory and image numbers from the interface
1108 subdir_civ1=get(handles.subdir_civ1,'String');%subdirectory subdir_civ1 for the netcdf data
1109 subdir_civ2=get(handles.subdir_civ2,'String');%subdirectory subdir_civ2 for the netcdf data
1110 first_i=str2num(get(handles.first_i,'String'));
1111 last_i=str2num(get(handles.last_i,'String'));
1112 incr=str2num(get(handles.incr_i,'String'));
1113 num1=first_i:incr:last_i;
1114 if isempty(num1)
1115     set(handles.list_pair_civ2,'String',{});
1116     return
1117 end
1118 ref_i=str2num(get(handles.ref_i,'String'));
1119 if isequal(mode,'pair j1-j2')|isequal(mode,'st_pair j1-j2')
1120     ref_j=0;
1121 else
1122     ref_j=str2num(get(handles.ref_j,'String'));
1123 end
1124 if isequal(get(handles.dt_text,'String'),'dt(ms)=')%simple series(Di) with equal interval
1125     ref_i=ceil((first_i+last_i)/2);
1126     ref_j=1;
1127 end
1128 %     ref_i=browse.num_ref;%field number initially selected by the browser
1129 time=get(handles.displ_filebase,'UserData'); %get the set of times
1130 if isempty(time)
1131     time=[0 1];%default
1132 end
1133 dt_unit=str2num(get(handles.dt,'String'));% used when there is no image documentation file
1134 displ_num=get(handles.list_pair_civ1,'UserData');
1135 
1136 
1137 %eliminate the first pairs inconsistent with the position
1138 if isempty(displ_num)
1139     nbpair=0;
1140 else
1141     nbpair=length(displ_num(1,:));%nbre of displayed pairs
1142     if  isequal(mode,'series(Di)') | isequal(mode,'st_series(Di)') 
1143         nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index
1144     elseif  isequal(mode,'series(Dj)') | isequal(mode,'st_series(Dj)') 
1145         nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index
1146     end
1147 end
1148 nbpair=min(200,nbpair);%limit the number of displayed pairs to 200
1149 
1150 %look for existing processed pairs involving the field at the middle of the series if civ1 will not
1151 % be performed, while the result is needed for next steps.
1152 displ_pair={''}; %default
1153 select=ones(size(1:nbpair));%default =1 for nubers of displayed pairs
1154 if get(handles.CIV2,'Value')==0 & get(handles.CIV1,'Value')==0 & get(handles.FIX1,'Value')==0 & get(handles.PATCH1,'Value')==0%&...
1155     if ~exist(fullfile(filepath,subdir_civ2,ext_dir),'dir') 
1156          errordlg(['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist'])
1157          set(handles.list_pair_civ2,'String',{});
1158          return
1159     end
1160     for ipair=1:nbpair       
1161         [filename,select(ipair)]=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,...
1162         ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1);
1163     end
1164     if  isequal(select,zeros(size(1:nbpair)))
1165         if isfield(browse,'incr_pair') 
1166             num_i1=ref_i-floor(browse.incr_pair(1)/2);
1167             num_i2=ref_i+floor((browse.incr_pair(1)+1)/2);
1168             num_j1=ref_j-floor(browse.incr_pair(2)/2);
1169             num_j2=ref_j+floor((browse.incr_pair(2)+1)/2);
1170             [filename,select(1)]=name_generator(filebase,num_i1,num_j1,'.nc',nom_type_nc,1,num_i2,num_j2,subdir_civ2);
1171         else
1172             if  isequal(mode,'series(Dj)') | isequal(mode,'st_series(Dj)') 
1173                 errordlg(['no civ2 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ2])
1174             else
1175                 errordlg(['no civ2 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ2])
1176             end
1177              set(handles.list_pair_civ2,'String',{});
1178             return
1179         end
1180     end
1181 end
1182 if isequal(mode,'series(Di)')  | isequal(mode,'st_series(Di)') 
1183     if  ~isequal(get(handles.dt_text,'String'),'dt(ms)=')
1184        for ipair=1:nbpair
1185           if select(ipair)
1186               dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt
1187               displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
1188           else 
1189              displ_pair{ipair}='...'; %pair not displayed in the menu
1190           end
1191        end
1192    else
1193        for ipair=1:nbpair
1194          if select(ipair)
1195             displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt_unit*ipair)];
1196          else 
1197             displ_pair{ipair}='...'; %pair not displayed in the menu
1198          end
1199        end
1200     end
1201 elseif isequal(mode,'series(Dj)') | isequal(mode,'st_series(Dj)') % series on the j index
1202        for ipair=1:nbpair
1203           if select(ipair)
1204               dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt
1205               displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
1206           else 
1207              displ_pair{ipair}='...'; %pair not displayed in the menu
1208           end
1209        end
1210 elseif isequal(mode,'pair j1-j2') | isequal(mode,'st_pair j1-j2') %case of pairs
1211     for ipair=1:nbpair
1212         if select(ipair)
1213            dt=time(ref_i+displ_num(4,ipair),displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),displ_num(1,ipair));%time interval dt
1214            displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ...
1215                         ' :dt= ' num2str(dt*1000)];
1216        else 
1217           displ_pair{ipair}='...'; %pair not displayed in the menu
1218        end   
1219    end
1220 elseif isequal(mode,'displacement')
1221     displ_pair={'Di=Dj=0'};  
1222 end   
1223 set(handles.list_pair_civ2,'String',displ_pair');
1224 ichoice=min(find(select));
1225 if (isempty(ichoice) | ichoice < 1); ichoice=1; end;
1226 if get(handles.CIV2,'Value')==0 & get(handles.CIV1,'Value')==0 & get(handles.FIX1,'Value')==0 & get(handles.PATCH1,'Value')==0
1227     set(handles.list_pair_civ2,'Value',ichoice);% first valid pair proposed by default in the menu
1228 end
1229 set(gcf,'Pointer','arrow')
1230 %----------------------------------------------------
1231 %  determine the list of index pairs of processing file
1232 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1233 function [num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=...
1234     find_pair_indices(handles,mode)
1235 first_i=str2num(get(handles.first_i,'String'));
1236 last_i=str2num(get(handles.last_i,'String'));
1237 incr=str2num(get(handles.incr_i,'String'));
1238 first_j=str2num(get(handles.first_j,'String'));
1239 last_j=str2num(get(handles.last_j,'String'));
1240 incr_j=str2num(get(handles.incr_j,'String'));
1241 list_civ1=get(handles.list_pair_civ1,'String');
1242 index_civ1=get(handles.list_pair_civ1,'Value');
1243 str_civ1=list_civ1{index_civ1};
1244 list_civ2=get(handles.list_pair_civ2,'String');
1245 index_civ2=get(handles.list_pair_civ2,'Value');
1246 str_civ2=list_civ2{index_civ2};
1247 if isequal(first_i,[])|isequal(first_j,[]), errordlg('first field number not defined'),...
1248     set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
1249 if isequal(last_i,[])| isequal(last_j,[]),errordlg('last field number not defined'),...
1250     set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
1251 if isequal(incr,[])| isequal(incr_j,[]),errordlg('increment in field number not defined'),...
1252     set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
1253 if last_i < first_i | last_j < first_j , errordlg('last field number must be larger than the first one'),...
1254     set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
1255 num1=[first_i:incr:last_i];
1256 num_j=[first_j:incr_j:last_j];
1257 if isequal (mode,'series(Di)') |isequal(mode,'st_series(Di)')
1258      %recognize the pair civ1 from the display
1259     indsel=find((double(str_civ1)<48)|(double(str_civ1)>57));% character indices of non numerical characters
1260     str_raw=str_civ1(indsel);
1261     indsepar=find(str_raw=='|'); %character index of the separator
1262     d1=str2num(str_civ1([indsel(indsepar-1)+1:indsel(indsepar)-1]));
1263     if indsepar==length(str_raw)
1264         d2=str2num(str_civ1([indsel(indsepar)+1:end]));
1265     else
1266         d2=str2num(str_civ1([indsel(indsepar)+1:indsel(indsepar+1)-1]));
1267     end   
1268     %recognize the pair civ2 from the display
1269     num1_civ1=num1-d1;% set of first image numbers
1270     num2_civ1=num1+d2;
1271     num_a_civ1=num_j;
1272     num_b_civ1=num_j;
1273     num1_civ2=num1-floor(index_civ2/2)*ones(size(num1));% set of first image numbers
1274     num2_civ2=num1+ceil(index_civ2/2)*ones(size(num1));
1275     num1_civ2=num1-d1;% set of first image numbers
1276     num2_civ2=num1+d2;
1277     num_a_civ2=num_j;
1278     num_b_civ2=num_j;
1279     % adjust the first and last field number
1280     lastfield=str2num(get(handles.nb_field,'String'));
1281     if isequal(lastfield,[])
1282         indsel=find((num1_civ1 >= 1)&(num1_civ2 >= 1));
1283     else
1284         indsel=find((num2_civ1 <= lastfield)&(num2_civ2 <= lastfield)&(num1_civ1 >= 1)&(num1_civ2 >= 1));
1285     end
1286     if length(indsel)>=1
1287         firstind=indsel(1);
1288         lastind=indsel(end);
1289         set(handles.first_i,'String',num2str(num1(firstind)))%update the display of first and last fields
1290         set(handles.last_i,'String',num2str(num1(lastind)))
1291         num1=num1(indsel);
1292         num1_civ1=num1_civ1(indsel);
1293         num1_civ2=num1_civ2(indsel);
1294         num2_civ1=num2_civ1(indsel);
1295         num2_civ2=num2_civ2(indsel);
1296     end
1297 elseif isequal (mode,'series(Dj)')|isequal (mode,'st_series(Dj)')
1298     lastfield_j=str2num(get(handles.nb_field2,'String'));
1299     num1_civ1=num1;% set of first image numbers
1300     num2_civ1=num1;
1301     num_a_civ1=num_j-floor(index_civ1/2)*ones(size(num_j));
1302     num_b_civ1=num_j+ceil(index_civ1/2)*ones(size(num_j));
1303     num1_civ2=num1;
1304     num2_civ2=num1;
1305     num_a_civ2=num_j-floor(index_civ2/2)*ones(size(num_j));
1306     num_b_civ2=num_j+ceil(index_civ2/2)*ones(size(num_j));
1307     % adjust the first and last field number
1308     if isequal(lastfield_j,[])
1309         indsel=find((num_a_civ1 >= 1)&(num_a_civ2 >= 1));
1310     else
1311         indsel=find((num_b_civ1 <= lastfield_j)&(num_b_civ2 <= lastfield_j)&(num_a_civ1 >= 1)&(num_a_civ2 >= 1));
1312     end
1313     if length(indsel)>=1
1314         firstind=indsel(1);
1315         lastind=indsel(end);
1316         set(handles.first_j,'String',num2str(num_j(firstind)))%update the display of first and last fields
1317         set(handles.last_j,'String',num2str(num_j(lastind)))
1318         num_j=num_j(indsel);
1319         num_a_civ1=num_a_civ1(indsel);
1320         num_a_civ2=num_a_civ2(indsel);
1321         num_b_civ1=num_b_civ1(indsel);
1322         num_b_civ2=num_b_civ2(indsel);
1323     end
1324 elseif isequal(mode,'pair j1-j2') | isequal(mode,'st_pair j1-j2') %case of bursts (png_old or png_2D)
1325     num1_civ1=num1;
1326     num1_civ2=num1;
1327     displ_num=get(handles.list_pair_civ1,'UserData');
1328     num2_civ1=num1;
1329     num_a_civ1=displ_num(1,index_civ1);
1330     num_b_civ1=displ_num(2,index_civ1);
1331     num2_civ2=num1;
1332     num_a_civ2=displ_num(1,index_civ2);
1333     num_b_civ2=displ_num(2,index_civ2);
1334 elseif isequal(mode,'displacement')
1335     num1_civ1=num1;
1336     num2_civ1=num1;
1337     num_a_civ1=num_j;
1338     num_b_civ1=num_j;
1339     num1_civ2=num1;
1340     num2_civ2=num1;
1341     num_a_civ2=num_j;
1342     num_b_civ2=num_j;
1343 end
1344 
1345 
1346 %-------------------------------------------------------------
1347 % --- Executes on selection change in list_pair_civ1.
1348 function list_pair_civ1_Callback(hObject, eventdata, handles)
1349 %------------------------------------------------------------
1350 %reproduce by default the chosen pair in the civ2 menu
1351 list_pair=get(handles.list_pair_civ1,'String');%get the menu of image pairs
1352 index_pair=get(handles.list_pair_civ1,'Value');
1353 displ_num=get(handles.list_pair_civ1,'UserData');
1354 num_a=displ_num(1,index_pair);
1355 num_b=displ_num(2,index_pair);
1356 set(handles.list_pair_civ2,'Value',index_pair);
1357 
1358 %update first_i and last_i according to the chosen image pairs
1359 mode_list=get(handles.mode,'String');
1360 mode_value=get(handles.mode,'Value');
1361 mode=mode_list{mode_value};
1362 if isequal(mode,'series(Di)')
1363     first_i=str2num(get(handles.first_i,'String'));
1364     last_i=str2num(get(handles.last_i,'String'));
1365     incr_i=str2num(get(handles.incr_i,'String'));
1366     num1=first_i:incr_i:last_i;
1367     lastfield=str2num(get(handles.nb_field,'String'));
1368     if ~isequal(lastfield,[])
1369         ind=find((num1-floor(index_pair/2)*ones(size(num1))>0)& ...
1370              (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield));
1371         num1=num1(ind);
1372     end
1373     set(handles.first_i,'String',num2str(num1(1)));
1374     set(handles.last_i,'String',num2str(num1(end)));
1375 elseif isequal(mode,'series(Dj)')
1376     first_j=str2num(get(handles.first_j,'String'));
1377     last_j=str2num(get(handles.last_j,'String'));
1378     incr_j=str2num(get(handles.incr_j,'String'));
1379     num_j=first_j:incr_j:last_j;
1380     lastfield2=str2num(get(handles.nb_field2,'String'));
1381     if ~isequal(lastfield2,[])
1382         ind=find((num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
1383              (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2));
1384         num1=num_j(ind);
1385     end
1386     set(handles.first_j,'String',num2str(num1(1)));
1387     set(handles.last_j,'String',num2str(num1(end)));
1388 end 
1389 
1390 %------------------------------------------------------------------
1391 % --- Executes on selection change in list_pair_civ2.
1392 function list_pair_civ2_Callback(hObject, eventdata, handles)
1393 
1394 index_pair=get(handles.list_pair_civ2,'Value');%get the selected position index in the menu
1395 
1396 %update first_i and last_i according to the chosen image pairs
1397 mode_list=get(handles.mode,'String');
1398 mode_value=get(handles.mode,'Value');
1399 mode=mode_list{mode_value};
1400 if isequal(mode,'series(Di)')
1401     first_i=str2num(get(handles.first_i,'String'));
1402     last_i=str2num(get(handles.last_i,'String'));
1403     incr_i=str2num(get(handles.incr_i,'String'));
1404     num1=first_i:incr_i:last_i;
1405     lastfield=str2num(get(handles.nb_field,'String'));
1406     if ~isequal(lastfield,[])
1407         ind=find((num1-floor(index_pair/2)*ones(size(num1))>0)& ...
1408              (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield));
1409         num1=num1(ind);
1410     end
1411     set(handles.first_i,'String',num2str(num1(1)));
1412     set(handles.last_i,'String',num2str(num1(end)));
1413 elseif isequal(mode,'series(Dj)')
1414     first_j=str2num(get(handles.first_j,'String'));
1415     last_j=str2num(get(handles.last_j,'String'));
1416     incr_j=str2num(get(handles.incr_j,'String'));
1417     num_j=first_j:incr_j:last_j;
1418     lastfield2=str2num(get(handles.nb_field2,'String'));
1419     if ~isequal(lastfield2,[])
1420         ind=find((num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
1421              (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield));
1422         num1=num_j(ind);
1423     end
1424     set(handles.first_j,'String',num2str(num1(1)));
1425     set(handles.last_j,'String',num2str(num1(end)));
1426 end 
1427 
1428 
1429 
1430 
1431 %-----------------------------------------------------------
1432 % --- Executes on button press in BATCH: remote processing
1433 %-----------------------------------------------------------
1434 function BATCH_Callback(hObject, eventdata, handles)
1435 global civ1_exe civ2_exe patch_exe patch_new_exe fix_exe todo_path sge Civ_exe
1436 
1437 pxcmx=get(handles.pxcmx,'String');
1438 pxcmy=get(handles.pxcmy,'String');
1439 npx=get(handles.pxcmx,'UserData');
1440 npy=get(handles.pxcmy,'UserData');
1441 
1442 %check the list of operations:
1443 operations={'CIV1','FIX1','PATCH1','CIV2','FIX2','PATCH2'};
1444 run_flag=1;
1445 box_test(1)=get(handles.CIV1,'Value');
1446 box_test(2)=get(handles.FIX1,'Value');
1447 box_test(3)=get(handles.PATCH1,'Value');
1448 box_test(4)=get(handles.CIV2,'Value');
1449 box_test(5)=get(handles.FIX2,'Value');
1450 box_test(6)=get(handles.PATCH2,'Value');
1451 index=find(box_test==1);
1452 if isempty(index)
1453     errordlg('no selected operation')
1454     set(handles.BATCH, 'Enable','On')
1455     set(handles.BATCH,'BackgroundColor',[1 0 0])
1456     return
1457 end
1458 index_first=min(index);
1459 index_last=max(index);
1460 box_used=box_test([index_first : index_last]);
1461 [box_missing,ind_missing]=min(box_used);
1462 if isequal(box_missing,0)
1463     errordlg(['missing' cell2mat(operations(ind_missing))]);
1464     set(handles.BATCH, 'Enable','On')
1465     set(handles.BATCH,'BackgroundColor',[1 0 0])
1466     return
1467 end
1468 
1469 %check mask if selecetd
1470 if isequal(get(handles.get_mask_civ1,'Value'),1)
1471      get_mask_civ1_Callback(hObject, eventdata, handles);
1472 end
1473 if isequal(get(handles.get_mask_fix1,'Value'),1)
1474      get_mask_fix1_Callback(hObject, eventdata, handles);
1475 end
1476 if isequal(get(handles.get_mask_civ2,'Value'),1)
1477      get_mask_civ2_Callback(hObject, eventdata, handles);
1478 end
1479 if isequal(get(handles.get_mask_fix2,'Value'),1)
1480      get_mask_fix2_Callback(hObject, eventdata, handles);
1481 end
1482 
1483 
1484 %read names of the .exe file
1485 path_uvmat=which('uvmat');% check the path detected for source file uvmat
1486 path_UVMAT=fileparts(path_uvmat); %path to UVMAT
1487 if isunix
1488     %fid = fopen(fullfile(path_UVMAT,'PARAM_LINUX.txt'),'r');%open the file with civ_3D binary names
1489     xmlfile=fullfile(path_UVMAT,'PARAM_LINUX.xml');
1490     if exist(xmlfile,'file')
1491         t=xmltree(xmlfile);
1492         sparam=convert(t);
1493     end
1494 else
1495     %fid = fopen(fullfile(path_UVMAT,'PARAM_WIN.txt'),'r');%open the file with civ_3D binary names
1496     xmlfile=fullfile(path_UVMAT,'PARAM_WIN.xml');
1497     if exist(xmlfile,'file')
1498         t=xmltree(xmlfile);
1499         sparam=convert(t);
1500     end
1501 end
1502  sge=0;
1503 if isfield(sparam,'Civ_exe')
1504     Civ_exe=sparam.Civ_exe
1505 end
1506 if isfield(sparam,'Civ1_exe')
1507     civ1_exe=sparam.Civ1_exe
1508 end
1509 if isfield(sparam,'Civ2_exe')
1510     civ2_exe=sparam.Civ2_exe
1511 end
1512 if isfield(sparam,'Patch_exe')
1513     patch_exe=sparam.Patch_exe
1514 end
1515 if isfield(sparam,'PatchNew_exe')
1516     patch_new_exe=sparam.PatchNew_exe
1517 end
1518 if isfield(sparam,'Fix_exe')
1519     fix_exe=sparam.Fix_exe
1520 end
1521 if isfield(sparam,'Todo_path')
1522     todo_path=sparam.Todo_path
1523 end
1524 if isfield(sparam,'SGE')
1525     sge=str2num(sparam.SGE)
1526 end 
1527 %choice of batch priority
1528 ind_answer=2;
1529 if sge
1530     [s,w]=unix('qstat -q civ_3D.q|grep job_| wc -l'); %check the waiting list (command unix)
1531     if isequal(s,0)
1532         w(end)=[];
1533         str_displ={[w ' jobs in the waiting list'];'Select a priority:'};
1534         str={'urgent';'normal';'low'};
1535         [ind_answer,v] = listdlg('PromptString',str_displ,...
1536                 'SelectionMode','single',...
1537                 'ListString',str,'ListSize',[200 200],'Name','job priority','InitialValue',3);
1538         if isequal(v,0) % to handle Cancel button and figure close,
1539            return % a better way should be create
1540         end
1541     else
1542         warndlg_uvmat('batch system not available','ERROR')
1543         return
1544     end
1545 end
1546 %initialize the waitbars
1547 set(handles.waitbar_1,'Position',[0.946 0.876 0.03 0.001])
1548 set(handles.waitbar_patch1,'Position',[0.946 0.439 0.03 0.001])
1549 set(handles.waitbar_civ2,'Position',[0.946 0.219 0.03 0.001])
1550 set(handles.waitbar_patch2,'Position',[0.946 0.0 0.03 0.001])
1551 set(handles.BATCH, 'Enable','Off')
1552 set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])
1553 
1554 %get the filename root, nomenclature and numbers
1555 filebase=get(handles.displ_filebase,'String');
1556 % for Windows system find the UBC path name if needed
1557 if ~isunix & isequal(todo_path(1:2),'\\') & isequal(filebase(2:3),':\')
1558     cur_dir=pwd;
1559     if ~isequal(cur_dir(2:3),':\')
1560         cd(matlabroot); %move to the Matlab root directory if the current Matlab dir does not allow the dos command or is M:
1561     end
1562     [ss,ww]=dos(['net use ' filebase(1:2)]);
1563     if isequal(ss,0)
1564         rankpath=findstr(ww,'\\');
1565         if ~isempty(rankpath)
1566             wwrest=ww(rankpath:end);
1567             rankend=min(find(double(wwrest)==10))-1;
1568             filebase=[wwrest(1:rankend) filebase(3:end)];
1569             set(handles.displ_filebase,'String',filebase);
1570         end
1571     else
1572          warndlg_uvmat('for BATCH option, UBC file names, beginning by \\, are needed','ERROR');
1573          set(handles.BATCH, 'Enable','On')
1574          set(handles.BATCH,'BackgroundColor',[1 0 0])
1575          return
1576     end
1577 end
1578 browse=get(handles.browse_root,'UserData')
1579 ext_ima=browse.ext_ima;
1580 nom_type_nc='_i1-i2';
1581 nom_type_ima=browse.nom_type_ima;
1582 % nom_type_nc=browse.nom_type_nc;
1583 % if isequal(nom_type_ima2,[]),nom_type_ima2='ima_num';end; %default
1584 % if isequal(nom_type_nc,[]),nom_type_nc='_i1-i2';end; %default
1585 mode_list=get(handles.mode,'String');
1586 mode_value=get(handles.mode,'Value');
1587 mode=mode_list{mode_value};
1588 time=get(handles.displ_filebase,'UserData'); %get the set of times
1589 
1590 [num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=...
1591 find_pair_indices(handles,mode); %determine the pairs of processing file
1592 
1593 %check dir
1594 subdir_civ1=get(handles.subdir_civ1,'String');%subdirectory subdir_civ1 for the netcdf output data
1595 subdir_civ2=get(handles.subdir_civ2,'String');
1596 if isequal(subdir_civ1,''),subdir_civ1='A'; end% put default subdir
1597 if isequal(subdir_civ2,''),subdir_civ2=subdir_civ1; end% put default subdir
1598 currentdir=pwd;%store the current working directory
1599 [Path_ima,Name]=fileparts(filebase);%Path of the image files (.civ_3D)
1600 if ~exist(Path_ima,'dir')
1601     warndlg_uvmat(['path to images ' Path_ima ' not found'],'ERROR')
1602     return
1603 end
1604 cd(Path_ima);%move to the directory of the images
1605 dircur=pwd; %current working directory
1606 m2='';
1607 [erread,message]=fileattrib(Path_ima);
1608 if ~isempty(message) & ~isequal(message.UserWrite,1)
1609       errordlg(['No writting access to ' Path_ima])
1610       cd(currentdir)
1611       return
1612 end
1613 
1614 %test for reference file in fix
1615 ref_fix1=get(handles.ref_fix1,'UserData');
1616 ref_fix2=get(handles.ref_fix2,'UserData');
1617 if (~isempty(ref_fix1) & box_test(2)==1)|(~isempty(ref_fix2) & box_test(5)==1)
1618     errordlg('reference file not implemented in BATCH mode, use RUN')
1619     set(handles.BATCH, 'Enable','On')
1620     set(handles.BATCH,'BackgroundColor',[1 0 0])
1621     return
1622 end
1623 nbfield=length(num1_civ1);
1624 nbslice=length(num_a_civ1);
1625    
1626 %check the existence of the netcdf and image files involved
1627 % if box_test(1)==1;%CIV1 activated
1628 detect=1; 
1629 while detect==1 %name a new subdir if one of the netcdf files already exists
1630       for ifile=1:nbfield
1631 %           for j=1:nbslice
1632               [filename,detect]=name_generator(filebase,num1_civ1(ifile),[],'.nc',...
1633                 nom_type_nc,1,num2_civ1(ifile),[],subdir_civ1);%
1634               if detect==1% if a netcdf file already exists
1635                  subdir_civ1=[subdir_civ1 '.0'];
1636                  subdir_civ2=subdir_civ1;
1637                  break
1638               end
1639               filecell_nc1(ifile)={filename};
1640           if detect==1% if a netcdf file already exists
1641               break
1642           end
1643       end
1644        %create the new subdir_civ1 if it does not exist
1645       if ~exist(fullfile(Path_ima,subdir_civ1),'dir')
1646           [m1,m2,m3]=mkdir(subdir_civ1)
1647            if ~isequal(m2,'')
1648                msgbox(m2);%error message for directory creation
1649           end
1650      end
1651 end
1652 %get image names
1653 for ifile=1:nbfield
1654     [filecell_ima1_civ1{ifile},idetect]=name_generator(filebase, num1_civ1(ifile),[],ext_ima,nom_type_ima);%first image
1655     [filecell_ima2_civ1{ifile},idetect_1]=name_generator(filebase, num2_civ1(ifile),[],ext_ima,nom_type_ima); %second image
1656      if idetect==0
1657             warndlg_uvmat([filecell_ima1_civ1{ifile} ' not found'],'ERROR')
1658             set(handles.BATCH, 'Enable','On')
1659             set(handles.BATCH,'BackgroundColor',[1 0 0])
1660             cd(currentdir)
1661             return
1662      end
1663      if idetect_1==0,
1664             errordlg([filecell_ima2_civ1{ifile} ' not found'])
1665             set(handles.BATCH, 'Enable','On')
1666             set(handles.BATCH,'BackgroundColor',[1 0 0])
1667             cd(currentdir)
1668             return
1669      end
1670 end
1671 
1672 cd(currentdir);%come back to the initial working directory
1673 % if ~isequal(m2,'')
1674 %      msgbox(m2);%error message for directory creation
1675 % end
1676 set(handles.subdir_civ1,'String',subdir_civ1);%update the edit box
1677 set(handles.subdir_civ2,'String',subdir_civ2);%update the edit box
1678 browse.nom_type_nc=nom_type_nc;
1679 set(handles.browse_root,'UserData',browse);%update the nomenclature type for uvmat
1680 
1681 %COPY IMAGES TO THE FORMAT .vol IF NEEDED
1682 if isequal(nom_type_ima,'avi')
1683     nom_type_imanew='_i';
1684 else
1685     nom_type_imanew=nom_type_ima;
1686 end
1687 
1688 if ~isequal(ext_ima,'.vol')
1689     if box_test(1)==1 %if civ1 is performed
1690        h = waitbar(0,['copy images to the .png format for civ1']);% display a wait bar
1691        for ifile=1:nbfield
1692             waitbar(ifile/nbfield);
1693             Atot=[];
1694             [filename_A,idetect_cur]=name_generator(filebase,num1_civ1(ifile),1,'.png','_i');%A VOIR
1695             for j=1:nbslice
1696                     if idetect_cur==0
1697                         A=read_image(cell2mat(filecell_ima1_civ1(ifile,j)),nom_type_ima2,npx,npy,num1_civ1(ifile));
1698                         Atot=[Atot;A];
1699                         %imwrite(A,filename,'BitDepth',16);
1700                     end
1701             end
1702             imwrite(Atot,filename_A,'BitDepth',16);
1703                     %filecell_ima1_civ1(ifile,j)={filename};
1704             Atot=[];
1705             [filename_B,idetect_cur]=name_generator(filebase, num2_civ1(ifile),1,'.png','_i');
1706             for j=1:nbslice
1707                     if idetect_cur==0
1708                         A=read_image(cell2mat(filecell_ima2_civ1(ifile,j)),nom_type_ima2,npx,npy,num2_civ1(ifile));
1709                         Atot=[Atot;A];
1710 %                         imwrite(A,filename,'BitDepth',16);
1711                     end
1712                     %filecell_ima2_civ1(ifile,j)={filename};
1713             end
1714             imwrite(Atot,filename_B,'BitDepth',16);
1715         end
1716         close(h)
1717     end    
1718 end
1719 
1720 if ~sge      
1721     %OPEN THE WAIT LIST FOR BATCH PROCESSES
1722     name_lock=fullfile(todo_path,'lock'); %lock file
1723     iwait=0;
1724     while(exist(name_lock) & iwait<15)
1725         pause(1); %wait 1 second
1726         iwait=iwait+1;
1727     end
1728     if iwait==15
1729         errordlg(['I''m tired to wait for the lock file, please delete it then click again on BATCH' name_lock ])
1730         set(handles.BATCH, 'Enable','On')
1731         set(handles.BATCH,'BackgroundColor',[1 0 0])
1732         return
1733     end
1734     p0=fopen(name_lock,'w'); %create the file name_lock: prevents other users to interfere
1735     name_todo=fullfile(todo_path,'TODO.txt');
1736     p1=fopen(name_todo,'a');
1737     if (p1<0)
1738         errordlg(['error in opening ' name_todo])
1739         set(handles.BATCH, 'Enable','On')
1740         set(handles.BATCH,'BackgroundColor',[1 0 0])
1741         return;
1742     end
1743 end
1744 
1745 for ifile=1:nbfield
1746     i_cmd=0; 
1747     cmd='';
1748     if sge
1749        cmd='#!/bin/bash';
1750        cmd=char({cmd;'#$ -cwd'});
1751        cmd=char({cmd;'hostname && date'});
1752     end
1753     filename_cmx=cell2mat(filecell_nc1(ifile));%output netcdf file
1754     filename_cmx([end-1:end])='cm';%name of cmx file
1755     filename_cmx=[filename_cmx 'x'];
1756     
1757 %CIV1
1758     if box_test(1)==1
1759         %GET civ_3D PARAMETERS:
1760         par_civ1=read_param_civ1(handles,cell2mat(filecell_ima1_civ1(1,1)));
1761         p1text=[];
1762         [par_civ1.path,resu_file,resu_ext]=fileparts(filecell_nc1{ifile});
1763         par_civ1.volume1=filecell_ima1_civ1{ifile};
1764         par_civ1.volume2=filecell_ima2_civ1{ifile}
1765         par_civ1.nx=1024;
1766         par_civ1.ny=1024;
1767         par_civ1.nz=par_civ1.gridLimits_Zmax - par_civ1.gridLimits_Zmin;
1768         'TEST'
1769         par_civ1
1770         % civAll=get(handles.Experimental,'Value'); % Boolean for new civ excution method
1771         % if isequal(civAll,1)
1772         civAllxml=struct2xml(par_civ1);% xml contents,  all parameters
1773         civAllxml=set(civAllxml,1,'name','civ3d3c');
1774     %    save(civAllxml)
1775         par_civ1_3d_xml=fullfile(par_civ1.path,[resu_file '.xml']);%[par_civ1.path '/test_to_change.xml'];
1776      pvalue=num2str((1-ind_answer)*500);
1777         save(civAllxml,par_civ1_3d_xml);
1778       if(isunix && sge)
1779      ['echo /CIVX/bin/MPI/lam-7.1.3_g95/bin/mpirun C  /CIVX/bin/civ3d3c -p ' par_civ1_3d_xml '|qsub -p ' pvalue ' -q lam.q -pe lam_loose 16 -e ' par_civ1_3d_xml '.errors -o ' par_civ1_3d_xml '.log' ]
1780      eval ( ['!echo /CIVX/bin/MPI/lam-7.1.3_g95/bin/mpirun C  /CIVX/bin/civ3d3c -p ' par_civ1_3d_xml '|qsub -p ' pvalue ' -q lam.q -pe lam_loose 16 -e ' par_civ1_3d_xml '.errors -o ' par_civ1_3d_xml '.log' ])
1781       else
1782          '3D mode is NOT supported without sge'
1783       end
1784      return
1785         % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1786         %  fichier xml produit
1787         %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1788         % A CONTINUER
1789         %civAllxml
1790         civAllCmd=[];
1791         civAllxml=set(civAllxml,1,'name','civ3d3c');
1792         namelog=[filename_cmx([1:end-3]) 'log'];
1793         %par_civ1.Dt=num2str(time(num2_civ1(ifile),num_b_civ1(j))-time(num1_civ1(ifile),num_a_civ1(1)));
1794         %par_civ1.T0=num2str((time(num2_civ1(ifile),num_b_civ1(j))+time(num1_civ1(ifile),num_a_civ1(1)))/2);
1795        % test_mask=get(handles.get_mask_civ1,'Value');
1796         i_cmd=i_cmd+1;
1797 %         if isequal(civAll,0)
1798 %             cmd=char({cmd;BATCH_CIV1(filename_cmx([1:end-4]),namelog,par_civ1,handles)});
1799 %         else
1800              civAllCmd=[civAllCmd ' civ1 '];
1801              str=BATCH_CIV1_Unified(filename_cmx([1:end-4]),namelog,par_civ1,handles);
1802             fieldnames=fields(str);
1803             [civAllxml,uid_civ1]=add(civAllxml,1,'element','civ1');
1804             for ilist=1:length(fieldnames)
1805               val=eval(['str.' fieldnames{ilist}]);
1806               if ischar(val)
1807                 [civAllxml,uid_t]=add(civAllxml,uid_civ1,'element',fieldnames{ilist});
1808                 [civAllxml,uid_t2]=add(civAllxml,uid_t,'chardata',val);
1809                end
1810             end   
1811 %         end
1812     end         
1813     if(isunix)
1814         cmd=char({cmd ; ['cp -f ' filename_cmx '2 ' filename_cmx]; cmd_CIV2});
1815     else
1816         cmd=char({cmd ; ['copy /Y ' filename_cmx '2 ' filename_cmx]; cmd_CIV2});
1817     end
1818 end
1819      
1820 %  if isequal(civAll,1)
1821     save(civAllxml,[filename_cmx([1:end-4]) '.xml']);
1822     cmd=char({cmd;[Civ_exe ' -f ' [filename_cmx([1:end-4]) '.xml'] ' ' civAllCmd]});
1823 
1824      %save(civAllxml,'/tmp/test.xml');
1825 %  end
1826 
1827 
1828 % create the .bat file:
1829 if sge
1830         [Rootbat,Filebat,extbat]=fileparts(filename_cmx);
1831         filename_bat=fullfile(Rootbat,['job_' Filebat extbat]);
1832 else
1833     filename_bat=filename_cmx;
1834 end
1835 filename_bat(end-2:end)='bat';
1836 
1837 %     pbat=fopen(filename_bat,'w'); %create the file filename_bat
1838 dlmwrite(filename_bat,cmd,'');%write commands in filename_bat
1839 if sge
1840     pvalue=num2str((1-ind_answer)*500);
1841     namelog=[filename_bat '.patch.log'];
1842     ['!qsub -p ' pvalue ' -q civ_3D.q -e ' filename_cmx(1:end-4) '.errors -o ' filename_cmx(1:end-4) '.log' ' ' filename_bat];
1843     eval(  ['!qsub -p ' pvalue ' -q civ_3D.q -e ' filename_cmx(1:end-4) '.errors -o ' filename_cmx(1:end-4) '.log' ' ' filename_bat]);
1844 else
1845     if(isunix)
1846       cmdtodo=['. ' filename_bat ];%removed for Mathieu tests %' && rm -f ' filename_bat] ;
1847     else
1848 %      cmdtodo=[filename_bat ' && del /F /Q ' filename_bat];
1849        cmdtodo=[filename_bat];%removed for Mathieu tests %' && del /F /Q ' filename_bat' ;
1850     end
1851     count= fprintf(p1,'%s\n', cmdtodo);
1852 end
1853 if ~sge
1854     fclose(p1);
1855     fclose(p0);
1856     delete(name_lock);
1857 end 
1858 set(handles.BATCH, 'Enable','On')
1859 set(handles.BATCH,'BackgroundColor',[1 0 0])
1860 %save interface state
1861 [Path,Name]=fileparts(filebase);
1862 namefig=fullfile(Path,subdir_civ2,Name);
1863 detect=1; 
1864 while detect==1
1865     namefigfull=[namefig '.fig'];
1866     hh=dir(namefigfull);
1867     if ~isempty(hh)
1868         detect=1;
1869         namefig=[namefig '.0'];
1870     else
1871         detect=0;
1872     end
1873 end
1874 saveas(gcbf,namefigfull);%save the interface with name namefigfull
1875 
1876 
1877 %----------------------------------------
1878 %PATCH
1879 %---------------------------------------
1880 function cmd_PATCH=RUN_PATCH(filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,test_interp)
1881 global patch_exe patch_new_exe
1882         namelog=[filename_nc([1:end-3]) '_patch.log'];
1883         if test_interp==0
1884             cmd_PATCH=[patch_exe ' -f ' filename_nc ' -m ' nx_patch  ' -n ' ny_patch ' -ro ' rho_patch ' -nopt ' subdomain_patch ...
1885             '  > ' namelog ' 2>&1'] % redirect standard output to the log file
1886          else %nouveau programme patch
1887              cmd_PATCH=[patch_new_exe ' -f ' filename_nc ' -m ' nx_patch  ' -n ' ny_patch ' -ro ' rho_patch ...
1888                 ' -max ' thresh_value ' -nopt ' subdomain_patch  '  > ' namelog ' 2>&1']; % redirect standard output to the log file
1889         end
1890 
1891   
1892 %----------------------------------------------------
1893 function first_j_Callback(hObject, eventdata, handles)
1894 last_j_Callback(hObject, eventdata, handles)
1895 
1896 %---------------------------------------------------------
1897 % --- Executes on button press in CIV1.
1898 function CIV1_Callback(hObject, eventdata, handles)
1899 enable_civ1(handles,get(handles.CIV1,'Value'))
1900 find_netcpair_civ1(hObject, eventdata, handles);
1901 
1902 %------------------------------------------------------
1903 % --- Executes on button press in FIX1.
1904 function FIX1_Callback(hObject, eventdata, handles)
1905 
1906 if get(handles.FIX1,'Value')==1
1907 enable_fix1(handles)
1908 else
1909 desable_fix1(handles)
1910 end
1911 
1912 %----------------------------------------------------------------
1913 % --- Executes on button press in PATCH1.
1914 function PATCH1_Callback(hObject, eventdata, handles)
1915 
1916 if get(handles.PATCH1,'Value')==1
1917 enable_patch1(handles)
1918 else
1919 desable_patch1(handles)
1920 end
1921 
1922 %----------------------------------------------------------
1923 % --- Executes on button press in CIV2.
1924 function CIV2_Callback(hObject, eventdata, handles)
1925 state=get(handles.CIV2,'Value');
1926 enable_civ2(handles,state)
1927 if state
1928     find_netcpair_civ2(hObject, eventdata, handles)
1929 end
1930 
1931 %---------------------------------------------------
1932 % --- Executes on button press in FIX2.
1933 function FIX2_Callback(hObject, eventdata, handles)
1934 if get(handles.FIX2,'Value')==1
1935     enable_fix2(handles)
1936     if get(handles.CIV2,'Value')==0
1937         find_netcpair_civ2(hObject, eventdata, handles) % select the available netcdf files
1938     end
1939 else
1940     desable_fix2(handles)
1941 end
1942 
1943 
1944 %-------------------------------------------------------
1945 % --- Executes on button press in PATCH2.
1946 function PATCH2_Callback(hObject, eventdata, handles)
1947 %--------------------------------------------------------
1948 if get(handles.PATCH2,'Value')==1
1949     enable_patch2(handles)
1950     if get(handles.CIV2,'Value')==0
1951         find_netcpair_civ2(hObject, eventdata, handles) % select the available netcdf files
1952     end
1953 else
1954     desable_patch2(handles)
1955 end
1956 
1957 
1958 
1959 %-----------------------------------------------------------
1960 function first_i_Callback(hObject, eventdata, handles)
1961 %------------------------------------------------------
1962 last_i_Callback(hObject, eventdata, handles)
1963 
1964 %-----------------------------------------------------------
1965 % --- Executes on button press in calcul_search: determine the search range isx,isy
1966 %--------------------------------------------------------
1967 function calcul_search_Callback(hObject, eventdata, handles)
1968 
1969 %determine pair numbers
1970 list_pair=get(handles.list_pair_civ1,'String');%get the menu of image pairs
1971 index=get(handles.list_pair_civ1,'Value');
1972 displ_num=get(handles.list_pair_civ1,'UserData');
1973 time=get(handles.displ_filebase,'UserData'); %get the set of times
1974 pxcm_xy=get(handles.calcul_search,'UserData')
1975 pxcmx=pxcm_xy(1);
1976 pxcmy=pxcm_xy(2);
1977 mode_list=get(handles.mode,'String');
1978 mode_value=get(handles.mode,'Value');
1979 mode=mode_list{mode_value};
1980 if isequal (mode, 'series(Di)' )
1981     ref_i=str2num(get(handles.ref_i,'String'));
1982     num1=ref_i-floor(index/2);%  first image numbers
1983     num2=ref_i+ceil(index/2);
1984     num_a=1;
1985     num_b=1;
1986 elseif isequal (mode, 'series(Dj)') 
1987     num1=1;
1988     num2=1;
1989     ref_j=str2num(get(handles.ref_j,'String'));
1990     num_a=ref_j-floor(index/2);%  first image numbers
1991     num_b=ref_j+ceil(index/2);
1992 elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)
1993     ref_i=str2num(get(handles.ref_i,'String'));
1994     num1=ref_i;
1995     num2=ref_i;
1996     num_a=displ_num(1,index);
1997     num_b=displ_num(2,index);
1998 end
1999 dt=time(num2,num_b)-time(num1,num_a);
2000 ibx=str2num(get(handles.ibx,'String'));
2001 iby=str2num(get(handles.iby,'String'));
2002 umin=dt*pxcmx*str2num(get(handles.umin,'String'));
2003 umax=dt*pxcmx*str2num(get(handles.umax,'String'));
2004 vmin=dt*pxcmy*str2num(get(handles.vmin,'String'));
2005 vmax=dt*pxcmy*str2num(get(handles.vmax,'String'));
2006 shiftx=round((umin+umax)/2);
2007 shifty=round((vmin+vmax)/2);
2008 isx=(umax+2-shiftx)*2+ibx;
2009 isx=2*ceil(isx/2)+1;
2010 isy=(vmax+2-shifty)*2+iby;
2011 isy=2*ceil(isy/2)+1;
2012 set(handles.shiftx,'String',num2str(shiftx));
2013 set(handles.shifty,'String',num2str(shifty));
2014 set(handles.isx,'String',num2str(isx));
2015 set(handles.isy,'String',num2str(isy));
2016 
2017 
2018 %---------------------------------------------------------
2019 % Executes on carriage return on the subdir civ1 edit window
2020 %--------------------------------------------------------
2021 function subdir_civ1_Callback(hObject, eventdata, handles)
2022 subdir=get(handles.subdir_civ1,'String');
2023 set(handles.subdir_civ2,'String',subdir);
2024 if get(handles.CIV1,'Value')==0 
2025     find_netcpair_civ1(hObject, eventdata, handles); %update the list of available pairs from netcdf files in the new directory
2026 end
2027 
2028 %---------------------------------------------------------
2029 % Executes on carriage return on the subdir civ1 edit window
2030 %---------------------------------------------------------
2031 function subdir_civ2_Callback(hObject, eventdata, handles)
2032 %update the list of available pairs from netcdf files in the new directory
2033 if get(handles.CIV2,'Value')==0 & get(handles.CIV1,'Value')==0 & get(handles.FIX1,'Value')==0 & get(handles.PATCH1,'Value')==0
2034     find_netcpair_civ2(hObject, eventdata, handles);
2035 end
2036 
2037 %------------------------------------------------------
2038 % --- Executes on button press in get_mask_civ1.
2039 %------------------------------------------------------
2040 function get_mask_civ1_Callback(hObject, eventdata, handles)
2041 maskval=get(handles.get_mask_civ1,'Value')
2042 if isequal(maskval,0)
2043     set(handles.mask_civ1,'String','')
2044 else
2045 mask_displ='no mask'; %default
2046 filebase=get(handles.displ_filebase,'String');
2047 [ nbslice, flag_mask]=get_mask(filebase,handles)
2048 if isequal(flag_mask,1)
2049       mask_displ=[num2str(nbslice) 'mask'];
2050 end
2051 if get(handles.compare,'Value')==1 & ~isequal(mask_displ,'no mask')% look for the second mask series
2052         filebase_a=get(handles.displ_filebase2,'String');
2053         [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles)
2054         if isequal(flag_mask_a,0) | ~isequal(nbslice_a,nbslice)
2055             mask_displ='no mask';
2056         end
2057 end
2058 if isequal(mask_displ,'no mask')
2059     set(handles.get_mask_civ1,'Value',0)
2060     set(handles.get_mask_fix1,'Value',0)
2061     set(handles.get_mask_civ2,'Value',0)
2062     set(handles.get_mask_fix2,'Value',0)
2063 else
2064     set(handles.get_mask_fix1,'Value',1)
2065     set(handles.get_mask_civ2,'Value',1)
2066     set(handles.get_mask_fix2,'Value',1)
2067 end
2068 set(handles.mask_civ1,'String',mask_displ)
2069 set(handles.mask_fix1,'String',mask_displ)
2070 set(handles.mask_civ2,'String',mask_displ)
2071 set(handles.mask_fix2,'String',mask_displ)
2072 end
2073 %--------------------------------------------------------------
2074 % --- Executes on button press in get_mask_fix1.
2075 function get_mask_fix1_Callback(hObject, eventdata, handles)
2076 maskval=get(handles.get_mask_fix1,'Value')
2077 if isequal(maskval,0)
2078     set(handles.mask_fix1,'String','')
2079 else
2080 mask_displ='no mask'; %default
2081 filebase=get(handles.displ_filebase,'String');
2082 [nbslice, flag_mask]=get_mask(filebase,handles)
2083 if isequal(flag_mask,1)
2084       mask_displ=[num2str(nbslice) 'mask'];
2085 end
2086 if get(handles.compare,'Value')==1 & ~isequal(mask_displ,'no mask')% look for the second mask series
2087         filebase_a=get(handles.displ_filebase2,'String');
2088         [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles)
2089         if isequal(flag_mask_a,0) | ~isequal(nbslice_a,nbslice)
2090             mask_displ='no mask';
2091         end
2092 end
2093 if isequal(mask_displ,'no mask')
2094     set(handles.get_mask_fix1,'Value',0)
2095     set(handles.get_mask_civ2,'Value',0)
2096     set(handles.get_mask_fix2,'Value',0)
2097 else
2098     set(handles.get_mask_civ2,'Value',1)
2099     set(handles.get_mask_fix2,'Value',1)
2100 end 
2101 set(handles.mask_fix1,'String',mask_displ)
2102 set(handles.mask_civ2,'String',mask_displ)
2103 set(handles.mask_fix2,'String',mask_displ)
2104 end
2105 %-----------------------------------------
2106 % --- Executes on button press in get_mask_civ2.
2107 function get_mask_civ2_Callback(hObject, eventdata, handles)
2108 maskval=get(handles.get_mask_civ2,'Value')
2109 if isequal(maskval,0)
2110     set(handles.mask_civ2,'String','')
2111 else
2112 mask_displ='no mask'; %default
2113 filebase=get(handles.displ_filebase,'String');
2114 [nbslice, flag_mask]=get_mask(filebase,handles)
2115 if isequal(flag_mask,1)
2116       mask_displ=[num2str(nbslice) 'mask'];
2117 end
2118 if get(handles.compare,'Value')==1 & ~isequal(mask_displ,'no mask')% look for the second mask series
2119         filebase_a=get(handles.displ_filebase2,'String');
2120         [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles)
2121         if isequal(flag_mask_a,0) | ~isequal(nbslice_a,nbslice)
2122             mask_displ='no mask';
2123         end
2124 end
2125 if isequal(mask_displ,'no mask')
2126     set(handles.get_mask_civ2,'Value',0)
2127     set(handles.get_mask_fix2,'Value',0)
2128 else
2129     set(handles.get_mask_fix2,'Value',1)
2130 end 
2131 set(handles.mask_civ2,'String',mask_displ)
2132 set(handles.mask_fix2,'String',mask_displ)
2133 end
2134 %-------------------------------------
2135 % --- Executes on button press in get_mask_fix2.
2136 function get_mask_fix2_Callback(hObject, eventdata, handles)
2137 maskval=get(handles.get_mask_fix2,'Value')
2138 if isequal(maskval,0)
2139     set(handles.mask_fix2,'String','')
2140 else
2141 mask_displ='no mask'; %default
2142 filebase=get(handles.displ_filebase,'String');
2143 [nbslice, flag_mask]=get_mask(filebase,handles)
2144 if isequal(flag_mask,1)
2145       mask_displ=[num2str(nbslice) 'mask'];
2146 end
2147 if get(handles.compare,'Value')==1 & ~isequal(mask_displ,'no mask')% look for the second mask series
2148         filebase_a=get(handles.displ_filebase2,'String');
2149         [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles)
2150         if isequal(flag_mask_a,0) | ~isequal(nbslice_a,nbslice)
2151             mask_displ='no mask';
2152         end
2153 end
2154 if isequal(mask_displ,'no mask')
2155     set(handles.get_mask_fix2,'Value',0)
2156 end 
2157 set(handles.mask_fix2,'String',mask_displ)
2158 end
2159 
2160 %---------------------------------------
2161 function [nbslice, flag_mask]=get_mask(filebase,handles)
2162 %detect mask files, images with appropriate file base
2163 %[filebase '_' xx 'mask'], xx=nbslice
2164 %flag_mask=1 indicates detection
2165 
2166 flag_mask=0;%default
2167 nbslice=1;
2168 
2169 % subdir=get(handles.subdir_civ1,'String');
2170 [Path,Name]=fileparts(filebase)
2171 currentdir=pwd;
2172 cd(Path);%move in the dir of the root name filebase
2173 maskfiles=dir([Name '_*mask_*.png'])%look for mask files
2174 cd(currentdir);%come back to the current working directory
2175 if isempty(maskfiles)
2176     browse=get(handles.browse_root,'UserData');
2177      varargin{1}='';
2178     [image_name,idetect]=name_generator(filebase,1,1,browse.ext_ima,browse.nom_type_ima);%name of an image
2179     if idetect==1
2180          varargin{1}=image_name;
2181     end
2182     warndlg_uvmat('no mask available, use TOOL menu in the uvmat interface to create it','ERROR')
2183 %     makemask(varargin); %open the makemask interface
2184 else
2185     maskname=maskfiles(1).name;% take the first mask file in the list
2186     [Path2,Name,ext]=fileparts(maskname);
2187     Namedouble=double(Name);
2188     val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
2189     ind_mask=findstr('mask',Name);
2190     i=ind_mask-1;
2191     while val(i)==0 & i>0
2192        i=i-1;
2193     end
2194     nbslice=str2num(Name(i+1:ind_mask-1));
2195     if ~isequal(nbslice,[]) & Name(i)=='_'
2196           flag_mask=1;
2197     else
2198           errordlg(['bad mask file ' Name ext ' found in ' Path2])
2199           return
2200           nbslice=1;
2201     end
2202 end    
2203 %------------------------------
2204 
2205 
2206 function grid_civ1_Callback(hObject, eventdata, handles)
2207 % hObject    handle to grid_civ1 (see GCBO)
2208 % eventdata  reserved - to be defined in a future version of MATLAB
2209 % handles    structure with handles and user data (see GUIDATA)
2210 
2211 % Hints: get(hObject,'String') returns contents of grid_civ1 as text
2212 %        str2double(get(hObject,'String')) returns contents of grid_civ1 as a double
2213 
2214 
2215 %-----------------------------------------------------------
2216 % transform numbers to letters
2217 %--------------------------------------------
2218 function str=num2stra(num,nom_type);
2219 if isequal(nom_type,'png_old') | isequal(nom_type,'netc_old') |isequal(nom_type,'raw_SMD')
2220     str=char(96+num);
2221 elseif isequal(nom_type,'_i')|isequal(nom_type,'_i1-i2')...
2222         |isequal(nom_type,'ima_num')| isequal(nom_type,'avi')| isequal(nom_type,'none')
2223     str='';
2224 else
2225     str=num2str(num);
2226 end
2227 %---------------------------------------------------
2228 function mask_civ1_Callback(hObject, eventdata, handles)
2229 set(handles.mask_civ1,'UserData',[])
2230 set(handles.mask_civ1,'String','')
2231 %----------------------------------------------------
2232 function mask_civ2_Callback(hObject, eventdata, handles)
2233 set(handles.mask_civ2,'UserData',[])
2234 set(handles.mask_civ2,'String','')
2235 %----------------------------------------------------
2236 function mask_fix1_Callback(hObject, eventdata, handles)
2237 set(handles.mask_fix1,'UserData',[])
2238 set(handles.mask_fix1,'String','')
2239 %----------------------------------------------------
2240 function mask_fix2_Callback(hObject, eventdata, handles)
2241 set(handles.mask_fix2,'UserData',[])
2242 set(handles.mask_fix2,'String','')
2243 
2244 %--------------------------------------------------------------------------
2245 % --- Executes on button press in list_subdir_civ1.
2246 function list_subdir_civ1_Callback(hObject, eventdata, handles)
2247 
2248 filebase=get(handles.displ_filebase,'String');
2249 dirinput = uigetdir(filebase)
2250     set(handles.subdir_civ1,'String',dirinput)
2251     set(handles.subdir_civ2,'String',dirinput)
2252 
2253 displ_filebase_Callback(hObject, eventdata, handles);
2254 
2255 
2256 function rho_civ2_Callback(hObject, eventdata, handles)
2257 % hObject    handle to rho_civ2 (see GCBO)
2258 % eventdata  reserved - to be defined in a future version of MATLAB
2259 % handles    structure with handles and user data (see GUIDATA)
2260 
2261 % Hints: get(hObject,'String') returns contents of rho_civ2 as text
2262 %        str2double(get(hObject,'String')) returns contents of rho_civ2 as a double
2263 
2264 %----------------------------------------------
2265 function last_i_Callback(hObject, eventdata, handles)
2266 first_i=str2num(get(handles.first_i,'String'));
2267 last_i=str2num(get(handles.last_i,'String'));
2268 ref_i=ceil((first_i+last_i)/2);
2269 set(handles.ref_i,'String', num2str(ref_i))
2270 ref_i_Callback(hObject, eventdata, handles)
2271 
2272 %-------------------------------------------------------
2273 function last_j_Callback(hObject, eventdata, handles)
2274 first_j=str2num(get(handles.first_j,'String'));
2275 last_j=str2num(get(handles.last_j,'String'));
2276 ref_j=ceil((first_j+last_j)/2);
2277 set(handles.ref_j,'String', num2str(ref_j))
2278 ref_j_Callback(hObject, eventdata, handles)
2279 
2280 %--------------------------------------------------------------------------
2281 % --- Executes on button press in browse_gridciv1.
2282 function browse_gridciv1_Callback(hObject, eventdata, handles)
2283 value=get(handles.browse_gridciv1,'Value');
2284 if value
2285     filebase=get(handles.displ_filebase,'String');
2286     [FileName, PathName, filterindex] = uigetfile( ...
2287            {'*.grid', ' (*.grid)';
2288             '*.grid',  '.grid files '; ...
2289             '*.*', 'All Files (*.*)'}, ...
2290             'Pick a file',filebase);
2291     filegrid=fullfile(PathName,FileName);
2292     if isempty(FileName)|isempty(PathName)|isequal(FileName,0)|~exist(filegrid,'file')
2293         set(handles.browse_gridciv1,'Value',0);
2294         set(handles.grid_civ1,'string','');
2295         set(handles.dx_civ1,'Visible','on');
2296         set(handles.dy_civ1,'Visible','on');
2297         set(handles.grid_civ2,'string','');
2298         if get(handles.CIV2,'Value')
2299             set(handles.dx_civ2,'Visible','on');
2300             set(handles.dy_civ2,'Visible','on');
2301         end
2302     else
2303         set(handles.grid_civ1,'string',filegrid);
2304         set(handles.dx_civ1,'Visible','off');
2305         set(handles.dy_civ1,'Visible','off');
2306         set(handles.grid_civ2,'string',filegrid);
2307         set(handles.dx_civ2,'Visible','off');
2308         set(handles.dy_civ2,'Visible','off');
2309 % set(handles.grid_patch1,'string',filegrid);
2310 % set(handles.grid_patch2,'string',filegrid);
2311     end
2312 else
2313     set(handles.grid_civ1,'string','');
2314     set(handles.dx_civ1,'Visible','on');
2315     set(handles.dy_civ1,'Visible','on');
2316     set(handles.grid_civ2,'string','');
2317     if get(handles.CIV2,'Value')
2318         set(handles.dx_civ2,'Visible','on');
2319         set(handles.dy_civ2,'Visible','on');
2320     end
2321 end
2322 
2323 
2324 
2325 function pxcmx_Callback(hObject, eventdata, handles)
2326 % hObject    handle to pxcmx (see GCBO)
2327 % eventdata  reserved - to be defined in a future version of MATLAB
2328 % handles    structure with handles and user data (see GUIDATA)
2329 
2330 % Hints: get(hObject,'String') returns contents of pxcmx as text
2331 %        str2double(get(hObject,'String')) returns contents of pxcmx as a double
2332 
2333 
2334 
2335 function pxcmy_Callback(hObject, eventdata, handles)
2336 % hObject    handle to pxcmy (see GCBO)
2337 % eventdata  reserved - to be defined in a future version of MATLAB
2338 % handles    structure with handles and user data (see GUIDATA)
2339 
2340 % Hints: get(hObject,'String') returns contents of pxcmy as text
2341 %        str2double(get(hObject,'String')) returns contents of pxcmy as a double
2342 
2343 
2344 % --- Executes on button press in browse_gridciv2.
2345 function browse_gridciv2_Callback(hObject, eventdata, handles)
2346 
2347 filebase=get(handles.displ_filebase,'String');
2348 [FileName, PathName, filterindex] = uigetfile( ...
2349        {'*.grid', ' (*.grid)';
2350         '*.grid',  '.grid files '; ...
2351         '*.*', 'All Files (*.*)'}, ...
2352         'Pick a file',filebase);
2353 filegrid=fullfile(PathName,FileName);
2354 set(handles.grid_civ2,'string',filegrid);
2355 set(handles.dx_civ2,'String',' ');
2356 set(handles.dy_civ2,'String',' ');
2357 % set(handles.grid_patch2,'string',filegrid);
2358 
2359 % --- Executes on button press in get_gridpatch1.
2360 function get_gridpatch1_Callback(hObject, eventdata, handles)
2361 % hObject    handle to get_gridpatch1 (see GCBO)
2362 % eventdata  reserved - to be defined in a future version of MATLAB
2363 % handles    structure with handles and user data (see GUIDATA)
2364 
2365 filebase=get(handles.displ_filebase,'String');
2366 [FileName, PathName, filterindex] = uigetfile( ...
2367        {'*.grid', ' (*.grid)';
2368         '*.grid',  '.grid files '; ...
2369         '*.*', 'All Files (*.*)'}, ...
2370         'Pick a file',filebase);
2371 filegrid=fullfile(PathName,FileName);
2372 set(handles.grid_patch1,'string',filegrid);
2373 % set(handles.grid_patch2,'string',filegrid
2374 
2375 %-----------------------------------------------------------------
2376 % --- Executes on button press in get_gridpatch2.
2377 function get_gridpatch2_Callback(hObject, eventdata, handles)
2378 % hObject    handle to get_gridpatch2 (see GCBO)
2379 % eventdata  reserved - to be defined in a future version of MATLAB
2380 % handles    structure with handles and user data (see GUIDATA)
2381 
2382 
2383 %----------------------------------------------------------
2384 function enable_civ1(handles,state)
2385 if isequal(state,0)
2386     state='off';
2387 end
2388 if isequal(state,1)
2389     state='on';
2390 end
2391 if isequal(state,'on')
2392     set(handles.frame_civ1,'BackgroundColor',[1 1 0])
2393     set(handles.frame_para_civ1,'BackgroundColor',[1 1 0])
2394     set(handles.frame_grid_civ1,'BackgroundColor',[1 1 0])
2395 else
2396     set(handles.frame_civ1,'BackgroundColor',[0.831 0.816 0.784])
2397     set(handles.frame_para_civ1,'BackgroundColor',[0.831 0.816 0.784])
2398     set(handles.frame_grid_civ1,'BackgroundColor',[0.831 0.816 0.784])
2399 end
2400 set(handles.ibx,'Visible',state)
2401 set(handles.iby,'Visible',state)
2402 set(handles.isx,'Visible',state)
2403 set(handles.isy,'Visible',state)
2404 set(handles.shiftx,'Visible',state)
2405 set(handles.shifty,'Visible',state)
2406 set(handles.rho,'Visible',state)
2407 set(handles.dx_civ1,'Visible',state)
2408 set(handles.dy_civ1,'Visible',state)
2409 set(handles.calcul_search,'Visible',state)
2410 set(handles.u_text,'Visible',state)
2411 set(handles.v_text,'Visible',state)
2412 set(handles.min,'Visible',state)
2413 set(handles.max,'Visible',state)
2414 set(handles.umin,'Visible',state)
2415 set(handles.umax,'Visible',state)
2416 set(handles.vmin,'Visible',state)
2417 set(handles.vmax,'Visible',state)
2418 set(handles.grid_civ1,'Visible',state)
2419 set(handles.mask_civ1,'Visible',state)
2420 set(handles.browse_gridciv1,'Visible',state)
2421 set(handles.get_mask_civ1,'Visible',state)
2422 set(handles.parameters,'Visible',state)
2423 set(handles.grid,'Visible',state)
2424 set(handles.dx_civ1,'Visible',state)
2425 set(handles.dy_civ1,'Visible',state)
2426 set(handles.ImaThreshold,'Visible',state)
2427 if isequal(state,'off')
2428     set(handles.MinIma,'Visible','off')
2429     set(handles.MaxIma,'Visible','off')
2430     set(handles.ImaThreshold,'Value',0)
2431 end
2432 set(handles.dx_civ1_title,'Visible',state)
2433 set(handles.dy_civ1_title,'Visible',state)
2434 set(handles.ImaThreshold_title,'Visible',state)
2435 set(handles.ib_title,'Visible',state)
2436 set(handles.is_title,'Visible',state)
2437 set(handles.shift_title,'Visible',state)
2438 set(handles.rho_title,'Visible',state)
2439 
2440 %----------------------------------------------------------
2441 function enable_fix1(handles)
2442 set(handles.frame_fix1,'BackgroundColor',[1 1 0])
2443 set(handles.REMOVE,'Visible','on')
2444 set(handles.vec_Fmin2,'Visible','on')
2445 set(handles.vec_F2,'Visible','on')
2446 set(handles.vec_F3,'Visible','on')
2447 set(handles.thresh_vecC,'Visible','on')
2448 set(handles.thresh_vecC_title,'Visible','on')
2449 set(handles.thresh_vel,'Visible','on')
2450 set(handles.thresh_vel_text,'Visible','on')
2451 set(handles.mask_fix1,'Visible','on')
2452 set(handles.get_mask_fix1,'Visible','on')
2453 set(handles.get_ref_fix1,'Visible','on')
2454 set(handles.ref_fix1,'Visible','on')
2455 set(handles.inf_sup1,'Visible','on')
2456 set(handles.field_ref1,'Visible','on')
2457 
2458 %----------------------------------------------------------
2459 function desable_fix1(handles)
2460 set(handles.frame_fix1,'BackgroundColor',[0.831 0.816 0.784])
2461 set(handles.REMOVE,'Visible','off')
2462 set(handles.vec_Fmin2,'Visible','off')
2463 set(handles.vec_F2,'Visible','off')
2464 set(handles.vec_F3,'Visible','off')
2465 set(handles.thresh_vecC,'Visible','off')
2466 set(handles.thresh_vecC_title,'Visible','off')
2467 set(handles.thresh_vel,'Visible','off')
2468 set(handles.thresh_vel_text,'Visible','off')
2469 set(handles.mask_fix1,'Visible','off')
2470 set(handles.get_mask_fix1,'Visible','off')
2471 set(handles.get_ref_fix1,'Visible','off')
2472 set(handles.ref_fix1,'Visible','off')
2473 set(handles.inf_sup1,'Visible','off')
2474 set(handles.field_ref1,'Visible','off')
2475 
2476 %--------------------------------------------------------------
2477 function enable_patch1(handles)
2478 global patch_new_exe
2479 set(handles.frame_patch1,'BackgroundColor',[1 1 0])
2480 set(handles.rho_patch1,'Visible','on')
2481 set(handles.rho_text1,'Visible','on')
2482 set(handles.thresh_patch1,'Visible','on')
2483 set(handles.thresh_text1,'Visible','on')
2484 set(handles.subdomain_patch1,'Visible','on')
2485 set(handles.subdomain_text1,'Visible','on')
2486 set(handles.nx_patch1,'Visible','on')
2487 set(handles.ny_patch1,'Visible','on')
2488 set(handles.nx_patch1_title,'Visible','on')
2489 set(handles.ny_patch1_title,'Visible','on')
2490 if (~isequal(patch_new_exe,[]) & ~isequal(patch_new_exe,[]))
2491     set(handles.test_interp,'Visible','on');
2492 end
2493 set(handles.get_gridpatch1,'Visible','on')
2494 set(handles.grid_patch1,'string','none');
2495 set(handles.grid_patch1,'Visible','on')
2496 
2497 %--------------------------------------------------------------
2498 function desable_patch1(handles)
2499 set(handles.frame_patch1,'BackgroundColor',[0.831 0.816 0.784])
2500 set(handles.rho_patch1,'Visible','off')
2501 set(handles.rho_text1,'Visible','off')
2502 set(handles.thresh_patch1,'Visible','off')
2503 set(handles.thresh_text1,'Visible','off')
2504 set(handles.subdomain_patch1,'Visible','off')
2505 set(handles.subdomain_text1,'Visible','off')
2506 set(handles.nx_patch1,'Visible','off')
2507 set(handles.ny_patch1,'Visible','off')
2508 set(handles.nx_patch1_title,'Visible','off')
2509 set(handles.ny_patch1_title,'Visible','off')
2510 set(handles.test_interp,'Visible','off')
2511 set(handles.get_gridpatch1,'Visible','off')
2512 set(handles.grid_patch1,'Visible','off')
2513 
2514 %----------------------------------------------------------
2515 function enable_civ2(handles,state)
2516 if isequal(state,0)
2517     state='off';
2518 end
2519 if isequal(state,1)
2520     state='on';
2521 end
2522 if isequal(state,'on')
2523     set(handles.frame_civ2,'BackgroundColor',[1 1 0])
2524     set(handles.frame_para_civ2,'BackgroundColor',[1 1 0])
2525     set(handles.frame_grid_civ2,'BackgroundColor',[1 1 0])
2526     set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
2527 else
2528     set(handles.frame_civ2,'BackgroundColor',[0.831 0.816 0.784])
2529     set(handles.frame_para_civ2,'BackgroundColor',[0.831 0.816 0.784])
2530     set(handles.frame_grid_civ2,'BackgroundColor',[0.831 0.816 0.784])
2531     set(handles.frame_subdirciv2,'BackgroundColor',[0.831 0.816 0.784])
2532 end
2533 set(handles.ibx_civ2,'Visible',state)
2534 set(handles.iby_civ2,'Visible',state)
2535 set(handles.decimal,'Visible',state)
2536 set(handles.deformation,'Visible',state)
2537 set(handles.rho_civ2,'Visible',state)
2538 set(handles.dx_civ2,'Visible',state)
2539 set(handles.dy_civ2,'Visible',state)
2540 set(handles.browse_gridciv2,'Visible',state)
2541 set(handles.get_mask_civ2,'Visible',state)
2542 set(handles.parameters,'Visible',state)
2543 set(handles.grid,'Visible',state)
2544 set(handles.parameters_text,'Visible',state)
2545 set(handles.grid_text,'Visible',state)
2546 set(handles.grid_civ2,'Visible',state)
2547 set(handles.mask_civ2,'Visible',state)
2548 set(handles.dx_civ2_title,'Visible',state)
2549 set(handles.dy_civ2_title,'Visible',state)
2550 set(handles.ibx_civ2_text,'Visible',state)
2551 set(handles.rho_civ2_title,'Visible',state)
2552 set(handles.ImaThreshold2,'Visible',state)
2553 set(handles.ImaThreshold_title2,'Visible',state)
2554 if isequal(state,'off')
2555     set(handles.MinIma2,'Visible','off')
2556     set(handles.MaxIma2,'Visible','off')
2557     set(handles.ImaThreshold2,'Value',0)
2558     if isequal(get(handles.FIX2,'Value'),0) & isequal(get(handles.PATCH2,'Value'),0) 
2559         set(handles.list_pair_civ2,'Visible','off')
2560         set(handles.subdir_civ2,'Visible','off')
2561         set(handles.subdir_civ2_text,'Visible','off')
2562     end
2563 else
2564     set(handles.list_pair_civ2,'Visible','on')
2565     set(handles.subdir_civ2,'Visible','on')
2566     set(handles.subdir_civ2_text,'Visible','on')
2567 end
2568 
2569 %----------------------------------------------------------
2570 % function desable_civ2(handles)
2571 % set(handles.frame_civ2,'BackgroundColor',[0.831 0.816 0.784])
2572 % set(handles.frame_para_civ2,'BackgroundColor',[0.831 0.816 0.784])
2573 % set(handles.frame_grid_civ2,'BackgroundColor',[0.831 0.816 0.784])
2574 % set(handles.ibx_civ2,'Visible','off')
2575 % set(handles.iby_civ2,'Visible','off')
2576 % set(handles.decimal,'Visible','off')
2577 % set(handles.deformation,'Visible','off')
2578 % set(handles.rho_civ2,'Visible','off')
2579 % set(handles.dx_civ2,'Visible','off')
2580 % set(handles.dy_civ2,'Visible','off')
2581 % set(handles.browse_gridciv2,'Visible','off')
2582 % set(handles.get_mask_civ2,'Visible','off')
2583 % set(handles.parameters,'Visible','off')
2584 % set(handles.grid,'Visible','off')
2585 % set(handles.grid,'Visible','on')
2586 % set(handles.parameters_text,'Visible','off')
2587 % set(handles.grid_text,'Visible','off')
2588 % set(handles.grid_civ2,'Visible','off')
2589 % set(handles.mask_civ2,'Visible','off')
2590 % set(handles.dx_civ2_title,'Visible','off')
2591 % set(handles.dy_civ2_title,'Visible','off')
2592 % set(handles.ibx_civ2_text,'Visible','off')
2593 % set(handles.rho_civ2_title,'Visible','off')
2594 % set(handles.frame_subdirciv2,'BackgroundColor',[0.831 0.816 0.784])
2595 % if isequal(get(handles.FIX2,'Value'),0) & isequal(get(handles.PATCH2,'Value'),0)
2596 %     set(handles.list_pair_civ2,'Visible','off')
2597 %     set(handles.subdir_civ2,'Visible','off')
2598 %     set(handles.subdir_civ2_text,'Visible','off')
2599 % end
2600 
2601 %----------------------------------------------------------
2602 function enable_fix2(handles)
2603 set(handles.frame_fix2,'BackgroundColor',[1 1 0])
2604 set(handles.REMOVE2,'Visible','on')
2605 set(handles.vec_Fmin2_2,'Visible','on')
2606 set(handles.vec_F4,'Visible','on')
2607 set(handles.vec_F3_2,'Visible','on')
2608 set(handles.thresh_vec2C,'Visible','on')
2609 set(handles.thresh_vec2C_text,'Visible','on')
2610 set(handles.thresh_vel2,'Visible','on')
2611 set(handles.thresh_vel2_text,'Visible','on')
2612 set(handles.mask_fix2,'Visible','on')
2613 set(handles.get_mask_fix2,'Visible','on')
2614 set(handles.list_pair_civ2,'Visible','on')
2615 set(handles.subdir_civ2,'Visible','on')
2616 set(handles.subdir_civ2_text,'Visible','on')
2617 set(handles.get_ref_fix2,'Visible','on')
2618 set(handles.ref_fix2,'Visible','on')
2619 set(handles.inf_sup2,'Visible','on')
2620 set(handles.field_ref2,'Visible','on')
2621 
2622 %----------------------------------------------------------
2623 function desable_fix2(handles)
2624 set(handles.frame_fix2,'BackgroundColor',[0.831 0.816 0.784])
2625 set(handles.REMOVE2,'Visible','off')
2626 set(handles.vec_Fmin2_2,'Visible','off')
2627 set(handles.vec_F4,'Visible','off')
2628 set(handles.vec_F3_2,'Visible','off')
2629 set(handles.thresh_vec2C,'Visible','off')
2630 set(handles.thresh_vec2C_text,'Visible','off')
2631 set(handles.thresh_vel2,'Visible','off')
2632 set(handles.thresh_vel2_text,'Visible','off')
2633 set(handles.mask_fix2,'Visible','off')
2634 set(handles.get_mask_fix2,'Visible','off')
2635 set(handles.get_ref_fix2,'Visible','off')
2636 set(handles.ref_fix2,'Visible','off')
2637 set(handles.inf_sup2,'Visible','off')
2638 set(handles.field_ref2,'Visible','off')
2639 if isequal(get(handles.CIV2,'Value'),0) & isequal(get(handles.PATCH2,'Value'),0) 
2640     set(handles.list_pair_civ2,'Visible','off')
2641     set(handles.subdir_civ2,'Visible','off')
2642     set(handles.subdir_civ2_text,'Visible','off')
2643 end
2644 
2645 %--------------------------------------------------------------
2646 function enable_patch2(handles)
2647 set(handles.frame_patch2,'BackgroundColor',[1 1 0])
2648 set(handles.rho_patch2,'Visible','on')
2649 set(handles.rho_text2,'Visible','on')
2650 set(handles.thresh_patch2,'Visible','on')
2651 set(handles.thresh_text2,'Visible','on')
2652 set(handles.subdomain_patch2,'Visible','on')
2653 set(handles.subdomain_text2,'Visible','on')
2654 set(handles.nx_patch2,'Visible','on')
2655 set(handles.ny_patch2,'Visible','on')
2656 set(handles.nx_patch2_title,'Visible','on')
2657 set(handles.ny_patch2_title,'Visible','on')
2658 set(handles.get_gridpatch2,'Visible','on')
2659 set(handles.grid_patch2,'Visible','on')
2660 set(handles.list_pair_civ2,'Visible','on')
2661 set(handles.subdir_civ2,'Visible','on')
2662 set(handles.subdir_civ2_text,'Visible','on')
2663 
2664 %--------------------------------------------------------------
2665 function desable_patch2(handles)
2666 set(handles.frame_patch2,'BackgroundColor',[0.831 0.816 0.784])
2667 set(handles.rho_patch2,'Visible','off')
2668 set(handles.rho_text2,'Visible','off')
2669 set(handles.thresh_patch2,'Visible','off')
2670 set(handles.thresh_text2,'Visible','off')
2671 set(handles.subdomain_patch2,'Visible','off')
2672 set(handles.subdomain_text2,'Visible','off')
2673 set(handles.nx_patch2,'Visible','off')
2674 set(handles.ny_patch2,'Visible','off')
2675 set(handles.nx_patch2_title,'Visible','off')
2676 set(handles.ny_patch2_title,'Visible','off')
2677 set(handles.get_gridpatch2,'Visible','off')
2678 set(handles.grid_patch2,'Visible','off')
2679 if isequal(get(handles.CIV2,'Value'),0) & isequal(get(handles.FIX2,'Value'),0) 
2680     set(handles.list_pair_civ2,'Visible','off')
2681     set(handles.subdir_civ2,'Visible','off')
2682     set(handles.subdir_civ2_text,'Visible','off')
2683 end
2684 
2685 % --- Executes on button press in test_interp.
2686 function test_interp_Callback(hObject, eventdata, handles)
2687 
2688 
2689 %------------------------------------------------
2690 %Read the parameters for civ1 on the interface
2691 %--------------------------------------------------
2692 function par=read_param_civ1(handles,file_ima)
2693 
2694 ibx_val=str2num(get(handles.ibx,'String'));
2695 par.correlationBoxesSize_X=num2str(ibx_val);
2696 iby_val=str2num(get(handles.iby,'String'));
2697 par.correlationBoxesSize_Y=num2str(iby_val);
2698 ibz_val=str2num(get(handles.ibz,'String'));
2699 par.correlationBoxesSize_Z=num2str(ibz_val);
2700 isx=get(handles.isx,'String');
2701 if isempty(str2num(isx)), isx='41'; set(handles.isx,'String','41'), end; %default
2702 maxDisplacement_X=floor((str2num(isx)-ibx_val)/2);
2703 par.maxDisplacement_X=num2str(maxDisplacement_X);
2704 isy=get(handles.isy,'String');
2705 if isempty(str2num(isy)), isy='41'; set(handles.isy,'String','41'), end; %default
2706 maxDisplacement_Y=floor((str2num(isy)-iby_val)/2);
2707 par.maxDisplacement_Y=num2str(maxDisplacement_Y);
2708 isz=get(handles.isz,'String');
2709 if isempty(str2num(isz)), isz='41'; set(handles.isz,'String','41'), end; %default
2710 maxDisplacement_Z=floor((str2num(isz)-ibz_val)/2);
2711 par.maxDisplacement_Z=num2str(maxDisplacement_Z);
2712 %      par.rho=get(handles.rho,'String');
2713 par.gridSpacing_X=get(handles.dx_civ1,'String');
2714 par.gridSpacing_Y=get(handles.dy_civ1,'String');
2715 par.gridSpacing_Z=get(handles.dz_civ1,'String');
2716 % Zmin=str2num(get(handles.first_j,'String'))-1;
2717 Zmax=str2num(get(handles.nb_field2,'String'));
2718 par.gridLimits_Xmin=0;
2719 par.gridLimits_Ymin=0;
2720 par.gridLimits_Zmin=0;
2721 % A=imread(file_ima);%read the first image to get the size
2722 %sizim=size(A);
2723 par.gridLimits_Xmax=1024;%num2str(sizim(2));
2724 par.gridLimits_Ymax=1024;%num2str(sizim(1));
2725 par.gridLimits_Zmax=Zmax;
2726 par.grid='grille';
2727 par.grid_division=4;
2728 par.hart=0;
2729 par.ratioHoverZ=1;
2730 
2731 %
2732 % %----------------------------------------------------------------
2733 % function par=read_param_civ2(handles,file_ima)
2734 %     par.ibx=get(handles.ibx_civ2,'String');
2735 %     par.iby=get(handles.iby_civ2,'String');
2736 %     par.rho=get(handles.rho_civ2,'String');
2737 %     par.decimal=int2str(get(handles.decimal,'Value'));
2738 %     par.deformation=int2str(get(handles.deformation,'Value'));
2739 %     par.dx=get(handles.dx_civ2,'String');
2740 %     par.dy=get(handles.dy_civ2,'String');
2741 %     if isequal(str2num(par.dx),[])
2742 %          if isempty(get(handles.grid_civ2,'String'));
2743 %              par.dx='0'; %just read by civ_3D program, not used
2744 %          else
2745 %             par.dx='20';%default
2746 %             set(handles.dx_civ2,'String','20');
2747 %          end
2748 %      end
2749 %      if isequal(str2num(par.dy),[])
2750 %          if isempty(get(handles.grid_civ2,'String'));
2751 %              par.dy='0';%just read by civ_3D program, not used
2752 %          else
2753 %             par.dy='20';%default
2754 %             set(handles.dy_civ2,'String','20');
2755 %          end
2756 %      end
2757 %     par.pxcmx=get(handles.pxcmx,'String');
2758 %     par.pxcmy=get(handles.pxcmy,'String');
2759 %     if isempty(str2num(par.pxcmx)) |isempty(str2num(par.pxcmy))
2760 %         par.pxcmx='1';
2761 %          par.pxcmy='1';
2762 %     end
2763 % %     par.npx=get(handles.pxcmx,'UserData');
2764 % %     par.npy=get(handles.pxcmy,'UserData');
2765 %     A=imread(file_ima);%read the first image to get the size
2766 %     sizim=size(A);
2767 %     par.npx=num2str(sizim(2));
2768 %     par.npy=num2str(sizim(1));
2769 %     time=get(handles.displ_filebase,'UserData'); %get the set of times
2770 %     par.gridname=get(handles.grid_civ2,'String');
2771 %     par.gridflag='y';
2772 %     if isequal(par.gridname,'')| isempty(par.gridname)
2773 %         par.gridname='nogrid';
2774 %         par.gridflag='n';
2775 %     end
2776 
2777 
2778 %---------------------------------------------------------
2779 %CIV1  CIV1  CIV1 CIV1
2780 %----------------------------------------------------------
2781 function cmd_CIV1=BATCH_CIV1(filename,namelog,par,handles)
2782 %pixels per cm and matrix of the image times, read from the .civ_3D file by uvmat
2783 global civ1_exe Civ_exe sge%name of the executable for civ1 calculation
2784 
2785 %changes : filename_cmx -> filename ( no extension )
2786 
2787             if isequal(par.Dt,'0')
2788                 par.Dt='1' ;%case of 'displacement' mode
2789             end         
2790  
2791     textcmx={'##############   CMX file';...
2792     ['FirstImage ' par.filename_ima_a];...
2793     ['LastImage  ' par.filename_ima_b];...
2794     'XX' ;...
2795     ['Mask ' par.maskflag] ;...
2796     ['MaskName ' par.maskname];...
2797     ['ImageSize ' par.npx ' ' par.npy];...   %VERIFIER CAS GENERAL ?
2798     ['CorrelationBoxesSize ' par.ibx ' ' par.iby];...
2799     ['SearchBoxeSize ' par.isx ' ' par.isy];...
2800     ['RO ' par.rho];...
2801     ['GridSpacing ' par.dx ' ' par.dy];...
2802     'XX 1.0';...
2803     ['Dt_TO ' par.Dt ' ' par.T0];...
2804     ['PixCmXY ' par.pxcmx ' ' par.pxcmy];...
2805     'XX 1';...
2806     ['ShiftXY ' par.shiftx ' '  par.shifty];...
2807     ['Grid ' par.gridflag];...
2808     ['GridName ' par.gridname] ;...
2809     'XX 85';...
2810     'XX 1.0';...
2811     'XX 1.0';...
2812     'Hart 1';...
2813     'DecimalShift 0';...
2814     'Deformation 0';...
2815     'CorrelationMin 0';...
2816     'IntensityMin 0';...
2817     'SeuilImage n';...
2818     'SeuilImageValues 0 4096';...
2819     ['ImageToUse ' par.term_a ' ' par.term_b];... % VERIFIER ?
2820     'ImageUsedBefore null null'};
2821 
2822             textout=char(textcmx);
2823     %         timeL1=clock;
2824             dlmwrite([filename '.cmx'],textout,'');
2825     %             timeL2=clock;
2826     %     timciv1=etime(timeL2,timeL1)
2827           if sge  
2828           cmd_CIV1=[civ1_exe ' -f ' filename '.cmx' ]; % redirect standard output to the log file
2829           else
2830               cmd_CIV1=[civ1_exe ' -f ' filename_cmx ' > ' namelog ' 2>&1']; % redirect standard output to the log file
2831           end
2832     if(isunix)
2833         [Rootbat,Filebat,extbat]=fileparts(namelog);
2834         ncName=fullfile(Rootbat,[ Filebat '.nc']);
2835         cmd_CIV1=char({cmd_CIV1 ; ['mv ' namelog  ' ' namelog '.civ1.log'];['chmod g+w ' ncName]});
2836     else
2837         cmd_CIV1=char({cmd_CIV1 ; ['copy /Y ' namelog ' ' namelog '.civ1.log']});
2838     end
2839 
2840 %---------------------------------------------------------
2841 %CIV1  Unified
2842 %----------------------------------------------------------
2843 function xml_civ1_parameters=BATCH_CIV1_Unified(filename,namelog,par,handles)
2844 %pixels per cm and matrix of the image times, read from the .civ_3D file by uvmat
2845 global civ1_exe Civ_exe%name of the executable for civ1 calculation
2846 
2847     civ1.image1=par.filename_ima_a;
2848     civ1.image2=par.filename_ima_b;
2849     civ1.imageSize_X=par.npx; 
2850     civ1.imageSize_Y=par.npy;
2851     civ1.outputFileName=[filename '.nc'];
2852     civ1.correlationBoxesSize_X=par.ibx;
2853     civ1.correlationBoxesSize_Y=par.iby;
2854     civ1.searchBoxesSize_X=par.isx;
2855     civ1.searchBoxesSize_Y=par.isy;
2856     civ1.globalShift_X=par.shiftx;
2857     civ1.globalShift_Y=par.shifty;
2858     civ1.ro=par.rho;
2859     civ1.hart='y';
2860     if isequal(par.gridflag,'y')
2861         civ1.grid=par.gridname;
2862     end
2863     civ1.gridSpacing_X=par.dx;
2864     civ1.gridSpacing_Y=par.dy;
2865     if isequal(par.maskflag,'y')
2866         civ1.mask=par.maskname;
2867     end
2868     civ1.dt=par.Dt;
2869     civ1.unit='pixel';
2870     civ1.absolut_time_T0=par.T0;
2871     civ1.pixcmx=par.pxcmx;
2872     civ1.pixcmy=par.pxcmy;
2873     civ1.convectFlow='n';
2874   
2875     xml_civ1_parameters=civ1;
2876    
2877 %---------------------------------------------------------
2878 %CIV2  CIV2  CIV2 CIV2
2879 %----------------------------------------------------------
2880 function cmd_CIV2=BATCH_CIV2(filename_cmx,namelog,par)
2881 %pixels per cm and matrix of the image times, read from the .civ_3D file by uvmat
2882 global civ2_exe sge%name of the executable for civ1 calculation
2883    if isequal(par.Dt,'0')
2884                 par.Dt='1' ;%case of 'displacement' mode
2885   end 
2886 textcmx={'##############   CMX file';...
2887 ['FirstImage ' par.filename_ima_a];...
2888 ['LastImage  ' par.filename_ima_b];...
2889 'XX' ;...
2890 ['Mask ' par.maskflag];...
2891 ['MaskName ' par.maskname];...
2892 ['ImageSize ' par.npx ' ' par.npy];...   
2893 ['CorrelationBoxesSize ' par.ibx ' ' par.iby];...
2894 ['SearchBoxeSize ' par.ibx ' ' par.iby];...
2895 ['RO ' par.rho];...
2896 ['GridSpacing ' par.dx ' ' par.dy];...
2897 'XX 1.0';...
2898 ['Dt_TO ' par.Dt ' ' par.T0];...
2899 ['PixCmXY ' par.pxcmx ' ' par.pxcmy];...
2900 'XX 1';...
2901 ['ShiftXY 0 0'];...
2902 ['Grid ' par.gridflag];...
2903 ['GridName ' par.gridname];...
2904 'XX 85';...
2905 'XX 1.0';...
2906 'XX 1.0';...
2907 'Hart 1';...
2908 ['DecimalShift ' par.decimal];...
2909 ['Deformation ' par.deformation];...
2910 'CorrelationMin 0';...
2911 'IntensityMin 0';...
2912 'SeuilImage n';...
2913 'SeuilImageValues 0 4096';...
2914 ['ImageToUse ' par.term_a ' ' par.term_b];... % VERIFIER ?
2915 ['ImageUsedBefore ' par.filename_nc1]};
2916         textout=char(textcmx);
2917         dlmwrite([filename_cmx '2'] ,textout,'');
2918         if sge
2919         cmd_CIV2=[civ2_exe ' -f ' filename_cmx ]; % redirect standard output to the log file
2920         else
2921           cmd_CIV2=[civ2_exe ' -f ' filename_cmx ' > ' namelog ' 2>&1']; % redirect standard output to the log file
2922       end
2923 
2924 
2925 % --- Executes on button press in HELP.
2926 function HELP_Callback(hObject, eventdata, handles)
2927 path_to_uvmat=which ('uvmat');% check the path of uvmat
2928 pathelp=fileparts(path_to_uvmat);
2929 helpfile=fullfile(pathelp,'UVMAT_DOC','uvmat_doc.html');
2930 if isempty(dir(helpfile)), errordlg('Please put the help file uvmat_doc.html in the directory UVMAT/UVMAT_DOC')
2931 else
2932 web([helpfile '#civ_3D'])    
2933 end
2934 
2935 
2936 %----------------------------------------------------------
2937 %--read images and convert them to the uint16 format used for PIV
2938 function A=read_image(filename,nom_type,npx,npy,num);
2939 %npx, npy are the dimensions needed for the raw SMD images
2940 %num is the view number needed for an avi movie
2941 if isequal(nom_type,'avi')
2942     mov=aviread(filename,num);
2943     A=frame2im(mov(1));
2944     A=sum(double(A),3);
2945     A=uint16(A);
2946 elseif isequal(nom_type,'raw_SMD')
2947     [fid,message]=fopen(filename,'r');    
2948     B=fread(fid,Inf,'int16',0,'ieee-le');%read 16 bit binary file
2949     A=(reshape(B,npx,npy))'; %remplissage ligne par ligne avec une matrice colonne ? transposer(uB) pour avoir une matrice ligne
2950     A=uint16(A);
2951     fclose(fid);
2952 else
2953     A=imread(filename);
2954     siz=size(A);
2955     if length(siz)==3;%color images
2956         A=sum(double(A),3);
2957     end
2958     A=uint16(A);
2959 end
2960         
2961 %----------------------------------------------------------------
2962 %Executes on carriage return on the time interval dt
2963 %----------------------------------------------------------------
2964 function dt_Callback(hObject, eventdata, handles)
2965 %determine the set of times and possible intervals for CIV_3D
2966 %                 answer=inputdlg('time interval between images?');
2967                 dt=(1/1000)*str2num(get(handles.dt,'String'));
2968                 nbfield=str2num(get(handles.nb_field,'String')); %last image number selected in the processing series
2969                 time=(dt*[0:nbfield-1])';
2970 %                 set(handles.incr_i,'UserData',dt);%store the time interval between successive images
2971                 set(handles.displ_filebase,'UserData',time); %store the set of times
2972                 for index=1:min(nbfield-1,200)
2973                     displ_num(1,index)=1;
2974                     displ_num(2,index)=1;
2975                     displ_num(3,index)=-floor(index/2);
2976                     displ_num(4,index)=ceil(index/2);
2977                 end
2978 set(handles.list_pair_civ1,'Value',1);
2979 set(handles.list_pair_civ1,'UserData',displ_num);
2980 set(handles.list_pair_civ2,'Value',1);
2981 %update the list of time intervals
2982 find_netcpair_civ1(hObject, eventdata, handles)
2983 find_netcpair_civ2(hObject, eventdata, handles)
2984 
2985 %-------------------------------------------------------
2986 function ref_i_Callback(hObject, eventdata, handles)
2987 mode_list=get(handles.mode,'String');
2988 mode_value=get(handles.mode,'Value');
2989 mode=mode_list{mode_value};
2990 if isequal(get(handles.CIV1,'Value'),0)| isequal(mode,'series(Di)') 
2991     find_netcpair_civ1(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files
2992 end
2993 if isequal(mode,'series(Di)') | ...% we do patch2 only
2994    (get(handles.CIV2,'Value')==0 & get(handles.CIV1,'Value')==0 & get(handles.FIX1,'Value')==0 & get(handles.PATCH1,'Value')==0)
2995     find_netcpair_civ2(hObject, eventdata, handles);
2996 end
2997 
2998 %----------------------------------------------------
2999 function ref_j_Callback(hObject, eventdata, handles)
3000 mode_list=get(handles.mode,'String');
3001 mode_value=get(handles.mode,'Value');
3002 mode=mode_list{mode_value};
3003 if isequal(get(handles.CIV1,'Value'),0)| isequal(mode,'series(Dj)') 
3004     find_netcpair_civ1(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files
3005 end
3006 if isequal(mode,'series(Dj)') | ...
3007    (get(handles.CIV2,'Value')==0 & get(handles.CIV1,'Value')==0 & get(handles.FIX1,'Value')==0 & get(handles.PATCH1,'Value')==0)
3008     find_netcpair_civ2(hObject, eventdata, handles);
3009 end
3010 %----------------------------------------------------
3011 % --- Executes on button press in compare.
3012 function compare_Callback(hObject, eventdata, handles)
3013 test=get(handles.compare,'Value');
3014 if test
3015     filebase=get(handles.displ_filebase,'String');
3016     browse=get(handles.browse_root,'Userdata');
3017     browse.nom_type_ima1=browse.nom_type_ima;
3018     set(handles.browse_root,'UserData',browse);
3019     set(handles.displ_filebase2,'Visible','On');%mkes the second file input window visible
3020     set(handles.displ_filebase2,'String',filebase);
3021     mode_store=get(handles.mode,'String');%get the present 'mode'
3022     set(handles.compare,'UserData',mode_store);%store the mode display
3023     set(handles.mode,'Value',1)
3024     set(handles.mode,'String',{'displacement';'st_pair j1-j2'})
3025 else
3026     set(handles.displ_filebase2,'Visible','Off');
3027     set(handles.displ_filebase2,'String',[]);
3028     mode_store=get(handles.compare,'UserData');
3029     set(handles.mode,'String',mode_store)
3030     set(handles.test_stereo1,'Value',0)
3031     set(handles.test_stereo2,'Value',0)
3032 end
3033 mode_Callback(hObject, eventdata, handles)
3034 
3035 %-----------------------------------------------------------
3036 % --- Executes on button press in get_ref_fix1.
3037 function get_ref_fix1_Callback(hObject, eventdata, handles)
3038 filebase=get(handles.displ_filebase,'String');
3039 [FileName, PathName, filterindex] = uigetfile( ...
3040        {'*.nc', ' (*.nc)';
3041         '*.nc',  'netcdf files '; ...
3042         '*.*', 'All Files (*.*)'}, ...
3043         'Pick a file',filebase);
3044     
3045 fileinput=[PathName FileName];
3046 sizf=size(fileinput);
3047 if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
3048 %[filebasesub,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
3049 [Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
3050 %filebase=fullfile(RootPath,RootFile);
3051 % [Pth,FileN]=fileparts(filebasesub);
3052 % Pth=fileparts(Pth);
3053 ref.filebase=fullfile(Path,File);
3054 ref.num_a=stra2num(str_a);
3055 ref.num_b=stra2num(str_b);
3056 ref.num1=str2num(field_count);
3057 ref.num2=str2num(str2);
3058 browse=[];%initialisation
3059 if ~isequal(ref.ext,'.nc')
3060     errordlg('the reference file must be in netcdf format (*.nc)')
3061     return
3062 end
3063 % [path,name]=fileparts(ref.filebase);
3064 set(handles.ref_fix1,'String',[fullfile(ref.subdir,File) '....nc']);
3065 set(handles.ref_fix1,'UserData',ref)
3066 menu_field{1}='civ1';
3067 Data=nc2struct(fileinput,[]);
3068 if isfield(Data,'patch') & isequal(Data.patch,1)
3069     menu_field{2}='filter1';
3070 end
3071 if isfield(Data,'civ2') & isequal(Data.civ2,1)
3072     menu_field{3}='civ2';
3073 end
3074 if isfield(Data,'patch2') & isequal(Data.patch2,1)
3075     menu_field{4}='filter2';
3076 end
3077 % [cte_detect,vdt,cte_read]=read_netcdf(fileinput,{'patch','civ2','patch2'});
3078 % if isequal(cte_detect(1),1) & isequal(cte_read(1),1)
3079 %          menu_field{2}='filter1';
3080 % end
3081 % if isequal(cte_detect(2),1) & isequal(cte_read(2),1)
3082 %          menu_field{3}='civ2';
3083 % end
3084 % if isequal(cte_detect(3),1) & isequal(cte_read(3),1)
3085 %          menu_field{4}='filter2';
3086 % end
3087 set(handles.field_ref1,'String',menu_field);
3088 set(handles.field_ref1,'Value',length(menu_field));
3089 set(handles.inf_sup1,'Value',2);
3090 set(handles.thresh_vel,'String','1');%default threshold
3091 set(handles.ref_fix1,'Enable','on')
3092  
3093 %---------------------------------------------------------------
3094 % --- Executes on button press in get_ref_fix2.
3095 function get_ref_fix2_Callback(hObject, eventdata, handles)
3096 if isequal(get(handles.get_ref_fix2,'Value'),1)
3097     filebase=get(handles.displ_filebase,'String');
3098     [FileName, PathName, filterindex] = uigetfile( ...
3099            {'*.nc', ' (*.nc)';
3100             '*.nc',  'netcdf files '; ...
3101             '*.*', 'All Files (*.*)'}, ...
3102             'Pick a file',filebase);
3103     fileinput=[PathName FileName];
3104     sizf=size(fileinput);
3105     if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
3106     %[filebasesub,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
3107     [Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
3108 %     [Pth,FileN]=fileparts(filebasesub);
3109 %     Pth=fileparts(Pth);
3110     ref.filebase=fullfile(Path,File)
3111     ref.num_a=stra2num(str_a);
3112     ref.num_b=stra2num(str_b);
3113     ref.num1=str2num(field_count);
3114     ref.num2=str2num(str2);
3115     browse=[];%initialisation
3116     if ~isequal(ref.ext,'.nc')
3117         errordlg('the reference file must be in netcdf format (*.nc)')
3118         return
3119     end
3120 %     [path,name]=fileparts(ref.filebase);
3121     set(handles.ref_fix2,'String',[fullfile(ref.subdir,File) '....nc']);
3122     set(handles.ref_fix2,'UserData',ref)    
3123     menu_field{1}='civ1';
3124 %     [cte_detect,vdt,cte_read]=read_netcdf(fileinput,{'patch','civ2','patch2'});
3125     Data=nc2struct(fileinput,[]);
3126     if isfield(Data,'patch') & isequal(Data.patch,1)
3127         menu_field{2}='filter1';
3128     end
3129     if isfield(Data,'civ2') & isequal(Data.civ2,1)
3130         menu_field{3}='civ2';
3131     end
3132     if isfield(Data,'patch2') & isequal(Data.patch2,1)
3133         menu_field{4}='filter2';
3134     end
3135 
3136 %     if isequal(cte_detect(1),1) & isequal(cte_read(1),1)
3137 %              menu_field{2}='filter1';
3138 %     end
3139 %     if isequal(cte_detect(2),1) & isequal(cte_read(2),1)
3140 %              menu_field{3}='civ2';
3141 %     end
3142 %     if isequal(cte_detect(3),1) & isequal(cte_read(3),1)
3143 %              menu_field{4}='filter2';
3144 %     end
3145     set(handles.field_ref2,'String',menu_field);
3146     set(handles.field_ref2,'Value',length(menu_field));
3147     set(handles.inf_sup2,'Value',2);
3148     set(handles.thresh_vel2,'String','1');%default threshold
3149     set(handles.ref_fix2,'Enable','on')
3150     set(handles.ref_fix2,'Visible','on')
3151     set(handles.field_ref2,'Visible','on')
3152 else
3153     set(handles.ref_fix2,'Visible','off')
3154     set(handles.field_ref2,'Visible','off')
3155 end
3156 %-------------------------------------------------------
3157 
3158 function ref_fix1_Callback(hObject, eventdata, handles)
3159     set(handles.inf_sup1,'Value',1);
3160     set(handles.field_ref1,'Value',1)
3161     set(handles.field_ref1,'String',{' '})
3162     set(handles.ref_fix1,'UserData',[]);
3163     set(handles.ref_fix1,'String','');
3164     set(handles.thresh_vel1,'String','0');
3165  
3166 
3167 %------------------------------------------------------
3168 
3169 function ref_fix2_Callback(hObject, eventdata, handles)
3170     set(handles.inf_sup2,'Value',1);
3171     set(handles.field_ref2,'Value',1)
3172     set(handles.field_ref2,'String',{' '})
3173     set(handles.ref_fix2,'UserData',[]);
3174     set(handles.ref_fix2,'String','');
3175     set(handles.thresh_vel2,'String','0');
3176 
3177 %--------------------------------------------------------
3178 % --- Executes on selection change in inf_sup1.
3179 function inf_sup1_Callback(hObject, eventdata, handles)
3180 
3181 %--------------------------------------------------------------------------
3182 
3183 
3184 % --- Executes on selection change in field_ref.
3185 function field_ref_Callback(hObject, eventdata, handles)
3186 
3187 %-------------------------------------------------------------------------
3188 
3189 % --- Executes on selection change in field_ref2.
3190 function field_ref2_Callback(hObject, eventdata, handles)
3191 
3192 % -----------------------------------------------------------
3193 % transform letters to numbers
3194 %--------------------------------------------
3195 function numres=stra2num(str)
3196 numres=double(str)-96;
3197 if double(str) >= 48 & double(str) <= 57 % = 1 for numbers
3198     numres=str2num(str);
3199 end
3200 
3201 
3202 % --- Executes on button press in test_stereo1.
3203 function test_stereo1_Callback(hObject, eventdata, handles)
3204 if isequal(get(handles.test_stereo1,'Value'),0)
3205     set(handles.subdomain_patch1,'Visible','on')
3206     set(handles.rho_patch1,'Visible','on')
3207 else
3208     set(handles.subdomain_patch1,'Visible','off')
3209     set(handles.rho_patch1,'Visible','off')
3210 end
3211 
3212 % --- Executes on button press in test_stereo2.
3213 function test_stereo2_Callback(hObject, eventdata, handles)
3214 if isequal(get(handles.test_stereo2,'Value'),0)
3215     set(handles.subdomain_patch2,'Visible','on')
3216     set(handles.rho_patch2,'Visible','on')
3217 else
3218     set(handles.subdomain_patch2,'Visible','off')
3219     set(handles.rho_patch2,'Visible','off')
3220 end
3221 
3222 % --- Executes on button press in ImaThreshold.
3223 function ImaThreshold_Callback(hObject, eventdata, handles)
3224 if isequal(get(handles.ImaThreshold,'Value'),1)
3225     set(handles.MinIma,'Visible','on')
3226     set(handles.MaxIma,'Visible','on')
3227 else
3228     set(handles.MinIma,'Visible','off')
3229     set(handles.MaxIma,'Visible','off')
3230 end
3231 
3232 
3233 % --- Executes on button press in ImaThreshold2.
3234 function ImaThreshold2_Callback(hObject, eventdata, handles)
3235 if isequal(get(handles.ImaThreshold2,'Value'),1)
3236     set(handles.MinIma2,'Visible','on')
3237     set(handles.MaxIma2,'Visible','on')
3238 else
3239     set(handles.MinIma2,'Visible','off')
3240     set(handles.MaxIma2,'Visible','off')
3241 end
3242 
3243 
3244 
3245 % --- Executes on button press in Experimental.
3246 function Experimental_Callback(hObject, eventdata, handles)
3247 
3248 
3249 
3250 function ibz_Callback(hObject, eventdata, handles)
3251 % hObject    handle to ibz (see GCBO)
3252 % eventdata  reserved - to be defined in a future version of MATLAB
3253 % handles    structure with handles and user data (see GUIDATA)
3254 
3255 % Hints: get(hObject,'String') returns contents of ibz as text
3256 %        str2double(get(hObject,'String')) returns contents of ibz as a double
3257 
3258 
3259 % --- Executes during object creation, after setting all properties.
3260 function ibz_CreateFcn(hObject, eventdata, handles)
3261 % hObject    handle to ibz (see GCBO)
3262 % eventdata  reserved - to be defined in a future version of MATLAB
3263 % handles    empty - handles not created until after all CreateFcns called
3264 
3265 % Hint: edit controls usually have a white background on Windows.
3266 %       See ISPC and COMPUTER.
3267 if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
3268     set(hObject,'BackgroundColor','white');
3269 end
3270 
3271 
3272 
3273 function edit74_Callback(hObject, eventdata, handles)
3274 % hObject    handle to edit74 (see GCBO)
3275 % eventdata  reserved - to be defined in a future version of MATLAB
3276 % handles    structure with handles and user data (see GUIDATA)
3277 
3278 % Hints: get(hObject,'String') returns contents of edit74 as text
3279 %        str2double(get(hObject,'String')) returns contents of edit74 as a double
3280 
3281 
3282 % --- Executes during object creation, after setting all properties.
3283 function edit74_CreateFcn(hObject, eventdata, handles)
3284 % hObject    handle to edit74 (see GCBO)
3285 % eventdata  reserved - to be defined in a future version of MATLAB
3286 % handles    empty - handles not created until after all CreateFcns called
3287 
3288 % Hint: edit controls usually have a white background on Windows.
3289 %       See ISPC and COMPUTER.
3290 if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
3291     set(hObject,'BackgroundColor','white');
3292 end
3293 
3294 
3295 
3296 function edit75_Callback(hObject, eventdata, handles)
3297 % hObject    handle to edit75 (see GCBO)
3298 % eventdata  reserved - to be defined in a future version of MATLAB
3299 % handles    structure with handles and user data (see GUIDATA)
3300 
3301 % Hints: get(hObject,'String') returns contents of edit75 as text
3302 %        str2double(get(hObject,'String')) returns contents of edit75 as a double
3303 
3304 
3305 % --- Executes during object creation, after setting all properties.
3306 function edit75_CreateFcn(hObject, eventdata, handles)
3307 % hObject    handle to edit75 (see GCBO)
3308 % eventdata  reserved - to be defined in a future version of MATLAB
3309 % handles    empty - handles not created until after all CreateFcns called
3310 
3311 % Hint: edit controls usually have a white background on Windows.
3312 %       See ISPC and COMPUTER.
3313 if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
3314     set(hObject,'BackgroundColor','white');
3315 end
3316 
3317 
3318 
3319 function dz_civ1_Callback(hObject, eventdata, handles)
3320 % hObject    handle to dz_civ1 (see GCBO)
3321 % eventdata  reserved - to be defined in a future version of MATLAB
3322 % handles    structure with handles and user data (see GUIDATA)
3323 
3324 % Hints: get(hObject,'String') returns contents of dz_civ1 as text
3325 %        str2double(get(hObject,'String')) returns contents of dz_civ1 as a double
3326 
3327 
3328 % --- Executes during object creation, after setting all properties.
3329 function dz_civ1_CreateFcn(hObject, eventdata, handles)
3330 % hObject    handle to dz_civ1 (see GCBO)
3331 % eventdata  reserved - to be defined in a future version of MATLAB
3332 % handles    empty - handles not created until after all CreateFcns called
3333 
3334 % Hint: edit controls usually have a white background on Windows.
3335 %       See ISPC and COMPUTER.
3336 if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
3337     set(hObject,'BackgroundColor','white');
3338 end
3339 
3340
civ_3D

PURPOSE

SYNOPSIS

DESCRIPTION

CROSS-REFERENCE INFORMATION

SUBFUNCTIONS

SOURCE CODE
