Changeset 298 for trunk/src/civ.m


Ignore:
Timestamp:
Nov 24, 2011, 4:33:06 PM (13 years ago)
Author:
sommeria
Message:

improve the input to the civ GUI

File:
1 edited

Legend:

Unmodified
Added
Removed

  • trunk/src/civ.m

    r297 r298  
    4545%------------------------------------------------------------------------
    4646% --- Executes just before civ is made visible.
    47 function civ_OpeningFcn(hObject, eventdata, handles, param)
     47function civ_OpeningFcn(hObject, eventdata, handles, fileinput)
    4848%------------------------------------------------------------------------
    4949% This function has no output args, see OutputFcn.
    50 %filebase: root name
    51 %nom_type: nomencalture used ('png_old','_i_j'...)
    52 %list of field numbers to process
    53 %subdir: subdirectory of the opened netcdf file
    54 %ind_opening: operation number advised for beginning (1=checkciv1,2=checkfix1,3=checkpatch1,4=checkciv2,5=checkfix2,6=checkpatch2),
    55 %ind_a_opening ind_b_opening chosen pair from the opened netcdf file
    56 % Choose default command line output for civ
     50
     51%% General settings
    5752handles.output = hObject;
    58 % Update handles structure
    59 guidata(hObject, handles);
    60 set(hObject,'WindowButtonDownFcn',{'mouse_alt_gui',handles}) % allows mouse action with right button (zoom for uicontrol display)
    61 %default initial parameters
    62 filebase=''; % root file name ('filebase'.civ)
    63 ext=[];
    64 
    65 %% read names of the .exe file to adjust the interface according to available binaries
    66 %path_uvmat=which('uvmat');% check the path detected for source file uvmat
     53guidata(hObject, handles); % Update handles structure
     54set(hObject,'WindowButtonDownFcn',{'mouse_down',handles}) % allows mouse action with right button (zoom for uicontrol display)
     55
     56%% Adjust the GUI according to the binaries available in PARAM.xml
    6757path_civ=fileparts(which('civ')); %path to civ
    68 addpath (path_civ) ; %add the path to UVMAT, (useful in case of change of working directory after civ has been s opened in the working directory)
     58addpath (path_civ) ; %add the path to civ, (useful in case of change of working directory after civ has been s opened in the working directory)
    6959errormsg=[];%default error message
    7060xmlfile='PARAM.xml';
    … …  
    8474    msgbox_uvmat('ERROR',errormsg);
    8575end
    86 
    8776test_batch=0;%default: ,no batch mode available
    8877if isfield(sparam,'BatchParam') && isfield(sparam.BatchParam,'BatchMode')
    … …  
    10190end
    10291
    103 %% load the list of previously browsed files in menu Open
     92%% load the list of previously browsed files in the upper bar menu Open/
    10493dir_perso=prefdir; % path to the directory .matlab for personal data
    10594profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmauvmat_perso.mat' in .matlab
    … …  
    113102end
    114103
    115 %default input parameters:
    116 num_i1=1; % set of field i numbers
    117 num_i2=1; % set of field i numbers
    118 num_j1=1; % set of field j numbers (fields a)
    119 num_j2=1; % second set of field j numbers (fields b)
    120 %subdir='A'; % subdir for the netcdf result files
    121 ind_opening=0; % proposed operation number (1=civ1,2=fix1,3=patch1,4=civ2,5=fix2,6=patch2)
    122 %load the initial parameters if the interface is started from uvmat
    123 if exist('param','var')&&isstruct(param)% the interface is opened from uvmat
    124     filebase=param.RootName;
    125     nom_type_read=param.NomType;
    126     num_i1=param.num1;
    127     if isnan(num_i1),num_i1=1;end
    128     num_i2=param.num2;
    129     if isnan(num_i2),num_i2=num_i1;end
    130     num_j1=param.num_a;
    131     if isnan(num_j1),num_j1=1;end
    132     num_j2=param.num_b;
    133     if isnan(num_j2),num_j2=num_j1;end
    134     subdir=param.SubDir;
    135     ind_opening=param.IndOpening;
    136     ext=param.ImaExt;
    137 end
    138 browse.num_i1=num_i1;
    139 browse.num_i2=num_i2;
    140 browse.num_j1=num_j1;
    141 browse.num_j2=num_j2;
    142 if ~isempty(ext) && (~isempty(imformats(ext(2:end)))||strcmpi(ext,'.avi'));%if an image file has been opened by uvmat
    143     set(handles.ImaExt,'String',ext)
    144     browse.ext_ima=ext;
    145     if exist('nom_type_read','var')
    146         browse.nom_type_ima=nom_type_read; % the image nomenclature is stored
    147     end
    148 elseif isequal(ext,'.nc')
    149     if exist('nom_type_read','var')
    150         browse.nom_type_nc=nom_type_read;% the netcdf  nomenclature is stored
    151     end
    152 end
    153 set(handles.RootName,'String',filebase);
    154 set(handles.ImaDoc,'String',ext)
    155 
    156 %initiate advised operations
    157 enable_civ1(handles,0)
    158 enable_civ2(handles,0)
    159 %enable_pair1(handles,'on')
    160 enable_fix1(handles,0)
    161 enable_patch1(handles,0)
    162 enable_fix2(handles,0)
    163 enable_patch2(handles,0)
    164 set(handles.CheckCiv1,'Value',0)
    165 set(handles.CheckFix1,'Value',0)
    166 set(handles.CheckPatch1,'Value',0)
    167 set(handles.CheckCiv2,'Value',0)
    168 set(handles.CheckFix2,'Value',0)
    169 set(handles.CheckPatch2,'Value',0)
    170 %set(handles.frame_subdirciv2,'BackgroundColor',[0.831 0.816 0.784])
    171 if isequal(ind_opening,1)
    172     set(handles.CheckCiv1,'Value',1)
    173     enable_civ1(handles,1)
    174 elseif isequal(ind_opening,2)
    175     set(handles.CheckFix1,'Value',1)
    176     enable_fix1(handles,1)
    177 elseif isequal(ind_opening,3)
    178     set(handles.CheckPatch1,'Value',1)
    179     enable_patch1(handles,1)
    180 elseif isequal(ind_opening,4)
    181     set(handles.CheckCiv2,'Value',1)
    182     enable_civ2(handles,1)
    183 elseif isequal(ind_opening,5)
    184     set(handles.CheckFix2,'Value',1)
    185     enable_fix2(handles,1)
    186     set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
    187     set(handles.ListPairCiv2,'Enable','On')
    188     set(handles.ListPairCiv2,'Enable','On')
    189     enable_pair1(handles,'off')
    190 elseif isequal(ind_opening,6)
    191     set(handles.CheckPatch2,'Value',1)
    192     enable_patch2(handles,1)
     104%% input parameters:
     105% param
     106% filebase=''; % root file name ('filebase'.civ)
     107% ext=[];
     108% num_i1=1; % set of field i numbers
     109% num_i2=1; % set of field i numbers
     110% num_j1=1; % set of field j numbers (fields a)
     111% num_j2=1; % second set of field j numbers (fields b)
     112% %subdir='A'; % subdir for the netcdf result files
     113% ind_opening=0; % proposed operation number (1=civ1,2=fix1,3=patch1,4=civ2,5=fix2,6=patch2)
     114% %load the initial parameters if the interface is started from uvmat
     115% if exist('param','var')&&isstruct(param)% the interface is opened from uvmat
     116%     filebase=param.RootName;
     117%     nom_type_read=param.NomType;
     118%     num_i1=param.num1;
     119%     if isnan(num_i1),num_i1=1;end
     120%     num_i2=param.num2;
     121%     if isnan(num_i2),num_i2=num_i1;end
     122%     num_j1=param.num_a;
     123%     if isnan(num_j1),num_j1=1;end
     124%     num_j2=param.num_b;
     125%     if isnan(num_j2),num_j2=num_j1;end
     126%     subdir=param.SubDir;
     127%     ind_opening=param.IndOpening;
     128%     ext=param.ImaExt;
     129% end
     130% browse.num_i1=num_i1;
     131% browse.num_i2=num_i2;
     132% browse.num_j1=num_j1;
     133% browse.num_j2=num_j2;
     134% if ~isempty(ext) && (~isempty(imformats(ext(2:end)))||strcmpi(ext,'.avi'));%if an image file has been opened by uvmat
     135%     set(handles.ImaExt,'String',ext)
     136% %     browse.ext_ima=ext;
     137% %     if exist('nom_type_read','var')
     138% %         browse.nom_type_ima=nom_type_read; % the image nomenclature is stored
     139% %     end
     140% % elseif isequal(ext,'.nc')
     141% %     if exist('nom_type_read','var')
     142% %         browse.nom_type_nc=nom_type_read;% the netcdf  nomenclature is stored
     143% %     end
     144% end
     145% set(handles.RootName,'String',filebase);
     146% set(handles.ImaDoc,'String',ext)
     147
     148
     149%% prepare the GUI with parameters from the input file if opened from uvmat
     150if exist('fileinput','var')% && isfield(param,'RootName') && ~isempty(param.RootName)
     151    errormsg=display_file_name(handles,fileinput);
     152    if ~isempty(errormsg)
     153        msgbox_uvmat('ERROR',errormsg)
     154    end
     155end
     156
     157% %initiate advised operations
     158% enable_civ1(handles,0)
     159% enable_civ2(handles,0)
     160% %enable_pair1(handles,'on')
     161% enable_fix1(handles,0)
     162% enable_patch1(handles,0)
     163% enable_fix2(handles,0)
     164% enable_patch2(handles,0)
     165% set(handles.CheckCiv1,'Value',0)
     166% set(handles.CheckFix1,'Value',0)
     167% set(handles.CheckPatch1,'Value',0)
     168% set(handles.CheckCiv2,'Value',0)
     169% set(handles.CheckFix2,'Value',0)
     170% set(handles.CheckPatch2,'Value',0)
     171%
     172% if isequal(ind_opening,1)
     173%     set(handles.CheckCiv1,'Value',1)
     174%     enable_civ1(handles,1)
     175% elseif isequal(ind_opening,2)
     176%     set(handles.CheckFix1,'Value',1)
     177%     enable_fix1(handles,1)
     178% elseif isequal(ind_opening,3)
     179%     set(handles.CheckPatch1,'Value',1)
     180%     enable_patch1(handles,1)
     181% elseif isequal(ind_opening,4)
     182%     set(handles.CheckCiv2,'Value',1)
     183%     enable_civ2(handles,1)
     184% elseif isequal(ind_opening,5)
     185%     set(handles.CheckFix2,'Value',1)
     186%     enable_fix2(handles,1)
    193187%     set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
    194     set(handles.ListPairCiv2,'Enable','On')
    195     enable_pair1(handles,'off')
    196 end
    197 
    198 % set the range of fields (1:1 by default) and selected pair
    199 if isequal(num_i2,num_i1)
    200     num_ref_i=num_i1;
    201 else
    202     num_ref_i=floor((num_i1+num_i2)/2);
    203     browse.incr_pair(1)=num_i2-num_i1;
    204     browse.incr_pair(2)=0;
    205 end
    206 if isequal(num_j1,num_j2)
    207     if isnan(num_j1)
    208         num_ref_j=1;
    209     else
    210         num_ref_j=num_j1;
    211     end
    212 else
    213     num_ref_j=floor((num_j1+num_j2)/2);
    214     browse.incr_pair(2)=num_j2-num_j1;
    215 end
    216 set(handles.first_i,'String',num2str(num_ref_i));
    217 set(handles.last_i,'String',num2str(num_ref_i));
    218 set(handles.first_j,'String',num2str(num_ref_j));
    219 set(handles.last_j,'String',num2str(num_ref_j));
    220 set(handles.ref_i,'String',num2str(num_ref_i));
    221 set(handles.ref_j,'String',num2str(num_ref_j));
    222 % set(handles.ref_i_civ2,'String',num2str(num_ref_i));
    223 % set(handles.ref_j_civ2,'String',num2str(num_ref_j));
    224 set(handles.RootName,'UserData',browse);
    225 if exist('param','var') && isfield(param,'RootName') && ~isempty(param.RootName)%varargin the interface is opened from uvmat
    226     RootName_Callback(hObject, eventdata, handles);
    227 end
     188%     set(handles.ListPairCiv2,'Enable','On')
     189%     set(handles.ListPairCiv2,'Enable','On')
     190%     enable_pair1(handles,'off')
     191% elseif isequal(ind_opening,6)
     192%     set(handles.CheckPatch2,'Value',1)
     193%     enable_patch2(handles,1)
     194%     set(handles.ListPairCiv2,'Enable','On')
     195%     enable_pair1(handles,'off')
     196% end
     197%
     198% % set the range of fields (1:1 by default) and selected pair
     199% if isequal(num_i2,num_i1)
     200%     num_ref_i=num_i1;
     201% else
     202%     num_ref_i=floor((num_i1+num_i2)/2);
     203%     browse.incr_pair(1)=num_i2-num_i1;
     204%     browse.incr_pair(2)=0;
     205% end
     206% if isequal(num_j1,num_j2)
     207%     if isnan(num_j1)
     208%         num_ref_j=1;
     209%     else
     210%         num_ref_j=num_j1;
     211%     end
     212% else
     213%     num_ref_j=floor((num_j1+num_j2)/2);
     214%     browse.incr_pair(2)=num_j2-num_j1;
     215% end
     216% set(handles.first_i,'String',num2str(num_ref_i));
     217% set(handles.last_i,'String',num2str(num_ref_i));
     218% set(handles.first_j,'String',num2str(num_ref_j));
     219% set(handles.last_j,'String',num2str(num_ref_j));
     220% set(handles.ref_i,'String',num2str(num_ref_i));
     221% set(handles.ref_j,'String',num2str(num_ref_j));
     222% set(handles.RootName,'UserData',browse);
    228223
    229224%------------------------------------------------------------------------
    … …  
    231226function varargout = civ_OutputFcn(hObject, eventdata, handles)
    232227%------------------------------------------------------------------------
    233 % varargout  cell array for returning output args (see VARARGOUT);
    234 % hObject    handle to figure
    235 % eventdata  reserved - to be defined in a future version of MATLAB
    236 % handles    structure with handles and user data (see GUIDATA)
    237228% Get default command line output from handles structure
    238229varargout{1} = handles.output;
    239230
    240 % --------------------------------------------------------------------
     231%------------------------------------------------------------------------
     232% --- function activated by the Open/Browse... option in the upper menu bar.
    241233function MenuBrowse_Callback(hObject, eventdata, handles)
    242 
    243 %get the input file properties
     234%------------------------------------------------------------------------
     235%get the current input root file name to initiate the browser
    244236filebase=get(handles.RootName,'String');
    245237oldfile=''; %default
    246 if isempty(filebase)|| isequal(filebase,'')%loads the previously stored file name and set it as default in the file_input box
     238if isempty(filebase)|| isequal(filebase,'')%loads the previously stored root file name
    247239    dir_perso=prefdir;
    248240    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
    … …  
    274266sizf=size(fileinput);
    275267if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
    276 [path,name,ext]=fileparts(fileinput);
    277 testeditxml=0;
    278 if isequal(ext,'.xml')
    279     testeditxml=1;
    280     t_browse=xmltree(fileinput);
    281     head_element=get(t_browse,1);
    282     if isfield(head_element,'name')&& isequal(head_element.name,'ImaDoc')
    283         testeditxml=0;
    284     end
    285 end
    286 if testeditxml==1 || isequal(ext,'.xls')
    287     heditxml=editxml({fileinput});
    288     set(heditxml,'Tag','browser')
    289     waitfor(heditxml,'Tag','idle')
    290     if ~ishandle(heditxml)
    291         return
    292     end
    293     attr=findobj(get(heditxml,'children'),'Tag','CurrentAttributes');
    294     set(handles.browse,'UserData',fileinput)% store for future opening with browser
    295     fileinput=get(attr,'UserData');
    296     if ~exist(fileinput,'file')
    297         return
    298     end
    299 end
    300 [RootPath,RootFile,str1,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fileinput);
    301 filebase=fullfile(RootPath,RootFile);
    302 num_i1=str2double(str1);
    303 if isnan(num_i1),num_i1=1;end
    304 num_i2=str2double(str2);
    305 if isnan(num_i2),num_i2=num_i1;end
    306 num_j1=stra2num(str_a);
    307 if isnan(num_j1),num_j1=1;end
    308 num_j2=stra2num(str_b);
    309 if isnan(num_j2),num_j2=num_j1;end
    310 if isequal(get(handles.ListCompareMode,'Value'),1)
    311     browse=[];%initialisation
    312 else
    313     browse=get(handlesRootName,'UserData');
    314 end
    315 browse.num_i1=num_i1;
    316 browse.num_i2=num_i2;
    317 browse.num_j1=num_j1;
    318 browse.num_j2=num_j2;
    319 if length(ext)>1 && (~isempty(imformats(ext(2:end)))||strcmpi(ext,'.avi'));%if an image file has been opened by uvmat
    320     browse.nom_type_ima=nom_type;
    321     browse.ext_ima=ext;
    322     set(handles.ImaExt,'String',ext)
    323 end
    324 set(handles.ImaDoc,'String',ext);
    325 
    326 %%%%% read the state of the selected netcdf file to advise default operation
    327 if isequal(ext,'.nc')
    328     browse.nom_type_nc=nom_type;
    329     ind_opening=2;% propose 'fix' as the default option
    330     Data=nc2struct(fileinput,'ListGlobalAttribute','CivStage','absolut_time_T0','fix','patch','civ2','fix2');
    331     if ~isempty(Data.CivStage)%test for civ files
    332         ind_opening=Data.CivStage;
    333         set(handles.ListPairMode,'Value',3)
    334     end
    335     if ~isempty(Data.absolut_time_T0)%test for civx files
    336         set(handles.ListPairMode,'Value',1)
    337         if isfield(Data,'fix') && isequal(Data.fix,1)
    338             ind_opening=3;
    339         end
    340         if isequal(Data.patch,1)
    341             ind_opening=4;
    342         end
    343         if isequal(Data.civ2,1)
    344             ind_opening=5;
    345         end
    346         if  isequal(Data.fix2,1)
    347             ind_opening=6;
    348         end
    349         testciv=1; %TO SUPPRESS WITH NEW VERSION OF CIVX
    350     else
    351         ind_opening=3; %GUI used only for patch
    352         testciv=0;
    353     end
    354     set(handles.txt_SubdirCiv1,'String',subdir);%set the default subdir directories for installing the .nc results
    355     set(handles.txt_SubdirCiv2,'String',subdir);
    356     browse.testciv=testciv;
    357     browse.ind_opening=ind_opening;
    358 end
    359 set(handles.RootName,'String',filebase);
    360 set(handles.ImaDoc,'String',ext);
    361 if ~isempty(num_i1)
    362     ref_i=num_i1;
    363     if ~isempty(num_i2)
    364         ref_i=floor((ref_i+num_i2)/2);% reference image number corresponding to the file
    365         browse.incr_pair(1)=num_i2-num_i1;
    366         browse.incr_pair(2)=0;
    367     end
    368     set(handles.first_i,'String',num2str(ref_i));
    369     set(handles.last_i,'String',num2str(ref_i));
    370     set(handles.ref_i,'String',num2str(ref_i));
    371 %     set(handles.ref_i_civ2,'String',num2str(ref_i))
    372 end
    373 if isempty(num_j1)
    374     set(handles.ref_j,'String','1');
    375     set(handles.ref_j_civ2,'String','1');
    376 else
    377     ref_j=num_j1;
    378     if ~isempty(num_j2)
    379         ref_j=floor((num_j1+num_j2)/2);
    380         browse.incr_pair(2)=num_j2-num_j1;
    381     end
    382     set(handles.first_j,'String',num2str(ref_j));
    383     set(handles.last_j,'String',num2str(ref_j));
    384     set(handles.ref_j,'String',num2str(ref_j));
    385 %     set(handles.ref_j_civ2,'String',num2str(ref_j));
    386 end
    387 
    388 % set default operation options
    389 enable_civ1(handles,0)
    390 enable_civ2(handles,0')
    391 enable_pair1(handles,'on')
    392 enable_fix1(handles,0)
    393 enable_patch1(handles,0)
    394 enable_fix2(handles,0)
    395 enable_patch2(handles,0)
    396 set(handles.CheckCiv1,'Value',0)
    397 set(handles.CheckFix1,'Value',0)
    398 set(handles.CheckPatch1,'Value',0)
    399 set(handles.CheckCiv2,'Value',0)
    400 set(handles.CheckFix2,'Value',0)
    401 set(handles.CheckPatch2,'Value',0)
    402 % set(handles.frame_subdirciv2,'BackgroundColor',[0.831 0.816 0.784])
    403 if isequal(ind_opening,1)
    404     set(handles.CheckCiv1,'Value',1)
    405     enable_civ1(handles,'on')
    406 elseif isequal(ind_opening,2)
    407     set(handles.CheckFix1,'Value',1)
    408     enable_fix1(handles,'on')
    409 elseif isequal(ind_opening,3)
    410     set(handles.CheckPatch1,'Value',1)
    411     enable_patch1(handles)
    412 elseif isequal(ind_opening,4)
    413     set(handles.CheckCiv2,'Value',1)
    414     enable_civ2(handles,'on')
    415 elseif isequal(ind_opening,5)
    416     enable_pair1(handles,'off')
    417     set(handles.CheckFix2,'Value',1)
    418     enable_fix2(handles)
    419     set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
    420     set(handles.ListPairCiv2,'Enable','On')
    421     set(handles.ListPairCiv2,'Enable','On')
    422 elseif isequal(ind_opening,6)
    423     enable_pair1(handles,'off')
    424     set(handles.CheckPatch2,'Value',1)
    425     enable_patch2(handles)
    426     set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
    427     set(handles.ListPairCiv2,'Enable','On')
    428 end
    429 set(handles.RootName,'UserData',browse);% store information from browser
    430 RootName_Callback(hObject, eventdata, handles);
    431 
     268
     269%% prepare the GUI with parameters from the input file if opened from uvmat
     270errormsg=display_file_name(handles,fileinput);
     271    if ~isempty(errormsg)
     272        msgbox_uvmat('ERROR',erromsg)
     273    end
     274
     275%
     276% [path,name,ext]=fileparts(fileinput);
     277% testeditxml=0;
     278% if isequal(ext,'.xml')
     279%     testeditxml=1;
     280%     t_browse=xmltree(fileinput);
     281%     head_element=get(t_browse,1);
     282%     if isfield(head_element,'name')&& isequal(head_element.name,'ImaDoc')
     283%         testeditxml=0;
     284%     end
     285% end
     286% if testeditxml==1 || isequal(ext,'.xls')
     287%     heditxml=editxml({fileinput});
     288%     set(heditxml,'Tag','browser')
     289%     waitfor(heditxml,'Tag','idle')
     290%     if ~ishandle(heditxml)
     291%         return
     292%     end
     293%     attr=findobj(get(heditxml,'children'),'Tag','CurrentAttributes');
     294%     set(handles.browse,'UserData',fileinput)% store for future opening with browser
     295%     fileinput=get(attr,'UserData');
     296%     if ~exist(fileinput,'file')
     297%         return
     298%     end
     299% end
     300% [RootPath,RootFile,str1,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fileinput);
     301% filebase=fullfile(RootPath,RootFile);
     302% num_i1=str2double(str1);
     303% if isnan(num_i1),num_i1=1;end
     304% num_i2=str2double(str2);
     305% if isnan(num_i2),num_i2=num_i1;end
     306% num_j1=stra2num(str_a);
     307% if isnan(num_j1),num_j1=1;end
     308% num_j2=stra2num(str_b);
     309% if isnan(num_j2),num_j2=num_j1;end
     310% if isequal(get(handles.ListCompareMode,'Value'),1)
     311%     browse=[];%initialisation
     312% else
     313%     browse=get(handlesRootName,'UserData');
     314% end
     315% browse.num_i1=num_i1;
     316% browse.num_i2=num_i2;
     317% browse.num_j1=num_j1;
     318% browse.num_j2=num_j2;
     319% if length(ext)>1 && (~isempty(imformats(ext(2:end)))||strcmpi(ext,'.avi'));%if an image file has been opened by uvmat
     320%     browse.nom_type_ima=nom_type;
     321%     browse.ext_ima=ext;
     322%     set(handles.ImaExt,'String',ext)
     323% end
     324% set(handles.ImaDoc,'String',ext);
     325%
     326%
     327% set(handles.RootName,'UserData',browse);% store information from browser
     328% RootName_Callback(hObject, eventdata, handles);
    432329
    433330% -----------------------------------------------------------------------
    … …  
    436333%------------------------------------------------------------------------
    437334fileinput=get(handles.MenuFile_1,'Label');
    438 display_file_name(hObject, eventdata, handles,fileinput)
     335errormsg=display_file_name(handles,fileinput);
     336if ~isempty(errormsg)
     337    msgbox_uvmat('ERROR',erromsg)
     338end
    439339
    440340% -----------------------------------------------------------------------
    … …  
    443343%------------------------------------------------------------------------
    444344fileinput=get(handles.MenuFile_2,'Label');
    445 display_file_name(hObject, eventdata, handles,fileinput)
    446 
     345errormsg=display_file_name(handles,fileinput);
     346if ~isempty(errormsg)
     347    msgbox_uvmat('ERROR',erromsg)
     348end
    447349% -----------------------------------------------------------------------
    448350% --- Open again the file whose name has been recorded in MenuFile_3
    … …  
    450352%------------------------------------------------------------------------
    451353fileinput=get(handles.MenuFile_3,'Label');
    452 display_file_name(hObject, eventdata, handles,fileinput)
    453 
     354errormsg=display_file_name(handles,fileinput);
     355if ~isempty(errormsg)
     356    msgbox_uvmat('ERROR',erromsg)
     357end
    454358% -----------------------------------------------------------------------
    455359% --- Open again the file whose name has been recorded in MenuFile_4
    … …  
    457361%------------------------------------------------------------------------
    458362fileinput=get(handles.MenuFile_4,'Label');
    459 display_file_name(hObject, eventdata, handles,fileinput)
    460 
     363errormsg=display_file_name(handles,fileinput);
     364if ~isempty(errormsg)
     365    msgbox_uvmat('ERROR',erromsg)
     366end
    461367% -----------------------------------------------------------------------
    462368% --- Open again the file whose name has been recorded in MenuFile_5
    … …  
    464370%------------------------------------------------------------------------
    465371fileinput=get(handles.MenuFile_5,'Label');
    466 display_file_name(hObject, eventdata, handles,fileinput)
    467 
     372errormsg=display_file_name(handles,fileinput);
     373if ~isempty(errormsg)
     374    msgbox_uvmat('ERROR',erromsg)
     375end
    468376%------------------------------------------------------------------------
    469377function ImaDoc_Callback(hObject, eventdata, handles)
    … …  
    476384%------------------------------------------------------------------------
    477385filebase=get(handles.RootName,'String');
    478 display_file_name(hObject, eventdata, handles,filebase)
    479 
    480 %------------------------------------------------------------------------
    481 function display_file_name(hObject, eventdata, handles,filebase)
     386errormsg=display_file_name(handles,filebase);
     387if ~isempty(errormsg)
     388    msgbox_uvmat('ERROR',erromsg)
     389end
     390%------------------------------------------------------------------------
     391function errormsg=display_file_name(handles,fileinput)
    482392%------------------------------------------------------------------------
    483393set(handles.ListCompareMode,'Visible','on')
     394errormsg='';%default empty error message
     395
     396%% enable RUN, BATCH button and 'status' display
     397set(handles.RUN, 'Enable','On')
     398set(handles.RUN,'BackgroundColor',[1 0 0])%set RUN button to red color
     399set(handles.BATCH,'Enable','On')
     400set(handles.BATCH,'BackgroundColor',[1 0 0])%set BATCH button to red color
     401if isfield(handles,'status')
     402    set(handles.status,'Value',0);       %suppress the 'status' display
     403    status_Callback([], [], handles)
     404end
     405
     406% %% default first_i and j and increments
     407% first_i=str2double(get(handles.first_i,'String'));%value possibly set by uvmat_Opening
     408% if isnan(first_i)|| first_i < 1
     409%     first_i=1; %default first_i
     410% end
     411% last_i=str2double(get(handles.last_i,'String'));
     412% if isnan(last_i)|| last_i < first_i
     413%     last_i=first_i;  %default last_i
     414% end
     415% first_j=str2double(get(handles.first_j,'String'));
     416% if isnan(first_j)|| first_j < 1
     417%     first_j=1; %default first_j
     418% end
     419% last_j=str2double(get(handles.last_j,'String'));
     420% if isnan(last_j)|| last_j < first_j
     421%     last_j=first_j; %default last_j
     422% end
     423% incr_i=str2double(get(handles.incr_i,'String'));
     424% if isnan(incr_i) || incr_i < 1;
     425%     set(handles.incr_i,'String','1') %default incr_i
     426% end
     427% incr_j=str2double(get(handles.incr_j,'String'));
     428% if isnan(incr_j) || incr_j < 1;
     429%     set(handles.incr_j,'String','1') %default incr_j
     430% end
     431
     432%% determine nomenclature types and extension of the input files
    484433ext_ima='';%default
    485 nom_type_ima=[];%default
    486 field_count=1;%default
    487 nom_type_nc=[];
     434nom_type_ima='';%default
     435nom_type_nc='';
     436[RootPath,FileName,i1_str,i2_str,j1_str,j2_str,ext_input,nom_type_input,subdir]=name2display(fileinput);
     437RootName=fullfile(RootPath,FileName);
     438set(handles.RootName,'String',RootName)
     439num_ref_i=str2double(i1_str);
     440num_ref_j=str2double(j1_str);
     441browse=[];%default
     442if ~isempty(imformats(ext_input(2:end)))||strcmp(lower(ext_input),'.avi')% if the extension corresponds to an image or movie format recognized by Matlab
     443    ext_ima=ext_input;
     444    nom_type_ima=nom_type_input;
     445else %case of netcdf input file, look for corresponding images
     446    nom_type_nc=nom_type_input;
     447    %TODO: read the image name in the netcdf file (if documented)
     448    dirima='';%default
     449    %look for double image series '_i_j'
     450    dirima=dir([RootName '_' i1_str '_' j1_str '.*']);
     451    if isempty(dirima)
     452        % look for images series  with sub marker '_'
     453        dirima=dir([RootName '_*' i1_str  '.*']);
     454        if isempty(dirima)
     455            % look for other images series
     456            dirima=dir([RootName '*' i1_str '.*']);
     457            if isempty(dirima)
     458                % look for other images series witth letter appendix
     459                appendix=char(96+j1_str);
     460                dirima=dir([RootName '*' i1_str appendix '.*']);
     461            end
     462        end
     463    end
     464    for ilist=1:numel(dirima)
     465        [pp,ff,i1,i2,j1,j2,ext_list,nom_type_list]=name2display(dirima(ilist).name);
     466        form=imformats(ext_list(2:end));
     467        if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
     468            ext_ima=ext_list;
     469            nom_type_ima=nom_type_list;
     470            num_i1=str2double(i1);
     471            num_j1=str2double(j1);
     472            num_i2=str2double(i2);
     473            num_j2=str2double(j2);
     474           
     475            % set the range of fields (1:1 by default) and selected pair
     476            if isequal(num_i2,num_i1)||isnan(num_i2)
     477                num_ref_i=num_i1;
     478            else
     479                num_ref_i=floor((num_i1+num_i2)/2);
     480                browse.incr_pair(1)=num_i2-num_i1;
     481                browse.incr_pair(2)=0;
     482            end
     483            if isequal(num_j1,num_j2)||isnan(num_j2)
     484                if isnan(num_j1)
     485                    num_ref_j=1;
     486                else
     487                    num_ref_j=num_j1;
     488                end
     489            else
     490                num_ref_j=floor((num_j1+num_j2)/2);
     491                browse.incr_pair(2)=num_j2-num_j1;
     492            end
     493            break
     494        end
     495    end
     496end
     497set(handles.RootName,'UserData',browse);
     498% ext_imadoc=get(handles.ImaDoc,'String');
     499% browse=get(handles.RootName,'UserData');%default
     500% if isfield(browse,'nom_type_ima')
     501%     nom_type_ima=browse.nom_type_ima;% get an image nomenclature type already determined by an input image name
     502% end
     503% if isfield(browse,'ext_ima')
     504%     ext_ima=browse.ext_ima;
     505% end
     506% if isfield(browse,'nom_type_nc')
     507%     nom_type_nc=browse.nom_type_nc;% get an image nomenclature type already determined by an input image name
     508% end
     509% if isfield(browse,'num_i1')
     510%     field_count=browse.num_i1;% get an image index type already determined by an input file
     511% end
     512%set(handles.civ,'UserData',[]); %refresh list of previous civ files (for STATUS)
     513
     514
     515%% look for an image documentation file
     516ext_imadoc='';%default
     517if exist([RootName '.xml'],'file')
     518    ext_imadoc='.xml';
     519elseif exist([RootName '.civxml'],'file')
     520    ext_imadoc='.civxml';
     521elseif exist([RootName '.civ'],'file')
     522    ext_imadoc='.civ';
     523elseif exist([RootName '.avi'],'file')
     524    ext_imadoc='.avi';
     525elseif exist([RootName '.AVI'],'file')
     526    ext_imadoc='.AVI';
     527end
     528set(handles.ImaDoc,'String',ext_imadoc)% display the extension name for the image documentation file used
     529set(handles.ImaDoc,'BackgroundColor',[1 1 0])
     530drawnow
     531%%%%%%%%   read image documentation file  %%%%%%%%%%%%%%%%%%%%%%%%%%%
     532mode=''; %default
    488533time=[];
    489534TimeUnit='frame'; %default
    … …  
    491536pxcmx_search=[];%default
    492537pxcmy_search=[];%default
    493 
    494 ext_imadoc=get(handles.ImaDoc,'String');
    495 browse=get(handles.RootName,'UserData');%default
    496 if isfield(browse,'nom_type_ima')
    497     nom_type_ima=browse.nom_type_ima;% get an image nomenclature type already determined by an input image name
    498 end
    499 if isfield(browse,'ext_ima')
    500     ext_ima=browse.ext_ima;
    501 end
    502 if isfield(browse,'nom_type_nc')
    503     nom_type_nc=browse.nom_type_nc;% get an image nomenclature type already determined by an input image name
    504 end
    505 if isfield(browse,'num_i1')
    506     field_count=browse.num_i1;% get an image index type already determined by an input file
    507 end
    508 set(handles.civ,'UserData',[]); %refresh list of previous civ files (for STATUS)
    509 
    510 %default first_i and j and increments
    511 first_i=str2double(get(handles.first_i,'String'));%value possibly set by uvmat_Opening
    512 if isnan(first_i)|| first_i < 1
    513     first_i=1; %default first_i
    514 end
    515 last_i=str2double(get(handles.last_i,'String'));
    516 if isnan(last_i)|| last_i < first_i
    517     last_i=first_i;  %default last_i
    518 end
    519 first_j=str2double(get(handles.first_j,'String'));
    520 if isnan(first_j)|| first_j < 1
    521     first_j=1; %default first_j
    522 end
    523 last_j=str2double(get(handles.last_j,'String'));
    524 if isnan(last_j)|| last_j < first_j
    525     last_j=first_j; %default last_j
    526 end
    527 incr_i=str2double(get(handles.incr_i,'String'));
    528 if isnan(incr_i) || incr_i < 1;
    529     set(handles.incr_i,'String','1') %default incr_i
    530 end
    531 incr_j=str2double(get(handles.incr_j,'String'));
    532 if isnan(incr_j) || incr_j < 1;
    533     set(handles.incr_j,'String','1') %default incr_j
    534 end
    535 dt=[];%default
    536 testmode=0;%default
    537 nbfield=[]; %default
    538 nburst=[];%default
    539 pxcmx=1;
    540 pxcmy=1;
    541 
    542 %look for an image documentation file
    543 if ~strcmp(ext_imadoc,'.xml') && ~strcmp(ext_imadoc,'.civ')&& ~strcmpi(ext_imadoc,'.avi')
    544     if exist([filebase '.xml'],'file')
    545         ext_imadoc='.xml';
    546     elseif exist([filebase '.civxml'],'file')
    547         ext_imadoc='.civxml';
    548     elseif exist([filebase '.civ'],'file')
    549         ext_imadoc='.civ';
    550     elseif exist([filebase '.avi'],'file')
    551         ext_imadoc='.avi';
    552     elseif exist([filebase '.AVI'],'file')
    553         ext_imadoc='.AVI';
    554     end
    555     set(handles.ImaDoc,'String',ext_imadoc)
    556 end
    557 
    558 %%%%%%%%   read image documentation file  %%%%%%%%%%%%%%%%%%%%%%%%%%%
    559 mode=''; %default
    560 set(handles.ImaDoc,'BackgroundColor',[1 1 0])
    561 drawnow
    562 if isequal(ext_imadoc,'.civxml') || isequal(ext_imadoc,'.xml')|| isequal(ext_imadoc,'.civ')
    563     set(handles.ref_i,'Visible','On')%use a reference index
    564     set(handles.ref_j,'Visible','On')
    565 elseif isequal(ext_imadoc,'.avi') || isequal(ext_imadoc,'.AVI')
    566     set(handles.ref_j,'Visible','Off')
    567 else
    568     set(handles.ref_i,'Visible','Off')
    569     set(handles.ref_j,'Visible','Off')
    570 end
    571 testima_xml=0;
     538% first_i=1;%default
     539% last_i=1;%default   
    572540if isequal(ext_imadoc,'.civxml')%TO ABANDON
    573     [nbfield,nbfield2,time]=read_civxml([filebase '.civxml']);
     541    [nbfield,nbfield2,time]=read_civxml([RootName '.civxml']);
    574542    mode='pair j1-j2';
    575543    if isempty(nom_type_ima)% dtermine types by default if not already selected by browser or uvmat
    … …  
    577545    end
    578546elseif isequal(ext_imadoc,'.xml')
    579     [XmlData,warntext]=imadoc2struct([filebase '.xml']);
     547    [XmlData,warntext]=imadoc2struct([RootName '.xml']);
    580548    ext_ima_read=[];
    581549    nom_type_read=[];
    582550    if isfield(XmlData,'Heading')&&isfield(XmlData.Heading','ImageName')&&ischar(XmlData.Heading.ImageName)% get image nom type and extension from the xml file
    583551        [PP,FF,fc,str2,str_a,str_b,ext_ima_read,nom_type_read]=name2display(XmlData.Heading.ImageName);
    584         fullname=fullfile(fileparts(filebase),XmlData.Heading.ImageName); %full name (including path) of the first image defined by the xmle file,
     552        fullname=fullfile(fileparts(RootName),XmlData.Heading.ImageName); %full name (including path) of the first image defined by the xmle file,
    585553        if ~exist(fullname,'file')
    586554            msgbox_uvmat('WARNING',['FirstImage ' fullname ' defined in the xml file does not exist'])
    … …  
    603571        TimeUnit=XmlData.TimeUnit;
    604572    end
    605     if isfield(XmlData,'Npx')
    606         npx=XmlData.Npx;
    607         npy=XmlData.Npy;
    608     end
    609573    pxcmx_search=1;
    610574    pxcmy_search=1;
    … …  
    621585    end
    622586elseif strcmp(ext_imadoc,'.civ')% case of .civ image documentation file
    623     [error,time,TimeUnit,mode,npx,npy]=read_imatext([filebase '.civ']);
    624     if error==2, msgbox_uvmat('WARNING',['no file ' filebase '.civ']);
     587    [error,time,TimeUnit,mode,npx,npy]=read_imatext([RootName '.civ']);
     588    if error==2, msgbox_uvmat('WARNING',['no file ' RootName '.civ']);
    625589    elseif error==1, msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file');
    626590    end
    … …  
    632596    set(handles.ListPairMode,'String',{'series(Di)'})
    633597    dt=0.04;%default
    634     if exist([filebase ext_imadoc],'file')==2
    635         info=aviinfo([filebase ext_imadoc]);%read infos on the avi movie
     598    if exist([RootName ext_imadoc],'file')==2
     599        info=aviinfo([RootName ext_imadoc]);%read infos on the avi movie
    636600        dt=1/info.FramesPerSecond;%time interval between successive frames
    637601        nbfield=info.NumFrames;%number of frames
    … …  
    642606    set(handles.ImaDoc,'String',''); %xml file not used for timing
    643607end
    644 set(handles.ImaDoc,'BackgroundColor',[1 1 1])
    645 
    646 %get the imabe nomenclature type if not defined by the input file nor by the xml file
    647 dirima=[];%default
    648 if isempty(nom_type_ima)
    649     %look for double image series '_i_j'
    650     dirima=dir([filebase '_' num2str(first_i) '_' num2str(first_j) '.*']);
    651     if isempty(dirima)
    652         % look for images series  with sub marker '_'
    653         dirima=dir([filebase '_*' num2str(first_i) '.*']);
    654         if isempty(dirima)
    655             % look for other images series
    656             dirima=dir([filebase '*' num2str(first_i) '.*']);
    657             if isempty(dirima)
    658                 % look for other images series witth letter appendix
    659                 appendix=char(96+first_j);
    660                 dirima=dir([filebase '*' num2str(first_i) appendix '.*']);
    661             end
    662         end
    663     end
    664 end
    665 for ilist=1:numel(dirima)
    666     [pp,ff,fc,str2,str_a,str_b,ext_list,nom_type_list]=name2display(dirima(ilist).name);
    667     form=imformats(ext_list(2:end));
    668     if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
    669         ext_ima=ext_list;
    670         nom_type_ima=nom_type_list;
    671             break
    672     end
    673 end
    674 % no image documentation file found: look for a series of existing files,images by priority or .nc files
    675 if isempty(nom_type_ima)
    676     ext_search=ext_imadoc;
    677     nom_type_search=nom_type_nc;
    678 else
    679     ext_search=ext_ima;
    680     nom_type_search=nom_type_ima;
    681 end
    682 if isempty(time) && ~strcmp(nom_type_search,'none') && ~strcmp(nom_type_search,'') && ~strcmp(nom_type_search,'*')
    683     subdir=get(handles.txt_SubdirCiv1,'String');
    684     incr_pair=[0 0];%default
    685     if isfield(browse,'incr_pair')
    686         incr_pair=browse.incr_pair;
    687     end
    688     %     nbdetect=0;%test of detected images
    689     field_i=browse.num_i2;
    690     imagename=name_generator(filebase,field_i,1,ext_search,nom_type_search);
    691     imagename_plus='';
    692     idetect=1;
    693     while idetect %look for the maximum file number in the series
    694         imagename_plus=name_generator(filebase,field_i+1,1,ext_search,nom_type_search);
    695         idetect=(exist(imagename_plus,'file')==2)&& ~strcmp(imagename,imagename_plus);
    696         if idetect
    697             field_i=field_i+1;
    698         end
    699         %SEE CASE OF NETCDF FILES
    700         %             nbdetect=nbdetect+(exist(imagename,'file')==2);
    701     end
    702     nbfield=field_i;% last detected field number
    703     field_i=browse.num_i1;%look for the minimum file number in the series
    704     imagename_min='';
    705     idetect=1;
    706     while idetect==1
    707         imagename_min=name_generator(filebase,field_i-1,1,ext_search,nom_type_search);
    708         idetect=(exist(imagename_min,'file')==2)&& ~strcmp(imagename,imagename_min);
    709         if idetect
    710             field_i=field_i-1;
    711         end
    712     end
    713     first_i=max(field_i,1);
    714     if numel(regexp(nom_type_search,'\D'))>=1%two indices i and j
    715         field_i=browse.num_i1;
    716         field_j=browse.num_j2;
    717         imagename=name_generator(filebase,field_i,field_j,ext_search,nom_type_search);
    718         imagename_plus='';
    719         jdetect=1;
    720         while jdetect==1 %look for the maximum file number in the series
    721             imagename_plus=name_generator(filebase,field_i,field_j+1,ext_search,nom_type_search);
    722             jdetect=(exist(imagename_plus,'file')==2)&& ~strcmp(imagename,imagename_plus);
    723             if jdetect
    724                 field_j=field_j+1;
    725             end
    726             %SEE CASE OF NETCDF FILES
    727             %             nbdetect=nbdetect+(exist(imagename,'file')==2);
    728         end
    729         nbfield2=field_j;% last detected field number
    730      end
    731  
    732     %determine the set of times and possible intervals for CIV
    733     %   dt=(1/1000)*str2double(get(handles.dt,'String'));
    734     time=(0:nbfield-1)';% time=file index -1  by default
    735     if numel(regexp(nom_type_search,'\D'))>=1%two indices i and j
    736         [x,y]=meshgrid(0:nbfield2-1,0:nbfield-1);
    737         time=x+y;
    738     end
    739 end
    740 
    741 if exist('time','var')
     608set(handles.ImaDoc,'BackgroundColor',[1 1 1])% set display box to yellow color
     609
     610
     611%% timing display
     612%show the reference image edit box if relevant (not needed for movies or in the absence of time information
     613% if isempty(time)|| strcmp(nom_type_ima,'*')||strcmp(nom_type_ima,'')
     614% %     set(handles.ref_i,'Visible','Off')% do not use a reference index to display time intervals
     615% %     set(handles.ref_j,'Visible','Off')
     616%     first_i=1;
     617%     last_i=1;
     618% else
     619% %     set(handles.ref_i,'Visible','On')%use a reference index
     620% %     set(handles.ref_j,'Visible','On')
     621%     set(handles.ref_i,'String',i1_str)
     622%     set(handles.ref_j,'String',j1_str)
     623% end
     624if ~isempty(time)
    742625    if size(time,1)+size(time,2)>=3 % if there are at least two time values to define dt
    743626        nbfield=size(time,1);
    … …  
    745628        set(handles.ImaDoc,'UserData',time); %store the set of times
    746629        set(handles.dt_unit,'String',['dt in m' TimeUnit]);
    747 %         set(handles.dt_unit_civ2,'String',['dt in m' TimeUnit]);
    748630        set(handles.TimeUnit,'String',TimeUnit);
    749631        set(handles.nb_field,'String',num2str(nbfield));
    … …  
    753635set(handles.CoordUnit,'String',CoordUnit)
    754636set(handles.SearchRange,'UserData',[pxcmx_search pxcmy_search]);
    755 % npxy=[npy npx];
    756637set(handles.ImaExt,'String',ext_ima)
    757 set(handles.first_i,'String',num2str(first_i));
    758 set(handles.last_i,'String',num2str(last_i));%
    759 set(handles.first_j,'String',num2str(first_j));
    760 set(handles.last_j,'String',num2str(last_j));%
     638set(handles.ref_i,'String',num2str(num_ref_i))
     639set(handles.first_i,'String',num2str(num_ref_i));
     640set(handles.last_i,'String',num2str(num_ref_i));%
     641set(handles.ref_j,'String',num2str(num_ref_j))
     642set(handles.first_j,'String',num2str(num_ref_j));
     643set(handles.last_j,'String',num2str(num_ref_j));%
    761644browse.nom_type_ima=nom_type_ima;
    762645set(handles.RootName,'UserData',browse)% store the nomenclature type
     646
     647%% set the civ options depending on the input file content
     648ind_opening=0;%default
     649if isequal(ext_input,'.nc')
     650    browse.nom_type_nc=nom_type_input;
     651    ind_opening=2;% propose 'fix' as the default option
     652    Data=nc2struct(fileinput,'ListGlobalAttribute','CivStage','absolut_time_T0','fix','patch','civ2','fix2');
     653    if ~isempty(Data.CivStage)%test for civ files
     654        ind_opening=Data.CivStage;
     655        set(handles.ListPairMode,'Value',3)
     656    end
     657end
     658ListOptions={'CheckCiv1', 'CheckFix1' 'CheckPatch1', 'CheckCiv2', 'CheckFix2', 'CheckPatch2'};
     659for index = 1:ind_opening
     660    set(handles.(ListOptions{index}),'value',0)
     661end
     662for index = ind_opening+1:length(ListOptions)
     663    set(handles.(ListOptions{index}),'value',1)
     664end
     665update_CivOptions(handles)
     666
    763667
    764668%%  set the menus of image pairs and default selection for civ   %%%%%%%%%%%%%%%%%%%
    … …  
    777681end
    778682
    779 
    780 %% desable status and RUN button
    781 set(handles.RUN, 'Enable','On')
    782 set(handles.RUN,'BackgroundColor',[1 0 0])
    783 set(handles.BATCH,'Enable','On')
    784 set(handles.BATCH,'BackgroundColor',[1 0 0])
    785 if isfield(handles,'status')
    786 set(handles.status,'Value',0);%suppress status display
    787 status_Callback(hObject, eventdata, handles)
    788 end
    789 
    790 %% store the root input filename for future opening
    791 dir_perso=prefdir;
    792 profil_perso=fullfile(prefdir,'uvmat_perso.mat');
    793 RootPath=fileparts(filebase);
    794 if exist(profil_perso,'file')
    795     save (profil_perso,'RootPath','-append'); %store the root name for future opening of uvmat
    796 else
    797     txt=ver('MATLAB');
    798     Release=txt.Release;
    799     relnumb=str2double(Release(3:4));
    800     if relnumb >= 14
    801         save (profil_perso,'RootPath','-V6'); %store the root name for future opening of uvmat
    802     else
    803         save (profil_perso,'RootPath'); %store the root name for future opening of uvmat
    804     end
    805 end
    806 
    807 %% update the subdir
    808 pathdir=fileparts(filebase);%path to the current xml file
    809 listot=dir(pathdir);
     683%% update the subdirectory display
     684listot=dir(RootPath);
    810685idir=0;
    811686listdir={''};%default
    … …  
    819694    end
    820695end
     696Value=find(strcmp(subdir,listdir));%search the index of subdir in the cell listdir
     697if isempty(Value)
     698    ValueCiv1=get(handles.ListSubdirCiv1,'Value');
     699    if ValueCiv1>numel(listdir)
     700        ValueCiv1=1;
     701    end
     702    set(handles.ListSubdirCiv1,'Value',ValueCiv1)
     703    ValueCiv2=get(handles.ListSubdirCiv2,'Value');
     704    if ValueCiv2>numel(listdir)
     705        ValueCiv2=1;
     706    end
     707    set(handles.ListSubdirCiv2,'Value',ValueCiv2)
     708else
     709    set(handles.ListSubdirCiv1,'Value',Value)
     710    set(handles.ListSubdirCiv2,'Value',Value)
     711end
    821712set(handles.ListSubdirCiv1,'Value',1)
    822713set(handles.ListSubdirCiv2,'Value',1)
    … …  
    824715set(handles.ListSubdirCiv2,'String',[listdir;'new...'])
    825716if isempty(listdir)
    826     dirname=listdir{1};
    827 else
    828     dirname='CIV'; %default civ directory name
     717    dirname='CIV';
     718else
     719    dirname=listdir{1}; %default civ directory name
    829720end
    830721set(handles.txt_SubdirCiv1,'String',dirname)
    831722set(handles.txt_SubdirCiv2,'String',dirname)
    832 %check wether the current subdir exists:
    833 % txt_SubdirCiv1=get(handles.txt_SubdirCiv1,'String');
    834 % txt_SubdirCiv2=get(handles.txt_SubdirCiv2,'String');
    835 
    836 ListPairMode_Callback(hObject, eventdata, handles)
     723
     724
     725%% list the possible index pairs, depending on the option set in ListPairMode
     726ListPairMode_Callback([], [], handles)
     727
     728%% store the root input filename for future opening
     729dir_perso=prefdir;
     730profil_perso=fullfile(prefdir,'uvmat_perso.mat');
     731% RootPath=fileparts(RootName);
     732if exist(profil_perso,'file')
     733    save (profil_perso,'RootPath','-append'); %store the root name for future opening of uvmat
     734else
     735    txt=ver('MATLAB');
     736    Release=txt.Release;
     737    relnumb=str2double(Release(3:4));
     738    if relnumb >= 14
     739        save (profil_perso,'RootPath','-V6'); %store the root name for future opening of uvmat
     740    else
     741        save (profil_perso,'RootPath'); %store the root name for future opening of uvmat
     742    end
     743end
    837744
    838745%------------------------------------------------------------------------
    … …  
    1068975testpair=0;
    1069976% case with no checkciv1 operation, netcdf files need to exist for reading
    1070 if get(handles.CheckCiv1,'Value')==0 %
     977if ~get(handles.CheckCiv1,'Value') %
    1071978    if ~exist(fullfile(filepath,subdir_civ1,ext_dir),'dir')
    1072979        msgbox_uvmat('ERROR',['no civ1 file available: subdirectory ' subdir_civ1 ' does not exist']);
    … …  
    12631170displ_pair={''}; %default
    12641171select=ones(size(1:nbpair));%default =1 for numbers of displayed pairs
    1265 if get(handles.CheckCiv2,'Value')==0 & get(handles.CheckCiv1,'Value')==0 & get(handles.CheckFix1,'Value')==0 & get(handles.CheckPatch1,'Value')==0%&...
     1172if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
    12661173    if ~exist(fullfile(filepath,subdir_civ2,ext_dir),'dir')
    12671174        errordlg(['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist'])
    … …  
    22942201
    22952202if isempty(filebase)||isequal(filebase,'')
    2296     msgbox_uvmat('ERROR','no input files')
     2203    msgbox_uvmat('ERROR','please open an image with the upper menu option Open/Browse...')
    22972204    return
    22982205end
    … …  
    31703077checkbox(4)=get(handles.CheckCiv2,'Value');
    31713078checkbox(5)=get(handles.CheckFix2,'Value');
    3172 checkbox(6)=get(handles.CheckPatch2,'Value');
     3079checkbox(6)=get(handles.CheckPatch2,'Value')
    31733080ind_selected=find(checkbox);
    31743081if ~isempty(ind_selected)
    … …  
    32073114end
    32083115
    3209 % end
    3210 
    3211 % set(handles.(operations(ind_selected)),'Visible','on')
    3212 %
    3213 % if state
    3214 %     RootName=get(handles.RootName,'String');
    3215 %     if isempty(RootName)
    3216 %          msgbox_uvmat('ERROR','No input file')
    3217 %         return
    3218 %     end
    3219 %     set(handles.Civ1,'Visible','on')   
    3220 %     set(handles.PairIndices,'Visible','on')
    3221 % else
    3222 %     set(handles.Civ1,'Visible','off') 
    3223 % end
    3224 
    3225 
    32263116%------------------------------------------------------------------------
    32273117function first_i_Callback(hObject, eventdata, handles)
    32283118%------------------------------------------------------------------------
    3229 % last_i_Callback(hObject, eventdata, handles)
    32303119first_i=str2double(get(handles.first_i,'String'));
    3231 % last_i=str2num(get(handles.last_i,'String'));
    3232 % ref_i=ceil((first_i+last_i)/2);
    32333120set(handles.ref_i,'String', num2str(first_i))% reference index for pair dt = first index
    3234 %set(handles.ref_i_civ2,'String', num2str(first_i))% reference index for pair dt = first index
    32353121ref_i_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
    32363122
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