Changeset 360

Timestamp:

Jan 9, 2012, 1:16:35 AM (13 years ago)

Author:

sommeria

Message:

civ: bugs corrected. Iintroduction of an xm file for parameters read using the new fct fill_GUI (to test and improve)
cleaning in uvmat. Possibility of using blank increment added (go to the next available file)
fullfile_uvmat: case of two equal indices in a pair, bug repair.
find_fileseries: improved speed.

Location:

trunk/src

Files:

• civ.fig (modified) (previous)
• civ.m (modified) (50 diffs)
• fill_GUI.m (added)
• find_file_series.m (modified) (4 diffs)
• fullfile_uvmat.m (modified) (6 diffs)
• series.m (modified) (7 diffs)
• uvmat.fig (modified) (previous)
• uvmat.m (modified) (69 diffs)

trunk/src/civ.m

@@ -23 +23 @@
 %TODO: search range
 
-% Last Modified by GUIDE v2.5 21-Dec-2011 00:34:49
+% Last Modified by GUIDE v2.5 08-Jan-2012 11:00:13
 % Begin initialization code - DO NOT EDIT
 gui_Singleton = 1;
@@ -139 +139 @@
     oldfile=filebase;
 end
-% ind_opening=1;%default
-% browse.incr_pair=[0 0]; %default
-%% get the new input fiel with the browser
+
+%% get the new input file with the browser
 menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)';
     '*.xml',  '.xml files '; ...
@@ -159 +158 @@
 [path,name,ext]=fileparts(fileinput);
 testeditxml=0;
-if isequal(ext,'.xml')
-    testeditxml=1;
-    t_browse=xmltree(fileinput);
-    head_element=get(t_browse,1);
-    if isfield(head_element,'name')&& isequal(head_element.name,'ImaDoc')
-        testeditxml=0;
-    end
-end
-if testeditxml==1 || isequal(ext,'.xls')
-    heditxml=editxml({fileinput});
-    set(heditxml,'Tag','browser')
-    waitfor(heditxml,'Tag','idle')
-    if ~ishandle(heditxml)
-        return
-    end
-    attr=findobj(get(heditxml,'children'),'Tag','CurrentAttributes');
-    set(handles.browse,'UserData',fileinput)% store for future opening with browser
-    fileinput=get(attr,'UserData');
-    if ~exist(fileinput,'file')
-        return
-    end
-end
-%[RootPath,RootFile,str1,str2,str_a,str_b,FileExt,NomType,subdir]=name2display(fileinput);
+% if isequal(ext,'.xml')
+%     testeditxml=1;
+%     t_browse=xmltree(fileinput);
+%     head_element=get(t_browse,1);
+%     if isfield(head_element,'name')&& isequal(head_element.name,'ImaDoc')
+%         testeditxml=0;
+%     end
+% end
+% if testeditxml==1 || isequal(ext,'.xls')
+%     heditxml=editxml({fileinput});
+%     set(heditxml,'Tag','browser')
+%     waitfor(heditxml,'Tag','idle')
+%     if ~ishandle(heditxml)
+%         return
+%     end
+%     attr=findobj(get(heditxml,'children'),'Tag','CurrentAttributes');
+%     set(handles.browse,'UserData',fileinput)% store for future opening with browser
+%     fileinput=get(attr,'UserData');
+%     if ~exist(fileinput,'file')
+%         return
+%     end
+% end
 [tild,tild,tild,i1,i2,j1,j2,FileExt,NomType]=fileparts_uvmat(fileinput);
-% filebase=fullfile(RootPath,RootFile);
-
-%% record the information obtained from the input file
-% if isempty(i1),i1=1;end
-% if isempty(i2),i2=i1;end
-% if isempty(j1),j1=1;end
-% if isempty(j2),j2=j1;end
-% if isequal(get(handles.ListCompareMode,'Value'),1)
-%     browse=[];%initialisation
-% else
-%     browse=get(handles.RootName,'UserData');
-% end
-% browse.num_i1=i1;
-% browse.num_i2=i2;
-% browse.num_j1=j1;
-% browse.num_j2=j2;
-% if length(FileExt)>1 && (~isempty(imformats(FileExt(2:end)))||strcmpi(FileExt,'.avi'));%if an image file has been opened by uvmat
-%     browse.nom_type_ima=NomType;
-%     browse.ext_ima=FileExt;
-%     set(handles.ImaExt,'String',FileExt)
-% end
-% set(handles.RootName,'UserData',browse);% store information from browser
 
 %% prepare the GUI with parameters from the input file 
@@ -321 +297 @@
 %------------------------------------------------------------------------
 set(handles.RootName,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
-filebase=get(handles.RootName,'String');
-errormsg=display_file_name(handles,filebase);
+[RootPath,RootFile]=fileparts(get(handles.RootName,'String'));
+ref_i=str2num(get(handles.ref_i,'String'));
+ref_j=str2num(get(handles.ref_j,'String'));
+NomType=get(handles.NomType,'String');
+ImaExt=get(handles.ImaExt,'String');
+fileinput=fullfile_uvmat(RootPath,'',RootFile,ImaExt,NomType,ref_i,[],ref_j)
+errormsg=display_file_name(handles,fileinput);
 if ~isempty(errormsg)
-    msgbox_uvmat('ERROR',erromsg)
+    msgbox_uvmat('ERROR',errormsg)
 end
 set(handles.RootName,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
@@ -346 +327 @@
 
 %% determine nomenclature types and extension of the input files
-ext_ima='';%default
-NomTypeIma='';%default
-NomTypeNc='';
-%[RootPath,RootFile,i1_str,i2_str,j1_str,j2_str,ext_input,nom_type_input,SubDir]=name2display(fileinput);
 [RootPath,SubDir,RootFile,i1,i2,j1,j2,ExtInput,NomTypeInput]=fileparts_uvmat(fileinput);
-[RootPath,RootFile,i1_series,i2_series,j1_series,j2_series,NomTypeInput,FileType,Object]=find_file_series(fileinput);
-if strcmp(NomTypeInput,'*')% movies will be opened at the first frame
-    i1=1;
-    i2=[];
-    j1=[];
-    j2=[];
-end  
+NomTypeNc='';%default
+
+%% case of netcdf file as input, look for a coresponding image
 ind_opening=0;%default
-switch FileType
-    case 'civdata'
-        Data=nc2struct(fileinput,'ListGlobalAttribute','CivStage','Civ1_ImageA');
-        if isfield(Data,'Txt')
-            errormsg=Data.Txt;
-            return
-        end
+if strcmp(ExtInput,'.xml')
+    Param=xml2struct(fileinput);
+    fill_GUI(Param,handles);%fill the GUI with the parameters retrieved from the xml file 
+    return
+end
+if strcmp(ExtInput,'.nc')
+    NomTypeNc=NomTypeInput;
+    Data=nc2struct(fileinput,'ListGlobalAttribute','Conventions','absolut_time_T0','CivStage','Civ2_ImageA','Civ1_ImageA','fix','patch','civ2','fix2');
+    if isfield(Data,'Txt')
+        errormsg=Data.Txt;
+        return
+    end
+    if strcmp(Data.Conventions,'uvmat/civdata')% case of new civ data,
+        set(handles.MenuMatlab,'checked','on') %select civ/Matlab by default
+        set(handles.MenuCivX,'checked','off')
         if ~isempty(Data.CivStage)%test for civ files
             ind_opening=Data.CivStage;
         end
-        if ~isempty(Data.Civ1_ImageA)%test for civ files
+        if ~isempty(Data.Civ2_ImageA)%get the corresponding input image in the netcdf file
             imageinput=Data.Civ1_ImageA;
-            if ~exist(imageinput,'file')
-                errormsg=['the image ' imageinput ' does not exist, please enter an image'];
-                return
-            end
-        end
-        set(handles.MenuMatlab,'checked','on')
-        set(handles.MenuCivX,'checked','off')
-        NomTypeNc=NomTypeInput;
-    case 'civx'
-        Data=nc2struct(fileinput,'ListGlobalAttribute','fix','patch','civ2','fix2');
+        elseif ~isempty(Data.Civ1_ImageA)
+            imageinput=Data.Civ1_ImageA;
+        end
+    elseif ~isempty(Data.absolut_time_T0')% case of  civx data,
+        set(handles.MenuMatlab,'checked','off') %select Cix by default
+        set(handles.MenuCivX,'checked','on')
         if ~isempty(Data.fix2)
             ind_opening=5;
@@ -390 +367 @@
             ind_opening=2;
         end
-        % look for the input images
+        % look for the corresponding input images
         check_letter=~isempty(regexp(NomTypeInput,'[ab|AB]$'));%detect pair label by letter
         NomTypeIma=NomTypeInput;
@@ -396 +373 @@
             NomTypeIma=NomTypeInput(1:end-1);
         else
-            r=regexp(NomTypeIma,'.-(?<num2>\d+$','names');
+            r=regexp(NomTypeIma,'.-(?<num2>\d+)$','names');
             if ~isempty(r)
                 NomTypeIma=regexprep(NomTypeIma,['-' r.num2],'');
             end
+            r=regexp(NomTypeIma,'.-(?<num2>\d+)','names');
+            if ~isempty(r)
+                NomTypeIma=regexprep(NomTypeIma,['-' r.num2],'');
+            end
         end
         imageinput=fullfile_uvmat(RootPath,'',RootFile,'.png',NomTypeIma,i1,[],j1);
-        if ~exist(imageinput,'file')
-            errormsg='no image corresponds to the input .nc file, please open an image';
-            return
-        end
+    else
+        errormsg='the input netcdf file is not civ data';
+        return
+    end
+end
+
+%% scan the image series when a nc file has been opened
+ImaExt=ExtInput;
+if ~isempty(NomTypeNc)
+    %no corresponding image found, select manually with the browser
+    if ~exist(imageinput,'file')
+        menu={'*.png;*.jpg;*.tif;*.avi;*.AVI', '(*.png,*.jpg ,*.tif, *.avi,*.AVI)';
+            '*.png','.png image files'; ...
+            '*.jpg',' jpeg image files'; ...
+            '*.tif','.tif image files'; ...
+            '*.avi;*.AVI','.avi movie files'; ...
+            '*.*',  'All Files (*.*)'};
+        [FileName, PathName] = uigetfile( menu, 'Pick an input image file',fileparts(fileparts(fileinput)));
+        imageinput=[PathName FileName];%complete file name
+     
+    end    
+    fileinput=imageinput;
+    [tild, tild,ImaExt]=fileparts(imageinput);
+end
+[RootPath,RootFile,i1_series,tild,j1_series,tild,NomTypeIma,FileType,Object]=find_file_series(fileinput);
+if strcmp(NomTypeInput,'*')% movies will be opened at the first frame
+    i1=1;
+    i2=[];
+    j1=[];
+    j2=[];
+end
+switch FileType
     case {'image','multimage','video'}
-         imageinput=fileinput;
-         NomTypeIma=NomTypeInput;
-         ext_ima=ExtInput;
     otherwise
-        errormsg='invalid input file: enter an image, a movie or .nc file';
-end
-[RootPath,RootFile,i1_series,i2_series,j1_series,j2_series,NomTypeIma,ImageType,Object]=find_file_series(imageinput);
+        errormsg='invalid input file: enter an image, a movie or civ .nc file';
+        return
+end
 RootName=fullfile(RootPath,RootFile);
 set(handles.RootName,'String',RootName)
+browse=get(handles.RootName,'UserData');
+browse.nom_type_nc=NomTypeNc;
+browse.incr_pair=[0 0];%default
+
+%% fill reference indices from the input file indices
+num_ref_i=i1;%efaulmt ref index
+if ~isempty(i2)
+    num_ref_i=floor((num_ref_i+i2)/2);
+end
+num_ref_j=j1;
+if ~isempty(j2)
+    num_ref_i=floor((num_ref_j+j2)/2);
+end
+
+%% scan the images if a civ file has been opened
+if ~isempty(NomTypeNc)
+[RootPath,RootFile,i1_series,tild,j1_series,tild,NomTypeIma,ImageType,Object]=find_file_series(imageinput);
+end
 MaxIndex_i=max(i1_series(i1_series>0));
 MaxIndex_j=max(j1_series(j1_series>0));
-
-num_ref_i=i1;%efaulmt ref index
-num_ref_j=j1;
-browse=get(handles.RootName,'UserData');
-browse.nom_type_nc=NomTypeNc;
-browse.nom_type_ima=NomTypeInput;
-browse.incr_pair=[0 0];%default
-
-% % form=imformats(ext_input(2:end));
-% check_letter=0;
-% check_separator=0;
-% if ~isempty(ext_input)&&(~isempty(imformats(ext_input(2:end)))||strcmpi(ext_input,'.avi'))% if the extension corresponds to an image or movie format recognized by Matlab
-%     ext_ima=ext_input;
-%     nom_type_ima=nom_type_input;
-%     imagename=fileinput;
-%     check_letter=~isempty(regexp(nom_type_ima,'[a|A]$'));%detect pair label by letter
-% else %case of netcdf input file, look for corresponding images
-%     nom_type_nc=nom_type_input;
-%     imagename=fullfile_uvmat(RootPath,[],RootFile,ext_ima,nom_type_ima,1,[],1);
-%     %imagename=name_generator(fullfile(RootPath,RootFile),1,1,ext_ima,nom_type_ima);
-%     i1_str='';
-%     j1_str='';
-%     if ~isnan(i2)
-%         num_ref_i=floor((num_ref_i+i2)/2);% reference image number corresponding to the file
-%         browse.incr_pair(1)=i2-i1;
-%         browse.incr_pair(2)=0;
-%     end
-%     %TODO: read the image name in the netcdf file (if documented)
-%     %look for double image series '_i_j'
-%     check_letter=~isempty(regexp(nom_type_nc,'[ab|AB]$'));%detect pair label by letter
-%     if check_letter
-%         j1_str=nom_type_nc(end-1);
-%         r=regexp(nom_type_nc,'_(?<num1>\d+)','names');
-%         if ~isempty(r)
-%             i1_str=r.num1;
-%         end
-%     else
-%         NomTypeIma=regexprep(nom_type_nc,'-\d','');%
-%         r_end=regexp(NomTypeIma,'.\D(?<num2>\d+$','names');
-%         if ~isempty(r_end)
-%             j1_str=r.num2;
-%         end
-%     end
-%     r=regexp(NomTypeIma,'_(?<num1>\d+)','names');
-%     if ~isempty(r)
-%         i1_str=r.num1;
-%     end  
-%     dirima=dir([RootName '_' i1_str '_' j1_str '.*']);
-%     if isempty(dirima)
-%         % look for images series  with sub marker '_'
-%         dirima=dir([RootName '_*' i1_str  '.*']);
-%         if isempty(dirima)
-%             % look for other images series
-%             dirima=dir([RootName '*' i1_str '.*']);
-%             if isempty(dirima)
-%                 % look for other images series witth letter appendix
-%                 appendix=char(96+j1_str);
-%                 dirima=dir([RootName '*' i1_str appendix '.*']);
-%             end
-%         end
-%     end
-%     for ilist=1:numel(dirima)
-%         %[pp,ff,i1_str,i2_str,j1_str,j2_str,ext_list,nom_type_list]=name2display(dirima(ilist).name);
-%         [tild,tild,tild,i1,i2,j1,j2,ext_list,nom_type_list]=fileparts_uvmat(dirima(ilist).name);
-%         form=imformats(ext_list(2:end));
-%         if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
-%             ext_ima=ext_list;
-%             nom_type_ima=nom_type_list;
-% %             i1=str2double(i1_str);
-% %             j1=str2double(j1_str);
-% %             i2=str2double(i2_str);
-% %             j2=str2double(j2_str);          
-%             % set the range of fields (1:1 by default) and selected pair
-%             if isempty(i2)
-%                 num_ref_i=i1;
-%             else
-%                 num_ref_i=floor((i1+i2)/2);
-%                 browse.incr_pair(1)=i2-i1;
-%                 browse.incr_pair(2)=0;
-%             end
-%             if isempty(j2)
-%                 if isempty(j1)
-%                     num_ref_j=1;
-%                 else
-%                     num_ref_j=j1;
-%                 end
-%             else
-%                 num_ref_j=floor((j1+j2)/2);
-%                 browse.incr_pair(2)=j2-j1;
-%             end 
-%             break
-%         end
-%     end
-% end
-
 
 %% look for an image documentation file
@@ -528 +457 @@
 end
 set(handles.ImaDoc,'String',ext_imadoc)% display the extension name for the image documentation file used
-
 
 %%  read the time in the image documentation file  
@@ -594 +522 @@
         case {'.avi','.AVI'}
             nom_type_ima='*';
-            ext_ima=ext_imadoc;
+            ImaExt=ext_imadoc;
             set(handles.ListPairMode,'Value',1);
             set(handles.ListPairMode,'String',{'series(Di)'})
@@ -632 +560 @@
 set(handles.CoordUnit,'String',CoordUnit)
 set(handles.SearchRange,'UserData',[pxcmx_search pxcmy_search]);
-set(handles.ImaExt,'String',ext_ima)
+set(handles.ImaExt,'String',ImaExt)
+set(handles.NomType,'String',NomTypeIma)
 set(handles.ref_i,'String',num2str(num_ref_i))
 set(handles.first_i,'String',num2str(num_ref_i));
@@ -639 +568 @@
 set(handles.first_j,'String',num2str(num_ref_j));
 set(handles.last_j,'String',num2str(num_ref_j));%
+% set(handles.civ,'UserData',CivData)
 
 %% set the civ options depending on the input file content
-% ind_opening=0;%default
-% if isequal(ext_input,'.nc')
-%     browse.nom_type_nc=nom_type_input;
-%     ind_opening=2;% propose 'fix' as the default option
-%     Data=nc2struct(fileinput,'ListGlobalAttribute','CivStage','absolut_time_T0','fix','patch','civ2','fix2');
-%     if isfield(Data,'Txt')
-%         msgbox_uvmat('ERROR',Data.Txt)
-%         return
-%     end
-%     if ~isempty(Data.CivStage)%test for civ files
-%         ind_opening=Data.CivStage;
-%         set(handles.ListPairMode,'Value',3)
-%     end
-% end
 ListOptions={'CheckCiv1', 'CheckFix1' 'CheckPatch1', 'CheckCiv2', 'CheckFix2', 'CheckPatch2'};
 for index = 1:ind_opening
@@ -664 +580 @@
 update_CivOptions(handles,1)
 
-
 %%  set the menus of image pairs and default selection for civ   %%%%%%%%%%%%%%%%%%%
-% test_ima_i=numel(nom_type_ima)>1 && isempty(regexp(nom_type_ima(2:end),'\D','once'))%=1 for images with single indexing
-% TODO: determine MaxIndex_i and MaxIndex_j using find_file_series (in the absence of xml file)
-% try
 check_letter=~isempty(regexp(NomTypeIma,'[ab|AB]$'));%detect pair label by letter
 if ~check_letter|| isequal(NomTypeNc,'_1-2')|| (MaxIndex_j==1)
@@ -680 +592 @@
 else
     set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)';'series(Di)'})%multiple choice
-    if  MaxIndex_j <= 10
+    if strcmp(NomTypeNc,'_1-2_1')
+        set(handles.ListPairMode,'Value',3)% advise 'series(Di)'
+    elseif  MaxIndex_j <= 10
         set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large
     end
 end
-% end
 
 %% update the subdirectory display
@@ -728 +641 @@
 
 %% store info
-% browse.nom_type_ima=nom_type_ima;
 set(handles.RootName,'UserData',browse)% store the nomenclature type
 
 %% list the possible index pairs, depending on the option set in ListPairMode
 ListPairMode_Callback([], [], handles)
-browse=get(handles.RootName,'UserData');
 
 %% store the root input filename for future opening
 profil_perso=fullfile(prefdir,'uvmat_perso.mat');
-% RootPath=fileparts(RootName);
 if exist(profil_perso,'file')
     save (profil_perso,'RootPath','-append'); %store the root name for future opening of uvmat
@@ -769 +679 @@
     set(handles.ListSubdirCiv2,'Value',ilist)
 else % if Civ1 data already exist
-    find_netcpair_civ1(handles); %update the list of available pairs from netcdf files in the new directory
+    find_netcpair_civ(handles,1); %update the list of available pairs from netcdf files in the new directory
 end
 
@@ -787 +697 @@
 %update the list of available pairs from netcdf files in the new directory
 if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
-    find_netcpair_civ2(handles);
+    find_netcpair_civ(handles,2);
 end
 
@@ -849 +759 @@
 set(handles.ListSubdirCiv1,'Visible','on')
 if ~opening
-find_netcpair_civ1(handles) % select the available netcdf files
+find_netcpair_civ(handles,1) % select the available netcdf files
 end
 if max(checkbox(4:6))% case of civ2 pair choice needed
@@ -858 +768 @@
     set(handles.ListPairCiv2,'Visible','on')
     if ~opening
-    find_netcpair_civ2(handles) % select the available netcdf files
+    find_netcpair_civ(handles,2) % select the available netcdf files
     end
 else
@@ -1757 +1667 @@
     end
 end
-%[RootPath,RootFile,field_count,str2,str_a,str_b,ext,nom_type,SubDir]=name2display(fileresu);
 [RootPath,SubDir,RootFile]=fileparts_uvmat(fileresu);
 namedoc=fullfile(RootPath,SubDir,RootFile);
@@ -1771 +1680 @@
     end
 end
+t=struct2xml(Param);
+save(t,[namedoc '.xml']); %save GUI  parameters as xml file
 saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER  .xml)
 
@@ -1844 +1755 @@
 val=get(handles.ListCompareMode,'Value');
 compare=compare_list{val};
-if strcmp(compare,'displacement')
+if strcmp(compare,'displacement')||strcmp(compare,'shift')
     mode='displacement';
 else
@@ -1853 +1764 @@
 %time=get(handles.RootName,'UserData'); %get the set of times
 ext_ima=get(handles.ImaExt,'String');
-nom_type_nc=browse.nom_type_nc;
-if isfield(browse,'nom_type_ima')
-    nom_type_ima2=browse.nom_type_ima;
-end
-if isempty(nom_type_ima2),nom_type_ima2='1';end; %default
-if isempty(nom_type_nc),nom_type_nc='_1-2';end; %default
+if strcmp(compare,'displacement')
+    nom_type_ima1='*';
+else
+    nom_type_ima1=get(handles.NomType,'String');
+end
+nom_type_nc=nomtype2pair(nom_type_ima1,mode);
+
 [num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=...
     find_pair_indices(handles,ref_i,ref_j,mode);
 %determine the new filebase for 'displacement' ListPairMode (comparison of two series)
 filebase_B=filebase;% root name of the second field series for stereo
-if strcmp(compare,'displacement') || strcmp(compare,'stereo PIV')
-%     test_disp=1;
-    nom_type_ima1=browse.nom_type_ima_1; %nomenclature type of the second file series
+if ~strcmp(compare,'PIV') 
     [Path2,Name2]=fileparts(filebase_B);
     Path1=Path2;
@@ -1880 +1790 @@
 %     test_disp=0;
     filebase_A=filebase;
-    nom_type_ima1=nom_type_ima2;
+    nom_type_ima2=nom_type_ima1;
     filebase_AB=filebase;
 end
-if strcmp(compare,'displacement')
+if strcmp(compare,'displacement')||strcmp(compare,'shift')
     filebase_ima1=filebase_A;
     filebase_ima2=filebase_B;
@@ -2353 +2263 @@
                 for j=1:nbslice
                     filename=fullfile_uvmat(RootPath_A,subdir_civ2,RootFile_A,'.nc',nom_type_nc,num1_civ2(ifile),num2_civ2(ifile),num_a_civ2(j),num_b_civ2(j));
-%                     filename=name_generator(filebase_A,num1_civ2(ifile),num_a_civ2(j),'.nc',...
-%                         nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
                     filecell.ncA.civ2(ifile,j)={filename};
                     if ~exist(filename,'file')
@@ -2372 +2280 @@
         for j=1:nbslice
             filename=fullfile_uvmat(RootPath_nc,subdir_civ2,RootFile_nc,'.nc',nom_type_nc,num1_civ2(ifile),num2_civ2(ifile),num_a_civ2(j),num_b_civ2(j));
-%             filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',...
-%                 nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);
             detect=exist(filename,'file')==2;
             filecell.nc.civ2(ifile,j)={filename};
@@ -2425 +2331 @@
             for j=1:nbslice
                  filename=fullfile_uvmat(RootPath_nc,subdir_civ2,RootFile_nc,'.nc',nom_type_nc,num1_civ2(ifile),num2_civ2(ifile),num_a_civ2(j),num_b_civ2(j));
-%                 filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',...
-%                     nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
                 filecell.nc.civ2(ifile,j)={filename};
                 if ~exist(filename,'file')
@@ -2455 +2359 @@
             for j=1:nbslice
                  filename=fullfile_uvmat(RootPath_AB,subdir_civ1,RootFile_AB,'.nc',nom_type_nc,num1_civ1(ifile),num2_civ1(ifile),num_a_civ1(j),num_b_civ1(j));
-%                 filename=name_generator(filebase_AB,num1_civ1(ifile),num_a_civ1(j),'.nc',...
-%                     nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
                 filecell.st(ifile,j)={filename};
             end
@@ -2465 +2367 @@
             for j=1:nbslice
                  filename=fullfile_uvmat(RootPath_AB,subdir_civ2,RootFile_AB,'.nc',nom_type_nc,num1_civ2(ifile),num2_civ2(ifile),num_a_civ2(j),num_b_civ2(j));
-%                 filename=name_generator(filebase_AB,num1_civ2(ifile),num_a_civ2(j),'.nc',...
-%                     nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
                 filecell.st(ifile,j)={filename};
             end
@@ -2690 +2590 @@
 function ListCompareMode_Callback(hObject, eventdata, handles)
 %------------------------------------------------------------------------
-test=get(handles.ListCompareMode,'Value');
-if test==2 || test==3 % case 'displacement' or 'stereo PIV'
+menu=get(handles.ListCompareMode,'String');
+val=get(handles.ListCompareMode,'Value');
+option=menu{val};
+if ~strcmp(option,'PIV') % case 'displacement' or 'stereo PIV'
     filebase=get(handles.RootName,'String');
     browse=get(handles.RootName,'Userdata');
-    browse.nom_type_ima1=browse.nom_type_ima;
+   % browse.nom_type_ima1=browse.nom_type_ima;
     set(handles.RootName,'UserData',browse);
     set(handles.sub_txt,'Visible','on')
@@ -2735 +2637 @@
         msgbox_uvmat('ERROR','The second image series must be in the same directory as the first one')
         return
-     end
-%     set(handles.RootName_1,'String',name);
-    %[RootPath,RootFile,field_count,str2,str_a,str_b,xx,nom_type,SubDir]=name2display(name);
+    end
     [tild,tild,RootFile,tild,tild,tild,tild,tild,nom_type]=fileparts_uvmat(name);
     set(handles.RootName_1,'String',RootFile);
     browse=get(handles.RootName,'UserData');
-    browse.nom_type_ima_1=nom_type;
+    %browse.nom_type_ima_1=nom_type;
     set(handles.RootName,'UserData',browse)
     
@@ -2749 +2649 @@
         return
     end
-    
-    %% check coincidence of image sizes
-%     ref_i=get(handles.ref_i,'string');
-%     ref_j=get(handles.ref_j,'string');
-%     [filecell,num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2,nom_type_nc]=set_civ_filenames(handles,ref_i,ref_j,[1 0 0 0 0 0]);
-%     A=imread(filecell.ima1.checkciv1{1});
-%     A_1=imread(fileinput);
-%     npxy=size(A);
-%     npxy_1=size(A_1);
-%     if ~isequal(size(A),size(A_1))
-%         msgbox_uvmat('ERROR','The two input image series do not have the same size')
-%         return
-%     end
+
 else
     set(handles.ListPairMode,'Visible','on')
@@ -2770 +2658 @@
     set(handles.ListPairMode,'Value',1)
     set(handles.ListPairMode,'String',mode_store)
-%     set(handles.test_stereo1,'Value',0)
     set(handles.CheckStereo,'Value',0)
     set(handles.ListPairMode,'Value',1) % mode 'civX' selected by default
 end
-if test==3 && get(handles.CheckPatch1,'Value')
+if strcmp(option,'stereo PIV') && get(handles.CheckPatch1,'Value')
     set(handles.CheckStereo,'Visible','on')
 else
     set(handles.CheckStereo,'Visible','off')
 end
-if test==3 && get(handles.CheckPatch2,'Value')
+if strcmp(option,'stereo PIV') && get(handles.CheckPatch2,'Value')
     set(handles.CheckStereo,'Visible','on')
 else
@@ -2797 +2684 @@
 val=get(handles.ListCompareMode,'Value');
 compare=compare_list{val};
-if strcmp(compare,'displacement')
+if strcmp(compare,'displacement')||strcmp(compare,'shift')
     mode='displacement';
 else
@@ -2821 +2708 @@
 % are relative to the reference indices ref_i and ref_j respectively.
 if isequal(mode,'pair j1-j2')%| isequal(mode,'st_pair j1-j2')
-
     dt=1;
     displ='';
@@ -2850 +2736 @@
     displ_num(3,:)=0;
     displ_num(4,:)=0;
-    set(handles.jtext,'Visible','Off')
-    set(handles.first_j,'Visible','Off')
-    set(handles.last_j,'Visible','Off')
-    set(handles.incr_j,'Visible','Off')
-    set(handles.nb_field2,'Visible','Off')
-    set(handles.ref_j,'Visible','Off')
+    enable_j(handles, 'off')
 elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)')
     index=1:200;
@@ -2861 +2742 @@
     displ_num(2,index)=ceil(index/2);
     displ_num(3:4,index)=zeros(2,200);
-%     for index=1:min(nbfield2-1,200)
-%         displ_num(1,index)=-floor(index/2);
-%         displ_num(2,index)=ceil(index/2);
-%         displ_num(3,index)=0;
-%         displ_num(4,index)=0;
-%     end
-    set(handles.jtext,'Visible','On')
-    set(handles.first_j,'Visible','On')
-    set(handles.last_j,'Visible','On')
-    set(handles.incr_j,'Visible','On')
-    set(handles.nb_field2,'Visible','On')
-    set(handles.ref_j,'Visible','On')
-%     if nbfield > 1
-%         set(handles.itext,'Visible','On')
-%         set(handles.first_i,'Visible','On')
-%         set(handles.last_i,'Visible','On')
-%         set(handles.incr_i,'Visible','On')
-%         set(handles.nb_field,'Visible','On')
-%         set(handles.ref_i,'Visible','On')
-%     else
-%         set(handles.itext,'Visible','Off')
-%         set(handles.first_i,'Visible','Off')
-%         set(handles.last_i,'Visible','Off')
-%         set(handles.incr_i,'Visible','Off')
-%         set(handles.nb_field,'Visible','Off')
-%         set(handles.ref_i,'Visible','Off')
-%     end
+    enable_j(handles, 'on')
 elseif isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)')
     index=1:200;
@@ -2893 +2748 @@
     displ_num(3,index)=-floor(index/2);
     displ_num(4,index)=ceil(index/2);
-%     for index=1:200%min(nbfield-1,200)
-%         displ_num(1,index)=0;
-%         displ_num(2,index)=0;
-%         displ_num(3,index)=-floor(index/2);
-%         displ_num(4,index)=ceil(index/2);
-%     end
-    set(handles.itext,'Visible','On')
-    set(handles.first_i,'Visible','On')
-    set(handles.last_i,'Visible','On')
-    set(handles.incr_i,'Visible','On')
-    set(handles.nb_field,'Visible','On')
-    set(handles.ref_i,'Visible','On')
+    enable_i(handles, 'on')
     if nbfield2 > 1
-        set(handles.jtext,'Visible','On')
-        set(handles.first_j,'Visible','On')
-        set(handles.last_j,'Visible','On')
-        set(handles.incr_j,'Visible','On')
-        set(handles.nb_field2,'Visible','On')
-        set(handles.ref_j,'Visible','On')
+        enable_j(handles, 'on')
     else
-        set(handles.jtext,'Visible','Off')
-        set(handles.first_j,'Visible','Off')
-        set(handles.last_j,'Visible','Off')
-        set(handles.incr_j,'Visible','Off')
-        set(handles.nb_field2,'Visible','Off')
-        set(handles.ref_j,'Visible','Off')
+        enable_j(handles, 'off')
     end
 elseif isequal(mode,'displacement')%the pairs have the same indices
@@ -2926 +2760 @@
     displ_num(4,1)=0;
     if nbfield > 1 || nbfield==0
-        set(handles.itext,'Visible','On')
-        set(handles.first_i,'Visible','On')
-        set(handles.last_i,'Visible','On')
-        set(handles.incr_i,'Visible','On')
-        set(handles.nb_field,'Visible','On')
-        set(handles.ref_i,'Visible','On')
+        enable_i(handles, 'on')
     else
-        set(handles.itext,'Visible','Off')
-        set(handles.first_i,'Visible','Off')
-        set(handles.last_i,'Visible','Off')
-        set(handles.incr_i,'Visible','Off')
-        set(handles.nb_field,'Visible','Off')
-        set(handles.ref_i,'Visible','Off')
+        enable_j(handles, 'off')
     end
     if nbfield2 > 1
-        set(handles.jtext,'Visible','On')
-        set(handles.first_j,'Visible','On')
-        set(handles.last_j,'Visible','On')
-        set(handles.incr_j,'Visible','On')
-        set(handles.nb_field2,'Visible','On')
-        set(handles.ref_j,'Visible','On')
+        enable_j(handles, 'on')
     else
-        set(handles.jtext,'Visible','Off')
-        set(handles.first_j,'Visible','Off')
-        set(handles.last_j,'Visible','Off')
-        set(handles.incr_j,'Visible','Off')
-        set(handles.nb_field2,'Visible','Off')
-        set(handles.ref_j,'Visible','Off')
+        enable_j(handles, 'off')
     end
 end
 set(handles.ListPairCiv1,'UserData',displ_num);
-find_netcpair_civ1( handles)
-find_netcpair_civ2(handles)
-browse=get(handles.RootName,'UserData');
+find_netcpair_civ( handles,1)
+% find_netcpair_civ2(handles)
+
+function enable_i(handles, state)
+set(handles.itext,'Visible',state)
+set(handles.first_i,'Visible',state)
+set(handles.last_i,'Visible',state)
+set(handles.incr_i,'Visible',state)
+set(handles.nb_field,'Visible',state)
+set(handles.ref_i,'Visible',state)
+
+function enable_j(handles, state)
+set(handles.jtext,'Visible',state)
+set(handles.first_j,'Visible',state)
+set(handles.last_j,'Visible',state)
+set(handles.incr_j,'Visible',state)
+set(handles.nb_field2,'Visible',state)
+set(handles.ref_j,'Visible',state)
+
 
 %------------------------------------------------------------------------
@@ -3052 +2882 @@
 mode_value=get(handles.ListPairMode,'Value');
 mode=mode_list{mode_value};
-find_netcpair_civ1(handles);% update the menu of pairs depending on the available netcdf files
+find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files
 if isequal(mode,'series(Di)') || ...% we do patch2 only
         (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
-    find_netcpair_civ2( handles);
+    find_netcpair_civ( handles,2);
 end
 
@@ -3065 +2895 @@
 mode=mode_list{mode_value};
 if isequal(get(handles.CheckCiv1,'Value'),0)|| isequal(mode,'series(Dj)')
-    find_netcpair_civ1(handles);% update the menu of pairs depending on the available netcdf files
+    find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files
 end
 if isequal(mode,'series(Dj)') || ...
         (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
-    find_netcpair_civ2(handles);
+    find_netcpair_civ(handles,2);
 end
 % 
+
 %------------------------------------------------------------------------
 % determine the menu for checkciv1 pairs depending on existing netcdf file at the middle of
 % the field series set by first_i, incr, last_i
-function find_netcpair_civ1(handles)
+function find_netcpair_civ(handles,index)
 %------------------------------------------------------------------------
 set(gcf,'Pointer','watch')
-%nomenclature types
 filebase=get(handles.RootName,'String');
 [filepath,Nme,ext_dir]=fileparts(filebase);
@@ -3095 +2925 @@
     mode=mode_list{mode_value};
 end
-
-% nomenclature type of the .nc files
-nom_type_ima=[];%default
-if isfield(browse,'nom_type_ima')
-    nom_type_ima=browse.nom_type_ima;
-end
-
-%determine nom_type_nc:
-nom_type_nc=[];%default
+nom_type_ima=get(handles.NomType,'String');
+
+%% determine nom_type_nc, nomenclature type of the .nc files:
+nom_type_nc='';%default
 if isfield(browse,'nom_type_nc')
     nom_type_nc=browse.nom_type_nc;
 end
 if isempty(nom_type_nc)
-    [nom_type_nc]=nomtype2pair(nom_type_ima,isequal(mode,'series(Di)'),isequal(mode,'series(Dj)'));
+    [nom_type_nc]=nomtype2pair(nom_type_ima,mode);
 end
 browse.nom_type_nc=nom_type_nc;
@@ -3115 +2940 @@
 %reads .nc subdirectoy and image numbers from the interface
 subdir_civ1=get(handles.txt_SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf data
+subdir_civ2=get(handles.txt_SubdirCiv2,'String');%subdirectory subdir_civ2 for the netcdf data
 ref_i=str2double(get(handles.ref_i,'String'));
 if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
@@ -3122 +2948 @@
 end
 time=get(handles.ImaDoc,'UserData');%get the set of times
-% if isempty(time)
-%     time=[0 1];
-% end
 TimeUnit=get(handles.TimeUnit,'String');
 checkframe=strcmp(TimeUnit,'frame');
-
 displ_num=get(handles.ListPairCiv1,'UserData');
 
@@ -3151 +2973 @@
 %% case with no Civ1 operation, netcdf files need to exist for reading
 [RootPath,RootFile]=fileparts(filebase);
+if index==1 % case civ1
 if ~get(handles.CheckCiv1,'Value') %
     if ~exist(fullfile(filepath,subdir_civ1,ext_dir),'dir')
@@ -3160 +2983 @@
         filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,...
             ref_i+displ_num(3,ipair),ref_i+displ_num(4,ipair),ref_j+displ_num(1,ipair),ref_j+displ_num(2,ipair));
-      %  filename=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,...
-       %     ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1);
         select(ipair)=exist(filename,'file')==2;% put flag to 0 if the file does not exist
     end   
@@ -3172 +2993 @@
             num_j2=ref_j+ceil(browse.incr_pair(2)/2);
             filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,num_i1,num_i2,num_j1,num_j2);
-            %filename=name_generator(filebase,num_i1,num_j1,'.nc',nom_type_nc,1,num_i2,num_j2,subdir_civ1);
             select(1)=exist(filename,'file')==2;
             testpair=1;
@@ -3186 +3006 @@
         end
     end
+end
+else %case civ2
+if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
+    if ~exist(fullfile(filepath,subdir_civ2,ext_dir),'dir')
+        errordlg(['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist'])
+        set(handles.ListPairCiv2,'Value',1);
+        set(handles.ListPairCiv2,'String',{''});
+        return
+    end
+    for ipair=1:nbpair
+        filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,...
+            ref_i+displ_num(3,ipair),ref_i+displ_num(4,ipair),ref_j+displ_num(1,ipair),ref_j+displ_num(2,ipair));
+        select(ipair)=exist(filename,'file')==2;
+    end
+    if  isequal(select,zeros(size(1:nbpair)))
+        if isfield(browse,'incr_pair')
+            num_i1=ref_i-floor(browse.incr_pair(1)/2);
+            num_i2=ref_i+floor((browse.incr_pair(1)+1)/2);
+            num_j1=ref_j-floor(browse.incr_pair(2)/2);
+            num_j2=ref_j+floor((browse.incr_pair(2)+1)/2);
+            filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile,'.nc',nom_type_nc,num_i1,num_i2,num_j1,num_j2);
+            select(1)=exist(filename,'file')==2;
+        else
+            if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
+                msgbox_uvmat('ERROR',['no civ2 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ2])
+            else
+                msgbox_uvmat('ERROR',['no civ2 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ2])
+            end
+            set(handles.ListPairCiv2,'Value',1);
+            set(handles.ListPairCiv2,'String',{''});
+            return
+        end
+    end
+end
 end
 
@@ -3270 +3124 @@
 % determine the menu for checkciv2 pairs depending on the existing netcdf file at the
 %middle of the series set by first_i, incr, last_i
-function find_netcpair_civ2(handles)
-%------------------------------------------------------------------------
-set(gcf,'Pointer','watch')
-%nomenclature types
-filebase=get(handles.RootName,'String');
-[filepath,Nme,ext_dir]=fileparts(filebase);
-browse=get(handles.RootName,'UserData');
-compare_list=get(handles.ListCompareMode,'String');
-val=get(handles.ListCompareMode,'Value');
-compare=compare_list{val};
-if strcmp(compare,'displacement')
-    mode='displacement';
-else
-    mode_list=get(handles.ListPairMode,'String');
-    if isempty(mode_list)
-        msgbox_uvmat('ERROR','please enter an input image or netcdf file')
-        return
-    end
-    mode_value=get(handles.ListPairMode,'Value');
-    mode=mode_list{mode_value};
-end
-
-% nomenclature type of the .nc files
-nom_type_ima='ima_num';%default
-if isfield(browse,'nom_type_ima')
-    nom_type_ima=browse.nom_type_ima;
-end
-nom_type_nc='_1-2';%default
-if isfield(browse,'nom_type_nc')
-    nom_type_nc=browse.nom_type_nc;
-end
-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')
-    nom_type_nc='netc_old';%nom_type for the netcdf files
-elseif isequal(nom_type_ima,'none')||isequal(nom_type_nc,'none')
-    nom_type_nc='none';
-elseif isequal(nom_type_ima,'avi')||isequal(nom_type_ima,'_i')||isequal(nom_type_ima,'ima_num')||isequal(nom_type_nc,'_1-2')
-    nom_type_nc='_1-2';
-else
-    if  isequal(mode,'series(Di)')%|isequal(mode,'st_series(Di)')
-        nom_type_nc='_1-2_1'; % PIV in volume
-    else
-        nom_type_nc='_1_1-2';
-    end
-end
-browse.nom_type_nc=nom_type_nc;
-set(handles.RootName,'UserData',browse)
-
-%reads .nc subdirectory and image numbers from the interface
-subdir_civ1=get(handles.txt_SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf data
-subdir_civ2=get(handles.txt_SubdirCiv2,'String');%subdirectory subdir_civ2 for the netcdf data
-ref_i=str2double(get(handles.ref_i,'String'));
-if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
-    ref_j=0;
-else
-    ref_j=str2double(get(handles.ref_j,'String'));
-end
-time=get(handles.ImaDoc,'UserData'); %get the set of times
-TimeUnit=get(handles.TimeUnit,'String');
-checkframe=strcmp(TimeUnit,'frame');
-% if isempty(time)
-%     time=[0 1];%default
+% function find_netcpair_civ2(handles)
+% %------------------------------------------------------------------------
+% set(gcf,'Pointer','watch')
+% %nomenclature types
+% filebase=get(handles.RootName,'String');
+% [filepath,Nme,ext_dir]=fileparts(filebase);
+% browse=get(handles.RootName,'UserData');
+% compare_list=get(handles.ListCompareMode,'String');
+% val=get(handles.ListCompareMode,'Value');
+% compare=compare_list{val};
+% if strcmp(compare,'displacement')
+%     mode='displacement';
+% else
+%     mode_list=get(handles.ListPairMode,'String');
+%     if isempty(mode_list)
+%         msgbox_uvmat('ERROR','please enter an input image or netcdf file')
+%         return
+%     end
+%     mode_value=get(handles.ListPairMode,'Value');
+%     mode=mode_list{mode_value};
 % end
-displ_num=get(handles.ListPairCiv1,'UserData');
-
-%eliminate the first pairs inconsistent with the position
-if isempty(displ_num)
-    nbpair=0;
-else
-    nbpair=length(displ_num(1,:));%nbre of displayed pairs
-    if  isequal(mode,'series(Di)')% | isequal(mode,'st_series(Di)')
-        nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index
-    elseif  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
-        nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index
-    end
-end
-nbpair=min(200,nbpair);%limit the number of displayed pairs to 200
-
-%% look for existing processed pairs at the reference indices if Civ1 will not
-% be performed, while the result is needed for next steps.
-displ_pair={''}; %default
-select=ones(size(1:nbpair));%default =1 for numbers of displayed pairs
-[RootPath,RootFile]=fileparts(filebase);
-if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
-    if ~exist(fullfile(filepath,subdir_civ2,ext_dir),'dir')
-        errordlg(['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist'])
-        set(handles.ListPairCiv2,'Value',1);
-        set(handles.ListPairCiv2,'String',{''});
-        return
-    end
-    for ipair=1:nbpair
-        filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,...
-            ref_i+displ_num(3,ipair),ref_i+displ_num(4,ipair),ref_j+displ_num(1,ipair),ref_j+displ_num(2,ipair));
-       % filename=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,...
-        %    ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1);
-        select(ipair)=exist(filename,'file')==2;
-    end
-    if  isequal(select,zeros(size(1:nbpair)))
-        if isfield(browse,'incr_pair')
-            num_i1=ref_i-floor(browse.incr_pair(1)/2);
-            num_i2=ref_i+floor((browse.incr_pair(1)+1)/2);
-            num_j1=ref_j-floor(browse.incr_pair(2)/2);
-            num_j2=ref_j+floor((browse.incr_pair(2)+1)/2);
-            filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile,'.nc',nom_type_nc,num_i1,num_i2,num_j1,num_j2);
-            %filename=name_generator(filebase,num_i1,num_j1,'.nc',nom_type_nc,1,num_i2,num_j2,subdir_civ2);
-            select(1)=exist(filename,'file')==2;
-        else
-            if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
-                msgbox_uvmat('ERROR',['no civ2 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ2])
-            else
-                msgbox_uvmat('ERROR',['no civ2 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ2])
-            end
-            set(handles.ListPairCiv2,'Value',1);
-            set(handles.ListPairCiv2,'String',{''});
-            return
-        end
-    end
-end
-if isequal(mode,'series(Di)') 
-    for ipair=1:nbpair
-        if select(ipair)
-            displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
-            if  ~checkframe && size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
-                dt=time(ref_i+displ_num(4,ipair)+1,ref_j+displ_num(2,ipair)+1)-time(ref_i+displ_num(3,ipair)+1,ref_j+displ_num(1,ipair)+1);%time interval dt
-                displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
-            end
-        else
-            displ_pair{ipair}='...'; %pair not displayed in the menu
-        end
-    end
-elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)') % series on the j index
-    for ipair=1:nbpair
-        if select(ipair)
-            displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
-            if ~checkframe && size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)&& displ_num(1,ipair)>=1 && displ_num(2,ipair)>=1
-                dt=time(ref_i+displ_num(4,ipair)+1,ref_j+displ_num(2,ipair)+1)-time(ref_i+displ_num(3,ipair)+1,ref_j+displ_num(1,ipair)+1);%time interval dt
-            else
-                dt=1;
-            end
-                displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
-        else
-            displ_pair{ipair}='...'; %pair not displayed in the menu
-        end
-    end
-elseif isequal(mode,'pair j1-j2')% | isequal(mode,'st_pair j1-j2') %case of pairs
-    for ipair=1:nbpair
-        if select(ipair)
-            if  ~checkframe && size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair) && displ_num(1,ipair)>=1 && displ_num(2,ipair)>=1
-            dt=time(ref_i+displ_num(4,ipair)+1,displ_num(2,ipair)+1)-time(ref_i+displ_num(3,ipair)+1,displ_num(1,ipair)+1);%time interval dt
-            else
-                dt=1;
-            end
-            displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair)+1,nom_type_ima) '-' num2stra(displ_num(2,ipair)+1,nom_type_ima) ...
-                ' :dt= ' num2str(dt*1000)];
-                
-        else
-            displ_pair{ipair}='...'; %pair not displayed in the menu
-        end
-    end
-elseif isequal(mode,'displacement')
-    displ_pair={'Di=Dj=0'};
-end
-val=get(handles.ListPairCiv2,'Value');
-ichoice=find(select,1);
-if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
-if get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0
-    val=ichoice;% first valid pair proposed by default in the menu
-end
-if val>length(displ_pair')
-    set(handles.ListPairCiv2,'Value',1);% first valid pair proposed by default in the menu
-else
-    set(handles.ListPairCiv2,'Value',val);
-end
-set(handles.ListPairCiv2,'String',displ_pair');
-set(gcf,'Pointer','arrow')
+% 
+% % nomenclature type of the .nc files
+% nom_type_ima='ima_num';%default
+% NomTypeIma=get(handles.NomType,'String');
+% nom_type_nc='_1-2';%default
+% if isfield(browse,'nom_type_nc')
+%     nom_type_nc=browse.nom_type_nc;
+% end
+% 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')
+%     nom_type_nc='netc_old';%nom_type for the netcdf files
+% elseif isequal(nom_type_ima,'none')||isequal(nom_type_nc,'none')
+%     nom_type_nc='none';
+% elseif isequal(nom_type_ima,'avi')||isequal(nom_type_ima,'_i')||isequal(nom_type_ima,'ima_num')||isequal(nom_type_nc,'_1-2')
+%     nom_type_nc='_1-2';
+% else
+%     if  isequal(mode,'series(Di)')%|isequal(mode,'st_series(Di)')
+%         nom_type_nc='_1-2_1'; % PIV in volume
+%     else
+%         nom_type_nc='_1_1-2';
+%     end
+% end
+% browse.nom_type_nc=nom_type_nc;
+% set(handles.RootName,'UserData',browse)
+% 
+% %reads .nc subdirectory and image numbers from the interface
+% subdir_civ1=get(handles.txt_SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf data
+% subdir_civ2=get(handles.txt_SubdirCiv2,'String');%subdirectory subdir_civ2 for the netcdf data
+% ref_i=str2double(get(handles.ref_i,'String'));
+% if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
+%     ref_j=0;
+% else
+%     ref_j=str2double(get(handles.ref_j,'String'));
+% end
+% time=get(handles.ImaDoc,'UserData'); %get the set of times
+% TimeUnit=get(handles.TimeUnit,'String');
+% checkframe=strcmp(TimeUnit,'frame');
+% % if isempty(time)
+% %     time=[0 1];%default
+% % end
+% displ_num=get(handles.ListPairCiv1,'UserData');
+% 
+% %eliminate the first pairs inconsistent with the position
+% if isempty(displ_num)
+%     nbpair=0;
+% else
+%     nbpair=length(displ_num(1,:));%nbre of displayed pairs
+%     if  isequal(mode,'series(Di)')% | isequal(mode,'st_series(Di)')
+%         nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index
+%     elseif  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
+%         nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index
+%     end
+% end
+% nbpair=min(200,nbpair);%limit the number of displayed pairs to 200
+% 
+% %% look for existing processed pairs at the reference indices if Civ1 will not
+% % be performed, while the result is needed for next steps.
+% displ_pair={''}; %default
+% select=ones(size(1:nbpair));%default =1 for numbers of displayed pairs
+% [RootPath,RootFile]=fileparts(filebase);
+% if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
+%     if ~exist(fullfile(filepath,subdir_civ2,ext_dir),'dir')
+%         errordlg(['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist'])
+%         set(handles.ListPairCiv2,'Value',1);
+%         set(handles.ListPairCiv2,'String',{''});
+%         return
+%     end
+%     for ipair=1:nbpair
+%         filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,...
+%             ref_i+displ_num(3,ipair),ref_i+displ_num(4,ipair),ref_j+displ_num(1,ipair),ref_j+displ_num(2,ipair));
+%        % filename=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,...
+%         %    ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1);
+%         select(ipair)=exist(filename,'file')==2;
+%     end
+%     if  isequal(select,zeros(size(1:nbpair)))
+%         if isfield(browse,'incr_pair')
+%             num_i1=ref_i-floor(browse.incr_pair(1)/2);
+%             num_i2=ref_i+floor((browse.incr_pair(1)+1)/2);
+%             num_j1=ref_j-floor(browse.incr_pair(2)/2);
+%             num_j2=ref_j+floor((browse.incr_pair(2)+1)/2);
+%             filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile,'.nc',nom_type_nc,num_i1,num_i2,num_j1,num_j2);
+%             %filename=name_generator(filebase,num_i1,num_j1,'.nc',nom_type_nc,1,num_i2,num_j2,subdir_civ2);
+%             select(1)=exist(filename,'file')==2;
+%         else
+%             if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
+%                 msgbox_uvmat('ERROR',['no civ2 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ2])
+%             else
+%                 msgbox_uvmat('ERROR',['no civ2 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ2])
+%             end
+%             set(handles.ListPairCiv2,'Value',1);
+%             set(handles.ListPairCiv2,'String',{''});
+%             return
+%         end
+%     end
+% end
+% if isequal(mode,'series(Di)') 
+%     for ipair=1:nbpair
+%         if select(ipair)
+%             displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
+%             if  ~checkframe && size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
+%                 dt=time(ref_i+displ_num(4,ipair)+1,ref_j+displ_num(2,ipair)+1)-time(ref_i+displ_num(3,ipair)+1,ref_j+displ_num(1,ipair)+1);%time interval dt
+%                 displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
+%             end
+%         else
+%             displ_pair{ipair}='...'; %pair not displayed in the menu
+%         end
+%     end
+% elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)') % series on the j index
+%     for ipair=1:nbpair
+%         if select(ipair)
+%             displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
+%             if ~checkframe && size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)&& displ_num(1,ipair)>=1 && displ_num(2,ipair)>=1
+%                 dt=time(ref_i+displ_num(4,ipair)+1,ref_j+displ_num(2,ipair)+1)-time(ref_i+displ_num(3,ipair)+1,ref_j+displ_num(1,ipair)+1);%time interval dt
+%             else
+%                 dt=1;
+%             end
+%                 displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
+%         else
+%             displ_pair{ipair}='...'; %pair not displayed in the menu
+%         end
+%     end
+% elseif isequal(mode,'pair j1-j2')% | isequal(mode,'st_pair j1-j2') %case of pairs
+%     for ipair=1:nbpair
+%         if select(ipair)
+%             if  ~checkframe && size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair) && displ_num(1,ipair)>=1 && displ_num(2,ipair)>=1
+%             dt=time(ref_i+displ_num(4,ipair)+1,displ_num(2,ipair)+1)-time(ref_i+displ_num(3,ipair)+1,displ_num(1,ipair)+1);%time interval dt
+%             else
+%                 dt=1;
+%             end
+%             displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair)+1,nom_type_ima) '-' num2stra(displ_num(2,ipair)+1,nom_type_ima) ...
+%                 ' :dt= ' num2str(dt*1000)];
+%                 
+%         else
+%             displ_pair{ipair}='...'; %pair not displayed in the menu
+%         end
+%     end
+% elseif isequal(mode,'displacement')
+%     displ_pair={'Di=Dj=0'};
+% end
+% val=get(handles.ListPairCiv2,'Value');
+% ichoice=find(select,1);
+% if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
+% if get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0
+%     val=ichoice;% first valid pair proposed by default in the menu
+% end
+% if val>length(displ_pair')
+%     set(handles.ListPairCiv2,'Value',1);% first valid pair proposed by default in the menu
+% else
+%     set(handles.ListPairCiv2,'Value',val);
+% end
+% set(handles.ListPairCiv2,'String',displ_pair');
+% set(gcf,'Pointer','arrow')
 
 %-------------------------------------------------------------------
@@ -3833 +3685 @@
 end
 set(handles.txt_SubdirCiv1,'String',SubDir);
-find_netcpair_civ1(handles) 
+find_netcpair_civ(handles,1) 
 
 %------------------------------------------------------------------------
@@ -4674 +4526 @@
 % Dtj: ~=0 if i index pairs are used
 
-function [nom_type_pair]=nomtype2pair(nom_type,Dti,Dtj)
+function NomTypeNc=nomtype2pair(NomTypeIma,mode)
 
 %determine nom_type_nc:
-nom_type_pair=[];%default
-if ischar(nom_type)
-    switch nom_type
-        case {'_i_j'}
-            if Dtj>0 || Dtj<0
-                nom_type_pair='_i_j1-j2';
-                if Dti>0 || Dti<0
-                    nom_type_pair='_i1-i2_j1-j2';
-                end
-                elseif Dti>0 || Dti<0
-                nom_type_pair='_i1-i21_j';   
-            else
-                 nom_type_pair='_i_j';
-            end
-        case {'_i1-i2_j'}
-            if Dtj>0 || Dtj<0
-               nom_type_pair='_i1-i2_j1-j2';
-            else
-                nom_type_pair='_i1-i2_j';
-            end
-        case {'i_j1-j2'}
-            if Dti>0 || Dti<0
-               nom_type_pair='_i1-i2_j1-j2';
-            else
-                nom_type_pair='_i1-i2_j';
-            end
-        case {'i1-i2_j1-j2'}
-             nom_type_pair='_i1-i2_j1-j2';
-        case '#a'
-            if Dtj>0 || Dtj<0
-                nom_type_pair='#_ab';
-            end
-        otherwise
-            if Dti>0 || Dti<0
-               nom_type_pair='_i1-i2'; 
-            end
-    end
-end
-
+NomTypeNc='';%default
+switch mode
+    case 'pair j1-j2'      
+    if ~isempty(regexp(NomTypeIma,'a$'))
+        NomTypeNc=[NomTypeIma 'b'];
+    elseif ~isempty(regexp(NomTypeIma,'A$'))
+        NomTypeNc=[NomTypeIma 'B'];
+    else
+        r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
+        if ~isempty(r)
+            NomTypeNc='_1_1-2';
+        end
+    end
+    case 'series(Dj)'  
+        r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
+        if ~isempty(r)
+            NomTypeNc='_1_1-2';
+        end
+   case 'series(Di)'
+        r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
+        if ~isempty(r)
+            NomTypeNc='_1-2_1';
+        else
+            NomTypeNc='_1-2';
+        end
+end
+
+function NomType_Callback(hObject, eventdata, handles)

trunk/src/find_file_series.m

@@ -88 +88 @@
             try
                 if exist('VideoReader','file')%recent version of Matlab
-                    Object=VideoReader(fileinput);    
+                    Object=VideoReader(fileinput);
                 else
-                    Object=mmreader(fileinput);%older Matlab function for movies                
+                    Object=mmreader(fileinput);%older Matlab function for movies
                 end
                 NomType='*';
-                FileType='video';  
+                FileType='video';
                 i1_series=(1:get(Object,'NumberOfFrames'))';
             end
@@ -99 +99 @@
 end
 
-%% get the list of existing files when relevant
 if strcmp(NomType,'')||strcmp(NomType,'*')
     if exist(fileinput,'file')
-    [RootPath,RootFile]=fileparts(fileinput);% case of constant name (no indexing)
+        [RootPath,RootFile]=fileparts(fileinput);% case of constant name (no indexing)
     else
-       RootPath='';
-       RootFile='';
-    end
-else
-    if strcmp(SubDir,'')
-        filebasesub=fullfile(RootPath,RootFile);
-    else
-        filebasesub=fullfile(RootPath,SubDir,RootFile);
-    end
-    detect_string=regexprep(NomType,'\d','*');%replace numbers by '*'
-    old_string='';
-    detect_string=regexprep(detect_string,'[ab]$','*');%suppress the possible letter ab at the end
-    detect_string=regexprep(detect_string,'[AB]$','*');%suppress the possible letter ab at the end
-    detect_string=regexprep(detect_string,'[a|A]$','*');%suppress a possible second letter a,A at the end
-    while ~strcmp(detect_string,old_string)%removes multiple '*'
-        old_string=detect_string;
-        detect_string=regexprep(detect_string,'**','*');
-    end
-    dirpair=dir([filebasesub detect_string FileExt]);
+        RootPath='';
+        RootFile='';
+    end
+else   
+    %% analyse the list of existing files when relevant
+    sep1='';
+    i1_str='(?<i1>)';
+    i1_star='';
+    sep2='';
+    i2_str='(?<i2>)';
+    i2_star='';
+    sep3='';
+    j1_str='(?<j1>)';
+    j1_star='';
+    sep4='';
+    j2_str='(?<j2>)';
+    j2_star='';
+    NomTypeStr=NomType;
+    if ~isempty(regexp(NomTypeStr,'^_\d'))
+        sep1='_';
+        NomTypeStr(1)=[];%remove '_' from the beginning of NomTypeStr
+    end
+    r=regexp(NomTypeStr,'^(?<num1>\d+)','names');%look for a number at the beginning of NomTypeStr
+    if ~isempty(r)
+        i1_str='(?<i1>\d+)';
+        i1_star='*';
+        NomTypeStr=regexprep(NomTypeStr,['^' r.num1],'');
+        r=regexp(NomTypeStr,'^-(?<num2>\d+)','names');%look for a pair i1-i2
+        if ~isempty(r)
+            sep2='-';
+            i2_str='(?<i2>\d+)';
+            i2_star='*';
+            NomTypeStr=regexprep(NomTypeStr,['^-' r.num2],'');
+        end
+        if ~isempty(regexp(NomTypeStr,'^_'));
+            sep3='_';
+            NomTypeStr(1)=[];%remove '_' from the beginning of NomTypeStr
+        end
+        if ~isempty(regexp(NomTypeStr,'^[a|A]'));
+            j1_str='(?<j1>[a-z]|[A-Z])';
+            j1_star='*';
+            if ~isempty(regexp(NomTypeStr,'[b|B]$'));
+                j2_str='(?<j1>[a-z]|[A-Z])';
+                j2_star='*';
+            end
+        else
+            r=regexp(NomTypeStr,'^(?<num3>\d+)','names');
+            if ~isempty(r)
+                j1_str='(?<j1>\d+)';
+                 j1_star='*';
+                NomTypeStr=regexprep(NomTypeStr,['^' r.num3],'');
+            end
+            r=regexp(NomTypeStr,'-(?<num4>\d+)','names');
+            if ~isempty(r)
+                sep4='-';
+                j2_str='(?<j2>\d+)';
+                 j2_star='*';
+            end
+        end
+    end
+    detect_string=[sep1 i1_str sep2 i2_str sep3 j1_str sep4 j2_str];%string used in regexp to detect file indices
+    %find the string used to extract the relevant files with the command dir
+    star_string=['*' sep1 i1_star sep2 i2_star sep3 j1_star sep4 j2_star '*'];
+    wd=pwd;%current working directory
+    RR=fullfile(RootPath,SubDir);
+    cd (RR)% move to the local dir to save time in the operation dir.
+    dirpair=dir([RootFile star_string FileExt]);% look for relevant files in the file directory
+    cd(wd)
     nbpair=numel(dirpair);
     ref_i_list=zeros(1,nbpair);
@@ -130 +178 @@
         RootFile='';
     end
+    % scan the list of relevant files, extract the indices
     for ifile=1:nbpair
-        [tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(dirpair(ifile).name);
+        rr=regexp(dirpair(ifile).name,detect_string,'names');
+        i1=str2num(rr.i1);
+        i2=str2num(rr.i2);
+        j1=stra2num(rr.j1);
+        j2=stra2num(rr.j2);
         ref_i=i1;
         if isempty(i2_input)
@@ -187 +240 @@
         ref_ij=ref_i_list*max_j+ref_j_list; % ordered by index i, then by j for a given i.
     end
-    [tild,ifile]=min(ref_ij(ref_ij>0));
-    if isempty(ifile)
+    [tild,ifile_min]=min(ref_ij(ref_ij>0));
+    if isempty(ifile_min)
         RootPath='';
         RootFile='';
         NomType='';
     else
-    [tild,tild,tild,tild,tild,tild,tild,tild,NomType]=fileparts_uvmat(dirpair(ifile).name);
+        [tild,tild,tild,tild,tild,tild,tild,tild,NomType]=fileparts_uvmat(dirpair(ifile_min).name);
     end
 end

trunk/src/fullfile_uvmat.m

@@ -36 +36 @@
 
 function filename=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,i1,i2,j1,j2)
-% sizf=size(filebase);
-% if (~ischar(filebase)||~isequal(sizf(1),1)),filebase='';end
-% if ~exist('ext','var')
-%     ext='';
-% end
-% if ~exist('nom_type','var')
-%     nom_type='';
-% end
-% if ~ischar(ext),ext='';end
-% % idetect=0;
-% if ~exist('i1','var') || isempty(i1) || isnan(i1)
-%     i1=1; %default
-% end
-% if ~exist('j1','var') ||  isempty(j1) || isnan(j1)
-%     j1=1; %default
-% end
-% if ~exist('i2','var') ||  isempty(i2) || isnan(i2)
-%     i2=i1; %default
-% end
-% if ~exist('j2','var') || isempty(j2) || isnan(j2)
-%     j2=j1; %default
-% end
-% if ~exist('subdir','var')|| isempty(subdir) 
-%     subdir='' ; %default
-% end
-
     
 %% display help and test function in the absence of input arument
@@ -75 +49 @@
 end
 if isequal(j1,j2)
-    j2=[];
+    j2=[];% suppress the secodn index if equal to the first
 end
 if ~exist('j1','var') 
@@ -84 +58 @@
 end
 if isequal(i1,i2)
-    i2=[];
+    i2=[];% suppress the secodn index if equal to the first
 end
 if ~exist('i1','var') 
@@ -108 +82 @@
 if ~isempty(r)
     i1_str=num2str(i1,['%0' num2str(length(r.num1)) 'd']);
-    NomType=regexprep(NomType,['^' r.num1],'');
+    NomType=regexprep(NomType,['^' r.num1],'');   
     r=regexp(NomType,'^-(?<num2>\d+)','names');%look for a pair i1-i2
     if ~isempty(r)
+         if ~isempty(i2)
         sep2='-';
          i2_str=num2str(i2,['%0' num2str(length(r.num2)) 'd']);
+         end
          NomType=regexprep(NomType,['^-' r.num2],'');
     end
@@ -121 +97 @@
     if ~isempty(regexp(NomType,'^[a|A]'));
         j1_str=num2stra(j1,NomType);
-        if ~isempty(regexp(NomType,'[b|B]$'));
+        if ~isempty(regexp(NomType,'[b|B]$'))&& ~isempty(j2);
             j2_str=num2stra(j2,NomType);
         end
@@ -130 +106 @@
             NomType=regexprep(NomType,['^' r.num3],'');
         end
+        if ~isempty(j2) 
         r=regexp(NomType,'-(?<num4>\d+)','names');
-        if ~isempty(r)&& ~isempty(j2)
+        if ~isempty(r)
             sep4='-';
             j2_str=num2str(j2,['%0' num2str(length(r.num4)) 'd']);
+        end
         end
     end

trunk/src/series.m

@@ -1087 +1087 @@
 function RUN_Callback(hObject, eventdata, handles)
 %------------------------------------------------------------------------
+%% Read parameters from series
+Series=read_GUI(handles.series)%TODO: extend to all input param
+Series.hseries=handles.series; % handles to the series GUI
+
 %% read root name and field type
 set(handles.RUN,'BusyAction','queue');
@@ -1096 +1100 @@
     Series.GetObject=0;
 end
-SeriesData=get(handles.series,'UserData');
+% SeriesData=get(handles.series,'UserData');
 
 % Series.hseries=handles.series; % handles to the series GUI
-
-%% Read parameters from series
-Series=read_GUI(handles.series);%TODO: extend to all input param
-Series.hseries=handles.series; % handles to the series GUI
-
    first_i=1;
    last_i=1;
@@ -1129 +1128 @@
 NomType=Series.InputTable(:,4);
 FileExt=Series.InputTable(:,5);
-% RootPath=get(handles.RootPath,'String');% path of the root name of the first field series
-% RootFile=get(handles.RootFile,'String');% root name of the first field series 
-% SubDir=get(handles.SubDir,'String');% subdirectory for netcdf files
-% FileExt=get(handles.FileExt,'String');%file extension
-if isempty(SeriesData)
-    msgbox_uvmat('ERROR','no input file series')
-    return
-end
+% if isempty(SeriesData)
+%     msgbox_uvmat('ERROR','no input file series')
+%     return
+% end
 % NomType=SeriesData.NomType;
-if length(RootPath)==1 %string character input for user fct
-    Series.RootPath=RootPath{1};
-    Series.RootFile=RootFile{1};
-    Series.SubDir=SubDir{1};
-    Series.FileExt=FileExt{1};
-    Series.NomType=NomType{1};
-else %cell input for user fct
-    Series.RootPath=RootPath;
-    Series.RootFile=RootFile;
-    Series.SubDir=SubDir;
-    Series.FileExt=FileExt;
-    Series.NomType=NomType;
-end
-if isequal(get(handles.FieldMenu,'Visible'),'on')
-    FieldMenu=get(handles.FieldMenu,'String');
-    FieldValue=get(handles.FieldMenu,'Value');
-    Series.Field=FieldMenu(FieldValue);
-end
+% if length(RootPath)==1 %string character input for user fct
+%     Series.RootPath=RootPath{1};
+%     Series.RootFile=RootFile{1};
+%     Series.SubDir=SubDir{1};
+%     Series.FileExt=FileExt{1};
+%     Series.NomType=NomType{1};
+% else %cell input for user fct
+%     Series.RootPath=RootPath;
+%     Series.RootFile=RootFile;
+%     Series.SubDir=SubDir;
+%     Series.FileExt=FileExt;
+%     Series.NomType=NomType;
+% end
+% if isequal(get(handles.FieldMenu,'Visible'),'on')
+%     FieldMenu=get(handles.FieldMenu,'String');
+%     FieldValue=get(handles.FieldMenu,'Value');
+%     Series.Field=FieldMenu(FieldValue);
+% end
 menu_coord_state=get(handles.transform_fct,'Visible');
 Series.CoordType='';%default
@@ -1164 +1159 @@
     Series.transform_fct=transform_list{menu_index};% transform function handles
 end
-    
-%     
-% first_i=str2num(get(handles.num_first_i,'String'));
-% last_i=str2num(get(handles.num_last_i,'String'));
-% incr_i=str2num(get(handles.num_incr_i,'String'));
-% first_j=str2num(get(handles.num_first_j,'String'));
-% last_j=str2num(get(handles.num_last_j,'String'));
-% incr_j=str2num(get(handles.num_incr_j,'String'));
-% if ~isequal(get(handles.num_first_i,'Visible'),'on')
-%    first_i=1;
-%    last_i=1;
-%    incr_i=1;
-% end
-% if ~isequal(get(handles.num_first_j,'Visible'),'on')
-%     first_j=1;
-%     last_j=1;
-%     incr_j=1;
-% end
 
 %reinitiate waitbar position
@@ -1202 +1179 @@
 nbfield=nb(1);
 nbfield2=nb(2);
-% nbfield2=cell2mat(Series.IndexRange.MaxIndex);
-% nbfield=min(nbfield);
-% % nbfield=[]; %default
-% % for iview=1:length(nbfield_cell)
-% %     nb=nbfield_cell{iview};
-% %     if ~isempty(nb)
-% %         nbfield=[nbfield nb];
-% %     end
-% % end
-% % nbfield=min(nbfield);
-% nbfield2_cell=get(handles.num_MaxIndex_j,'String');
-% nbfield2=[]; %default
-% for iview=1:length(nbfield2_cell)
-%     nb=str2num(nbfield2_cell{iview});
-%     if ~isempty(nb)
-%         nbfield2=[nbfield2 nb];
-%     end
-% end
-% nbfield2=min(nbfield2);
 
 %get complementary information from the 'series' interface
@@ -1233 +1191 @@
 %determine the list of input file names
 nbmissing=0;
-for iview=1:length(RootPath)
-    %case of pairs (.nc files)
-    fileinput=name_generator(fullfile(RootPath{iview},RootFile{iview}),first_i,first_j,FileExt{iview},NomType{iview},1,first_i+1,first_j+1,SubDir{iview});
-    if strcmp(get(handles.Pairs,'Visible'),'on')
-       pair_list=get(handles.list_pair_civ,'String');
-       val=get(handles.list_pair_civ,'Value');
-       pair_string=pair_list{val};
-       r=regexp(pair_string,'.*\D(?<num1>[\d+|*])(?<delim>[-||])(?<num2>[\d+|*])','names');
-       if ~isempty(r)
-           if strcmp(r.num1,'*')%free pairs
-               [tild,RootFile,i1_series,i2_series,j1_series,j2_series,tild,tild,Object]=find_file_series(fileinput)% TODO: choice pair when multiple choice
- 
-               if isempty(i2_series) %j pairs
-                   ind_sel=i1_series>=i1_series>=first_i & i1_series<=last_i & j1_series>first_j & j2_series<last_j;
-                   j2_series=j2_series(ind_sel);
-               else%i pairs
-                   if isempty(j1_series) %j pairs
-                        ind_sel=i1_series>=first_i & i2_series<=last_i ;
-                   else
-                       ind_sel=i1_series>=first_i & i2_series<=last_i& j1_series>first_j & j1_series<last_j; 
-                       j1_series=j1_series(ind_sel);
-                       i2_series=i2_series(ind_sel);
-                   end
-               end
-               i1_series=i1_series(ind_sel);             
-           else
-               if strcmp(r.delim,'-')
-                   ind_shift(1)=str2num(r.num1);
-                   ind_shift(2)=str2num(r.num2);
-               else
-                   ind_shift(1)=-str2num(r.num1);
-                   ind_shift(2)=str2num(r.num2);
-               end
-               [i1_series,i2_series,j1_series,j2_series,nbmissing]=find_file_indices(num_i,num_j,ind_shift,NomType{iview},mode);
-           end
-       end
-       if isempty(i1_series)
-           msgbox_uvmat('ERROR','no file in the considered range')
-           return
-       end
-       if isempty(i2_series)
-           i2_series=i1_series;
-       end
-       if isempty(j2_series)
-           j2_series=j1_series;
-       end 
-%     if isequal(NomType{iview},'_1_1-2')|| isequal(NomType{iview},'_1-2_1')|| isequal(NomType{iview},'_1-2')|| isequal(NomType{iview},'#_ab')
-%         ind_shift=SeriesData.displ_num(iview,:);
-%         if isequal(ind_shift,[0 0 0 0]) % undefined pairs
-%             if isequal(NomType{iview},'#_ab')
-%                 mode='#_ab';
-%             end
-%             [num_i1,i2_series,j1_series,num_j2,nbmissing]=netseries_generator(fullfile(RootPath{iview},RootFile{iview}),SubDir{iview},mode,num_first_i,num_incr_i,num_last_i,num_first_j,num_incr_j,num_last_j);
-%         else    
-%             [num_i1,num_i2,num_j1,num_j2,num_i,num_j]=find_file_indices(num_i,num_j,ind_shift,NomType{iview},mode);
-%             if isempty(num_i)
-%                 msgbox_uvmat('ERROR','ERROR: empty set of input files chosen')
-%                 return
-%             end
-%             if num_i(1)>num_first_i
-%                set(handles.num_first_i,'String',num2str(num_i(1)))%update the display of first field
-%                last_i_Callback(hObject, eventdata, handles)
-%             end
-%             if num_i(end)<num_last_i
-%                set(handles.num_last_i,'String',num2str(num_i(end)))%update the display of last field
-%                last_i_Callback(hObject, eventdata, handles)
-%             end
-%             if num_j(1)>num_first_j
-%                set(handles.num_first_j,'String',num2str(num_j(1)))%update the display of first field
-%                last_j_Callback(hObject, eventdata, handles)
-%             end
-%             if num_j(end)<num_last_j
-%                set(handles.num_last_j,'String',num2str(num_j(end)))%update the display of last field
-%                last_j_Callback(hObject, eventdata, handles)
-%             end 
-%         end
-    else%case of images
-        [i1_series,j1_series]=meshgrid(num_i,num_j);
-        i2_series=i1_series;
-        j2_series=j1_series;
-    end
-    if length(RootPath)>1
-        i1_series_cell{iview}=i1_series;
-        i2_series_cell{iview}=i2_series;
-        j1_series_cell{iview}=j1_series;
-        j2_series_cell{iview}=j2_series;
-    end
-end
+% for iview=1:length(RootPath)
+%     %case of pairs (.nc files)
+%     fileinput=name_generator(fullfile(RootPath{iview},RootFile{iview}),first_i,first_j,FileExt{iview},NomType{iview},1,first_i+1,first_j+1,SubDir{iview});
+%     if strcmp(get(handles.Pairs,'Visible'),'on')
+%        pair_list=get(handles.list_pair_civ,'String');
+%        val=get(handles.list_pair_civ,'Value');
+%        pair_string=pair_list{val};
+%        r=regexp(pair_string,'.*\D(?<num1>[\d+|*])(?<delim>[-||])(?<num2>[\d+|*])','names');
+%        if ~isempty(r)
+%            if strcmp(r.num1,'*')%free pairs
+%                [tild,RootFile,i1_series,i2_series,j1_series,j2_series,tild,tild,Object]=find_file_series(fileinput);% TODO: choice pair when multiple choice
+%  
+%                if isempty(i2_series) %j pairs
+%                    ind_sel=i1_series>=i1_series>=first_i & i1_series<=last_i & j1_series>first_j & j2_series<last_j;
+%                    j2_series=j2_series(ind_sel);
+%                else%i pairs
+%                    if isempty(j1_series) %j pairs
+%                         ind_sel=i1_series>=first_i & i2_series<=last_i ;
+%                    else
+%                        ind_sel=i1_series>=first_i & i2_series<=last_i& j1_series>first_j & j1_series<last_j; 
+%                        j1_series=j1_series(ind_sel);
+%                        i2_series=i2_series(ind_sel);
+%                    end
+%                end
+%                i1_series=i1_series(ind_sel);             
+%            else
+%                if strcmp(r.delim,'-')
+%                    ind_shift(1)=str2num(r.num1);
+%                    ind_shift(2)=str2num(r.num2);
+%                else
+%                    ind_shift(1)=-str2num(r.num1);
+%                    ind_shift(2)=str2num(r.num2);
+%                end
+%                [i1_series,i2_series,j1_series,j2_series,nbmissing]=find_file_indices(num_i,num_j,ind_shift,NomType{iview},mode);
+%            end
+%        end
+%        if isempty(i1_series)
+%            msgbox_uvmat('ERROR','no file in the considered range')
+%            return
+%        end
+%        if isempty(i2_series)
+%            i2_series=i1_series;
+%        end
+%        if isempty(j2_series)
+%            j2_series=j1_series;
+%        end 
+%     else%case of images
+%         [i1_series,j1_series]=meshgrid(num_i,num_j);
+%         i2_series=i1_series;
+%         j2_series=j1_series;
+%     end
+%     if length(RootPath)>1
+%         i1_series_cell{iview}=i1_series;
+%         i2_series_cell{iview}=i2_series;
+%         j1_series_cell{iview}=j1_series;
+%         j2_series_cell{iview}=j2_series;
+%     end
+% end
 
 %% defining the ACTION function handle
@@ -1344 +1272 @@
 %% RUN ACTION
 Series.Action=action;%name of the processing programme
+Series
 set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
-if length(RootPath)>1
-    h_fun(i1_series_cell,i2_series_cell,j1_series_cell,j2_series_cell,Series);
-else
-    h_fun(i1_series,i2_series,j1_series,j2_series,Series);
-end
+h_fun(Series);
+% if length(RootPath)>1
+%     h_fun(i1_series_cell,i2_series_cell,j1_series_cell,j2_series_cell,Series);
+% else
+%     h_fun(i1_series,i2_series,j1_series,j2_series,Series);
+% end
 set(handles.RUN,'BackgroundColor',[1 0 0])
 

trunk/src/uvmat.m

@@ -469 +469 @@
 function display_file_name(hObject, eventdata, handles,fileinput,index)
 %------------------------------------------------------------------------
-%% analyse the input file
+%% look for the input file existence
 if ~exist(fileinput,'file')
     msgbox_uvmat('ERROR',['input file ' fileinput  ' does not exist'])
@@ -475 +475 @@
 end
 
-%% have a unique function for fileinput (index=1) and fileinput_1 (index=2)
+%% set the mouse pointer to 'watch'
+set(handles.uvmat,'Pointer','watch')
+set(handles.RootPath,'BackgroundColor',[1 1 0])
+drawnow
+
+%% define the relevant handles for the first fiel series (index=1) or the second file series (index=2)
 if ~exist('index','var')
     index=1;
@@ -502 +507 @@
     set(handles.NomType_1,'Visible','on');
 end
-% detect root name, nomenclature and indices in the input file name:
+
+%% detect root name, nomenclature and indices in the input file name:
 [tild,SubDir,tild,i1,i2,j1,j2,FileExt]=fileparts_uvmat(fileinput);
 % detect the file type, get the movie object if relevant, and look for the corresponding file series:
@@ -512 +518 @@
     j2=[];
 end  
-% open the file or fill the GUI uvmat according to the detected file type
+
+%% open the file or fill the GUI uvmat according to the detected file type
 switch FileType
     case ''
@@ -536 +543 @@
         set(handles_FileExt,'String',FileExt);
         if index==1
-            % fill file index counters
+            % fill file index counters if the first file series is opened
             set(handles.i1,'String',num2str(i1));
             set(handles.i2,'String',num2str(i2));
             set(handles.j1,'String',num2stra(j1,NomType));
             set(handles.j2,'String',num2stra(j2,NomType));
-        else %read the current field index
+        else %read the current field index if the second file series is opened
             i1=str2num(get(handles.i1,'String'));
             i2=str2num(get(handles.i2,'String'));
@@ -547 +554 @@
             j2=stra2num(get(handles.j2,'String'));
         end
+        
         % synchronise indices of the second  input file if it exists
         if get(handles.SubField,'Value')==1% if the subfield button is activated, update the field numbers
-            %             if index==1
             Input=read_GUI(handles.InputFile);
             if ~isfield(Input,'RootPath_1')||strcmp(Input.RootPath_1,'"')
@@ -564 +571 @@
             if exist(FileName_1,'file')
                 FileIndex_1=fullfile_uvmat('','','','',Input.NomType_1,i1,i2,j1,j2);
-                %FileIndex_1=name_generator('',i1,i2,'',NomType_1,1,j1,j2,'');
                 set(handles.FileIndex_1,'String',FileIndex_1)
             else
@@ -588 +594 @@
         set(handles.frame_object,'Visible','on')
         
-        % initiate input file series and refresh the current field view:
-       
+        % initiate input file series and refresh the current field view:     
         update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,index);
 
 end
+
+%% set back the mouse pointer to arrow
+set(handles.uvmat,'Pointer','arrow')
 
 %------------------------------------------------------------------------
@@ -601 +609 @@
 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
 fileinput=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
-% fileinput=read_file_boxes(handles);
 % detect the file type, get the movie object if relevant, and look for the corresponding file series:
 [RootPath,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fileinput);
@@ -640 +647 @@
 function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,index)
 %------------------------------------------------------------------------
-%% TODO: have a unique function for update_rootinfo and update_rootinfo_1
+%% define the relevant handles depending on the index (1=first file series, 2= second file series)
 if ~exist('index','var')
     index=1;
@@ -650 +657 @@
     handles_RootPath=handles.RootPath_1;
     handles_Fields=handles.Fields_1;
-    %..........................
 end
 
@@ -664 +670 @@
 UvData.j1_series{index}=j1_series;
 UvData.j2_series{index}=j2_series;
-set(handles.fix_pair,'Value',1) % activate by default the comp_input '-'input window
+% set(handles.CheckFixPair,'Value',1) % activate by default the comp_input '-'input window
 set(handles.FixVelType,'Value',0); %desactivate fixed veltype
-%[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles);
 if index==1
-[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
+    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
 else
     [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
@@ -681 +686 @@
 nbfield_j=[];%default
 
-% read timing and total frame number from the current file (movie files) !! may be overrid by xml file
+%% read timing and total frame number from the current file (movie files) !! may be overrid by xml file
 XmlData.Time=[];%default
 XmlData.GeometryCalib=[];%default
@@ -732 +737 @@
 set(handles.CheckBW,'Value',strcmp(ColorType,'grayscale'))% select handles.CheckBW if grayscale image
 
-% read parameters (time, geometric calibration..) from a documentation file (.xml advised)
+%% read parameters (time, geometric calibration..) from a documentation file (.xml advised)
 filexml=[FileBase '.xml'];
 fileciv=[FileBase '.civ'];
 warntext='';%default warning message
 NbSlice=1;%default
-
+set(handles.RootPath,'BackgroundColor',[1 1 1])
 if exist(filexml,'file')
     set(handles.view_xml,'Visible','on')
     set(handles.view_xml,'BackgroundColor',[1 1 0])
-    set(handles.RootPath,'BackgroundColor',[1 1 1])
     set(handles.view_xml,'String','view .xml')
     drawnow
@@ -815 +819 @@
     if isequal(nbfield,1) && ~isequal(nbfield_j,1)% .Time is a line vector
         NomType=get(handles.NomType,'String');
-%         NomType=get(handles.FileIndex,'UserData');
         if numel(NomType)>=2 &&(strcmp(NomType,'_i')||strcmp(NomType(1:2),'%0')||strcmp(NomType(1:2),'_%'))
             XmlData.Time=(XmlData.Time)';
@@ -838 +841 @@
 set(handles.last_j,'String',last_j_cell);
 
-% store geometric calibration in UvData
+%% store geometric calibration in UvData
 if isfield(XmlData,'GeometryCalib')
     GeometryCalib=XmlData.GeometryCalib;
@@ -877 +880 @@
 end
 
-%update the data attached to the uvmat interface
+%% update the data attached to the uvmat interface
 if ~isempty(TimeUnit)
     set(handles.time_txt,'String',['time (' TimeUnit ')'])
 end
 UvData.TimeUnit=TimeUnit;
-UvData.XmlData=XmlData;
+UvData.XmlData{index}=XmlData;
 UvData.NewSeries=1;
 % UvData.MovieObject=MovieObject;
@@ -891 +894 @@
 end
 
-% set default options in menu 'Fields'
+%% set default options in menu 'Fields'
 if ~testima
     testcivx=0;
@@ -919 +922 @@
 
 %% set index navigation options and refresh plots
-set(handles.RootPath,'BackgroundColor',[1 1 1])
-drawnow
-set_scan_options(handles)
-
-%% update list of recent files in the menubar
-MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
-    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
-str_find=strcmp(FileName,MenuFile);
-if isempty(find(str_find,1))
-    MenuFile=[{FileName};MenuFile];%insert the current file if not already in the list
-end
-for ifile=1:min(length(MenuFile),5)
-    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
-    eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',MenuFile{ifile});'])
-end
-dir_perso=prefdir;
-profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
-if exist(profil_perso,'file')
-    save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
-else
-    save (profil_perso,'MenuFile','-V6'); %store the file names for future opening of uvmat
-end
-
-%------------------------------------------------------------------------
-%--- Set index navigation options for new series input and refresh plot
-%------------------------------------------------------------------------
-function set_scan_options(handles)
-
-%  set the corresponding index navigation options 
- NomType=get(handles.NomType,'String');       
- NomType_1=get(handles.NomType_1,'String');
-% NomType=get(handles.FileIndex,'UserData');       
-% NomType_1=get(handles.FileIndex_1,'UserData');
-last_i_str=get(handles.last_i,'String');
-nbfield=str2num(last_i_str{1});
-if numel(last_i_str)==2
-    nbfield=min(nbfield,str2num(last_i_str{2}));
-end  
+scan_option='i';%default
 state_j='off'; %default
-scan_option='i';%default
-NomTypeRaw=regexprep(NomType(2:end), '-', '');
-if numel(regexp(NomTypeRaw,'\D'))>=1 
+if index==2
+    if get(handles.scan_j,'Value')
+        scan_option='j'; %keep the scan option for the second fiel series
+    end
+    if strcmp(get(handles.j1,'Visible'),'on')
         state_j='on';
-        if isequal(nbfield,1)
+    end
+end
+if ~isempty(j1_series) 
+        state_j='on';
+        if isequal(nbfield,1) &&index==1
             scan_option='j'; %scan j index by default if nbfield=1                
         end 
-end
-if ~isempty(NomType_1)
-    NomTypeRaw=regexprep(NomType_1(2:end), '-', '');
-    if numel(regexp(NomTypeRaw,'\D'))>=1
-            state_j='on';
-            if isequal(nbfield,1)
-                scan_option='j';                 
-            end           
-    end
 end
 if isequal(scan_option,'i')
@@ -988 +951 @@
 set(handles.frame_j,'Visible',state_j);
 set(handles.j_text,'Visible',state_j);
-if strcmp(state_j,'on')
-    set(handles.fix_pair,'Visible','on')
-else
-    set(handles.fix_pair,'Visible','off')
+if ~isempty(i2_series)||~isempty(j2_series)
+    set(handles.CheckFixPair,'Visible','on')
+elseif index==1
+    set(handles.CheckFixPair,'Visible','off')
 end
 
@@ -1004 +967 @@
     CheckMask_Callback([],[],handles)
 end
+
+%% update list of recent files in the menubar
+MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
+    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
+str_find=strcmp(FileName,MenuFile);
+if isempty(find(str_find,1))
+    MenuFile=[{FileName};MenuFile];%insert the current file if not already in the list
+end
+for ifile=1:min(length(MenuFile),5)
+    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
+    eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',MenuFile{ifile});'])
+end
+dir_perso=prefdir;
+profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
+if exist(profil_perso,'file')
+    save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
+else
+    save (profil_perso,'MenuFile','-V6'); %store the file names for future opening of uvmat
+end
+
 
 %------------------------------------------------------------------------
@@ -1110 +1093 @@
 display_file_name(hObject,eventdata,handles,fileinput_1,2)
 
-%------------------------------------------------------------------------
-% NOT USED  fills the edit boxes RootPath_1, RootFile_1,NomType_1...from an input file name 'fileinput_1'
-%------------------------------------------------------------------------
-% function display_file_name_1(hObject,eventdata,handles,fileinput_1)
-% 
-% %[path,name,ext]=fileparts(fileinput_1);
-% [tild,SubDir_1,tild,i1,i2,j1,j2,FileExt_1]=fileparts_uvmat(fileinput_1);
-% [RootPath_1,RootFile_1,i1_series,i2_series,j1_series,j2_series,NomType,FileType,MovieObject]=find_file_series(fileinput_1);
-% % [RootPath_1,RootFile_1,field_count,str2,str_a,str_b,FileExt_1,NomType_1,SubDir_1]=name2display(fileinput_1);
-% switch FileType
-%     case ''
-%        msgbox_uvmat('ERROR','invalid input file type')
-%     case 'txt'
-%         edit(fileinput)  
-%     case 'figure'                           %display matlab figure
-%         hfig=open(fileinput_1);
-%         set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
-%         set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
-%         set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
-%     case {'xml','xls'}                % edit xml or Excel files
-%        editxml(fileinput_1);
-% %     case {'.avi','.image','.vol','.nc','.cdf'}  
-%     otherwise
-%         set(handles.RootPath_1,'String',RootPath_1);
-%         if  isequal(SubDir_1,'')
-%             rootname=fullfile(RootPath_1,RootFile_1);
-%         else
-%             rootname=fullfile(RootPath_1,SubDir_1,RootFile_1);
-%             SubDir=['/' SubDir_1]; %display the separator
-%         end
-%         set(handles.SubDir_1,'String',SubDir_1);
-%         set(handles.RootFile_1,'String',['/' RootFile_1]); %display the separator
-%         indices=fileinput_1(length(rootname)+1:end);
-%         indices(end-length(FileExt_1)+1:end)=[]; %remove extension
-%         set(handles.FileIndex,'String',indices);        
-% %         set(handles.FileIndex,'UserData',NomType);
-%         set(handles.NomType_1,'String',NomType);
-%         set(handles.FileExt_1,'String',FileExt_1);
-%         % fill file index counters
-%         set(handles.i1,'String',num2str(i1));    
-%         set(handles.i2,'String',num2str(i2));
-%         set(handles.j1,'String',num2str(j1));
-%         set(handles.j2,'String',num2str(j2));
-%         
-%         % synchronise indices of the second  input file if it exists
-%         if get(handles.SubField,'Value')==1% if the subfield button is activated, update the field numbers
-%             [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
-%             %[ff,rr,FileBase_1,ii,FileExt_1,SubDir_1]=read_file_boxes_1(handles);
-%             NomType_1=get(handles.NomType_1,'String'); 
-% %             NomType_1=get(handles.FileIndex_1,'UserData');     
-%             %FileName_1=name_generator(FileBase_1,i1,i2,FileExt_1,NomType_1,1,j1,j2,SubDir_1);
-%             FileName_1=fullfile_uvmat(RootPath_1,SubDir_1,RootFile_1,FileExt_1,NomType_1,i1,i2,j1,j2);
-%             if exist(FileName_1,'file')
-%                 FileIndex_1=fullfile_uvmat('','','','',NomType_1,i1,i2,j1,j2);
-%                 %FileIndex_1=name_generator('',i1,i2,'',NomType_1,1,j1,j2,'');
-%                 set(handles.FileIndex_1,'String',FileIndex_1)
-%             else
-%                 set(handles.SubField,'Value',0)
-%                 SubField_Callback(hObject, eventdata, handles)
-%             end
-%         end  
-% end
-% 
-% % test for image series in a single file and synchronise file indices of the two series
-% if nbfield_1 >1 %case of image with multiple frames
-%     if nbfield_1 < num_i1
-%         msgbox_uvmat('ERROR','current frame index beyond the input movie length')
-%         return
-%     else
-%         NomType_1='*'; %indicate a set of indexed frames within a single file
-%         filename_new=fileinput_1;
-%     end
-% else  % cases of data files   
-%     RootPath=get(handles.RootPath,'String');
-%     RootFile=get(handles.RootFile,'String');
-%     FileBase=fullfile(RootPath,RootFile);
-%     FileBase_1=fullfile(RootPath_1,RootFile_1);
-%     if isequal(FileBase,FileBase_1)
-%         filename_new=fileinput_1;
-%     else        
-%         num_i1=stra2num(get(handles.i1,'String'));%get the current file indices from counters
-%         num_j1=stra2num(get(handles.j1,'String'));
-%         num_i2=stra2num(get(handles.i2,'String'));
-%         num_j2=stra2num(get(handles.j2,'String'));
-%         [filename_new,idetect]=...
-%            name_generator(FileBase_1,num_i1,num_j1,FileExt_1,NomType_1,1,num_i2,num_j2,SubDir_1);%create name with indices synchronised with the first file
-%         indices=''; %default
-%         if ~idetect
-%             msgbox_uvmat('ERROR','second input file with indices corresponding to the first one does not exist')
-%             return
-%         end 
-%     end
-% end
-% set(handles.NomType_1,'String',NomType_1);
-% % set(handles.FileIndex_1,'UserData',NomType_1);
-% 
-% % make visible and fill the second raw of edit boxes
-% set(handles.RootPath_1,'Visible','on')
-% set(handles.RootFile_1,'Visible','on')
-% set(handles.SubDir_1,'Visible','on');
-% set(handles.FileIndex_1,'Visible','on');
-% set(handles.FileExt_1,'Visible','on');
-% %[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles);
-% [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
-% FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
-% FileBase=fullfile(RootPath,RootFile);
-% if isequal(FileBase,FileBase_1)
-%     set(handles.RootPath_1,'String','"')
-%     set(handles.RootFile_1,'String','"');
-% else
-%     set(handles.RootPath_1,'String',RootPath_1)
-%     set(handles.RootFile_1,'String',['/' RootFile_1]);
-% end 
-% if  isequal(SubDir_1,'')
-%      set(handles.SubDir_1,'String','');
-%      FileBaseSub_1=FileBase_1;
-% else  
-%     set(handles.SubDir_1,'String',['/' SubDir_1]);
-%     FileBaseSub_1=fullfile(FileBase_1,SubDir_1);
-% end
-% indices=filename_new(length(FileBaseSub_1)+1:end);
-% indices(end-length(FileExt_1)+1:end)=[]; %remove extension
-% set(handles.FileIndex_1,'String',indices)
-% set(handles.NomType_1,'String',NomType_1)
-% % set(handles.FileIndex_1,'UserData',NomType_1)
-% set(handles.FileExt_1,'String',FileExt_1);
-% 
-% % % default choice of fields
-% %set(handles.SubField,'Visible','on')
-% set(handles.SubField,'Value',1)
-% RootPath_1_Callback(hObject,eventdata,handles);  
-
 %-----------------------------------------------------------------------
 % --- Called by action in RootPath_1 edit box
 function RootPath_1_Callback(hObject,eventdata,handles)
 % -----------------------------------------------------------------------
-update_rootinfo_1(hObject,eventdata,handles)
-
+% update_rootinfo_1(hObject,eventdata,handles)
+[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
+fileinput=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
+% detect the file type, get the movie object if relevant, and look for the corresponding file series:
+[tild,tild,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fileinput);
+% initiate the input file series and refresh the current field view: 
+update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,2);
 %-----------------------------------------------------------------------
 % --- Called by action in RootFile_1 edit box
 function RootFile_1_Callback(hObject, eventdata, handles)
 % -----------------------------------------------------------------------
-update_rootinfo_1(hObject,eventdata,handles)
+RootPath_1_Callback(hObject,eventdata,handles)
 
 %------------------------------------------------------------------------
@@ -1259 +1115 @@
 %------------------------------------------------------------------------
 run0_Callback(hObject, eventdata, handles)
-
-% %------------------------------------------------------------------------
-% % --- Update information about a new second field series (indices to scan, timing,
-% %     calibration from an xml file, then refresh current plots
-% function update_rootinfo_1(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject) %A REVOIR
-% % -----------------------------------------------------------------------
-% set(handles.RootPath_1,'BackgroundColor',[1 1 0])% indicate active program by yellow color
-% drawnow
-% UvData=get(handles.uvmat,'UserData');%huvmat=handles of the uvmat interface
-% UvData.NewSeries=1; %flag for run0: begin a new series
-% [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
-% FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
-% %[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes_1(handles);
-% if ~exist(FileName,'file')
-%     msgbox_uvmat('ERROR',['input file ' FileName ' not found']);
-% end
-% set(handles.FixVelType,'Value',0); %desactivate fixed veltype
-% nbfield_1=[];%default
-% nbfield_j_1=[];%default
-% XmlData.Time=[];
-% XmlData.GeometryCalib=[];%default
-% TimeUnit=[];
-% if isfield(UvData,'TimeUnit')
-%     TimeUnit=UvData.TimeUnit;
-% end
-% TimeUnit_1=[];
-% hhh='';%default, test for  movie reading with mmreader
-% imainfo=[];
-% FileBase=fullfile(RootPath,RootFile);
-% if isequal(lower(FileExt),'.avi') %.avi file
-%     imainfo=aviinfo([FileBase FileIndices FileExt]);
-%     nbfield_1=imainfo.NumFrames;
-%     nbfield_j_1=1;
-%     set(handles.Dt_txt,'String',['Dt=' num2str(1000/info.FramesPerSecond) 'ms']);%display the elementary time interval in millisec
-%     time=(0:1/imainfo.FramesPerSecond:(imainfo.NumFrames-1)/imainfo.FramesPerSecond)';
-%     ColorType=imainfo.ImageType;%='truecolor' for color images
-%     hhh=which('mmreader');
-% elseif ~isempty(imformats(FileExt(2:end)))|| isequal(FileExt,'.vol')
-%     if ~isequal(SubDir,'')
-%         RootFile=get(handles.RootFile,'String');
-%         imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]);
-%     else
-%         imainfo=imfinfo([FileBase FileIndices FileExt]);
-%     end
-%     ColorType=imainfo.ColorType;%='truecolor' for color images
-%     if length(imainfo) >1 %case of image with multiple frames
-%         nbfield_1=length(imainfo);
-%         nbfield_j_1=1;
-%     end 
-% end
-% if ~strcmp(hhh,'')&& mmreader.isPlatformSupported()% if the function is found (recent version of matlab)
-%     UvData.MovieObject_1=mmreader([FileBase FileIndices FileExt]);
-% elseif isfield(UvData,'MovieObject_1')
-%     UvData=rmfield(UvData,'MovieObject_1');
-% end
-% if ~isempty(imainfo)% (an image has been introduced as second fierld input)
-%     if strcmp(get(handles.num_Npx,'String'),'') || strcmp(get(handles.num_Npy,'String'),'')%update npx and npy if it is not already filled by the first input field
-%         if  isfield(imainfo,'Width') && isfield(imainfo,'Height')
-%             set(handles.num_Npx,'String',num2str(imainfo.Width));%fills nbre of pixels x box
-%             set(handles.num_Npy,'String',num2str(imainfo.Height));%fills nbre of pixels x box
-%         else
-%             set(handles.num_Npx,'String','');%fills nbre of pixels x box
-%             set(handles.num_Npy,'String','');%fills nbre of pixels x box
-%         end
-%         set(handles.CheckBW,'Value',strcmp(ColorType,'grayscale'))% select handles.CheckBW if grayscale image
-%     end
-% end
-% % find scaling parameters
-% filexml=[FileBase '.xml'];
-% fileciv=[FileBase '.civ'];
-% warntext='';%default warning text
-% if exist(filexml,'file')
-%     [XmlData,warntext]=imadoc2struct(filexml);
-%     if ~isempty(warntext)
-%         msgbox_uvmat('WARNING',warntext)
-%     end
-%     if isfield(XmlData,'Camera')
-%         if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
-%             TimeUnit=XmlData.Camera.TimeUnit;
-%         end
-%     end 
-% elseif exist(fileciv,'file')% if .civ file found 
-%     [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']);
-%     GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
-%     GeometryCalib.Tx=0;
-%     GeometryCalib.Ty=0;
-%     GeometryCalib.Tz=1;
-%     GeometryCalib.dpx=1;
-%     GeometryCalib.dpy=1;
-%     GeometryCalib.sx=1;
-%     GeometryCalib.Cx=0;
-%     GeometryCalib.Cy=0;
-%     GeometryCalib.f=1;
-%     GeometryCalib.kappa1=0;
-%     GeometryCalib.CoordUnit='cm';
-%     XmlData.GeometryCalib=GeometryCalib;
-%     if error==2, warntext=['no file ' FileBase '.civ'];
-%     elseif error==1, warntext='inconsistent number of fields in the .civ file';
-%     end
-%     
-%     set(handles.num_Npx,'String',num2str(npx));%fills nbre of pixels x box
-%     set(handles.num_Npy,'String',num2str(npy));%fills nbre of pixels y box
-%     set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box
-%     set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box
-%     set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box 
-%     set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box 
-% end   
-% if ~isempty(TimeUnit_1) && ~isequal(TimeUnit_1,TimeUnit)
-%         msgbox_uvmat('WARNING','the time units for the second series differs from the first one')
-% end
-%         
-% % store last index in handles.lat_i and .last_j
-% if ~isempty(XmlData.Time)
-%     nbfield_1=size(XmlData.Time,1);
-%     nbfield_j_1=size(XmlData.Time,2);   
-% end
-% last_i_cell=get(handles.last_i,'String');
-% if isempty(nbfield_1)
-%     last_i_cell{2}='';
-% else
-%     last_i_cell{2}=num2str(nbfield_1);
-% end
-% set(handles.last_i,'String',last_i_cell)
-% last_j_cell=get(handles.last_j,'String');
-% if isempty(nbfield_j_1)
-%      last_j_cell{2}='';
-% else
-%      last_j_cell{2}=num2str(nbfield_j_1);
-% end
-% set(handles.last_j,'String',last_j_cell);
-% if ~isequal(last_i_cell{1},last_i_cell{2}) || ~isequal(last_j_cell{1},last_j_cell{2})
-%         msgbox_uvmat('WARNING','the numbers of input file of the second series differs from the first one')
-% end
-% 
-% % store calibration data
-% GeometryCalib=XmlData.GeometryCalib;
-% if isempty(GeometryCalib)
-%     if isfield(UvData, 'GeometryCalib_1')
-%         UvData=rmfield(UvData,'GeometryCalib_1');
-%     end
-% else
-%     UvData.GeometryCalib_1=GeometryCalib;
-%     if (isfield(GeometryCalib,'R')&& ~isequal(GeometryCalib.R(2,1),0) && ~isequal(GeometryCalib.R(1,2),0)) ||...
-%         (isfield(GeometryCalib,'kappa1')&& ~isequal(GeometryCalib.kappa1,0))
-%         set(handles.pxcm,'String','var')
-%         set(handles.pycm,'String','var')
-%     else
-%         if isfield(GeometryCalib,'fx_fy')
-%             pixcmx=GeometryCalib.fx_fy(1);
-%             pixcmy=GeometryCalib.fx_fy(2);
-%             set(handles.pxcm,'String',num2str(pixcmx))
-%             set(handles.pycm,'String',num2str(pixcmy))
-%         end
-%     end
-% end
-% UvData.XmlData_1=XmlData;
-% set(handles.uvmat,'UserData',UvData)%update the data attached to the uvmat interface
-% 
-% if ~isequal(warntext,'')
-%     msgbox_uvmat('WARNING',warntext)
-% end
-% 
-% set(handles.RootPath_1,'BackgroundColor',[1 1 1])% signa the end the input operation
-% drawnow
-% 
-% set_scan_options(handles)
 
 %------------------------------------------------------------------------
@@ -1433 +1123 @@
     set(handles.scan_i,'BackgroundColor',[1 1 0])
     set(handles.scan_j,'Value',0)
-%     set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
 else
     set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
     set(handles.scan_j,'Value',1)
-%     set(handles.scan_j,'BackgroundColor',[1 1 0])
 end
 scan_j_Callback(hObject, eventdata, handles)
@@ -1449 +1137 @@
     set(handles.scan_i,'Value',0)
     set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
-    NomType=get(handles.NomType,'String');
-%     NomType=get(handles.FileIndex,'UserData');
-    switch NomType
-    case {'_1_1-2','#_ab','%3dab'},% pair with j index
-        set(handles.fix_pair,'Visible','on')% option fixed pair on/off made visible (choice of avaible pair with buttons + and - if ='off')
-    otherwise
-        set(handles.fix_pair,'Visible','off')
-    end 
+%     NomType=get(handles.NomType,'String');
+%     switch NomType
+%     case {'_1_1-2','#_ab','%3dab'},% pair with j index
+%         set(handles.CheckFixPair,'Visible','on')% option fixed pair on/off made visible (choice of avaible pair with buttons + and - if ='off')
+%     otherwise
+%         set(handles.CheckFixPair,'Visible','off')
+%     end 
 else
     set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
     set(handles.scan_i,'Value',1)
     set(handles.scan_i,'BackgroundColor',[1 1 0])
-    set(handles.fix_pair,'Visible','off')
+    set(handles.CheckFixPair,'Visible','off')
 end
 
@@ -1705 +1392 @@
         transform=transform_list{choice_value};
         if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
-            if isfield(UvData,'XmlData') && isfield(UvData.XmlData,'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
-                Calib=UvData.XmlData.GeometryCalib;
-                Mask=transform(Mask,UvData.XmlData);
+            if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
+                Calib=UvData.XmlData{1}.GeometryCalib;
+                Mask=transform(Mask,UvData.XmlData{1});
             end
         end
@@ -1763 +1450 @@
 drawnow
 %TODO: introduce the option: increment ='*' to move to the next available view
-increment=str2double(get(handles.increment_scan,'String')); %get the field increment d
-if isnan(increment)
-    set(handles.increment_scan,'String','1')%default value
-    increment=1;
-end
+increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
+% if isnan(increment)
+%     set(handles.increment_scan,'String','1')%default value
+%     increment=1;
+% end
 errormsg=runpm(hObject,eventdata,handles,increment);
 if ~isempty(errormsg)
@@ -1782 +1469 @@
 set(handles.runmin,'BackgroundColor',[1 1 0])%paint the command button in yellow
 drawnow
-increment=-str2double(get(handles.increment_scan,'String')); %get the field increment d
-if isnan(increment)
-    set(handles.increment_scan,'String','1')%default value
-    increment=1;
-end
+increment=-str2num(get(handles.increment_scan,'String')); %get the field increment d
+% if isnan(increment)
+%     set(handles.increment_scan,'String','1')%default value
+%     increment=1;
+% end
 errormsg=runpm(hObject,eventdata,handles,increment);
 if ~isempty(errormsg)
@@ -1799 +1486 @@
 set(handles.Movie,'BackgroundColor',[1 1 0])%paint the command button in yellow
 drawnow
-increment=str2double(get(handles.increment_scan,'String')); %get the field increment d
-if isnan(increment)
-    set(handles.increment_scan,'String','1')%default value
-    increment=1;
-end
+increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
+% if isnan(increment)
+%     set(handles.increment_scan,'String','1')%default value
+%     increment=1;
+% end
 set(handles.STOP,'Visible','on')
 set(handles.speed,'Visible','on')
@@ -1830 +1517 @@
 set(handles.MovieBackward,'BackgroundColor',[1 1 0])%paint the command button in yellow
 drawnow
-increment=-str2double(get(handles.increment_scan,'String')); %get the field increment d
-if isnan(increment)
-    set(handles.increment_scan,'String','1')%default value
-    increment=1;
-end
+increment=-str2num(get(handles.increment_scan,'String')); %get the field increment d
 set(handles.STOP,'Visible','on')
 set(handles.speed,'Visible','on')
@@ -1871 +1554 @@
 function errormsg=runpm(hObject,eventdata,handles,increment)
 %------------------------------------------------------------------------
+errormsg='';%default
 %% check for movie pair status
 movie_status=get(handles.movie_pair,'Value');
@@ -1881 +1565 @@
 InputFile.RootFile=regexprep(InputFile.RootFile,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
 InputFile.SubDir=regexprep(InputFile.SubDir,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
-% if isempty(InputFile.RootFile)
-%     filebase=InputFile.RootPath;
-% else
- filebase=fullfile(InputFile.RootPath,InputFile.RootFile);
-% end
 FileExt=InputFile.FileExt;
-% [FileName,RootPath,filebase,FileIndices,FileExt,subdir]=read_file_boxes(handles);
 NomType=get(handles.NomType,'String');
-% NomType=get(handles.FileIndex,'UserData');
 i1=str2num(get(handles.i1,'String'));%read the field indices (for movie, it is not given by the file name)
 i2=str2num(get(handles.i2,'String'));
@@ -1895 +1572 @@
 j2=stra2num(get(handles.j2,'String'));
 sub_value= get(handles.SubField,'Value');
-if sub_value % a second input file has been entered
-    
+if sub_value % a second input file has been entered 
     [FileName_1,RootPath_1,filebase_1,FileIndices_1,FileExt_1,SubDir_1]=read_file_boxes_1(handles);
     [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(FileIndices_1);
-  %  [pp,ff,i1_1_str,i2_1_str,j1_1_str,j2_1_str]=name2display(FileIndices_1);
-%     i1_1=stra2num(i1_1_str);%current set of indices for the second field (may be set different than the main indices)
-%     i2_1=stra2num(i2_1_str);
-%     j1_1=stra2num(j1_1_str);
-%     j2_1=stra2num(j2_1_str);
     NomType_1=get(handles.NomType_1,'String');
-%     NomType_1=get(handles.FileIndex_1,'UserData');
 else
     filename_1=[];
 end   
-comp_input=get(handles.fix_pair,'Value');
 
 %% increment (or decrement) the field indices and update the input filename(s)
-if get(handles.scan_i,'Value')==1% case of scanning along index i
-    i1=i1+increment;
-    i2=i2+increment;
-    if sub_value
-        i1_1=i1_1+increment;
-        i2_1=i2_1+increment;
-    end
-else % case of scanning along index j (burst numbers)
-    j1=j1+increment;
-    j2=j2+increment;
-    if sub_value
-        j1_1=j1_1+increment;
-        j2_1=j2_1+increment;
-    end
-end
-if ~comp_input
+CheckSearch=0;
+if isempty(increment)
+    CheckSearch=1;% search for the next available file
+    set(handles.CheckFixPair,'Value',0)
+end
+CheckFixPair=get(handles.CheckFixPair,'Value');
+if CheckFixPair
+    if get(handles.scan_i,'Value')==1% case of scanning along index i
+        i1=i1+increment;
+        i2=i2+increment;
+        if sub_value
+            i1_1=i1_1+increment;
+            i2_1=i2_1+increment;
+        end
+    else % case of scanning along index j (burst numbers)
+        j1=j1+increment;
+        j2=j2+increment;
+        if sub_value
+            j1_1=j1_1+increment;
+            j2_1=j2_1+increment;
+        end
+    end
+else
     UvData=get(handles.uvmat,'UserData');
     ref_i=i1;
@@ -1940 +1616 @@
         end
     end
-    if ref_i+1>size(UvData.i1_series{1},1)
-        msgbox_uvmat('ERROR','maximum i index exceeded');
-        return
-    end
-    if ref_j+1>size(UvData.i1_series{1},2)
-        msgbox_uvmat('ERROR','maximum j index exceeded');
+    if ~isempty(increment)
+        if get(handles.scan_i,'Value')==1% case of scanning along index i
+            ref_i=ref_i+increment;
+        else % case of scanning along index j (burst numbers)
+            ref_j=ref_j+increment;
+        end
+    else% free increment
+        if isequal(get(handles.runplus,'BackgroundColor'),[1 1 0])% if runplus is activated
+            step=1;
+        else
+            step=-1;
+        end
+        if get(handles.scan_i,'Value')==1% case of scanning along index i
+            ref_i=ref_i+step;
+            while ref_i>=0  && size(UvData.i1_series{1},1)>=ref_i+1 && UvData.i1_series{1}(ref_i+1,ref_j+1,1)==0
+                ref_i=ref_i+step;
+            end
+        else % case of scanning along index j (burst numbers)
+            ref_j=ref_j+step;
+            while ref_j>=0  && size(UvData.i1_series{1},2)>=ref_j+1 && UvData.i1_series{1}(ref_i+1,ref_j+1,1)==0
+                ref_j=ref_j+step;
+            end
+        end
+    end
+    if ref_i<0
+        errormsg='minimum i index reached';
+    elseif ref_j<0
+        errormsg='minimum j index reached';
+    elseif ref_i+1>size(UvData.i1_series{1},1)
+        errormsg='maximum i index reached';
+    elseif ref_j+1>size(UvData.i1_series{1},2)
+        errormsg='maximum j index reached';
+    end
+    if ~isempty(errormsg)
         return
     end
@@ -2121 +1825 @@
 transform=transform_list{choice_value};
 if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
-    if test_1 && isfield(UvData,'XmlData_1') && isfield(UvData.XmlData_1,'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
-        Field_a=transform(Field_a,UvData.XmlData_1);%the first field has been stored without transform
-        Field_b=transform(Field_b,UvData.XmlData_1);
-    elseif ~test_1 && isfield(UvData,'XmlData') && isfield(UvData.XmlData,'GeometryCalib')%use geometry calib
-        Field_b=transform(Field_b,UvData.XmlData);
+    if test_1 && isfield(UvData,'XmlData') && numel(UvData.XmlData)==2 && isfield(UvData.XmlData{2},'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
+        Field_a=transform(Field_a,UvData.XmlData{2});%the first field has been stored without transform
+        Field_b=transform(Field_b,UvData.XmlData{2});
+    elseif ~test_1 && isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'GeometryCalib')%use geometry calib
+        Field_b=transform(Field_b,UvData.XmlData{1});
     end
 end
@@ -2329 +2033 @@
             end
     end
-%     if strcmp(get(handles.FileExt_1,'Visible'),'on')
-%         FileExt_1=get(handles.FileExt_1,'String');
-%     else
-%         FileExt_1=get(handles.FileExt,'String');%read the file extension for the first series (case of veltype comparison within a single file)
-%     end
     NomType_1=get(handles.NomType_1,'String');
-%     %         NomType_1=get(handles.FileIndex_1,'UserData');
-%     if isequal(Ext_1,'.nc')||isequal(Ext_1,'.cdf')
-%         FileType_1='netcdf';
-%     elseif isfield(UvData,'MovieObject_1')
-%         Name=UvData.MovieObject_1;
-%         FileType_1='movie';
-%     elseif isequal(lower(Ext_1),'.avi')
-%         FileType_1='avi';
-%     elseif isequal(lower(Ext_1),'.vol')
-%         FileType_1='vol';
-%         if isfield(UvData.XmlData_1,'Npy') && isfield(UvData.XmlData_1,'Npx')
-%             ParamIn.Npy=UvData.XmlData_1.Npy;
-%             ParamIn.Npx=UvData.XmlData_1.Npx;
-%         else
-%             errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
-%             return
-%         end
-%     else
-%         if length(Ext_1)>=2
-%             form=imformats(Ext_1(2:end));
-%             if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
-%                 if isequal(NomType_1,'*');
-%                     FileType_1='multimage';
-%                 else
-%                     FileType_1='image';
-%                 end
-%             end
-%         end
-%     end
-%     if strcmp(FileType_1,'netcdf')
-%         list_fields=get(handles.Fields_1,'String');% list menu fields
-%         index_fields=get(handles.Fields_1,'Value');% selected string index
-%         FieldName_1= list_fields{index_fields}; % selected field
-%         if ~isequal(FieldName_1,'get_field...')% read the field names on the interface get_field...
-%             VelType_1='';
-%             if get(handles.FixVelType,'Value')
-%                 VelTypeList=get(handles.VelType_1,'String');
-%                 index=get(handles.VelType_1,'Value');
-%                 VelType_1=VelTypeList{index};
-%             end
-%         end
-%         if strcmp(VelType_1,'*')% free veltype choice
-%             VelType_1=[];
-%         elseif strcmp(VelType_1,'"')% veltype the same as for the first field
-%             if isempty(VelType)
-%                 VelType_1=[];
-%             else
-%                 VelType_1=VelType;
-%             end
-%         end
-%         if strcmp(FieldName_1,'velocity')
-%             list_code=get(handles.ListColorCode,'String');% list menu fields
-%             index_code=get(handles.ListColorCode,'Value');% selected string index
-%             if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
-%                 list_code=get(handles.ListColorScalar,'String');% list menu fields
-%                 index_code=get(handles.ListColorScalar,'Value');% selected string index
-%                 ParamIn.ColorVar= list_code{index_code}; % selected field
-%             end
-%         end
-%     end
     test_keepdata_1=0;% test for keeping the previous stored data if the input files are unchanged
     if ~isequal(NomType_1,'*')%in case of a series of files (not avi movie)
@@ -2513 +2152 @@
 %% apply coordinate transform or other user fct
 XmlData=[];%default
+XmlData_1=[];%default
 if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority
-    XmlData=UvData.XmlData;
-end
-XmlData_1=[];%default
-if isfield(UvData,'XmlData_1')
-   XmlData_1=UvData.XmlData_1;
-end
+    XmlData=UvData.XmlData{1};
+    if numel(UvData.XmlData)==2
+        XmlData_1=UvData.XmlData{2};
+    end
+end
+
 % menu_transform=get(handles.transform_fct,'String');
 choice_value=get(handles.transform_fct,'Value');
@@ -2684 +2324 @@
 elseif isfield(UvData,'Z')
     if isfield(UvData,'CoordType')&& isequal(UvData.CoordType,'phys') && isfield(UvData,'XmlData')
-        XmlData=UvData.XmlData;
+        XmlData=UvData.XmlData{1};
         if isfield(XmlData,'PlanePos')
             UvData.Object{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:);
@@ -2726 +2366 @@
     UvData.Object={[]}; 
     set(handles.ListObject,'Value',1)
-%     set(handles.list_object_2,'Value',1)
-%     set(handles.list_object_2,'String',{''})
-%     set(handles.list_object_2,'Visible','off')
 end
 IndexObj=get(handles.ListObject,'Value');%selected projection object for main view
@@ -2928 +2565 @@
 end
 % time from xml file overset previous result
-if isfield(UvData,'XmlData') && isfield(UvData.XmlData,'Time')
+if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'Time')
     if isempty(num_i2)||isnan(num_i2)
         num_i2=num_i1;
@@ -2938 +2575 @@
         num_j2=num_j1;
     end
-    siz=size(UvData.XmlData.Time);
+    siz=size(UvData.XmlData{1}.Time);
     if siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
-        abstime=(UvData.XmlData.Time(num_i1,num_j1)+UvData.XmlData.Time(num_i2,num_j2))/2;%overset the time read from files
-        dt=(UvData.XmlData.Time(num_i2,num_j2)-UvData.XmlData.Time(num_i1,num_j1));
+        abstime=(UvData.XmlData{1}.Time(num_i1,num_j1)+UvData.XmlData{1}.Time(num_i2,num_j2))/2;%overset the time read from files
+        dt=(UvData.XmlData{1}.Time(num_i2,num_j2)-UvData.XmlData{1}.Time(num_i1,num_j1));
         testimedoc=1;
-        if isfield(UvData.XmlData,'TimeUnit')
-            TimeUnit=UvData.XmlData.TimeUnit;
-        end
-    end
-end
-if isfield(UvData,'XmlData_1') && isfield(UvData.XmlData_1,'Time')
-    [tild,tild,tild,num_i1,num_i2,num_j1,num_j2]=fileparts_uvmat(['xx' get(handles.FileIndex_1,'String') get(handles.FileExt_1,'String')]);
-  %  [P,F,str1,str2,str_a,str_b,E]=name2display(['xx' get(handles.FileIndex_1,'String') get(handles.FileExt_1,'String')]);
-    if isempty(num_i2)
-        num_i2=num_i1;
-    end
-    if isempty(num_j1)
-        num_j1=1;
-    end
-    if isempty(num_j2)
-        num_j2=num_j1;
-    end
-    siz=size(UvData.XmlData_1.Time);
-    if siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
-        abstime_1=(UvData.XmlData_1.Time(num_i1,num_j1)+UvData.XmlData_1.Time(num_i2,num_j2))/2;%overset the time read from files
-    end
-end
+        if isfield(UvData.XmlData{1},'TimeUnit')
+            TimeUnit=UvData.XmlData{1}.TimeUnit;
+        end
+    end
+    if numel(UvData.XmlData)==2
+        [tild,tild,tild,num_i1,num_i2,num_j1,num_j2]=fileparts_uvmat(['xx' get(handles.FileIndex_1,'String') get(handles.FileExt_1,'String')]);
+        %  [P,F,str1,str2,str_a,str_b,E]=name2display(['xx' get(handles.FileIndex_1,'String') get(handles.FileExt_1,'String')]);
+        if isempty(num_i2)
+            num_i2=num_i1;
+        end
+        if isempty(num_j1)
+            num_j1=1;
+        end
+        if isempty(num_j2)
+            num_j2=num_j1;
+        end
+        siz=size(UvData.XmlData{2}.Time);
+        if siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
+            abstime_1=(UvData.XmlData{2}.Time(num_i1,num_j1)+UvData.XmlData{2}.Time(num_i2,num_j2))/2;%overset the time read from files
+        end
+    end
+end
+
 if ~isequal(numel(abstime),1)
     abstime=[];
@@ -3020 +2658 @@
 end
 
-
 %-------------------------------------------------------------------
 
@@ -3035 +2672 @@
     set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
 end
-
 
 %-------------------------------------------------------------------
@@ -3098 +2734 @@
 fin=close(nc);
 
-
 %-------------------------------------------------------------------
 %determines the fields to read from the interface
@@ -3107 +2742 @@
 VelType=VelTypeList{index};
 
-% VelType=[]; %default
-% if (get(handles.VelType,'Value') == 1);
-%         VelType='civ1';
-% % interp1   
-% elseif (get(handles.interp1,'Value') == 1);
-%     VelType='interp1';
-% % filter1   
-% elseif (get(handles.filter1,'Value') == 1); 
-%     VelType='filter1';  
-% % CIV2
-% elseif (get(handles.civ2,'Value') == 1);
-%     VelType='civ2';
-% % interp2   
-% elseif (get(handles.interp2,'Value') == 1); 
-%     VelType='interp2';
-% % filter2   
-% elseif (get(handles.filter2,'Value') == 1);  
-%     VelType='filter2'; 
-% end 
-% 
-% if isequal(get(handles.filter2,'Visible'),'on');
-%     civ=6;
-% % interp1   
-% elseif isequal(get(handles.interp2,'Visible'),'on');
-%     civ=5;
-% % filter1   
-% elseif isequal(get(handles.civ2,'Visible'),'on'); 
-%     civ=4;  
-% % CIV2
-% elseif isequal(get(handles.filter1,'Visible'),'on');
-%    civ=3;
-% % interp2   
-% elseif isequal(get(handles.interp1,'Visible'),'on'); 
-%     civ=2;
-% % filter2   
-% elseif isequal(get(handles.VelType,'Visible'),'on');  
-%     civ=1; 
-% else
-%     civ=0;
-% end 
-
 %-------------------------------------------------------------------
 %determines the veltype of the second field to read from the iinterface
@@ -3155 +2749 @@
 index=get(handles.VelType_1,'Value');
 VelType=VelTypeList{index};
-% VelType=[]; %default
-% if (get(handles.VelType_1,'Value') == 1);
-%     VelType='civ1';
-% % interp1   
-% elseif (get(handles.interp1_1,'Value') == 1);
-%     VelType='interp1';
-% % filter1   
-% elseif (get(handles.filter1_1,'Value') == 1); 
-%     VelType='filter1';  
-% % CIV2
-% elseif (get(handles.civ2_1,'Value') == 1);
-%     VelType='civ2';
-% % interp2   
-% elseif (get(handles.interp2_1,'Value') == 1); 
-%     VelType='interp2';
-% % filter2   
-% elseif (get(handles.filter2_1,'Value') == 1);  
-%     VelType='filter2'; 
-% end 
-
 
 %---------------------------------------------------
@@ -3288 +2862 @@
 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
 FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
-% [FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles);
 [tild,tild,tild,i1,i2,j1,j2,tild,NomType]=fileparts_uvmat(['xxx' get(handles.FileIndex,'String') FileExt]);
-% [P,F,str1,str2,str_a,str_b,E,NomType]=name2display(['xxx' get(handles.FileIndex,'String') FileExt]);
-NomTypeNew=NomType;%default
+% NomTypeNew=NomType;%default
 if isequal(field,'image')
-    if isequal(NomType,'_1-2_1')||isequal(NomType,'_1_1-2')
-        NomTypeNew='_1_1';
-    elseif isequal(NomType,'#_ab')
-        NomTypeNew='#a';
-    elseif isequal(NomType,'_1-2')
-        NomTypeNew='_1';
-    end
-    imagename=fullfile_uvmat(RootPath,SubDir,RootFile,'.png',NomTypeNew,i1,i2,j1,j2);
-%     imagename=name_generator(FileBase,i1,j1,'.png',NomTypeNew,1,i2,j2,'');
+%     if isequal(NomType,'_1-2_1')||isequal(NomType,'_1_1-2')
+%         NomTypeNew='_1_1';
+%     elseif isequal(NomType,'#_ab')
+%         NomTypeNew='#a';
+%     elseif isequal(NomType,'_1-2')
+%         NomTypeNew='_1';
+%     end
+    imagename=fullfile_uvmat(RootPath,SubDir,RootFile,'.png',NomType,i1,[],j1,[]);
     if ~exist(imagename,'file')
         [FileName,PathName] = uigetfile( ...
@@ -3331 +2902 @@
     end
 end
-% indices=name_generator('',i1,j1,'',NomTypeNew,1,i2,j2,'');
-indices=fullfile_uvmat('','','','',NomTypeNew,i1,i2,j1,j2);
+indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
 set(handles.FileIndex,'String',indices)
-set(handles.NomType,'String',NomTypeNew)
-% set(handles.FileIndex,'UserData',NomTypeNew)
+% set(handles.NomType,'String',NomType)
+
 %common to Fields_1_Callback
 if isequal(field,'image')||isequal(field_1,'image')
@@ -3361 +2931 @@
 UvData=get(handles.uvmat,'UserData');
 if check_new && isfield(UvData,'XmlData')
-    UvData.XmlData_1=UvData.XmlData;
+    UvData.XmlData{2}=UvData.XmlData{1};
 end
 list_fields=get(handles.Fields,'String');% list menu fields
@@ -3387 +2957 @@
 switch field_1
     case 'get_field...'
-        %veltype_handles=[handles.VelType handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2];
         set_veltype_display(0) % no veltype display
-        %      [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
-        %      filename=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
         hget_field=findobj(allchild(0),'name','get_field_1');
         if ~isempty(hget_field)
@@ -3406 +2973 @@
         NomType=get(handles.NomType,'string');
         check_letter=~isempty(regexp(NomType,'[ab|AB]$'));%detect pair label by letter
-        NomType_1=NomType;
-        if check_letter
-            NomType_1=NomType_1(1:end-1);
-        else
-            r=regexp(NomType_1,'.-(?<num2>\d+$','names');
-            if ~isempty(r)
-                NomType_1=regexprep(NomType_1,['-' r.num2],'');
-            end
-        end
-        imagename=fullfile_uvmat(RootPath_1,'',RootFile_1,'.png',NomType_1,i1,[],j1);
+%         NomType_1=NomType;
+%         if check_letter
+%             NomType_1=NomType_1(1:end-1);
+%         else
+%             r=regexp(NomType_1,'.-(?<num2>\d+$','names');
+%             if ~isempty(r)
+%                 NomType_1=regexprep(NomType_1,['-' r.num2],'');
+%             end
+%         end
+        imagename=fullfile_uvmat(RootPath_1,'',RootFile_1,'.png',NomType,i1,[],j1);
         if ~exist(imagename,'file')
             [FileName,PathName] = uigetfile( ...
@@ -3452 +3019 @@
         end
 end
-
 
 %------------------------------------------------------------------------
@@ -3638 +3204 @@
             testphys=0; %coordinates in pixels by default
             if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys')
-                if isfield(UvData,'XmlData')&& isfield(UvData.XmlData,'GeometryCalib')
-                    Calib=UvData.XmlData.GeometryCalib;
+                if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
+                    Calib=UvData.XmlData{1}.GeometryCalib;
                     testphys=1;
                 end
@@ -3891 +3457 @@
      UvData.Object=UvData.Object(1);
 end 
-%list_object=get(handles.ListObject,'String');
 set(handles.ListObject,'Value',1)
 set(handles.ListObject,'String',{''})
-%set(handles.list_object_2,'Value',1)
-%set(handles.list_object_2,'String',{''})
-%list_object_2_Callback(hObject, eventdata, handles)
 
 %delete mask if it is displayed 
@@ -3986 +3548 @@
             end
         end
-%         set(haxes,'XLimMode','auto')%reset auto mode (after CheckZoom effect)
-%         set(haxes,'YLimMode','auto')
-%         PlotParam.Auto_xy=1;
         plot_field(Histo,haxes);
     end
@@ -4211 +3770 @@
 [PP,PlotParamOut]= plot_field(AxeData,handles.axes3,PlotParam);
 write_plot_param(handles,PlotParamOut); %update the auto plot parameters
-
-% %-------------------------------------------------------------------
-% % --- Executes on button press in grid.
-% function grid_Callback(hObject, eventdata, handles)
-
 
 %-------------------------------------------------------------------
@@ -4237 +3791 @@
     UvData.MouseAction='none';
     set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])   
-%     hset_object=findobj(allchild(0),'tag','set_object');% look for the set_object GUI
-%     if ~isempty(hset_object)
-%         delete(hset_object)% delete the current GUI set_object
-%     end
 end
 set(handles.uvmat,'UserData',UvData);
@@ -4353 +3903 @@
 ProjData= proj_field(UvData.Field,ObjectData);%project the current interface field on ObjectData
 plot_field(ProjData,ViewObjectAxes,read_GUI(get(ViewObjectAxes,'Parent')));%read plotting parameters on the uvmat interfacPlotHandles);
-% 
-% UvData.Object=update_obj(UvData,IndexObj(1),IndexObj(2));
-% set(handles.uvmat,'UserData',UvData)
 
 %------------------------------------------------------------------------
@@ -4406 +3953 @@
 end
 end
-
-%         SubObjectData=get(ObjectData.DisplayHandle_uvmat,'UserData');
-
-
-
-
-
-
 
 %------------------------------------------------------
@@ -4506 +4045 @@
 UvData.plotaxes=newaxes;% the axis in the new figure becomes the current main plotting axes
 set(huvmat,'UserData',UvData);
-increment=str2double(get(handles.increment_scan,'String')); %get the field increment d
-if isnan(increment)
-    set(handles.increment_scan,'String','1')%default value
-    increment=1;
-end
+increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
 set(handles.STOP,'Visible','on')
 set(handles.speed,'Visible','on')
@@ -4607 +4142 @@
                 testphys=0; %coordinates in pixels by default
                 if isfield(ObjectData,'CoordUnit') && ~isequal(ObjectData.CoordUnit,'pixel')
-                    if isfield(UvData,'XmlData')&& isfield(UvData.XmlData,'GeometryCalib')
-                        Calib=UvData.XmlData.GeometryCalib;
+                    if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
+                        Calib=UvData.XmlData{1}.GeometryCalib;
                         testphys=1;
                     end
@@ -4695 +4230 @@
 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
 FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
-%FileName=read_file_boxes(handles);
 CoordList=get(handles.transform_fct,'String');
 val=get(handles.transform_fct,'Value');
@@ -4707 +4241 @@
 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
 param.FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
-%[param.FileName]=read_file_boxes(handles);
 if isequal(get(handles.SubField,'Value'),1)
     [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
@@ -4720 +4253 @@
 param.NomType_1=get(handles.NomType_1,'String');
 % param.NomType_1=get(handles.FileIndex_1,'UserData');
-param.comp_input=get(handles.fix_pair,'Value');
+param.CheckFixPair=get(handles.CheckFixPair,'Value');
 huvmat=get(handles.MenuSeries,'parent');
 UvData=get(huvmat,'UserData');
-if isfield(UvData,'Time')
-    param.Time=UvData.XmlData.Time;
+if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'Time')
+    param.Time=UvData.XmlData{1}.Time;
 end
 if isequal(get(handles.scan_i,'Value'),1)
-    param.incr_i=str2double(get(handles.increment_scan,'String'));
+    param.incr_i=str2num(get(handles.increment_scan,'String'));
 elseif isequal(get(handles.scan_j,'Value'),1)
-    param.incr_j=str2double(get(handles.increment_scan,'String'));
+    param.incr_j=str2num(get(handles.increment_scan,'String'));
 end
 param.list_fields=get(handles.Fields,'String');% list menu fields
@@ -4753 +4286 @@
  [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
  FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
-%FileName=read_file_boxes(handles);
-%[FileName,RootPath,filebase,FileIndices,ext,SubDir]=read_file_boxes(handles)
-% num1=stra2num(get(handles.i1,'String'));
-% num2=stra2num(get(handles.i2,'String'));
-% num_a=stra2num(get(handles.j1,'String'));
-% num_b=stra2num(get(handles.j2,'String'));
-% NomType=get(handles.FileIndex,'UserData');
-% ind_opening=1; % default (images): will advice civ1 option by default in the civ interface
-% if isequal(ext,'.nc') ||  isequal(ext,'.cdf')% netcdf files
-%     ind_opening=2;% propose 'fix' as the default option
-% % +read the current netcdf rootfile
-%     Data=nc2struct(FileName,'ListGlobalAttribute','fix','patch','civ2','fix2');
-%     if isfield(Data,'fix') && isequal(Data.fix,1)
-%         ind_opening=3;
-%     end
-%     if isfield(Data,'patch') && isequal(Data.patch,1)
-%         ind_opening=4;
-%     end
-%     if isfield(Data,'civ2') && isequal(Data.civ2,1)
-%         ind_opening=5;
-%     end
-%     if isfield(Data,'fix2') && isequal(Data.fix2,1)
-%         ind_opening=6;
-%     end
-% end      
-% param.RootName=filebase;
-% param.NomType=NomType;
-% param.num1=num1;
-% param.num2=num2;
-% param.num_a=num_a;
-% param.num_b=num_b;
-% param.SubDir=SubDir;
-% param.IndOpening=ind_opening;% A REVOIR +TRANSMETTRE IMADOC INFO
-% param.ImaExt=ext;
 civ(FileName);% interface de civ(not in the uvmat file)
 
@@ -4897 +4396 @@
         'Pick an xml Object file',get(handles.RootPath,'String'));
 fileinput=[PathName FileName];%complete file name 
-% testblank=findstr(fileinput,' ');%look for blanks
-% if ~isempty(testblank)
-%     msgbox_uvmat('ERROR','forbidden input file name: contain blanks')
-%     return
-% end
 sizf=size(fileinput);
 if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
@@ -4915 +4409 @@
     delete(hset_object)% delete existing version of set_object
 end
-% UvData=get(handles.uvmat,'UserData');
 set_object(data);% call the set_object interface
-% %position the set_object GUI with respect to uvmat
-% pos_uvmat=get(handles.uvmat,'Position');
-% if isfield(UvData,'SetObjectOrigin')
-%     pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2);
-%     pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4);
-%     set(hset_object,'Position',pos_set_object)
-% end
 set(handles.edit_object,'Value',0); %suppress the object edit mode
 set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])  
 set(handles.MenuObject,'checked','on')
-%UvData.MouseAction='create_object';
-% set(handles.uvmat,'UserData',UvData)
 set(handles.delete_object,'Visible','on')
-% set(handles.uvmat_title,'Visible','on')
-% set(handles.view_field_title,'Visible','on')
 
 %------------------------------------------------------------------------
@@ -5042 +4524 @@
 end
 
-
 % --- Executes on button press in ViewObject.
 function ViewObject_Callback(hObject, eventdata, handles)
@@ -5065 +4546 @@
 
 
-
 function NomType_Callback(hObject, eventdata, handles)