Changeset 363

Timestamp:

Jan 10, 2012, 9:13:31 AM (13 years ago)

Author:

sommeria

Message:

civ2 introduced in civ_matlab (still bugs)
bugs corrected in civ and fill_GUI, read_GUI
comments in get_field

Location:

trunk/src

Files:

• civ.fig (modified) (previous)
• civ.m (modified) (20 diffs)
• civ_matlab.m (modified) (15 diffs)
• fill_GUI.m (modified) (1 diff)
• get_field.m (modified) (4 diffs)
• read_GUI.m (modified) (2 diffs)

trunk/src/civ.m

@@ -23 +23 @@
 %TODO: search range
 
-% Last Modified by GUIDE v2.5 08-Jan-2012 11:00:13
+% Last Modified by GUIDE v2.5 09-Jan-2012 20:42:45
 % Begin initialization code - DO NOT EDIT
 gui_Singleton = 1;
@@ -619 +619 @@
         ValueCiv1=1;
     end
-    set(handles.txt_SubdirCiv1,'String',listdir{ValueCiv1})
+    set(handles.SubdirCiv1,'String',listdir{ValueCiv1})
     ValueCiv2=get(handles.ListSubdirCiv2,'Value');
     if ValueCiv2>numel(listdir)
         ValueCiv2=1;
     end
-    set(handles.txt_SubdirCiv2,'String',listdir{ValueCiv2})
+    set(handles.SubdirCiv2,'String',listdir{ValueCiv2})
 else
     ValueCiv1=Value;
     ValueCiv2=Value;
-     set(handles.txt_SubdirCiv1,'String',listdir{Value})
-     set(handles.txt_SubdirCiv2,'String',listdir{Value})
+     set(handles.SubdirCiv1,'String',listdir{Value})
+     set(handles.SubdirCiv2,'String',listdir{Value})
 end
 set(handles.ListSubdirCiv1,'Value',ValueCiv1)
@@ -636 +636 @@
 set(handles.ListSubdirCiv2,'String',[listdir;'new...'])
 if isempty(listdir)
-    set(handles.txt_SubdirCiv1,'String','CIV')
-    set(handles.txt_SubdirCiv2,'String','CIV')
+    set(handles.SubdirCiv1,'String','CIV')
+    set(handles.SubdirCiv2,'String','CIV')
 end
 
@@ -664 +664 @@
 %------------------------------------------------------------------------
 % --- Executes on carriage return on the subdir checkciv1 edit window
-function txt_SubdirCiv1_Callback(hObject, eventdata, handles)
-%------------------------------------------------------------------------
-SubDir=get(handles.txt_SubdirCiv1,'String');
+function SubdirCiv1_Callback(hObject, eventdata, handles)
+%------------------------------------------------------------------------
+SubDir=get(handles.SubdirCiv1,'String');
 menu_str=get(handles.ListSubdirCiv1,'String');% read the list of subdirectories for update
 ichoice=find(strcmp(SubDir,menu_str),1);
@@ -676 +676 @@
 set(handles.ListSubdirCiv1,'Value',ilist)% select the selected subdir in the menu
 if get(handles.CheckCiv1,'Value')% if Civ1 is performed
-    set(handles.txt_SubdirCiv2,'String',SubDir);% set by default civ2 directory the same as civ1 
+    set(handles.SubdirCiv2,'String',SubDir);% set by default civ2 directory the same as civ1 
     set(handles.ListSubdirCiv2,'Value',ilist)
 else % if Civ1 data already exist
@@ -687 +687 @@
 %------------------------------------------------------------------------
 % --- Executes on carriage return on the SubDir checkciv1 edit window
-function txt_SubdirCiv2_Callback(hObject, eventdata, handles)
-%------------------------------------------------------------------------
-SubDir=get(handles.txt_SubdirCiv1,'String');
+function SubdirCiv2_Callback(hObject, eventdata, handles)
+%------------------------------------------------------------------------
+SubDir=get(handles.SubdirCiv1,'String');
 menu_str=get(handles.ListSubdirCiv2,'String');% read the list of subdirectories for update
 ichoice=find(strcmp(SubDir,menu_str),1);
@@ -762 +762 @@
 end
 set(handles.PairIndices,'Visible','on')
-set(handles.txt_SubdirCiv1,'Visible','on')
+set(handles.SubdirCiv1,'Visible','on')
 set(handles.ListSubdirCiv1,'Visible','on')
 if ~opening
@@ -773 +773 @@
     set(handles.TitlePairCiv2,'Visible','on')
     set(handles.TitleSubdirCiv2,'Visible','on')
-    set(handles.txt_SubdirCiv2,'Visible','on')
+    set(handles.SubdirCiv2,'Visible','on')
     set(handles.ListSubdirCiv2,'Visible','on')
     set(handles.ListPairCiv2,'Visible','on')
@@ -784 +784 @@
 else
     set(handles.TitleSubdirCiv2,'Visible','off')
-    set(handles.txt_SubdirCiv2,'Visible','off')
+    set(handles.SubdirCiv2,'Visible','off')
     set(handles.ListSubdirCiv2,'Visible','off')
     set(handles.ListPairCiv2,'Visible','off')
@@ -1692 +1692 @@
     end
 end
+Param=rmfield(Param,'status');
+Param=rmfield(Param,'xml');
 t=struct2xml(Param);
+t=set(t,1,'Name','CivDoc');% set the head label
 save(t,[namedoc '.xml']); %save GUI  parameters as xml file
 saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER  .xml)
@@ -1934 +1937 @@
 
 %check dir
-subdir_civ1=get(handles.txt_SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf output data
-subdir_civ2=get(handles.txt_SubdirCiv2,'String');
+subdir_civ1=get(handles.SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf output data
+subdir_civ2=get(handles.SubdirCiv2,'String');
 if isequal(subdir_civ1,''),subdir_civ1='CIV'; end% put default subdir
 if isequal(subdir_civ2,''),subdir_civ2=subdir_civ1; end% put default subdir
@@ -1985 +1988 @@
         end
   
-        %create the new txt_SubdirCiv1
+        %create the new SubdirCiv1
         if ~exist(fullfile(Path_ima,subdir_civ1_new),'dir')
 %             cd(Path_ima);          
@@ -2028 +2031 @@
                 end
             end
-            %create the new txt_SubdirCiv1
+            %create the new SubdirCiv1
             if ~exist(fullfile(Path_ima,subdir_civ1_new),'dir')
 %                    cd(Path_ima);          
@@ -2210 +2213 @@
             end
             subdir_civ2=subdir_civ2_new;
-            %create the new txt_SubdirCiv1
+            %create the new SubdirCiv1
             if ~exist(fullfile(Path_ima,subdir_civ2_new),'dir')
                 [xx,m2]=mkdir(subdir_civ2_new);
@@ -2384 +2387 @@
     end
 end
-set(handles.txt_SubdirCiv1,'String',subdir_civ1);%update the edit box
-set(handles.txt_SubdirCiv2,'String',subdir_civ2);%update the edit box
+set(handles.SubdirCiv1,'String',subdir_civ1);%update the edit box
+set(handles.SubdirCiv2,'String',subdir_civ2);%update the edit box
 browse.nom_type_nc=nom_type_nc;
 set(handles.RootName,'UserData',browse); %update the nomenclature type for uvmat
@@ -2962 +2965 @@
 
 %% 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
+subdir_civ1=get(handles.SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf data
+subdir_civ2=get(handles.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')
@@ -3193 +3196 @@
 % 
 % %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
+% subdir_civ1=get(handles.SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf data
+% subdir_civ2=get(handles.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')
@@ -3611 +3614 @@
 nbslice=1;
 
-% subdir=get(handles.txt_SubdirCiv1,'String');
+% subdir=get(handles.SubdirCiv1,'String');
 [Path,Name]=fileparts(filebase);
 if ~isdir(Path)
@@ -3707 +3710 @@
     end    
 end
-set(handles.txt_SubdirCiv1,'String',SubDir);
+set(handles.SubdirCiv1,'String',SubDir);
 errormsg=find_netcpair_civ(handles,1);
 if ~isempty(errormsg)
@@ -3728 +3731 @@
     end
 end
-set(handles.txt_SubdirCiv2,'String',SubDir);
+set(handles.SubdirCiv2,'String',SubDir);
 
 %------------------------------------------------------------------------

trunk/src/civ_matlab.m

@@ -77 +77 @@
     for ilist=1:length(list_param)
         Civ1_param{ilist}=['Civ1_' list_param{ilist}];
-        %         eval(['Data.Civ1_' list_param{ilist} '=Param.Civ1.' list_param{ilist} ';'])
         Data.(['Civ1_' list_param{ilist}])=Param.Civ1.(list_param{ilist});
     end
     Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ1_param];% {'Civ1_Time','Civ1_Dt'}];
-    %     if exist('ncfile','var')% TEST for use interactively with mouse_motion (no file created)
     Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F'};%  cell array containing the names of the fields to record
     Data.VarDimName={'NbVec1','NbVec1','NbVec1','NbVec1','NbVec1','NbVec1'};
@@ -103 +101 @@
         CivFile=Param.Patch1.CivFile;
     end
-    Data=nc2struct(CivFile,'ListGlobalAttribute','absolut_time_T0') %look for the constant 'absolut_time_T0' to detect old civx data format
+    Data=nc2struct(CivFile,'ListGlobalAttribute','absolut_time_T0'); %look for the constant 'absolut_time_T0' to detect old civx data format
     if isfield(Data,'Txt')
         errormsg=Data.Txt;
@@ -112 +110 @@
         [Data,vardetect,ichoice]=nc2struct(CivFile);%read the variables in the netcdf file
     else
-        if isfield(Param,'Fix1')
-            Data=nc2struct(CivFile,ListVarCiv1);%read civ1 data in the existing netcdf file
-        else
-            Data=nc2struct(CivFile,ListVarFix1);%read civ1 and fix1 data in the existing netcdf file
-        end
+        Data=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file
+%         if isfield(Param,'Fix1')
+%             Data=nc2struct(CivFile,ListVarCiv1);%read civ1 data in the existing netcdf file
+%         else
+%             Data=nc2struct(CivFile,ListVarFix1);%read civ1 and fix1 data in the existing netcdf file
+%         end
     end
 end
@@ -153 +152 @@
     end
     check_patch1=1;
-    Param.Patch1
     Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch1_Rho','Patch1_Threshold','Patch1_SubDomain'}];
     Data.Patch1_Rho=Param.Patch1.SmoothingParam;
@@ -168 +166 @@
     if isfield(Data,'Civ1_FF')
         ind_good=find(Data.Civ1_FF==0);
-    else
-        
+    else 
         ind_good=1:numel(Data.Civ1_X);
     end
@@ -183 +180 @@
 if isfield (Param,'Civ2')
     par_civ2=Param.Civ2;
-    if ~check_civ1 || ~strcmp(par_civ1.filename_ima_a,par_civ2.filename_ima_a)
-            par_civ2.ImageA=imread(par_civ2.filename_ima_a);%read first image if not already done for civ1 
-    end
-    if ~check_civ1|| ~strcmp(par_civ1.filename_ima_b,par_civ2.filename_ima_b)
-            par_civ2.ImageB=imread(par_civ2.filename_ima_b);%read second image if not already done for civ1 
-    end
-%     stepx=str2double(par_civ2.dx);
-%     stepy=str2double(par_civ2.dy);
-    ibx2=ceil(str2double(par_civ2.ibx)/2);
-    iby2=ceil(str2double(par_civ2.iby)/2);
+    if ~isfield (Param,'Civ1') || ~strcmp(Param.Civ1.ImageA,par_civ2.ImageA)
+        par_civ2.ImageA=imread(par_civ2.ImageA);%read first image if not already done for civ1
+    else
+        par_civ2.ImageA=Param.Civ1.ImageA;
+    end
+    if ~isfield (Param,'Civ1') || ~strcmp(Param.Civ1.ImageB,par_civ2.ImageB)
+        par_civ2.ImageB=imread(par_civ2.ImageB);%read second image if not already done for civ1
+         else
+        par_civ2.ImageB=Param.Civ1.ImageB;
+    end
+    ibx2=ceil(par_civ2.Bx/2);
+    iby2=ceil(par_civ2.By/2);
     isx2=ibx2+2;
     isy2=iby2+2;
-
-
-%         Data.Civ1_U_Diff=zeros(size(Data.Civ1_X));
-%         Data.Civ1_V_Diff=zeros(size(Data.Civ1_X));
-%         if isfield(Data,'Civ1_FF')
-%             ind_good=find(Data.Civ1_FF==0);
-%         else
-%             ind_good=1:numel(Data.Civ1_X);
-%         end
-%             [Data.Civ1_X_SubRange,Data.Civ1_Y_SubRange,Data.Civ1_NbSites,FFres,Ures, Vres,Data.Civ1_X_tps,Data.Civ1_Y_tps,Data.Civ1_U_tps,Data.Civ1_V_tps]=...
-%                                 patch(Data.Civ1_X(ind_good)',Data.Civ1_Y(ind_good)',Data.Civ1_U(ind_good)',Data.Civ1_V(ind_good)',Data.Patch1_Rho,Data.Patch1_Threshold,Data.Patch1_SubDomain);
-%         end 
-%     shiftx=str2num(par_civ1.shiftx);
-%     shifty=str2num(par_civ1.shifty);
-% TO GET shift from par_civ2.filename_nc1
-    % shiftx=velocity interpolated at position 
-    miniy=max(1+isy2+shifty,1+iby2);
-    minix=max(1+isx2-shiftx,1+ibx2);
-    maxiy=min(size(par_civ2.ImageA,1)-isy2+shifty,size(par_civ2.ImageA,1)-iby2);
-    maxix=min(size(par_civ2.ImageA,2)-isx2-shiftx,size(par_civ2.ImageA,2)-ibx2);
+    % shift from par_civ2.filename_nc1
+    % shiftx=velocity interpolated at position
+    miniy=max(1+isy2,1+iby2);
+    minix=max(1+isx2,1+ibx2);
+    maxiy=min(size(par_civ2.ImageA,1)-isy2,size(par_civ2.ImageA,1)-iby2);
+    maxix=min(size(par_civ2.ImageA,2)-isx2,size(par_civ2.ImageA,2)-ibx2);
     [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy);
-    PointCoord(:,1)=reshape(GridX,[],1);
-    PointCoord(:,2)=reshape(GridY,[],1);
-
-    Guess = tps_eval(PointCoord,[Data.Civ1_X_tps Data.Civ1_Y_tps])
-    Shiftx=Guess*Data.Civ1_U_tps;
-    Shifty=Guess*Data.Civ1_V_tps;
-    
-    if ~isempty(par_civ2.maskname)&& ~strcmp(maskname,par_civ2.maskname)% mask exist, not already read in civ1
+    GridX=reshape(GridX,[],1);
+    GridY=reshape(GridY,[],1);
+    Shiftx=zeros(size(GridX));% shift expected from civ1 data
+    Shifty=zeros(size(GridX));
+    nbval=zeros(size(GridX));
+    if par_civ2.CheckDeformation
+        DUDX=zeros(size(GridX));
+        DUDY=zeros(size(GridX));
+        DVDX=zeros(size(GridX));
+        DVDY=zeros(size(GridX));
+    end
+    [NbSubDomain,xx]=size(Data.Civ1_X_SubRange);
+    % get the guess from patch1
+    for isub=1:NbSubDomain
+        nbvec_sub=Data.Civ1_NbSites(isub);
+        ind_sel=find(GridX>=Data.Civ1_X_SubRange(isub,1) & GridX<=Data.Civ1_X_SubRange(isub,2) & GridY>=Data.Civ1_Y_SubRange(isub,1) & GridY<=Data.Civ1_Y_SubRange(isub,2));
+        epoints = [GridX(ind_sel) GridY(ind_sel)];% coordinates of interpolation sites
+        ctrs=[Data.Civ1_X_tps(1:nbvec_sub,isub) Data.Civ1_Y_tps(1:nbvec_sub,isub)];%(=initial points) ctrs
+        nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for eacn interpolation point (in case of subdomain overlap)
+        EM = tps_eval(epoints,ctrs);
+        Shiftx(ind_sel)=Shiftx(ind_sel)+EM*Data.Civ1_U_tps(1:nbvec_sub+3,isub);
+        Shifty(ind_sel)=Shifty(ind_sel)+EM*Data.Civ1_V_tps(1:nbvec_sub+3,isub);
+        if par_civ2.CheckDeformation
+            [EMDX,EMDY] = tps_eval_dxy(epoints,ctrs);%2D matrix of distances between extrapolation points epoints and spline centres (=site points) ctrs
+            DUDX(ind_sel)=DUDX(ind_sel)+EMDX*Data.Civ1_U_tps(1:nbvec_sub+3,isub);
+            DUDY(ind_sel)=DUDY(ind_sel)+EMDY*Data.Civ1_U_tps(1:nbvec_sub+3,isub);
+            DVDX(ind_sel)=DVDX(ind_sel)+EMDX*Data.Civ1_V_tps(1:nbvec_sub+3,isub);
+            DVDY(ind_sel)=DVDY(ind_sel)+EMDY*Data.Civ1_V_tps(1:nbvec_sub+3,isub);
+        end
+    end
+    mask='';
+    if par_civ2.CheckMask&&~isempty(par_civ2.maskname)&& ~strcmp(maskname,par_civ2.maskname)% mask exist, not already read in civ1
         mask=imread(par_civ2.maskname);
     end
+    par_civ2.Searchx=2*isx2+1;
+    par_civ2.Searchy=2*isy2+1;
+    par_civ2.Shiftx=Shiftx./nbval;
+    par_civ2.Shifty=Shifty./nbval;
+    par_civ2.Grid=[GridX GridY];   
+    if par_civ2.CheckDeformation
+        DUDX=DUDX./nbval;
+        DUDY=DUDY./nbval;
+        DVDX=DVDX./nbval;
+        DVDY=DVDY./nbval;
+    end
     % caluclate velocity data (y and v in indices, reverse to y component)
-    [xtable ytable utable vtable ctable F] = civ (par_civ2.ImageA,par_civ1.ImageB,ibx2,iby2,isx2,isy2,shiftx,-shifty,PointCoord,str2num(par_civ1.rho),mask);
-    list_param=(fieldnames(par_civ1))';
+    [xtable ytable utable vtable ctable F] = civ (par_civ2);
+    list_param=(fieldnames(Param.Civ2))';
     list_remove={'pxcmx','pxcmy','npx','npy','gridflag','maskflag','term_a','term_b','T0'};
-    index=zeros(size(list_param));
     for ilist=1:length(list_remove)
         index=strcmp(list_remove{ilist},list_param);
@@ -238 +257 @@
     end
     for ilist=1:length(list_param)
-        Civ1_param{ilist}=['Civ1_' list_param{ilist}];
-        eval(['Data.Civ1_' list_param{ilist} '=Param.Civ1.' list_param{ilist} ';'])
-    end
-    if isfield(Data,'Civ1_gridname') && strcmp(Data.Civ1_gridname(1:6),'noFile')
+        Civ2_param{ilist}=['Civ2_' list_param{ilist}];
+        eval(['Data.Civ2_' list_param{ilist} '=Param.Civ2.' list_param{ilist} ';'])
+    end
+    if isfield(Data,'Civ2_gridname') && strcmp(Data.Civ1_gridname(1:6),'noFile')
         Data.Civ1_gridname='';
     end
-    if isfield(Data,'Civ1_maskname') && strcmp(Data.Civ1_maskname(1:6),'noFile')
-        Data.Civ1_maskname='';
-    end
-    Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ1_param {'Civ1_Time','Civ1_Dt'}];
-    Data.Civ1_Time=str2double(par_civ1.T0);
-    Data.Civ1_Dt=str2double(par_civ1.Dt);
-    Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F'};%  cell array containing the names of the fields to record
-    Data.VarDimName={'NbVec1','NbVec1','NbVec1','NbVec1','NbVec1','NbVec1'};
+    if isfield(Data,'Civ2_maskname') && strcmp(Data.Civ1_maskname(1:6),'noFile')
+        Data.Civ2_maskname='';
+    end
+    Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param {'Civ2_Time','Civ2_Dt'}];
+    Data.Civ2_Time=str2double(par_civ2.Time);
+    Data.Civ2_Dt=str2double(par_civ2.Dt);
+    Data.ListVarName=[Data.ListVarName {'Civ2_X','Civ2_Y','Civ2_U','Civ2_V','Civ2_C','Civ2_F'}];%  cell array containing the names of the fields to record
+    Data.VarDimName=[Data.VarDimName {'NbVec2','NbVec2','NbVec2','NbVec2','NbVec2','NbVec2'}];
     Data.VarAttribute{1}.Role='coord_x';
     Data.VarAttribute{2}.Role='coord_y';
@@ -257 +276 @@
     Data.VarAttribute{4}.Role='vector_y';
     Data.VarAttribute{5}.Role='warnflag';
-    Data.Civ1_X=reshape(xtable,[],1);
-    Data.Civ1_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1);
-    Data.Civ1_U=reshape(utable,[],1);
-    Data.Civ1_V=reshape(-vtable,[],1);
-    Data.Civ1_C=reshape(ctable,[],1);
-    Data.Civ1_F=reshape(F,[],1);
+    Data.Civ2_X=reshape(xtable,[],1);
+    Data.Civ2_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1);
+    Data.Civ2_U=reshape(utable,[],1);
+    Data.Civ2_V=reshape(-vtable,[],1);
+    Data.Civ2_C=reshape(ctable,[],1);
+    Data.Civ2_F=reshape(F,[],1);
     Data.CivStage=Data.CivStage+1;
 end
@@ -361 +380 @@
 if isfield(par_civ,'Grid')
     if ischar(par_civ.Grid)
-        par_civ.Grid;
         par_civ.Grid=dlmread(par_civ.Grid);
         par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file)
@@ -370 +388 @@
     isx2=ceil(par_civ.Searchx/2);
     isy2=ceil(par_civ.Searchy/2);
-    shiftx=par_civ.Shiftx;
-    shifty=-par_civ.Shifty;
     miniy=max(1+isy2+shifty,1+iby2);
     minix=max(1+isx2-shiftx,1+ibx2);
@@ -380 +396 @@
     par_civ.Grid(:,2)=reshape(GridY,[],1);
 end
-
+nbvec=size(par_civ.Grid,1);
+if numel(shiftx)==1
+    shiftx=round(shiftx)*ones(nbvec,1);
+    shifty=round(shifty)*ones(nbvec,1);
+end
 %% Default output
-nbvec=size(par_civ.Grid,1);
 xtable=par_civ.Grid(:,1);
 ytable=par_civ.Grid(:,2);
@@ -462 +481 @@
     %     ytable(ivec)=jref;%default
     if ~(checkmask && par_civ.Mask(jref,iref)<=20) %velocity not set to zero by the black mask
-        if jref-iby2<1 || jref+iby2>par_civ.ImageHeight|| iref-ibx2<1 || iref+ibx2>par_civ.ImageWidth% we are outside the image
+        if jref-iby2<1 || jref+iby2>par_civ.ImageHeight|| iref-ibx2<1 || iref+ibx2>par_civ.ImageWidth||...
+              jref+shifty(ivec)-isy2<1||jref+shifty(ivec)+isy2>par_civ.ImageHeight|| iref+shiftx(ivec)-isx2<1 || iref+shiftx(ivec)+isx2>par_civ.ImageWidth  % we are outside the image
             F(ivec)=3;
         else
             image1_crop=par_civ.ImageA(jref-iby2:jref+iby2,iref-ibx2:iref+ibx2);%extract a subimage (correlation box) from image A
-            image2_crop=par_civ.ImageB(jref+shifty-isy2:jref+shifty+isy2,iref+shiftx-isx2:iref+shiftx+isx2);%extract a larger subimage (search box) from image B
+            image2_crop=par_civ.ImageB(jref+shifty(ivec)-isy2:jref+shifty(ivec)+isy2,iref+shiftx(ivec)-isx2:iref+shiftx(ivec)+isx2);%extract a larger subimage (search box) from image B
             image1_mean=mean(mean(image1_crop));
             image2_mean=mean(mean(image2_crop));
@@ -496 +516 @@
                         [vector,F(ivec)] = SUBPIX2DGAUSS (result_conv,x,y);
                     end
-                    utable(ivec)=vector(1)+shiftx;
-                    vtable(ivec)=vector(2)+shifty;
+                    utable(ivec)=vector(1)+shiftx(ivec);
+                    vtable(ivec)=vector(2)+shifty(ivec);
                     xtable(ivec)=iref+utable(ivec)/2;% convec flow (velocity taken at the point middle from imgae1 and 2)
                     ytable(ivec)=jref+vtable(ivec)/2;
@@ -509 +529 @@
                     ctable(ivec)=corrmax/sum_square;% correlation value
                 catch ME
-                    %                     vector=[0 0]; %if something goes wrong with cross correlation.....
                     F(ivec)=3;
                 end
@@ -619 +638 @@
 function FF=fix(Param,F,C,U,V,X,Y)
 FF=zeros(size(F));%default
-Param
 
 %criterium on warn flags

trunk/src/fill_GUI.m

@@ -17 +17 @@
     else
         hh=[];
+        input_data=Param.(fields{ifield});
         if isfield(handles,fields{ifield})
             hh=handles.(fields{ifield});
             if strcmp(get(hh,'Type'),'uitable')
-                set(hh,'Data',input)
+                set(hh,'Data',input_data)
                 break
             end
-        elseif isnumeric(input) && isfield(handles,['num_' fields{ifield}])
+        elseif isnumeric(input_data) && isfield(handles,['num_' fields{ifield}])
             hh=handles.(['num_' fields{ifield}]);
         end
         if ~isempty(hh)
             set(hh,'Visible','on')
+            get(hh,'style')
+            input_data
             switch get(hh,'style')
-                case {'checkbox','pushbutton','radiobutton','togglebutton'}
-                    if isnumeric(input)
-                        set(hh,'Value',input)
+                case {'checkbox','radiobutton','togglebutton'}
+                    if isnumeric(input_data)
+                        set(hh,'Value',input_data)
                     end
                 case 'edit'
-                    if isnumeric(input)
-                        input=num2str(input);
+                    if isnumeric(input_data)
+                        input_data=num2str(input_data);
                     end
-                    set(hh,'String',input)
+                    set(hh,'String',input_data)
                 case{'Listbox','popupmenu'}
-                    if isnumeric(input)
-                        input=num2str(input);
+                    if isnumeric(input_data)
+                        input_data=num2str(input_data);
                     end
                     menu=get(hh,'String');
-                    iline=find(strcmp(input,menu));
+                    iline=find(strcmp(input_data,menu));
                     if isempty(iline)
                         iline=numel(menu)+1;
-                        set(hh,'String',[menu;{input}])
+                        set(hh,'String',[menu;{input_data}])
                     end
                     set(hh,'Value',iline)

trunk/src/get_field.m

@@ -1075 +1075 @@
 Field=get(handles.get_field,'UserData');
 index=get(handles.variables,'Value');%index in the list 'variables'
+
+%% list global TimeAttribute names and values if index=1 (blank TimeVariable display) is selected
 if isequal(index,1) 
     set(handles.attributes_txt,'String','global attributes')
-% list global TimeAttribute names and values if index=1 (blank TimeVariable display) is selected
     if isfield(Field,'ListGlobalAttribute') && ~isempty(Field.ListGlobalAttribute)
         for iline=1:length(Field.ListGlobalAttribute)
@@ -1092 +1093 @@
         Tabchar=cell2tab(Tabcell,'=');
     end
+%% list Attribute names and values associated to the Variable # index-1   
 else
-%list TimeAttribute names and values associated to the TimeVariable # injdex-1   
     list_var=get(handles.variables,'String');
     var_select=list_var{index};
@@ -1122 +1123 @@
 set(handles.attributes,'String',Tabchar);
 
-% update dimensions;
+%% update dimensions;
 if isfield(Field,'ListDimName')
     Tabdim={};%default
@@ -1139 +1140 @@
             dim_indices=[dim_indices dim_index];
         end
-        %dim_indices=find(dim_list) %removes 0 values
         set(handles.dimensions_txt,'String', ['dimensions of ' var_select])
     end

trunk/src/read_GUI.m

@@ -16 +16 @@
                 check_input=1;%default
                 switch object_style
-                    case {'checkbox','pushbutton','radiobutton','togglebutton'}
+                    case {'checkbox','radiobutton','togglebutton'}
                         input=get(hchild(ichild),'Value');
                     case 'edit'
-                        separator=regexp(tag,'_');
+                        separator=regexp(tag,'^num_');
                         if isempty(separator)
                             input=get(hchild(ichild),'String');
                         else
-                            switch(tag(1:separator))
-                                case 'num_'
-                                    input=str2double(get(hchild(ichild),'String'));
-                                    tag=tag(separator+1:end);
-                                    %deal with undefined input: retrieve the default value stored as UserData
-                                    if isnan(input)
-                                        input=get(hchild(ichild),'UserData');
-                                        set(hchild(ichild),'String',num2str(input))
-                                    end
-                                case 'txt_'
-                                    input=get(hchild(ichild),'String');
-                                    tag=tag(separator+1:end);
-                                otherwise
-                                    input=get(hchild(ichild),'String');
+                            input=str2double(get(hchild(ichild),'String'));
+                            tag=regexprep(tag,'^num_','');
+                            %deal with undefined input: retrieve the default value stored as UserData
+                            if isnan(input)
+                                input=get(hchild(ichild),'UserData');
+                                set(hchild(ichild),'String',num2str(input))
                             end
-                        end
-
-                        %                         key=tag(7:end);
-                    case{'Listbox','popupmenu'}
+                        end                        
+                    case{'listbox','popupmenu'}
                         listinput=get(hchild(ichild),'String');
                         value=get(hchild(ichild),'Value');
                         if ~isempty(listinput)
-                        input=listinput(value);
+                            input=listinput{value};
+                        else
+                            check_input=0;
                         end
-                        separator=regexp(tag,'_');
-                        if strcmp(tag(1:separator),'num_')
+                        separator=regexp(tag,'^num_');
+                        if ~isempty(separator)
                             input=str2double(input);% transform to numerical values if the uicontrol tag begins with 'num_'
-                            tag=tag(separator+1:end);
+                            tag=regexprep(tag,'^num_','');
                         end
                     otherwise
@@ -57 +49 @@
                 if check_input
                     struct.(tag)=input;
-                  %  eval(['struct.' tag '=input;'])
                 end
             case 'uitable'
-                 struct.(tag)=get(hchild(ichild),'Data');
+                struct.(tag)=get(hchild(ichild),'Data');
         end
     end